Conference proceedings
Dong, T., Jamnik, M. and Liò, P., 2025 (Published online). Neural Reasoning for Sure Through Constructing Explainable Models Proceedings of the AAAI Conference on Artificial Intelligence, v. 39
Doi: 10.1609/aaai.v39i11.33262
Dong, T., Jamnik, M. and Liò, P., 2025. Neural Reasoning for Sure Through Constructing Explainable Models. AAAI,
Zhao, X., Li, Z., Shen, M., Stan, GB., Liò, P. and Zhao, Y., 2024. Enhancing Node Representations for Real-World Complex Networks with Topological Augmentation Frontiers in Artificial Intelligence and Applications, v. 392
Doi: http://doi.org/10.3233/FAIA240652
Komorowska, UJ., Mathis, S., Didi, K., Vargas, F., Lio, P. and Jamnik, M., 2024. Dynamics-Informed Protein Design with Structure Conditioning
Shen, Y., Chen, Z., Mamalakis, M., Liu, Y., Li, T., Su, Y., He, J., Liò, P. and Wang, YG., 2024. TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering Proceedings - 2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024,
Doi: http://doi.org/10.1109/BIBM62325.2024.10822695
Bazaga, A., Lio, P. and Micklem, G., 2024. Unsupervised Pretraining for Fact Verification by Language Model Distillation. ICLR,
Papamarkou, T., Birdal, T., Bronstein, M., Carlsson, G., Curry, J., Gao, Y., Hajij, M., Kwitt, R., Liò, P., Di Lorenzo, P., Maroulas, V., Miolane, N., Nasrin, F., Ramamurthy, KN., Rieck, B., Scardapane, S., Schaub, MT., Veličković, P., Wang, B., Wang, Y., Wei, G-W. and Zamzmi, G., 2024. Position: Topological Deep Learning is the New Frontier for Relational Learning. Proc Mach Learn Res, v. 235
Kovac, V., Bekkers, EJ., Liò, P. and Eijkelboom, F., 2024. E(n) Equivariant Message Passing Cellular Networks Proceedings of Machine Learning Research, v. 251
Zaghen, O., Longa, A., Azzolin, S., Telyatnikov, L., Passerini, A. and Liò, P., 2024. Sheaf Diffusion Goes Nonlinear: Enhancing GNNs with Adaptive Sheaf Laplacians Proceedings of Machine Learning Research, v. 251
Giusti, L., Reu, T., Ceccarelli, F., Bodnar, C. and Liò, P., 2024. Topological Message Passing for Higher - Order and Long - Range Interactions Proceedings of the International Joint Conference on Neural Networks,
Doi: 10.1109/IJCNN60899.2024.10650343
Huang, K., Cao, W., Ta, H., Xiao, X. and Liò, P., 2024. Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach WWW 2024 - Proceedings of the ACM Web Conference,
Doi: 10.1145/3589334.3645705
Ceccarelli, F., Prinzi, F., Liò, P., Vitabile, S. and Holden, SB., 2024. MUGI-MRI: Enhancing Breast Cancer Classification through Multiplex Graph Neural Networks in DCE-MRI Proceedings of the International Joint Conference on Neural Networks,
Doi: 10.1109/IJCNN60899.2024.10650117
Bazaga, A., Lio, P. and Micklem, G., 2024. HyperBERT: Mixing Hypergraph-Aware Layers with Language Models for Node Classification on Text-Attributed Hypergraphs. EMNLP (Findings),
Bazaga, A., Lio, P. and Micklem, G., 2024. Language Model Knowledge Distillation for Efficient Question Answering in Spanish. Tiny Papers @ ICLR,
Ceccarelli, F., Prinzi, F., Liò, P., Vitabile, S. and Holden, SB., 2024. MUGI-MRI: Enhancing Breast Cancer Classification through Multiplex Graph Neural Networks in DCE-MRI. IJCNN,
Huang, K., Wang, YG., Li, M. and Lio, P., 2024. How Universal Polynomial Bases Enhance Spectral Graph Neural Networks: Heterophily, Over-smoothing, and Over-squashing. ICML,
Denker, A., Vargas, F., Padhy, S., Didi, K., Mathis, S., Dutordoir, V., Barbano, R., Mathieu, E., Komorowska, UJ. and Lio, P., 2024. DEFT: Efficient Fine-Tuning of Diffusion Models by Learning the Generalised h-transform Advances in Neural Information Processing Systems, v. 37
Ceccarelli, F., Giusti, L., Holden, S. and Lio, P., 2024. Integrating Structure and Sequence: Protein Graph Embeddings via GNNs and LLMs
Doi: 10.5220/0012453600003654
Iuliano, A., Lio, P., Manfredi, G. and Romaniello, F., 2024. Denoising Probabilistic Diffusion Models for Synthetic Healthcare Image Generation 2024 IEEE International Workshop on Metrology for Living Environment, MetroLivEnv 2024 - Proceedings,
Doi: 10.1109/MetroLivEnv60384.2024.10615511
Liu, L., Prost, J., Zhu, L., Papadakis, N., Liò, P., Schönlieb, C-B. and Avilés-Rivero, AI., 2023. SCOTCH and SODA: A Transformer Video Shadow Detection Framework. CVPR,
Liu, L., Prost, J., Zhu, L., Papadakis, N., Liò, P., Schönlieb, CB. and Aviles-Rivero, AI., 2023. SCOTCH and SODA: A Transformer Video Shadow Detection Framework Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, v. 2023-June
Doi: 10.1109/CVPR52729.2023.01007
Georgiev, D., Numeroso, D., Bacciu, D. and Lio, P., 2023. Neural Algorithmic Reasoning for Combinatorial Optimisation. LoG, v. 231
Opolka, FL., Zhi, YC., Liò, P. and Dong, X., 2023. Graph Classification Gaussian Processes via Spectral Features Proceedings of Machine Learning Research, v. 216
Borde, HSDO., Kazi, A., Barbero, F. and Liò, P., 2023. Latent Graph Inference using Product Manifolds. ICLR,
Azzolin, S., Longa, A., Barbiero, P., Liò, P. and Passerini, A., 2023. Global Explainability of GNNs via Logic Combination of Learned Concepts. ICLR,
Sun, Z., Cristea, AI., Lio, P. and Yu, J., 2023. Adaptive Distance Message Passing From the Multi-Relational Edge View. Tiny Papers @ ICLR,
Keskin, O., Lupidi, A., Giannini, F., Fioravanti, S., Magister, LC., Barbiero, P. and Liò, P., 2023. Bridging Equational Properties and Patterns on Graphs: an AI-Based Approach Proceedings of Machine Learning Research, v. 221
Lu, X., Zhang, X. and Lio, P., 2023. GAT-DNS: DNS Multivariate Time Series Prediction Model Based on Graph Attention Network ACM Web Conference 2023 - Companion of the World Wide Web Conference, WWW 2023,
Doi: 10.1145/3543873.3587329
Bernárdez, G., Telyatnikov, L., Alarcón, E., Cabellos-Aparicio, A., Barlet-Ros, P. and Liò, P., 2023. Topological Network Traffic Compression GNNet 2023 - Proceedings of the 2nd Graph Neural Networking Workshop 2023,
Doi: 10.1145/3630049.3630172
Mittone, G., Svoboda, F., Aldinucci, M., Lane, N. and Lió, P., 2023. A Federated Learning Benchmark for Drug-Target Interaction ACM Web Conference 2023 - Companion of the World Wide Web Conference, WWW 2023,
Doi: 10.1145/3543873.3587687
Norcliffe, A., Cebere, B., Imrie, F., Liò, P. and van der Schaar, M., 2023. SurvivalGAN: Generating Time-to-Event Data for Survival Analysis Proceedings of Machine Learning Research, v. 206
Bi, X., Tang, S., Yang, Z., Deng, X., Xiao, B. and Lio, P., 2023. MMCTNet: Multi-Modal Cony-Transformer Network for Predicting Good and Poor Outcomes in Cardiac Arrest Patients Computing in Cardiology,
Doi: 10.22489/CinC.2023.099
Jang, A., Patel, S., Patel, S., Shah, S. and Lio, P., 2023. Predicting mortality in systemic sclerosis patients using machine learning approaches JOURNAL OF INVESTIGATIVE DERMATOLOGY, v. 143
Sun, Z., Harit, A., Cristea, AI., Wang, J. and Lio, P., 2023. A Rewiring Contrastive Patch PerformerMixer Framework for Graph Representation Learning Proceedings - 2023 IEEE International Conference on Big Data, BigData 2023,
Doi: 10.1109/BigData59044.2023.10386951
Norcliffe, A., Cebere, B., Imrie, F., Liò, P. and Schaar, MVD., 2023. SurvivalGAN: Generating Time-to-Event Data for Survival Analysis. AISTATS,
Di Giovanni, F., Giusti, L., Barbero, F., Luise, G., Liò, P. and Bronstein, M., 2023. On Over-Squashing in Message Passing Neural Networks: The Impact of Width, Depth, and Topology Proceedings of Machine Learning Research, v. 202
Margeloiu, A., Simidjievski, N., Liò, P. and Jamnik, M., 2023. Weight Predictor Network with Feature Selection for Small Sample Tabular Biomedical Data Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023, v. 37
Doi: 10.1609/aaai.v37i8.26090
Barbiero, P., Ciravegna, G., Giannini, F., Zarlenga, ME., Magister, LC., Tonda, A., Lió, P., Precioso, F., Jamnik, M. and Marra, G., 2023. Interpretable Neural-Symbolic Concept Reasoning Proceedings of Machine Learning Research, v. 202
Duta, I., Cassarà, G., Silvestri, F. and Lió, P., 2023. Sheaf Hypergraph Networks. NeurIPS,
Zou, X., Zhao, X., Lio, P. and Zhao, Y., 2023. Will More Expressive Graph Neural Networks Do Better on Generative Tasks? LoG, v. 231
Joshi, CK., Bodnar, C., Mathis, SV., Cohen, T. and Liò, P., 2023. On the Expressive Power of Geometric Graph Neural Networks Proceedings of Machine Learning Research, v. 202
Tilly, T., Auckland, K., Nibhani, R., Martin, J., Nihr, N., Morrell, NW., Lio', P. and Graf, S., 2022. Deep learning of regulatory regions discovers enhancer variants implicated in PAH EUROPEAN RESPIRATORY JOURNAL, v. 60
Doi: 10.1183/13993003.congress-2022.2543
Yi, K., Chen, J., Wang, YG., Zhou, B., Liò, P., Fan, Y. and Hamann, J., 2022. APPROXIMATE EQUIVARIANCE SO(3) NEEDLET CONVOLUTION Proceedings of Machine Learning Research, v. 196
Liu, L., Huang, Z., Liò, P., Schönlieb, CB. and Aviles-Rivero, AI., 2022. You only Look at Patches: A Patch-wise Framework for 3D Unsupervised Medical Image Registration Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 13386 LNCS
Doi: 10.1007/978-3-031-11203-4_21
Cardozo, S., Montero, GI., Kazhdan, D., Dimanov, B., Wijaya, M., Jamnik, M. and Lio, P., 2022. Explainer Divergence Scores (EDS): Some Post-Hoc Explanations May be Effective for Detecting Unknown Spurious Correlations CEUR Workshop Proceedings, v. 3318
Day, B., Viñas, R., Simidjievski, N. and Liò, P., 2022. Attentional Meta-learners for Few-shot Polythetic Classification Proceedings of Machine Learning Research, v. 162
Stärk, H., Beaini, D., Corso, G., Tossou, P., Dallago, C., Günnemann, S. and Liò, P., 2022. 3D Infomax improves GNNs for Molecular Property Prediction Proceedings of Machine Learning Research, v. 162
Fan, J., Pei, J., Bi, X., Xiao, B. and Lio, P., 2022. Context Correlation Aware Network for Cardiac Segmentation Proceedings - IEEE International Conference on Multimedia and Expo, v. 2022-July
Doi: 10.1109/ICME52920.2022.9859985
Buterez, D., Janet, JP., Kiddle, SJ., Oglic, D. and Liò, P., 2022. Graph Neural Networks with Adaptive Readouts. NeurIPS,
Lu, X. and Lio, P., 2022. Second International Workshop On Artificial Intelligence To Security - AITS 2022 Proceedings - 52nd Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshop Volume, DSN-W 2022,
Doi: 10.1109/DSN-W54100.2022.00010
Manouchehrinia, A., Ebrahimi, A., Wiil, UK., Kiani, NA., Lio, P., Olsson, T. and Kockum, I., 2022. A susceptibility network analysis of disease pathways leading to multiple sclerosis MULTIPLE SCLEROSIS JOURNAL, v. 28
Zarlenga, ME., Barbiero, P., Ciravegna, G., Marra, G., Giannini, F., Diligenti, M., Shams, Z., Precioso, F., Melacci, S., Weller, A., Lio, P. and Jamnik, M., 2022. Concept Embedding Models: Beyond the Accuracy-Explainability Trade-Off Advances in Neural Information Processing Systems, v. 35
Qian, P., Yang, J., Lió, P., Hu, P. and Qi, H., 2022. Joint Group-Wise Motion Estimation and Segmentation of Cardiac Cine MR Images Using Recurrent U-Net Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 13413 LNCS
Doi: 10.1007/978-3-031-12053-4_5
Opolka, FL. and Liò, P., 2022. Bayesian Link Prediction with Deep Graph Convolutional Gaussian Processes Proceedings of Machine Learning Research, v. 151
Barbiero, P., Ciravegna, G., Giannini, F., Lió, P., Gori, M. and Melacci, S., 2022. Entropy-Based Logic Explanations of Neural Networks Proceedings of the 36th AAAI Conference on Artificial Intelligence, AAAI 2022, v. 36
Doi: 10.1609/aaai.v36i6.20551
Opolka, FL., Zhi, YC., Liò, P. and Dong, X., 2022. Adaptive Gaussian Processes on Graphs via Spectral Graph Wavelets Proceedings of Machine Learning Research, v. 151
Cardozo, S., Montero, GI., Kazhdan, D., Dimanov, B., Wijaya, MA., Jamnik, M. and Liò, P., 2022. Explainer Divergence Scores (EDS): Some Post-Hoc Explanations May be Effective for Detecting Unknown Spurious Correlations. CIKM Workshops, v. 3318
Georgiev, D., Barbiero, P., Kazhdan, D., Veličković, P. and Liò, P., 2022. Algorithmic Concept-Based Explainable Reasoning Proceedings of the 36th AAAI Conference on Artificial Intelligence, AAAI 2022, v. 36
Doi: 10.1609/aaai.v36i6.20623
Jain, R., Ciravegna, G., Barbiero, P., Giannini, F., Buffelli, D. and Lio, P., 2022. Extending Logic Explained Networks to Text Classification Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing, EMNLP 2022,
Doi: 10.18653/v1/2022.emnlp-main.604
Pándy, M., Qiu, W., Corso, G., Veličković, P., Ying, R., Leskovec, J. and Liò, P., 2022. Learning Graph Search Heuristics Proceedings of Machine Learning Research, v. 198
Tailor, SA., Opolka, FL., Liò, P. and Lane, ND., 2022. DO WE NEED ANISOTROPIC GRAPH NEURAL NETWORKS? ICLR 2022 - 10th International Conference on Learning Representations,
Lu, X., Zhao, J. and Lio, P., 2022. Robust android malware detection based on subgraph network and denoising GCN network MobiSys 2022 - Proceedings of the 2022 20th Annual International Conference on Mobile Systems, Applications and Services,
Doi: 10.1145/3498361.3538778
He, Y., Veličković, P., Liò, P. and Deac, A., 2022. Continuous Neural Algorithmic Planners Proceedings of Machine Learning Research, v. 198
Aghakhanyan, G., Barucci, A., Colantonio, S., Colcelli, V., Pasquinelli, F., Gini, R., Lio, P., Mazzei, M., Erba, P., Miele, V. and Neri, E., 2022. NAVIGATOR: An Imaging Biobank to Precisely Prevent and Predict cancer, and facilitate the Participation of oncologic patients to Diagnosis and Treatment EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING, v. 49
Imrie, F., Norcliffe, A., Lió, P. and Schaar, MVD., 2022. Composite Feature Selection Using Deep Ensembles. NeurIPS,
Imrie, F., Norcliffe, A., Liò, P. and van der Schaar, M., 2022. Composite Feature Selection Using Deep Ensembles Advances in Neural Information Processing Systems, v. 35
Buffelli, D., Liò, P. and Vandin, F., 2022. SizeShiftReg: a Regularization Method for Improving Size-Generalization in Graph Neural Networks Advances in Neural Information Processing Systems, v. 35
Buffelli, D., Lió, P. and Vandin, F., 2022. SizeShiftReg: a Regularization Method for Improving Size-Generalization in Graph Neural Networks. NeurIPS,
Bodnar, C., Di Giovanni, F., Chamberlain, BP., Liò, P. and Bronstein, M., 2022. Neural Sheaf Diffusion: A Topological Perspective on Heterophily and Oversmoothing in GNNs Advances in Neural Information Processing Systems, v. 35
Lu, X., Pang, R. and Lio, P., 2022. Poster: CFMAP: A Robust CPU Clock Fingerprint Model for Device Authentication Proceedings of the ACM Conference on Computer and Communications Security,
Doi: 10.1145/3548606.3563528
Jamasb, AR., Viñas, R., Ma, EJ., Harris, C., Huang, K., Hall, D., Lió, P. and Blundell, TL., 2022. Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction Networks Advances in Neural Information Processing Systems, v. 35
Barbero, F., Bodnar, C., de Ocáriz Borde, HS., Bronstein, M., Veličković, P. and Liò, P., 2022. SH EA F NEU RA L NETWO RK S W ITH CO NN ECTIO N LAPLACIANS Proceedings of Machine Learning Research, v. 196
Bodnar, C., Giovanni, FD., Chamberlain, BP., Lió, P. and Bronstein, MM., 2022. Neural Sheaf Diffusion: A Topological Perspective on Heterophily and Oversmoothing in GNNs. NeurIPS,
Opolka, FL., Zhi, Y-C., Liò, P. and Dong, X., 2022. Adaptive Gaussian Processes on Graphs via Spectral Graph Wavelets. AISTATS, v. 151
Campbell, A., Qendro, L., Liò, P. and Mascolo, C., 2022. ROBUST AND EFFICIENT UNCERTAINTY AWARE BIOSIGNAL CLASSIFICATION VIA EARLY EXIT ENSEMBLES ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings, v. 2022-May
Doi: 10.1109/ICASSP43922.2022.9746330
Buterez, D., Janet, JP., Kiddle, SJ., Oglic, D. and Liò, P., 2022. Graph Neural Networks with Adaptive Readouts Advances in Neural Information Processing Systems, v. 35
Scherer, P., Liò, P. and Jamnik, M., 2022. Distributed Representations of Graphs for Drug Pair Scoring Proceedings of Machine Learning Research, v. 198
Zhou, B., Liu, X., Liu, Y., Huang, Y., Liò, P. and Wang, YG., 2022. Well-conditioned Spectral Transforms for Dynamic Graph Representation Proceedings of Machine Learning Research, v. 198
Zheng, X., Zhou, B., Gao, J., Wang, YG., Liò, P., Li, M. and Montúfar, G., 2021. How Framelets Enhance Graph Neural Networks Proceedings of Machine Learning Research, v. 139
Norcliffe, A., Bodnar, C., Day, B., Moss, J. and Liò, P., 2021. Neural ODE Processes
Beaini, D., Passaro, S., Létourneau, V., Hamilton, WL., Corso, G. and Liò, P., 2021. Directional Graph Networks Proceedings of Machine Learning Research, v. 139
Bodnar, C., Frasca, F., Otter, N., Wang, YG., Lio, P., Montufar, G. and Bronstein, M., 2021. Weisfeiler and Lehman Go Cellular: CW Networks ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 34 (NEURIPS 2021),
Bellini, E., Bagnoli, F., Caporuscio, M., Damiani, E., Flammini, F., Linkov, I., Lio, P. and Marrone, S., 2021. Resilience learning through self adaptation in digital twins of human-cyber-physical systems Proceedings of the 2021 IEEE International Conference on Cyber Security and Resilience, CSR 2021,
Doi: 10.1109/CSR51186.2021.9527913
Corso, G., Ying, R., Pandy, M., Veličković, P., Leskovec, J. and Lio, P., 2021. Neural Distance Embeddings for Biological Sequences Advances in Neural Information Processing Systems, v. 22
Kazhdan, D., Dimanov, B., Terre, HA., Jamnik, M., Liò, P. and Weller, A., 2021. Is Disentanglement all you need? Comparing Concept-based &
Disentanglement Approaches
Qendro, L., Campbell, A., Liò, P. and Mascolo, C., 2021. Early Exit Ensembles for Uncertainty Quantification Proceedings of Machine Learning Research, v. 158
Drotár, P., Jamasb, AR., Day, B., Cangea, C. and Liò, P., 2021. Structure-aware generation of drug-like molecules. CoRR, v. abs/2111.04107
Rocheteau, E., Liò, P. and Hyland, SL., 2021. Temporal pointwise convolutional networks for length of stay prediction in the intensive care unit. CHIL,
Norcliffe, A., Bodnar, C., Day, B., Moss, J. and Liò, P., 2021. NEURAL ODE PROCESSES ICLR 2021 - 9th International Conference on Learning Representations,
Zhu, J., Tan, C., Yang, J., Yang, G. and Lio', P., 2021. Arbitrary Scale Super-Resolution for Medical Images International Journal of Neural Systems, v. 31
Doi: 10.1142/S0129065721500374
Zubic, N. and Liò, P., 2021. An Effective Loss Function for Generating 3D Models from Single 2D Image Without Rendering. AIAI, v. 627
Moss, JD., Opolka, FL., Dumitrascu, B. and Lió, P., 2021. Approximate Latent Force Model Inference
Sebenius, I., Campbell, A., Morgan, SE., Bullmore, ET. and Lio, P., 2021. Multimodal Graph Coarsening for Interpretable, MRI-Based Brain Graph Neural Network IEEE International Workshop on Machine Learning for Signal Processing, MLSP, v. 2021-January
Doi: 10.1109/MLSP52302.2021.9690626
Wei, X., Pu, C., He, Z. and Lio, P., 2021. Deep Reinforcement Learning-based Vaccine Distribution Strategies Proceedings - 2021 2nd International Conference on Electronics, Communications and Information Technology, CECIT 2021,
Doi: 10.1109/CECIT53797.2021.00082
Bodnar, C., Frasca, F., Wang, YG., Otter, N., Montúfar, G., Liò, P. and Bronstein, MM., 2021. Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks Proceedings of Machine Learning Research, v. 139
Lu, X. and Lio, P., 2021. International Workshop on Application of Intelligent Technology in Security - AITS 2021 Proceedings - 51st Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops, DSN-W 2021,
Doi: 10.1109/DSN-W52860.2021.00008
Dmitry, K., Shams, Z. and Pietro, L., 2020 (Published online). MARLeME: A Multi-Agent Reinforcement Learning Model Extraction Library. 2020 International Joint Conference on Neural Networks (IJCNN),
Doi: 10.1109/IJCNN48605.2020.9207564
Bardozzo, F., Lio', P. and Tagliaferri, R., 2020 (No publication date). A machine learning approach to investigate regulatory control circuits in bacterial metabolic pathways
Norcliffe, A., Bodnar, C., Day, B., Simidjievski, N. and Lió, P., 2020. On Second Order Behaviour in Augmented Neural ODEs. NeurIPS,
Deasy, J., Simidjievski, N. and Lió, P., 2020. Constraining Variational Inference with Geometric Jensen-Shannon Divergence. NeurIPS,
Filip, A-C., Azevedo, T., Passamonti, L., Toschi, N. and Lio, P., 2020. A novel Graph Attention Network Architecture for modeling multimodal brain connectivity. Annu Int Conf IEEE Eng Med Biol Soc, v. 2020
Doi: 10.1109/EMBC44109.2020.9176613
Kazhdan, D., Dimanov, B., Jamnik, M., Liò, P. and Weller, A., 2020. Now you see me (CME): Concept-based model extraction CEUR Workshop Proceedings, v. 2699
Corso, G., Cavalleri, L., Beaini, D., Liò, P. and Velickovic, P., 2020. Principal Neighbourhood Aggregation for Graph Nets. NeurIPS,
Ma, Z., Xuan, J., Wang, YG., Li, M. and Liò, P., 2020. Path Integral Based Convolution and Pooling for Graph Neural Networks. NeurIPS,
Bodnar, C., Day, B. and Lió, P., 2020. Proximal Distilled Evolutionary Reinforcement Learning. AAAI,
D’Agostino, D., Liò, P., Aldinucci, M. and Merelli, I., 2020. NeoHiC: A web application for the analysis of Hi-C data Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 12313 LNBI
Doi: 10.1007/978-3-030-63061-4_10
Wang, D., Jamnik, M. and Lio, P., 2020. Abstract Diagrammatic Reasoning with Multiplex Graph Networks
Kusztos, R., Dimitri, GM. and Lió, P., 2020. Neural Models for Brain Networks Connectivity Analysis Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 11925 LNBI
Doi: 10.1007/978-3-030-34585-3_19
Deasy, J., Ercole, A. and Liò, P., 2020. Adaptive Prediction Timing for Electronic Health Records
Dimitri, GM., Beqiri, E., Placek, MM., Czosnyka, M., Ercole, A., Smielewski, P. and Lio, P., 2020. Introducing brain-heart crosstalks information in clinical decision support systems for TBI patients, through ICM+ 2020 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ESGCO 2020,
Doi: 10.1109/ESGCO49734.2020.9158050
Di Stefano, A., Maesa, DDF., Das, SK. and Liò, P., 2020. Resolution of Blockchain Conflicts through Heuristics-based Game Theory and Multilayer Network Modeling ACM International Conference Proceeding Series, v. Part F165625
Doi: 10.1145/3369740.3372914
Dimitri, GM., Spasov, S., Duggento, A., Passamonti, L., Lio, P. and Toschi, N., 2020. Unsupervised stratification in neuroimaging through deep latent embeddings. Annu Int Conf IEEE Eng Med Biol Soc, v. 2020
Doi: 10.1109/EMBC44109.2020.9175810
Azevedo, T., Passamonti, L., Lio, P. and Toschi, N., 2020. A deep spatiotemporal graph learning architecture for brain connectivity analysis. Annu Int Conf IEEE Eng Med Biol Soc, v. 2020
Doi: 10.1109/EMBC44109.2020.9175360
Yeghikyan, G., Opolka, FL., Nanni, M., Lepri, B. and Lio, P., 2020. Learning Mobility Flows from Urban Features with Spatial Interaction Models and Neural Networks**To appear in the Proceedings of 2020 IEEE International Conference on Smart Computing (SMARTCOMP 2020) Proceedings - 2020 IEEE International Conference on Smart Computing, SMARTCOMP 2020,
Doi: 10.1109/SMARTCOMP50058.2020.00028
Veličković, P., Fedus, W., Hamilton, WL., Liò, P., Bengio, Y. and Hjelm, RD., 2019 (No publication date). Deep Graph Infomax
Opolka, FL., Solomon, A., Cangea, C., Veličković, P., Liò, P. and Hjelm, RD., 2019 (No publication date). Spatio-Temporal Deep Graph Infomax
Zhu, J., Yang, G. and Lió, P., 2019. Lesion focused super-resolution. Image Processing, v. 10949
Di Stefano, A., Scatà, M., La Corte, A., Das, SK. and Liò, P., 2019. Improving QoE in multi-layer social sensing: A cognitive architecture and game theoretic model SocialSense'19 Proceedings of the Fourth International Workshop on Social Sensing,
Doi: 10.1145/3313294.3313384
Zhu, J., Yang, G. and Lio, P., 2019. How can we make gan perform better in single medical image super-resolution? A lesion focused multi-scale approach Proceedings - International Symposium on Biomedical Imaging, v. 2019-April
Doi: 10.1109/ISBI.2019.8759517
Cangea, C., Belilovsky, E., Liò, P. and Courville, A., 2019. VideoNavQA: Bridging the Gap between Visual and Embodied Question
Answering
Prokhorov, V., Pilehvar, MT., Kartsaklis, D., Liò, P. and Collier, N., 2019. Unseen word representation by aligning heterogeneous lexical semantic spaces 33rd AAAI Conference on Artificial Intelligence, AAAI 2019, 31st Innovative Applications of Artificial Intelligence Conference, IAAI 2019 and the 9th AAAI Symposium on Educational Advances in Artificial Intelligence, EAAI 2019,
Doi: 10.1609/aaai.v33i01.33016900
Azevedo, T., Passamonti, L., Lió, P. and Toschi, N., 2019. A Machine Learning Tool for Interpreting Differences in Cognition Using Brain Features IFIP Advances in Information and Communication Technology, v. 559
Doi: 10.1007/978-3-030-19823-7_40
Satu, MS., Chandra Howlader, K., Niamat Ullah Akhund, TM., Quinn, JMW., Lio, P. and Moni, MA., 2019. Comorbidity effects of mitochondrial dysfunction to the progression of neurological disorders: Insights from a systems biomedicine perspective 2019 22nd International Conference on Computer and Information Technology, ICCIT 2019,
Doi: 10.1109/ICCIT48885.2019.9038388
Spasov, SE. and Liò, P., 2019. Dynamic Neural Network Channel Execution for Efficient Training. BMVC,
Rossi, E., Monti, F., Bronstein, M. and Liò, P., 2019. ncRNA Classification with Graph Convolutional Networks
Taylor, D., Spasov, S. and Liò, P., 2019. Co-Attentive Cross-Modal Deep Learning for Medical Evidence Synthesis
and Decision Making
Veličković, P., Fedus, W., Hamilton, WL., Bengio, Y., Liò, P. and Devon Hjelm, R., 2019. Deep graph infomax 7th International Conference on Learning Representations, ICLR 2019,
Tangherloni, A., Rundo, L., Spolaor, S., Nobile, MS., Merelli, I., Besozzi, D., Mauri, G., Cazzaniga, P. and Liò, P., 2019. High performance computing for haplotyping: Models and platforms Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 11339 LNCS
Doi: 10.1007/978-3-030-10549-5_51
Webb, E., Day, B., Andres-Terre, H. and Lió, P., 2019. Factorised Neural Relational Inference for Multi-Interaction Systems
Prokhorov, V., Pilehvar, MT., Kartsaklis, D., Liò, P. and Collier, N., 2019. Unseen Word Representation by Aligning Heterogeneous Lexical Semantic Spaces. AAAI,
Despeyroux, J., Felty, A., Liò, P. and Olarte, C., 2019. A Logical Framework for Modelling Breast Cancer Progression Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 11415 LNCS
Doi: 10.1007/978-3-030-19432-1_8
Serra, A., Guida, MD., Lió, P. and Tagliaferri, R., 2019. Hierarchical block matrix approach for multi-view clustering Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 10834 LNBI
Doi: 10.1007/978-3-030-14160-8_19
Cangea, C., Belilovsky, E., Liò, P. and Courville, AC., 2019. VideoNavQA: Bridging the Gap between Visual and Embodied Question Answering. ViGIL@NeurIPS,
Zhu, J., Yang, G. and Liò, P., 2019. How Can We Make Gan Perform Better in Single Medical Image Super-Resolution? A Lesion Focused Multi-Scale Approach. ISBI,
Angione, C., Carapezza, G., Costanza, J., Lio, P. and Nicosia, G., 2018 (No publication date). Computing with Metabolic Machines EPiC Series in Computing, v. 10
Doi: 10.29007/t48n
Wang, D., Jamnik, M. and Lio, P., 2018 (Accepted for publication). Investigating diagrammatic reasoning with deep neural networks
Doi: 10.1007/978-3-319-91376-6_36
Bica, I., Veličković, P., Xiao, H. and Liò, P., 2018. Multi-omics data integration using cross-modal neural networks ESANN 2018 - Proceedings, European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning,
Mathur, A., Zhang, T., Bhattacharya, S., Velickovic, P., Joffe, L., Lane, ND., Kawsar, F. and Liò, P., 2018. Using deep data augmentation training to address software and hardware heterogeneities in wearable and smartphone sensing devices. IPSN '18 Proceedings of the 17th ACM/IEEE International Conference on Information Processing in Sensor Networks,
Doi: 10.1109/IPSN.2018.00048
Veličković, P., Casanova, A., Liò, P., Cucurull, G., Romero, A. and Bengio, Y., 2018. Graph attention networks 6th International Conference on Learning Representations, ICLR 2018 - Conference Track Proceedings,
Velickovic, P., Karazija, L., Lane, ND., Bhattacharya, S., Liberis, E., Liò, P., Chieh, A., Bellahsen, O. and Vegreville, M., 2018. Cross-modal Recurrent Models for Weight Objective Prediction from Multimodal Time-series Data. PervasiveHealth,
Spasov, SE., Passamonti, L., Duggento, A., Lio, P. and Toschi, N., 2018. A Multi-modal Convolutional Neural Network Framework for the Prediction of Alzheimer's Disease. Annu Int Conf IEEE Eng Med Biol Soc, v. 2018
Doi: 10.1109/EMBC.2018.8512468
2018. 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing, PDP 2018, Cambridge, United Kingdom, March 21-23, 2018 PDP,
Merelli, I., Lio, P. and Kotenko, I., 2018. Message from General Chairs Proceedings - 26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018,
Doi: 10.1109/PDP2018.2018.00005
Merelli, I., Lio, P. and Kotenko, I., 2018. Message from Organizing Chairs Proceedings - 26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2018,
Doi: 10.1109/PDP2018.2018.00006
Lu, X., Liang, C., Zhang, S., Lio, P. and Jing, S., 2018. Terminal sensitive data protection by adjusting access time bidirectionally and automatically Proceedings - International Conference on Computer Communications and Networks, ICCCN, v. 2018-July
Doi: 10.1109/ICCCN.2018.8487465
Bakas, S., Reyes, M., Jakab, A., Bauer, S., Rempfler, M., Crimi, A., Shinohara, RT., Berger, C., Ha, SM., Rozycki, M., Prastawa, M., Alberts, E., Lipkova, J., Freymann, J., Kirby, J., Bilello, M., Fathallah-Shaykh, H., Wiest, R., Kirschke, J., Wiestler, B., Colen, R., Kotrotsou, A., Lamontagne, P., Marcus, D., Milchenko, M., Nazeri, A., Weber, M-A., Mahajan, A., Baid, U., Gerstner, E., Kwon, D., Acharya, G., Agarwal, M., Alam, M., Albiol, A., Albiol, A., Albiol, FJ., Alex, V., Allinson, N., Amorim, PHA., Amrutkar, A., Anand, G., Andermatt, S., Arbel, T., Arbelaez, P., Avery, A., Azmat, M., Pranjal, B., Bai, W., Banerjee, S., Barth, B., Batchelder, T., Batmanghelich, K., Battistella, E., Beers, A., Belyaev, M., Bendszus, M., Benson, E., Bernal, J., Bharath, HN., Biros, G., Bisdas, S., Brown, J., Cabezas, M., Cao, S., Cardoso, JM., Carver, EN., Casamitjana, A., Castillo, LS., Catà, M., Cattin, P., Cerigues, A., Chagas, VS., Chandra, S., Chang, Y-J., Chang, S., Chang, K., Chazalon, J., Chen, S., Chen, W., Chen, JW., Chen, Z., Cheng, K., Choudhury, AR., Chylla, R., Clérigues, A., Colleman, S., Colmeiro, RGR., Combalia, M., Costa, A., Cui, X., Dai, Z., Dai, L., Daza, LA., Deutsch, E., Ding, C., Dong, C., Dong, S., Dudzik, W., Eaton-Rosen, Z., Egan, G., Escudero, G., Estienne, T., Everson, R., Fabrizio, J., Fan, Y., Fang, L., Feng, X., Ferrante, E., Fidon, L., Fischer, M., French, AP., Fridman, N., Fu, H., Fuentes, D., Gao, Y., Gates, E., Gering, D., Gholami, A., Gierke, W., Glocker, B., Gong, M., González-Villá, S., Grosges, T., Guan, Y., Guo, S., Gupta, S., Han, W-S., Han, IS., Harmuth, K., He, H., Hernández-Sabaté, A., Herrmann, E., Himthani, N., Hsu, W., Hsu, C., Hu, X., Hu, X., Hu, Y., Hu, Y., Hua, R., Huang, T-Y., Huang, W., Huffel, SV., Huo, Q., Vivek, HV., Iftekharuddin, KM., Isensee, F., Islam, M., Jackson, AS., Jambawalikar, SR., Jesson, A., Jian, W., Jin, P., Jose, VJM., Jungo, A., Kainz, B., Kamnitsas, K., Kao, P-Y., Karnawat, A., Kellermeier, T., Kermi, A., Keutzer, K., Khadir, MT., Khened, M., Kickingereder, P., Kim, G., King, N., Knapp, H., Knecht, U., Kohli, L., Kong, D., Kong, X., Koppers, S., Kori, A., Krishnamurthi, G., Krivov, E., Kumar, P., Kushibar, K., Lachinov, D., Lambrou, T., Lee, J., Lee, C., Lee, Y., Lee, M., Lefkovits, S., Lefkovits, L., Levitt, J., Li, T., Li, H., Li, W., Li, H., Li, X., Li, Y., Li, H., Li, Z., Li, X., Li, Z., Li, X., Li, W., Lin, Z-S., Lin, F., Lio, P., Liu, C., Liu, B., Liu, X., Liu, M., Liu, J., Liu, L., Llado, X., Lopez, MM., Lorenzo, PR., Lu, Z., Luo, L., Luo, Z., Ma, J., Ma, K., Mackie, T., Madabushi, A., Mahmoudi, I., Maier-Hein, KH., Maji, P., Mammen, CP., Mang, A., Manjunath, BS., Marcinkiewicz, M., McDonagh, S., McKenna, S., McKinley, R., Mehl, M., Mehta, S., Mehta, R., Meier, R., Meinel, C., Merhof, D., Meyer, C., Miller, R., Mitra, S., Moiyadi, A., Molina-Garcia, D., Monteiro, MAB., Mrukwa, G., Myronenko, A., Nalepa, J., Ngo, T., Nie, D., Ning, H., Niu, C., Nuechterlein, NK., Oermann, E., Oliveira, A., Oliveira, DDC., Oliver, A., Osman, AFI., Ou, Y-N., Ourselin, S., Paragios, N., Park, MS., Paschke, B., Pauloski, JG., Pawar, K., Pawlowski, N., Pei, L., Peng, S., Pereira, SM., Perez-Beteta, J., Perez-Garcia, VM., Pezold, S., Pham, B., Phophalia, A., Piella, G., Pillai, GN., Piraud, M., Pisov, M., Popli, A., Pound, MP., Pourreza, R., Prasanna, P., Prkovska, V., Pridmore, TP., Puch, S., Puybareau, É., Qian, B., Qiao, X., Rajchl, M., Rane, S., Rebsamen, M., Ren, H., Ren, X., Revanuru, K., Rezaei, M., Rippel, O., Rivera, LC., Robert, C., Rosen, B., Rueckert, D., Safwan, M., Salem, M., Salvi, J., Sanchez, I., Sánchez, I., Santos, HM., Sartor, E., Schellingerhout, D., Scheufele, K., Scott, MR., Scussel, AA., Sedlar, S., Serrano-Rubio, JP., Shah, NJ., Shah, N., Shaikh, M., Shankar, BU., Shboul, Z., Shen, H., Shen, D., Shen, L., Shen, H., Shenoy, V., Shi, F., Shin, HE., Shu, H., Sima, D., Sinclair, M., Smedby, O., Snyder, JM., Soltaninejad, M., Song, G., Soni, M., Stawiaski, J., Subramanian, S., Sun, L., Sun, R., Sun, J., Sun, K., Sun, Y., Sun, G., Sun, S., Suter, YR., Szilagyi, L., Talbar, S., Tao, D., Tao, D., Teng, Z., Thakur, S., Thakur, MH., Tharakan, S., Tiwari, P., Tochon, G., Tran, T., Tsai, YM., Tseng, K-L., Tuan, TA., Turlapov, V., Tustison, N., Vakalopoulou, M., Valverde, S., Vanguri, R., Vasiliev, E., Ventura, J., Vera, L., Vercauteren, T., Verrastro, CA., Vidyaratne, L., Vilaplana, V., Vivekanandan, A., Wang, G., Wang, Q., Wang, CJ., Wang, W., Wang, D., Wang, R., Wang, Y., Wang, C., Wang, G., Wen, N., Wen, X., Weninger, L., Wick, W., Wu, S., Wu, Q., Wu, Y., Xia, Y., Xu, Y., Xu, X., Xu, P., Yang, T-L., Yang, X., Yang, H-Y., Yang, J., Yang, H., Yang, G., Yao, H., Ye, X., Yin, C., Young-Moxon, B., Yu, J., Yue, X., Zhang, S., Zhang, A., Zhang, K., Zhang, X., Zhang, L., Zhang, X., Zhang, Y., Zhang, L., Zhang, J., Zhang, X., Zhang, T., Zhao, S., Zhao, Y., Zhao, X., Zhao, L., Zheng, Y., Zhong, L., Zhou, C., Zhou, X., Zhou, F., Zhu, H., Zhu, J., Zhuge, Y., Zong, W., Kalpathy-Cramer, J., Farahani, K., Davatzikos, C., Leemput, KV. and Menze, B., 2018. Identifying the Best Machine Learning Algorithms for Brain Tumor
Segmentation, Progression Assessment, and Overall Survival Prediction in the
BRATS Challenge
Wang, D., Zhang, R., Zhu, J., Teng, Z., Huang, Y., Spiga, F., Hong-Fei Du, M., Gillard, JH., Lu, Q. and Liò, P., 2018. Neural network fusion: a novel CT-MR Aortic Aneurysm image segmentation method. Proc SPIE Int Soc Opt Eng, v. 10574
Doi: 10.1117/12.2293371
Heffernan, K., Liò, P. and Teufel, S., 2017. Multilayer data and document stratification for comorbidity analysis Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 10477 LNBI
Doi: 10.1007/978-3-319-67834-4_17
Felicetti, L., Femminella, M., Ivanov, T., Lio, P. and Reali, G., 2017. A big-data layered architecture for analyzing molecular communications systems in blood vessels Proceedings of the 4th ACM International Conference on Nanoscale Computing and Communication, NanoCom 2017,
Doi: 10.1145/3109453.3109468
Brouwer, T. and Lio, P., 2017. Bayesian Hybrid Matrix Factorisation for Data Integration Proceedings of Machine Learning Research, v. 54
Brouwer, T., Frellsen, J. and Liò, P., 2017. Comparative Study of Inference Methods for Bayesian Nonnegative Matrix Factorisation. ECML/PKDD (1), v. 10534
Doi: 10.1007/978-3-319-71249-9_31)
He, P., Mao, Y., Liu, Q., Liò, P. and Yang, K., 2016. Channel modelling of molecular communications across blood vessels and nerves 2016 IEEE International Conference on Communications, ICC 2016,
Doi: 10.1109/ICC.2016.7510860
Velickovic, P., Wang, D., Lane, ND. and Liò, P., 2016. X-CNN: Cross-modal convolutional neural networks for sparse datasets. SSCI,
Angione, C., Liò, P., Pucciarelli, S., Can, B., Conway, M., Lotti, M., Bokhari, H., Mancini, A., Sezerman, U. and Telatin, A., 2016. Bioinformatics challenges and potentialities in studying extreme environments Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 9874 LNCS
Doi: 10.1007/978-3-319-44332-4_16
Tordini, F., Merelli, I., Liò, P., Milanesi, L. and Aldinucci, M., 2016. NuchaRT: Embedding high-level parallel computing in R for augmented Hi-C data analysis Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 9874 LNCS
Doi: 10.1007/978-3-319-44332-4_20
Pratanwanich, N., Lió, P. and Stegle, O., 2016. Warped matrix factorisation for multi-view data integration Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 9852 LNAI
Doi: 10.1007/978-3-319-46227-1_49
Alarcon, E., Cid-Fuentes, RG., Davy, A., Felicetti, L., Femminella, M., Lio, P., Reali, G. and Solé-Pareta, J., 2016. MolComML: The molecular communication markup language Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication, ACM NANOCOM 2016,
Doi: 10.1145/2967446.2967460
2016. Computational Methods in Systems Biology - 14th International Conference, CMSB 2016, Cambridge, UK, September 21-23, 2016, Proceedings CMSB, v. 9859
Moni, M. and Lio, P., 2016. Infectome, diseasome and comorbidities of Zika infection INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, v. 53
Doi: 10.1016/j.ijid.2016.11.040
Lu, X. and Lio, P., 2016. Privacy Information Security Classification and Comparison between the Westerner and Chinese Proceedings - 2015 International Conference on Identification, Information, and Knowledge in the Internet of Things, IIKI 2015,
Doi: 10.1109/IIKI.2015.10
Lu, X., Lio, P. and Hui, P., 2015. A content dissemination model for mobile internet to minimize load on cellular network Electronics, Communications and Networks IV - Proceedings of the 4th International Conference on Electronics, Communications and Networks, CECNet2014,
Doi: 10.1201/b18592-54
Tordini, F., Drocco, M., Misale, C., Milanesi, L., Lio, P., Merelli, I. and Aldinucci, M., 2015. Parallel Exploration of the Nuclear Chromosome Conformation with <i>NuChart</i>-<i>II</i> 23RD EUROMICRO INTERNATIONAL CONFERENCE ON PARALLEL, DISTRIBUTED, AND NETWORK-BASED PROCESSING (PDP 2015),
Doi: 10.1109/PDP.2015.104
Boutorh, A., Pratanwanich, N., Guessoum, A. and Liò, P., 2015. Drug repurposing by optimizing mining of genes target association Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8623
Doi: 10.1007/978-3-319-24462-4_18
Di Serio, C., Liò, P., Nonis, A. and Tagliaferri, R., 2015. Computational intelligence methods for bioinformatics and biostatistics: 11th international meeting, CIBB 2014 Cambridge, UK, june 26–28, 2014 revised selected papers Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8623
Bardozzo, F., Lió, P. and Tagliaferri, R., 2015. Multi omic oscillations in bacterial pathways Proceedings of the International Joint Conference on Neural Networks, v. 2015-September
Doi: 10.1109/IJCNN.2015.7280853
Tordini, F., Drocco, M., Merelli, I., Milanesi, L., Liò, P. and Aldinucci, M., 2015. NuChart-II: A graph-based approach for analysis and interpretation of Hi-C data Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8623
Doi: 10.1007/978-3-319-24462-4_25
Pratanwanich, N. and Lio, P., 2015. Who wrote this? Textual modeling with authorship attribution in big data IEEE International Conference on Data Mining Workshops, ICDMW, v. 2015-January
Doi: 10.1109/ICDMW.2014.140
Hamey, FK., Shavit, Y., Maciulyte, V., Town, C., Liò, P. and Tosi, S., 2015. Automated detection of fluorescent probes in molecular imaging Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8623
Doi: 10.1007/978-3-319-24462-4_6
Iuliano, A., Occhipinti, A., Angelini, C., De Feis, I. and Lió, P., 2015. Applications of network-based survival analysis methods for pathways detection in cancer Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8623
Doi: 10.1007/978-3-319-24462-4_7
Korhonen, A., Guo, Y., Baker, S., Yetisgen-Yildiz, M., Stenius, U., Narita, M. and Liò, P., 2015. Improving literature-based discovery with advanced text mining Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8623
Doi: 10.1007/978-3-319-24462-4_8
Tordini, F., Drocco, M., Misale, C., Milanesi, L., Lió, P., Merelli, I. and Aldinucci, M., 2015. Parallel exploration of the nuclear Chromosome Conformation with NuChart-II Proceedings - 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2015,
Doi: 10.1109/PDP.2015.104
Angione, C., Bartocci, E., Bortolussi, L., Lio, P., Occhipinti, A. and Sanguinetti, G., 2014 (No publication date). Bayesian Design for Whole Cell Synthetic Biology Models Proceedings of the Third International Workshop on Hybrid Systems Biology (HSB 2014),
Angione, C., Pratanwanich, N. and Lio, P., 2014 (No publication date). A hybrid of multi-omics FBA and Bayesian factor modeling to identify pathway crosstalks Proceedings of the 6th International Workshop on Bio-Design Automation (IWBDA),
Scatà, M., Di Stefano, A., Giacchi, E., La Corte, A. and Liò, P., 2014. The bio-inspired and social evolution of node and data in a multilayer network DCNET 2014 - Proceedings of the 5th International Conference on Data Communication Networking, Part of ICETE 2014 - 11th International Joint Conference on e-Business and Telecommunications,
Doi: 10.5220/0005119600410046
Fernandes, PL., Liò, P. and Milanesi, L., 2014. Challenges in building an e-health infrastructure for P5 medicine Conference on Computer Science and Information Systems, MCCSIS 2014 ...,
Lu, X., Lio, P., Hui, P. and Qu, Z., 2014. Nodes density adaptive opportunistic forwarding protocol for intermittently connected networks Proceedings - 2014 International Conference on Identification, Information and Knowledge in the Internet of Things, IIKI 2014,
Doi: 10.1109/IIKI.2014.67
Lió, P., 2014. Computing longevity: Insights from controls Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8738 LNBI
Doi: 10.1007/978-3-319-10398-3_4
Felicetti, L., Femminella, M., Reali, G. and Liò, P., 2014. Endovascular mobile sensor network for detecting circulating tumoral cells BODYNETS 2014 - 9th International Conference on Body Area Networks,
Doi: 10.4108/icst.bodynets.2014.256917
Bartoszek, K. and Lio, P., 2014. A novel algorithm to reconstruct phylogenies using gene sequences and expression data
Nguyen, VA. and Lio, P., 2013 (No publication date). Filling in the gaps of biological network
Liò, P., 2013. Methodologies for Systems Medicine: Time to Join the Forces of Bioengineering and Bioinformatics. BIOINFORMATICS,
Pratanwanich, N. and Lio, P., 2013. Bayesian Inference for Learning Between-Pathway Network: A New Tool for Studying Drug-Disease Interactions HUMAN HEREDITY, v. 76
2013. Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life, ECAL 2013, Sicily, Italy, September 2-6, 2013 ECAL,
Bansal, A., Azad, S. and Lio, P., 2013. Malaria Incidence Forecasting and Its Implication to Intervention Proceedings of the European Conference on Complex Systems 2012,
Liò, P., Jacovella, L. and Nguyen, V., 2013. Information filtering and learning: From heuristics to social eudaimonia
Doi: 10.1007/978-3-319-00395-5_125
Angione, C., Carapezza, G., Costanza, J., Lió, P. and Nicosia, G., 2013. The role of the genome in the evolution of the complexity of metabolic machines
Doi: 10.1007/978-3-319-00395-5_127
Bianchi, L., Fernandes, P. and Lio, P., 2013. Improving collective awareness and education about the privacy and ethical issues connected with the genome technologies The Future of Education, Conference Proceedings 2013,
Kim, H., Khoo, WM. and Lio, P., 2012. Polymorphic Attacks against Sequence-based Software Birthmarks
2012. Artificial Immune Systems - 11th International Conference, ICARIS 2012, Taormina, Italy, August 28-31, 2012. Proceedings ICARIS, v. 7597
Lio, P., 2011 (No publication date). Long Range Properties of DNA Sequences Collana Franco Angeli Editore,
2011. Artificial Immune Systems - 10th International Conference, ICARIS 2011, Cambridge, UK, July 18-21, 2011. Proceedings ICARIS, v. 6825
Lio, P., Emanuela Merelli, and Nicola Paoletti, NP., 2011. Multiple verification in computational modeling of bone pathologies EPTCS, v. 67
Merelli, E., Paoletti, N. and Lio, P., 2011. Methodological Bridges for Multi-Level Systems Procedia Computer Science, v. 7
Bartoszek, K., Lio, P. and Sorathiya, A., 2010. INFLUENZA DIFFERENTIATION AND EVOLUTION SUMMER SOLSTICE 2009 INTERNATIONAL CONFERENCE ON DISCRETE MODELS OF COMPLEX SYSTEMS, v. 3
Aldinucci, M., Bracciali, A., Liò, P., Sorathiya, A. and Torquati, M., 2010. StochKit-FF: Efficient Systems Biology on Multicore Architectures. Euro-Par Workshops, v. 6586
Ostilli, M., Yoneki, E., Leung, IXY., Mendes, JFF., Lio, P. and Crowcroft, J., 2010. Statistical mechanics of rumour spreading in network communities ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, v. 1
Doi: 10.1016/j.procs.2010.04.262
Kitchovitch, S. and Lio, P., 2010. Risk perception and disease spread on social networks ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, v. 1
Doi: 10.1016/j.procs.2010.04.264
Chan, TM., Leung, KS., Lee, KH. and Lio, P., 2010. Generic Spaced DNA Motif Discovery Using Genetic Algorithm 2010 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION (CEC),
Guazzini, A., Lio, P., Bagnoli, F., Passarella, A. and Conti, M., 2010. Cognitive network dynamics in chatlines ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, v. 1
Doi: 10.1016/j.procs.2010.04.265
Papini, A., Nicosia, G., Stracquadanio, G., Lio, P. and Umeton, R., 2010. Key Enzymes for the Optimization of CO2 Uptake and Nitrogen Consumption in the C-3 Photosynthetic Carbon Metabolism JOURNAL OF BIOTECHNOLOGY, v. 150
Doi: 10.1016/j.jbiotec.2010.09.846
Papini, A., Mosti, S., Lio, P. and Haider, S., 2010. BIOLIP, a biotechnology-oriented database of oil content in plants, algae, fungi and cyanobacteria JOURNAL OF BIOTECHNOLOGY, v. 150
Doi: 10.1016/j.jbiotec.2010.09.012
Xu, K., Hui, P., Li, VOK., Crowcroft, J., Latora, V. and Lio, P., 2009. Impact of Altruism on Opportunistic Communications 2009 FIRST INTERNATIONAL CONFERENCE ON UBIQUITOUS AND FUTURE NETWORKS,
Kitchovitch, S., Song, YD., van der Wath, R. and Lio, P., 2009. Substitution Matrices and Mutual Information Approaches to Modeling Evolution LEARNING AND INTELLIGENT OPTIMIZATION, v. 5851
Kitchovitch, S., Leung, I., Song, YD. and Lio, P., 2009. Using Mutual Information and Models of Evolution for improved pattern detection 2009 INTERNATIONAL JOINT CONFERENCE ON BIOINFORMATICS, SYSTEMS BIOLOGY AND INTELLIGENT COMPUTING, PROCEEDINGS,
Doi: 10.1109/IJCBS.2009.77
Sorathiya, A., Jucikas, T., Piecewicz, S., Sengupta, S. and Lio, P., 2009. Searching for Glycomics Role in Stem Cell Development COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS, v. 5488
Guazzini, A., Lio, P., Passarella, A. and Conti, M., 2009. Information Processing and Timing Mechanisms in Vision ARTIFICIAL NEURAL NETWORKS - ICANN 2009, PT I, v. 5768
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Nguyen, VA., Koukolikova-Nicola, Z., Bagnoli, F. and Lio, P., 2008. Bayesian Inference on Hidden Knowledge in High-Throughput Molecular Biology Data PRICAI 2008: TRENDS IN ARTIFICIAL INTELLIGENCE, v. 5351
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Doi: 10.1109/ISM.Workshops.2007.61
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Doi: 10.1186/1471-2148-7-S2-S5
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Doi: 10.1186/1471-2148-7-S2-S4
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Doi: 10.1186/1471-2148-7-S2-S8
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Lu, YE., Hand, S. and Lio, P., 2005. Keyword searching in hypercubic manifolds Fifth IEEE International Conference on Peer-to-Peer Computing, Proceedings,
Lio, P., 2005. Phylogenetic and structural analysis of mitochondrial complex I proteins GENE, v. 345
Doi: 10.1016/j.gene.2004.11.033
Brilli, M., Lio, P., Lazcano, A. and Fani, R., 2002. Evolution of TIM barrel: Multiple gene elongation events in HisA. Origins of Life and Evolution of the Biosphere, v. 22
Lio, P., 2002. Structure and evolution of the histidine biosynthetic pathway Origins of Life and Evolution of the Biosphere, v. 22
Hagelberg, E., Kayser, M., Nagy, M., Roewer, L., Zimdahl, H., Krawczak, M., Lió, P. and Schiefenhövel, W., 1999. Molecular genetic evidence for the human settlement of the Pacific: analysis of mitochondrial DNA, Y chromosome and HLA markers. Philos Trans R Soc Lond B Biol Sci, v. 354
Doi: 10.1098/rstb.1999.0367
Thomas, NS., Wilkinson, J., Lio, P., Doull, I., Morton, NE. and Holgate, ST., 1997. Investigation of the genetic factors underlying asthma and atopy in outbred UK populations 5TH WEST-PACIFIC ALLERGY SYMPOSIUM / 7TH KOREA-JAPAN JOINT ALLERGY SYMPOSIUM,
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Fani, R., Bandi, C., Bazzicalupo, M., Damiani, G., Di Cello, F., Fancelli, S., Gerace, L., Grifoni, A., Lio, P. and Mori, E., 1994. Phylogenetic Studies of the Genus Azospirillum Related Microorganisms:: Genetics - Physiology - Ecology (NATO ASI Series / Ecological Sciences),
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Doi: 10.1038/s41421-024-00728-2
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Wang, Z., Ma, J., Gao, Q., Bain, C., Imoto, S., Liò, P., Cai, H., Chen, H. and Song, J., 2024. Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. Med Image Anal, v. 97
Doi: 10.1016/j.media.2024.103252
Kulyte, P., Vargas, F., Mathis, SV., Wang, YG., Hernández-Lobato, JM. and Liò, P., 2024. Improving Antibody Design with Force-Guided Sampling in Diffusion Models. CoRR, v. abs/2406.05832
Braithwaite, L., Duta, I. and Liò, P., 2024. Heterogeneous Sheaf Neural Networks. CoRR, v. abs/2409.08036
Somathilaka, S., Ratwatte, A., Balasubramaniam, S., Vuran, MC., Srisa-an, W. and Liò, P., 2024. Wet TinyML: Chemical Neural Network Using Gene Regulation and Cell Plasticity. CoRR, v. abs/2403.08549
Moss, J., England, J. and Lió, P., 2024. Deep Kernel Learning of Nonlinear Latent Force Models Transactions on Machine Learning Research, v. 2024
Huang, K., Wang, YG., Li, M. and Liò, P., 2024. How Universal Polynomial Bases Enhance Spectral Graph Neural Networks: Heterophily, Over-smoothing, and Over-squashing Proceedings of Machine Learning Research, v. 235
Su, S., Duta, I., Magister, LC. and Liò, P., 2024. Explaining Hypergraph Neural Networks: From Local Explanations to Global Concepts. CoRR, v. abs/2410.07764
Georgiev, D., Wilson, JJ., Buffelli, D. and Liò, P., 2024. Deep Equilibrium Algorithmic Reasoning Advances in Neural Information Processing Systems, v. 37
Dong, T., Jamnik, M. and Liò, P., 2024. Sphere Neural-Networks for Rational Reasoning. CoRR, v. abs/2403.15297
Raisa, RA., Rodela, AS., Yousuf, MA., Azad, A., Alyami, SA., Lio, P., Islam, MZ., Pogrebna, G. and Moni, MA., 2024. Deep and Shallow Learning Model-Based Sleep Apnea Diagnosis Systems: A Comprehensive Study IEEE Access, v. 12
Doi: 10.1109/ACCESS.2024.3426928
Lope, EGD., Deshpande, S., Torné, RV., Liò, P., Glaab, E. and Bordas, SPA., 2024. Graph Representation Learning Strategies for Omics Data: A Case Study on Parkinson's Disease. CoRR, v. abs/2406.14442
Sabari, A., Hasan, I., Alyami, SA., Liò, P., Ali, MS., Moni, MA. and Azad, AKM., 2024. LandSin: A differential ML and google API-enabled web server for real-time land insights and beyond[Formula presented] Software Impacts, v. 22
Doi: http://doi.org/10.1016/j.simpa.2024.100718
Buterez, D., Janet, JP., Kiddle, SJ., Oglic, D. and Lió, P., 2024. Transfer learning with graph neural networks for improved molecular property prediction in the multi-fidelity setting. Nat Commun, v. 15
Doi: 10.1038/s41467-024-45566-8
Zaki, JK., Tomasik, J., McCune, JA., Bahn, S., Liò, P. and Scherman, OA., 2024. Explainable Deep Learning Framework for SERS Bio-quantification. CoRR, v. abs/2411.08082
Defilippo, A., Veltri, P., Lió, P. and Guzzi, PH., 2024. Leveraging graph neural networks for supporting automatic triage of patients. Sci Rep, v. 14
Doi: 10.1038/s41598-024-63376-2
Rowbottom, J., Maierhofer, G., Deveney, T., Schratz, K., Liò, P., Schönlieb, C-B. and Budd, CJ., 2024. G-Adaptive mesh refinement - leveraging graph neural networks and differentiable finite element solvers. CoRR, v. abs/2407.04516
Schneuing, A., Harris, C., Du, Y., Didi, K., Jamasb, A., Igashov, I., Du, W., Gomes, C., Blundell, TL., Lio, P., Welling, M., Bronstein, M. and Correia, B., 2024. Structure-based drug design with equivariant diffusion models. Nat Comput Sci, v. 4
Doi: http://doi.org/10.1038/s43588-024-00737-x
Mumenin, N., Yousuf, MA., Nashiry, MA., Azad, AKM., Alyami, SA., Lio', P. and Moni, MA., 2024. ASDNet: A robust involution-based architecture for diagnosis of autism spectrum disorder utilising eye-tracking technology IET Computer Vision, v. 18
Doi: 10.1049/cvi2.12271
Singh, V., Khanzadeh, M., Davis, V., Rush, H., Rossi, E., Shrader, J. and Lio, P., 2024. Bayesian Binary Search. CoRR, v. abs/2410.01771
Buterez, D., Janet, JP., Oglic, D. and Lio, P., 2024. Masked Attention is All You Need for Graphs. CoRR, v. abs/2402.10793
Zhao, X., Li, Z., Shen, M., Stan, G-B., Liò, P. and Zhao, Y., 2024. Enhancing Real-World Complex Network Representations with Hyperedge Augmentation. CoRR, v. abs/2402.13033
Jamasb, AR., Morehead, A., Joshi, CK., Zhang, Z., Didi, K., Mathis, S., Harris, C., Tang, J., Cheng, J., Liò, P. and Blundell, TL., 2024. Evaluating Representation Learning on the Protein Structure Universe. ArXiv,
Zhu, M., Bazaga, A. and Liò, P., 2024. FLUID-LLM: Learning Computational Fluid Dynamics with Spatiotemporal-aware Large Language Models. CoRR, v. abs/2406.04501
Nobel, SMN., Swapno, SMMR., Islam, MB., Azad, AKM., Alyami, SA., Alamin, M., Liò, P. and Moni, MA., 2024. A Novel Mixed Convolution Transformer Model for the Fast and Accurate Diagnosis of Glioma Subtypes Advanced Intelligent Systems,
Doi: http://doi.org/10.1002/aisy.202400566
Bazaga, A., Liò, P. and Micklem, G., 2024. HyperBERT: Mixing Hypergraph-Aware Layers with Language Models for Node Classification on Text-Attributed Hypergraphs EMNLP 2024 - 2024 Conference on Empirical Methods in Natural Language Processing, Findings of EMNLP 2024,
Doi: 10.18653/v1/2024.findings-emnlp.537
Ceccarelli, F., Liò, P. and Holden, SB., 2024. AnnoGCD: a generalized category discovery framework for automatic cell type annotation. NAR Genom Bioinform, v. 6
Doi: http://doi.org/10.1093/nargab/lqae166
Margeloiu, A., Simidjievski, N., Liò, P. and Jamnik, M., 2023 (Published online). Weight Predictor Network with Feature Selection for Small Sample Tabular Biomedical Data Proceedings of the AAAI Conference on Artificial Intelligence, v. 37
Doi: 10.1609/aaai.v37i8.26090
Breger, A., Selby, I., Roberts, M., Babar, J., Gkrania-Klotsas, E., Preller, J., Escudero Sanchez, L., Rudd, J., Aston, J., Weir-McCall, J., Sala, E. and Schoenlieb, C., 2023 (Accepted for publication). A pipeline to further enhance quality, integrity and reusability of the NCCID clinical data Scientific data,
Doi: 10.1038/s41597-023-02340-7
Petrović, A., Nikolić, M., Bugarić, U., Delibašić, B. and Lio, P., 2023. Controlling highway toll stations using deep learning, queuing theory, and differential evolution Engineering Applications of Artificial Intelligence, v. 119
Doi: 10.1016/j.engappai.2022.105683
Zou, X., Zhao, X., Liò, P. and Zhao, Y., 2023. Will More Expressive Graph Neural Networks do Better on Generative Tasks? Proceedings of Machine Learning Research, v. 231
Bujel, K., Gideoni, Y., Joshi, CK. and Liò, P., 2023. Group Invariant Global Pooling. CoRR, v. abs/2305.19207
Ambags, EL., Capitoli, G., Imperio, VL., Provenzano, M., Nobile, MS. and Liò, P., 2023. Assisting clinical practice with fuzzy probabilistic decision trees. CoRR, v. abs/2304.07788
Nayan, SI., Rahman, MH., Hasan, MM., Raj, SMRH., Almoyad, MAA., Liò, P. and Moni, MA., 2023. Network based approach to identify interactions between Type 2 diabetes and cancer comorbidities. Life Sci, v. 335
Doi: 10.1016/j.lfs.2023.122244
de Ocáriz Borde, HS., Kazi, A., Barbero, F. and Liò, P., 2023. LATENT GRAPH INFERENCE USING PRODUCT MANIFOLDS 11th International Conference on Learning Representations, ICLR 2023,
Kidwai, S., Barbiero, P., Meijerman, I., Tonda, A., Perez-Pardo, P., Lio, P., van der Maitland-Zee, AH., Oberski, DL., Kraneveld, AD. and Lopez-Rincon, A., 2023. A robust mRNA signature obtained via recursive ensemble feature selection predicts the responsiveness of omalizumab in moderate-to-severe asthma. Clin Transl Allergy, v. 13
Doi: 10.1002/clt2.12306
Caso, F., Trappolini, G., Bacciu, A., Liò, P. and Silvestri, F., 2023. Renormalized Graph Neural Networks. CoRR, v. abs/2306.00707
Xuanyuan, H., Barbiero, P., Georgiev, D., Magister, LC. and Liò, P., 2023. Global Concept-Based Interpretability for Graph Neural Networks via Neuron Analysis Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI 2023, v. 37
Doi: 10.1609/aaai.v37i9.26267
Bergna, R., Opolka, FL., Liò, P. and Hernández-Lobato, JM., 2023. Graph Neural Stochastic Differential Equations. CoRR, v. abs/2308.12316
Huang, K. and Liò, P., 2023. An Effective Universal Polynomial Basis for Spectral Graph Neural Networks. CoRR, v. abs/2311.18177
Buterez, D., Janet, JP., Kiddle, SJ., Oglic, D. and Liò, P., 2023. Modelling local and general quantum mechanical properties with attention-based pooling. Commun Chem, v. 6
Doi: 10.1038/s42004-023-01045-7
Sathyanarayanan, A., Mueller, TT., Ali Moni, M., Schueler, K., ECNP TWG Network members, , Baune, BT., Lio, P., Mehta, D., Baune, BT., Dierssen, M., Ebert, B., Fabbri, C., Fusar-Poli, P., Gennarelli, M., Harmer, C., Howes, OD., Janzing, JGE., Lio, P., Maron, E., Mehta, D., Minelli, A., Nonell, L., Pisanu, C., Potier, M-C., Rybakowski, F., Serretti, A., Squassina, A., Stacey, D., van Westrhenen, R. and Xicota, L., 2023. Multi-omics data integration methods and their applications in psychiatric disorders. Eur Neuropsychopharmacol, v. 69
Doi: 10.1016/j.euroneuro.2023.01.001
Purificato, A., Cassarà, G., Liò, P. and Silvestri, F., 2023. Sheaf Neural Networks for Graph-based Recommender Systems. CoRR, v. abs/2304.09097
Jain, R., Velickovic, P. and Liò, P., 2023. Neural Priority Queues for Graph Neural Networks. CoRR, v. abs/2307.09660
Longa, A., Lachi, V., Santin, G., Bianchini, M., Lepri, B., Liò, P., Scarselli, F. and Passerini, A., 2023. Graph Neural Networks for Temporal Graphs: State of the Art, Open Challenges, and Opportunities Transactions on Machine Learning Research, v. 2023
Lu, Y., Borde, HSDO. and Liò, P., 2023. AMES: A Differentiable Embedding Space Selection Framework for Latent Graph Inference. CoRR, v. abs/2311.11891
Lu, X., Liu, C., Zhu, S., Mao, Y., Lio, P. and Hui, P., 2023. RLPTO: A Reinforcement Learning-Based Performance-Time Optimized Task and Resource Scheduling Mechanism for Distributed Machine Learning IEEE Transactions on Parallel and Distributed Systems, v. 34
Doi: 10.1109/TPDS.2023.3317388
Waqas, M., Aziz, S., Liò, P., Khan, Y., Ali, A., Iqbal, A., Khan, F. and Almajhdi, FN., 2023. Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets. Front Immunol, v. 14
Doi: 10.3389/fimmu.2023.1091941
Ceccarelli, F., Giusti, L., Holden, SB. and Liò, P., 2023. Neural Embeddings for Protein Graphs. CoRR, v. abs/2306.04667
Azevedo, T., Bethlehem, RAI., Whiteside, DJ., Swaddiwudhipong, N., Rowe, JB., Lió, P., Rittman, T. and Alzheimer’s Disease Neuroimaging Initiative, , 2023. Identifying healthy individuals with Alzheimer's disease neuroimaging phenotypes in the UK Biobank. Commun Med (Lond), v. 3
Doi: 10.1038/s43856-023-00313-w
Yi, K., Zhou, B., Shen, Y., Liò, P. and Wang, YG., 2023. Graph Denoising Diffusion for Inverse Protein Folding Advances in Neural Information Processing Systems, v. 36
Zhu, J., Yang, G. and Liò, P., 2023. A residual dense vision transformer for medical image super-resolution with segmentation-based perceptual loss fine-tuning. CoRR, v. abs/2302.11184
Jiang, Y., Ding, Q., Wang, YG., Liò, P. and Zhang, X., 2023. VISION GRAPH U-NET: GEOMETRIC LEARNING ENHANCED ENCODER FOR MEDICAL IMAGE SEGMENTATION AND RESTORATION Inverse Problems and Imaging, v. 2023
Doi: 10.3934/ipi.2023049
Yang, J. and Liò, P., 2023. Unsupervised Adaptive Implicit Neural Representation Learning for Scan-Specific MRI Reconstruction. CoRR, v. abs/2312.00677
Georgiev, D., Numeroso, D., Bacciu, D. and Liò, P., 2023. Neural Algorithmic Reasoning for Combinatorial Optimisation Proceedings of Machine Learning Research, v. 231
Kazhdan, D., Dimanov, B., Magister, LC., Barbiero, P., Jamnik, M. and Liò, P., 2023. GCI: A (G)raph (C)oncept (I)nterpretation Framework. CoRR, v. abs/2302.04899
Shadbahr, T., Roberts, M., Stanczuk, J., Gilbey, J., Teare, P., Dittmer, S., Thorpe, M., Torné, RV., Sala, E., Lió, P., Patel, M., Preller, J., AIX-COVNET Collaboration, , Rudd, JHF., Mirtti, T., Rannikko, AS., Aston, JAD., Tang, J. and Schönlieb, C-B., 2023. The impact of imputation quality on machine learning classifiers for datasets with missing values. Commun Med (Lond), v. 3
Doi: 10.1038/s43856-023-00356-z
Duval, A., Mathis, SV., Joshi, CK., Schmidt, V., Miret, S., Malliaros, FD., Cohen, T., Lio, P., Bengio, Y. and Bronstein, MM., 2023. A Hitchhiker's Guide to Geometric GNNs for 3D Atomic Systems. CoRR, v. abs/2312.07511
COVID-19 Host Genetics Initiative, , 2023. A second update on mapping the human genetic architecture of COVID-19. Nature, v. 621
Doi: 10.1038/s41586-023-06355-3
Azzolin, S., Longa, A., Barbiero, P., Liò, P. and Passerini, A., 2023. GLOBAL EXPLAINABILITY OF GNNS VIA LOGIC COMBINATION OF LEARNED CONCEPTS 11th International Conference on Learning Representations, ICLR 2023,
Shen, Z., Cheng, Y., Chan, RH., Liò, P., Schönlieb, C-B. and Avilés-Rivero, AI., 2023. TRIDENT: The Nonlinear Trilogy for Implicit Neural Representations. CoRR, v. abs/2311.13610
Joshi, CK., Jamasb, AR., Viñas, R., Harris, C., Mathis, SV. and Liò, P., 2023. Multi-State RNA Design with Geometric Multi-Graph Neural Networks. CoRR, v. abs/2305.14749
Crisostomi, D., Cannistraci, I., Moschella, L., Barbiero, P., Ciccone, M., Liò, P. and Rodolà, E., 2023. From Charts to Atlas: Merging Latent Spaces into One. CoRR, v. abs/2311.06547
Didi, K., Vargas, F., Mathis, SV., Dutordoir, V., Mathieu, E., Komorowska, UJ. and Lio, P., 2023. A framework for conditional diffusion modelling with applications in motif scaffolding for protein design. CoRR, v. abs/2312.09236
Dimitri, GM., Spasov, SE., Duggento, A., Passamonti, L., Liò, P. and Toschi, N., 2023. Multimodal and multicontrast image fusion via deep generative models. CoRR, v. abs/2303.15963
Viñas, R., Joshi, CK., Georgiev, D., Lin, P., Dumitrascu, B., Gamazon, ER. and Liò, P., 2023. Hypergraph factorization for multi-tissue gene expression imputation. Nat Mach Intell, v. 5
Doi: 10.1038/s42256-023-00684-8
Brant, I., Norcliffe, A. and Liò, P., 2023. Fourier Neural Differential Equations for learning Quantum Field Theories. CoRR, v. abs/2311.17250
Mei, X., Yang, Y., Li, M., Huang, C., Zhang, K. and Lió, P., 2023. A Feature Reuse Framework with Texture-adaptive Aggregation for Reference-based Super-Resolution. CoRR, v. abs/2306.01500
Liu, L., Cheng, Y., Chen, D., He, J., Liò, P., Schönlieb, C-B. and Avilés-Rivero, AI., 2023. Traffic Video Object Detection using Motion Prior. CoRR, v. abs/2311.10092
Ciravegna, G., Barbiero, P., Giannini, F., Gori, M., Liò, P., Maggini, M. and Melacci, S., 2023. Logic Explained Networks. Artif. Intell., v. 314
Jürß, J., Magister, LC., Barbiero, P., Liò, P. and Simidjievski, N., 2023. Everybody Needs a Little HELP: Explaining Graphs via Hierarchical Concepts. CoRR, v. abs/2311.15112
Campbell, A., Zippo, AG., Passamonti, L., Toschi, N. and Liò, P., 2023. DBGSL: Dynamic Brain Graph Structure Learning Proceedings of Machine Learning Research, v. 227
Islam, MS., Hasan, KF., Sultana, S., Uddin, S., Lio', P., Quinn, JMW. and Moni, MA., 2023. HARDC : A novel ECG-based heartbeat classification method to detect arrhythmia using hierarchical attention based dual structured RNN with dilated CNN. Neural Netw, v. 162
Doi: 10.1016/j.neunet.2023.03.004
Bernárdez, G., Telyatnikov, L., Alarcón, E., Cabellos-Aparicio, A., Barlet-Ros, P. and Liò, P., 2023. Topological Graph Signal Compression. CoRR, v. abs/2308.11068
Dittmer, S., Roberts, M., Gilbey, J., Biguri, A., Selby, I., Breger, A., Thorpe, M., Weir-McCall, JR., Gkrania-Klotsas, E., Korhonen, A., Jefferson, E., Langs, G., Yang, G., Prosch, H., Stanczuk, J., Tang, J., Babar, J., Escudero Sánchez, L., Teare, P., Patel, M., Wassin, M., Holzer, M., Walton, N., Lió, P., Shadbahr, T., Sala, E., Preller, J., Rudd, JHF., Aston, JAD. and Schönlieb, CB., 2023. Navigating the development challenges in creating complex data systems Nature Machine Intelligence, v. 5
Doi: 10.1038/s42256-023-00665-x
Yeh, KF., Flood, PDL., Redman, W. and Liò, P., 2023. Learning Linear Embeddings for Non-Linear Network Dynamics with Koopman Message Passing. CoRR, v. abs/2305.09060
Bardozzo, F., Terlizzi, A., Liò, P. and Tagliaferri, R., 2023. ElegansNet: a brief scientific report and initial experiments. CoRR, v. abs/2304.13538
Zhao, X., Stärk, H., Beaini, D., Liò, P. and Zhao, Y., 2023. Task-Agnostic Graph Neural Network Evaluation via Adversarial Collaboration. CoRR, v. abs/2301.11517
Bazaga, A., Liò, P. and Micklem, G., 2023. Language Model Knowledge Distillation for Efficient Question Answering in Spanish. CoRR, v. abs/2312.04193
Yang, J. and Liò, P., 2023. Dual-Domain Multi-Contrast MRI Reconstruction with Synthesis-based Fusion Network. CoRR, v. abs/2312.00661
Lu, M., Christensen, CN., Weber, JM., Konno, T., Läubli, NF., Scherer, KM., Avezov, E., Lio, P., Lapkin, AA., Kaminski Schierle, GS. and Kaminski, CF., 2023. ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology. Nat Methods, v. 20
Doi: 10.1038/s41592-023-01815-0
Zhu, M., Kobalczyk, K., Petrovic, A., Nikolic, M., Schaar, MVD., Delibasic, B. and Liò, P., 2023. Tabular Few-Shot Generalization Across Heterogeneous Feature Spaces. CoRR, v. abs/2311.10051
Bisercic, A., Nikolic, M., Schaar, MVD., Delibasic, B., Liò, P. and Petrovic, A., 2023. Interpretable Medical Diagnostics with Structured Data Extraction by Large Language Models. CoRR, v. abs/2306.05052
Chen, J., Wang, Y., Bodnar, C., Ying, R., Lio, P. and Wang, Y., 2023. Dirichlet Energy Enhancement of Graph Neural Networks by Framelet Augmentation. CoRR, v. abs/2311.05767
Del Duca, S., Semenzato, G., Esposito, A., Liò, P. and Fani, R., 2023. The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis. Genes (Basel), v. 14
Doi: 10.3390/genes14040949
Giannini, F., Fioravanti, S., Keskin, O., Lupidi, AM., Magister, LC., Lió, P. and Barbiero, P., 2023. Interpretable Graph Networks Formulate Universal Algebra Conjectures Advances in Neural Information Processing Systems, v. 36
Villaforesta, AFD., Magister, LC., Barbiero, P. and Liò, P., 2023. Digital Histopathology with Graph Neural Networks: Concepts and Explanations for Clinicians. CoRR, v. abs/2312.02225
Buterez, D., Janet, JP., Kiddle, SJ. and Liò, P., 2023. MF-PCBA: Multifidelity High-Throughput Screening Benchmarks for Drug Discovery and Machine Learning. J Chem Inf Model, v. 63
Doi: 10.1021/acs.jcim.2c01569
Bazaga, A., Liò, P. and Micklem, G., 2023. SQLformer: Deep Auto-Regressive Query Graph Generation for Text-to-SQL Translation. CoRR, v. abs/2310.18376
Zhu, M., Stanivuk, S., Petrovic, A., Nikolic, M. and Lio, P., 2023. Incorporating LLM Priors into Tabular Learners. CoRR, v. abs/2311.11628
Chowdhury, AA., Hasan Mahmud, SM., Shahjalal Hoque, KK., Ahmed, K., Bui, FM., Lio, P., Moni, MA. and Al-Zahrani, FA., 2023. StackFBAs: Detection of fetal brain abnormalities using CNN with stacking strategy from MRI images Journal of King Saud University - Computer and Information Sciences, v. 35
Doi: 10.1016/j.jksuci.2023.101647
Wölflein, G., Magister, LC., Liò, P., Harrison, DJ. and Arandjelovic, O., 2023. Deep Multiple Instance Learning with Distance-Aware Self-Attention. CoRR, v. abs/2305.10552
Bongini, P., Scarselli, F., Bianchini, M., Dimitri, GM., Pancino, N. and Lio, P., 2023. Modular Multi-Source Prediction of Drug Side-Effects With DruGNN. IEEE/ACM Trans Comput Biol Bioinform, v. 20
Doi: 10.1109/TCBB.2022.3175362
Duta, I., Silvestri, F., Cassarà, G. and Liò, P., 2023. Sheaf Hypergraph Networks Advances in Neural Information Processing Systems, v. 36
Lu, X., Yang, F., Zou, L., Lio, P. and Hui, P., 2023. An LTE Authentication and Key Agreement Protocol Based on the ECC Self-Certified Public Key IEEE/ACM Transactions on Networking, v. 31
Doi: 10.1109/TNET.2022.3207360
Lachi, V., Dimitri, GM., Stefano, AD., Liò, P., Bianchini, M. and Mocenni, C., 2023. Impact of the Covid 19 outbreaks on the italian twitter vaccination debat: a network based analysis. CoRR, v. abs/2306.02838
Campbell, A., Spasov, S., Toschi, N. and Liò, P., 2023. DBGDGM: Dynamic Brain Graph Deep Generative Model Proceedings of Machine Learning Research, v. 227
Charoenkwan, P., Pipattanaboon, C., Nantasenamat, C., Hasan, MM., Moni, MA., Lio', P. and Shoombuatong, W., 2023. PSRTTCA: A new approach for improving the prediction and characterization of tumor T cell antigens using propensity score representation learning. Comput Biol Med, v. 152
Doi: 10.1016/j.compbiomed.2022.106368
Wang, Z., Gao, Q., Yi, X., Zhang, X., Zhang, Y., Zhang, D., Liò, P., Bain, C., Bassed, R., Li, S., Guo, Y., Imoto, S., Yao, J., Daly, RJ. and Song, J., 2023. Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. Comput Methods Programs Biomed, v. 241
Doi: 10.1016/j.cmpb.2023.107733
Giusti, L., Reu, T., Ceccarelli, F., Bodnar, C. and Liò, P., 2023. CIN++: Enhancing Topological Message Passing. CoRR, v. abs/2306.03561
Sun, Z., Harit, A., Cristea, AI., Wang, J. and Lio, P., 2023. MONEY: Ensemble learning for stock price movement prediction via a convolutional network with adversarial hypergraph model AI Open, v. 4
Doi: 10.1016/j.aiopen.2023.10.002
Ciravegna, G., Barbiero, P., Giannini, F., Gori, M., Liò, P., Maggini, M. and Melacci, S., 2023. Logic Explained Networks Artificial Intelligence, v. 314
Doi: 10.1016/j.artint.2022.103822
Dominici, G., Barbiero, P., Magister, LC., Liò, P. and Simidjievski, N., 2023. SHARCS: Shared Concept Space for Explainable Multimodal Learning. CoRR, v. abs/2307.00316
Li, Z., Zhao, X., Shen, M., Stan, G-B., Liò, P. and Zhao, Y., 2023. Hybrid Graph: A Unified Graph Representation with Datasets and Benchmarks for Complex Graphs. CoRR, v. abs/2306.05108
Faruqui, N., Yousuf, MA., Whaiduzzaman, M., Azad, AKM., Alyami, SA., Liò, P., Kabir, MA. and Moni, MA., 2023. SafetyMed: A Novel IoMT Intrusion Detection System Using CNN-LSTM Hybridization Electronics (Switzerland), v. 12
Doi: 10.3390/electronics12173541
Barbiero, P., Fioravanti, S., Giannini, F., Tonda, A., Liò, P. and Lavore, ED., 2023. Categorical Foundations of Explainable AI: A Unifying Formalism of Structures and Semantics. CoRR, v. abs/2304.14094
Yang, J., Li, X-X., Liu, F., Nie, D., Lio, P., Qi, H. and Shen, D., 2023. Fast Multi-Contrast MRI Acquisition by Optimal Sampling of Information Complementary to Pre-Acquired MRI Contrast. IEEE Trans Med Imaging, v. 42
Doi: 10.1109/TMI.2022.3227262
Lishkova, Y., Scherer, P., Ridderbusch, S., Jamnik, M., Liò, P., Ober-Blöbaum, S. and Offen, C., 2022 (Accepted for publication). Discrete Lagrangian Neural Networks with Automatic Symmetry Discovery IFAC-PapersOnLine, v. 56
Doi: 10.1016/j.ifacol.2023.10.1457
Meoni, G., Tenori, L., Schade, S., Licari, C., Pirazzini, C., Bacalini, MG., Garagnani, P., Turano, P., PROPAG-AGEING Consortium, , Trenkwalder, C., Franceschi, C., Mollenhauer, B. and Luchinat, C., 2022. Metabolite and lipoprotein profiles reveal sex-related oxidative stress imbalance in de novo drug-naive Parkinson's disease patients. NPJ Parkinsons Dis, v. 8
Doi: 10.1038/s41531-021-00274-8
Goh, CWJ., Bodnar, C. and Liò, P., 2022. Simplicial Attention Networks
Lu, X., Liao, Y., Liu, C., Lio, P. and Hui, P., 2022. Heterogeneous Model Fusion Federated Learning Mechanism Based on Model Mapping IEEE Internet of Things Journal, v. 9
Doi: 10.1109/JIOT.2021.3110908
Chen, Y., Schonlieb, CB., Lio, P., Leiner, T., Dragotti, PL., Wang, G., Rueckert, D., Firmin, D. and Yang, G., 2022. AI-Based Reconstruction for Fast MRI-A Systematic Review and Meta-Analysis Proceedings of the IEEE, v. 110
Doi: 10.1109/JPROC.2022.3141367
Borgheresi, R., Barucci, A., Colantonio, S., Aghakhanyan, G., Assante, M., Bertelli, E., Carlini, E., Carpi, R., Caudai, C., Cavallero, D., Cioni, D., Cirillo, R., Colcelli, V., Dell'Amico, A., Di Gangi, D., Erba, PA., Faggioni, L., Falaschi, Z., Gabelloni, M., Gini, R., Lelii, L., Liò, P., Lorito, A., Lucarini, S., Manghi, P., Mangiacrapa, F., Marzi, C., Mazzei, MA., Mercatelli, L., Mirabile, A., Mungai, F., Miele, V., Olmastroni, M., Pagano, P., Paiar, F., Panichi, G., Pascali, MA., Pasquinelli, F., Shortrede, JE., Tumminello, L., Volterrani, L., Neri, E. and NAVIGATOR Consortium Group, , 2022. NAVIGATOR: an Italian regional imaging biobank to promote precision medicine for oncologic patients. Eur Radiol Exp, v. 6
Doi: 10.1186/s41747-022-00306-9
Charoenkwan, P., Schaduangrat, N., Hasan, MM., Moni, MA., Lió, P. and Shoombuatong, W., 2022. Empirical comparison and analysis of machine learning-based predictors for predicting and analyzing of thermophilic proteins. EXCLI J, v. 21
Doi: 10.17179/excli2022-4723
Barbero, F., Bodnar, C., Borde, HSDO., Bronstein, M., Veličković, P. and Liò, P., 2022. Sheaf Neural Networks with Connection Laplacians
Charoenkwan, P., Schaduangrat, N., Lio', P., Moni, MA., Shoombuatong, W. and Manavalan, B., 2022. Computational prediction and interpretation of druggable proteins using a stacked ensemble-learning framework. iScience, v. 25
Doi: 10.1016/j.isci.2022.104883
Margeloiu, A., Simidjievski, N., Lio', P. and Jamnik, M., 2022. Graph-Conditioned MLP for High-Dimensional Tabular Biomedical Data. CoRR, v. abs/2211.06302
Liu, L., Huang, Z., Liò, P., Schönlieb, C-B. and Aviles-Rivero, AI., 2022. PC-SwinMorph: Patch Representation for Unsupervised Medical Image
Registration and Segmentation
Huang, J., Fang, Y., Nan, Y., Wu, H., Wu, Y., Gao, Z., Li, Y., Wang, Z., Lio, P., Rueckert, D., Eldar, YC. and Yang, G., 2022. Data and Physics Driven Learning Models for Fast MRI -- Fundamentals and
Methodologies from CNN, GAN to Attention and Transformers
Yi, K., Chen, J., Wang, YG., Zhou, B., Liò, P., Fan, Y. and Hamann, J., 2022. Approximate Equivariance SO(3) Needlet Convolution
Purves, C., Liò, P. and Cangea, C., 2022. Goal-Conditioned Reinforcement Learning in the Presence of an Adversary. CoRR, v. abs/2211.06929
Charoenkwan, P., Schaduangrat, N., Lio', P., Moni, MA., Manavalan, B. and Shoombuatong, W., 2022. NEPTUNE: A novel computational approach for accurate and large-scale identification of tumor homing peptides. Comput Biol Med, v. 148
Doi: 10.1016/j.compbiomed.2022.105700
Wang, Y., Wang, YG., Hu, C., Li, M., Fan, Y., Otter, N., Sam, I., Gou, H., Hu, Y., Kwok, T., Zalcberg, J., Boussioutas, A., Daly, RJ., Montúfar, G., Liò, P., Xu, D., Webb, GI. and Song, J., 2022. Cell graph neural networks enable the precise prediction of patient survival in gastric cancer. NPJ Precis Oncol, v. 6
Doi: 10.1038/s41698-022-00285-5
Dimitri, GM., Spasov, S., Duggento, A., Passamonti, L., Lió, P. and Toschi, N., 2022. Multimodal and multicontrast image fusion via deep generative models Information Fusion, v. 88
Doi: 10.1016/j.inffus.2022.07.017
Zafeiriou, S., Bronstein, M., Cohen, T., Vinyals, O., Song, L., Leskovec, J., Lio, P., Bruna, J. and Gori, M., 2022. Guest Editorial: Non-Euclidean Machine Learning IEEE Transactions on Pattern Analysis and Machine Intelligence, v. 44
Doi: 10.1109/TPAMI.2021.3129857
Chaturvedi, A., Tiwari, A., Chaturvedi, S. and Lio, P., 2022. System Neural Network: Evolution and Change Based Structure Learning IEEE Transactions on Artificial Intelligence, v. 3
Doi: 10.1109/TAI.2022.3143778
Dhillon, SK., Ganggayah, MD., Sinnadurai, S., Lio, P. and Taib, NA., 2022. Theory and Practice of Integrating Machine Learning and Conventional Statistics in Medical Data Analysis. Diagnostics (Basel), v. 12
Doi: 10.3390/diagnostics12102526
Pisanu, C., Severino, G., De Toma, I., Dierssen, M., Fusar-Poli, P., Gennarelli, M., Lio, P., Maffioletti, E., Maron, E., Mehta, D., Minelli, A., Potier, M-C., Serretti, A., Stacey, D., van Westrhenen, R., Xicota, L., European College of Neuropsychopharmacology (ECNP) Pharmacogenomics & Transcriptomics Network, , Baune, BT. and Squassina, A., 2022. Transcriptional biomarkers of response to pharmacological treatments in severe mental disorders: A systematic review. Eur Neuropsychopharmacol, v. 55
Doi: 10.1016/j.euroneuro.2021.12.005
Magister, LC., Barbiero, P., Kazhdan, D., Siciliano, F., Ciravegna, G., Silvestri, F., Liò, P. and Jamnik, M., 2022. Encoding Concepts in Graph Neural Networks. CoRR, v. abs/2207.13586
Charoenkwan, P., Schaduangrat, N., Moni, MA., Lio', P., Manavalan, B. and Shoombuatong, W., 2022. SAPPHIRE: A stacking-based ensemble learning framework for accurate prediction of thermophilic proteins. Comput Biol Med, v. 146
Doi: 10.1016/j.compbiomed.2022.105704
Aslam, AA., Baksh, RA., Pape, SE., Strydom, A., Gulliford, MC., Chan, LF. and GO-DS21 Consortium, , 2022. Diabetes and Obesity in Down Syndrome Across the Lifespan: A Retrospective Cohort Study Using U.K. Electronic Health Records. Diabetes Care, v. 45
Doi: 10.2337/dc22-0482
Charoenkwan, P., Chumnanpuen, P., Schaduangrat, N., Lio', P., Moni, MA. and Shoombuatong, W., 2022. Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides. J Comput Aided Mol Des, v. 36
Doi: 10.1007/s10822-022-00476-z
Scherer, P., Trebacz, M., Simidjievski, N., Viñas, R., Shams, Z., Andrés-Terré, H., Jamnik, M. and Liò, P., 2022. Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases. Bioinform., v. 38
Charoenkwan, P., Chiangjong, W., Nantasenamat, C., Moni, MA., Lio', P., Manavalan, B. and Shoombuatong, W., 2022. SCMTHP: A New Approach for Identifying and Characterizing of Tumor-Homing Peptides Using Estimated Propensity Scores of Amino Acids. Pharmaceutics, v. 14
Doi: 10.3390/pharmaceutics14010122
Azevedo, T., Campbell, A., Romero-Garcia, R., Passamonti, L., Bethlehem, RAI., Liò, P. and Toschi, N., 2022. A deep graph neural network architecture for modelling spatio-temporal dynamics in resting-state functional MRI data. Med Image Anal, v. 79
Doi: 10.1016/j.media.2022.102471
Zhi, Y-C., Opolka, FL., Ng, YC., Liò, P. and Dong, X., 2022. Transductive Kernels for Gaussian Processes on Graphs. CoRR, v. abs/2211.15322
Zago, E., Dal Molin, A., Dimitri, GM., Xumerle, L., Pirazzini, C., Bacalini, MG., Maturo, MG., Azevedo, T., Spasov, S., Gómez-Garre, P., Periñán, MT., Jesús, S., Baldelli, L., Sambati, L., Calandra-Buonaura, G., Garagnani, P., Provini, F., Cortelli, P., Mir, P., Trenkwalder, C., Mollenhauer, B., Franceschi, C., Liò, P., Nardini, C. and PROPAG-AGEING Consortium, , 2022. Early downregulation of hsa-miR-144-3p in serum from drug-naïve Parkinson's disease patients. Sci Rep, v. 12
Doi: 10.1038/s41598-022-05227-6
Zarlenga, ME., Barbiero, P., Ciravegna, G., Marra, G., Giannini, F., Diligenti, M., Shams, Z., Precioso, F., Melacci, S., Weller, A., Liò, P. and Jamnik, M., 2022. Concept Embedding Models. CoRR, v. abs/2209.09056
Scherer, P., Trębacz, M., Simidjievski, N., Viñas, R., Shams, Z., Terre, HA., Jamnik, M. and Liò, P., 2022. Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases. Bioinformatics, v. 38
Doi: 10.1093/bioinformatics/btab830
Christensen, CN., Lu, M., Ward, EN., Liò, P. and Kaminski, CF., 2022. Spatio-temporal Vision Transformer for Super-resolution Microscopy. CoRR, v. abs/2203.00030
Bodnar, C., Giovanni, FD., Chamberlain, BP., Liò, P. and Bronstein, MM., 2022. Neural Sheaf Diffusion: A Topological Perspective on Heterophily and
Oversmoothing in GNNs
Charoenkwan, P., Ahmed, S., Nantasenamat, C., Quinn, JMW., Moni, MA., Lio', P. and Shoombuatong, W., 2022. AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning. Sci Rep, v. 12
Doi: 10.1038/s41598-022-11897-z
Tong, C., Rocheteau, E., Veličković, P., Lane, N. and Liò, P., 2022. Predicting Patient Outcomes with Graph Representation Learning Studies in Computational Intelligence, v. 1013
Doi: 10.1007/978-3-030-93080-6_20
Shadbahr, T., Roberts, M., Stanczuk, J., Gilbey, JD., Teare, P., Dittmer, S., Thorpe, M., Torné, RV., Sala, E., Lió, P., Patel, M., Collaboration, A-C., Rudd, JHF., Mirtti, T., Rannikko, A., Aston, JAD., Tang, J. and Schönlieb, C-B., 2022. Classification of datasets with imputed missing values: does imputation quality matter? CoRR, v. abs/2206.08478
Yang, J., Küstner, T., Hu, P., Liò, P. and Qi, H., 2022. End-to-End Deep Learning of Non-rigid Groupwise Registration and Reconstruction of Dynamic MRI. Front Cardiovasc Med, v. 9
Doi: 10.3389/fcvm.2022.880186
Coggan, H., Andres Terre, H. and Liò, P., 2022. A novel interpretable machine learning algorithm to identify optimal parameter space for cancer growth. Front Big Data, v. 5
Doi: 10.3389/fdata.2022.941451
Dimitri, GM., Beqiri, E., Placek, MM., Czosnyka, M., Stocchetti, N., Ercole, A., Smielewski, P., Lió, P. and CENTER-TBI Collaborators, , 2022. Modeling Brain-Heart Crosstalk Information in Patients with Traumatic Brain Injury. Neurocrit Care, v. 36
Doi: 10.1007/s12028-021-01353-7
Goh, CWJ., Bodnar, C. and Liò, P., 2022. Simplicial Attention Networks. CoRR, v. abs/2204.09455
Chen, Y., Schönlieb, C-B., Liò, P., Leiner, T., Dragotti, PL., Wang, G., Rueckert, D., Firmin, DN. and Yang, G., 2022. AI-Based Reconstruction for Fast MRI - A Systematic Review and Meta-Analysis. Proc. IEEE, v. 110
Patel, S. and Lio, P., 2022. Efficacy, Safety, and Applications of Skin Protectants. J Drugs Dermatol, v. 21
Doi: 10.36849/JDD.6705
Liu, L., Huang, Z., Liò, P., Schönlieb, C-B. and Avilés-Rivero, AI., 2022. PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation. CoRR, v. abs/2203.05684
Lu, X., Xue, A., Lio, P. and Hui, P., 2022. Intelligent Decision Making Based on the Combination of Deep Reinforcement Learning and an Influence Map Applied Sciences (Switzerland), v. 12
Doi: 10.3390/app122211458
Viñas, R., Andrés-Terré, H., Liò, P. and Bryson, K., 2022. Adversarial generation of gene expression data. Bioinform., v. 38
Buffelli, D., Liò, P. and Vandin, F., 2022. SizeShiftReg: a Regularization Method for Improving Size-Generalization
in Graph Neural Networks
Charoenkwan, P., Nantasenamat, C., Hasan, MM., Moni, MA., Lio', P., Manavalan, B. and Shoombuatong, W., 2022. StackDPPIV: A novel computational approach for accurate prediction of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides. Methods, v. 204
Doi: 10.1016/j.ymeth.2021.12.001
Charoenkwan, P., Schaduangrat, N., Lio, P., Moni, MA., Chumnanpuen, P. and Shoombuatong, W., 2022. iAMAP-SCM: A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides. ACS Omega, v. 7
Doi: 10.1021/acsomega.2c04465
Christensen, CN., Lu, M., Ward, EN., Lio, P. and Kaminski, CF., 2022. Spatio-temporal Vision Transformer for Super-resolution Microscopy
Schaduangrat, N., Anuwongcharoen, N., Moni, MA., Lio', P., Charoenkwan, P. and Shoombuatong, W., 2022. StackPR is a new computational approach for large-scale identification of progesterone receptor antagonists using the stacking strategy. Sci Rep, v. 12
Doi: 10.1038/s41598-022-20143-5
Buterez, D., Bica, I., Tariq, I., Andrés-Terré, H. and Liò, P., 2022. CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks. Bioinformatics, v. 38
Doi: 10.1093/bioinformatics/btab804
Bongini, P., Scarselli, F., Bianchini, M., Dimitri, GM., Pancino, N. and Liò, P., 2022. Modular multi-source prediction of drug side-effects with DruGNN. CoRR, v. abs/2202.08147
Ahamad, MM., Aktar, S., Uddin, MJ., Rashed-Al-Mahfuz, M., Azad, AKM., Uddin, S., Alyami, SA., Sarker, IH., Khan, A., Liò, P., Quinn, JMW. and Moni, MA., 2022. Adverse Effects of COVID-19 Vaccination: Machine Learning and Statistical Approach to Identify and Classify Incidences of Morbidity and Postvaccination Reactogenicity. Healthcare (Basel), v. 11
Doi: 10.3390/healthcare11010031
Jain, A., Mishra, C. and Liò, P., 2022. A physics-informed search for metric solutions to Ricci flow, their embeddings, and visualisation. CoRR, v. abs/2212.05892
Ahmad, S., Charoenkwan, P., Quinn, JMW., Moni, MA., Hasan, MM., Lio', P. and Shoombuatong, W., 2022. SCORPION is a stacking-based ensemble learning framework for accurate prediction of phage virion proteins. Sci Rep, v. 12
Doi: 10.1038/s41598-022-08173-5
Dimitri, GM., Meoni, G., Tenori, L., Luchinat, C. and Lió, P., 2022. NMR Spectroscopy Combined with Machine Learning Approaches for Age Prediction in Healthy and Parkinson’s Disease Cohorts through Metabolomic Fingerprints Applied Sciences (Switzerland), v. 12
Doi: 10.3390/app12188954
Ayorinde, JOO., Citterio, F., Landrò, M., Peruzzo, E., Islam, T., Tilley, S., Taylor, G., Bardsley, V., Liò, P., Samoshkin, A. and Pettigrew, GJ., 2022. Artificial Intelligence You Can Trust: What Matters Beyond Performance When Applying Artificial Intelligence to Renal Histopathology? J Am Soc Nephrol, v. 33
Doi: 10.1681/ASN.2022010069
Mitchell, H., Norcliffe, A. and Liò, P., 2022. Learning Feynman Diagrams using Graph Neural Networks. CoRR, v. abs/2211.15348
Tailor, SA., Opolka, FL., Liò, P. and Lane, ND., 2021 (Published online). Adaptive Filters and Aggregator Fusion for Efficient Graph Convolutions arxiv,
Christensen, CN., Ward, E., Lio, P. and Kaminski, C., 2021 (No publication date). ML-SIM: Universal reconstruction of structured illumination microscopy images using transfer learning Biomedical Optics Express,
Doi: 10.1364/boe.414680
Banerjee, S., Lio, P., Jones, P. and Cardinal, R., 2021 (Accepted for publication). A class-contrastive human-interpretable machine learning approach to predict mortality in severe mental illness npj Schizophrenia,
Doi: 10.1038/s41537-021-00191-y
Charoenkwan, P., Nantasenamat, C., Hasan, MM., Moni, MA., Lio', P. and Shoombuatong, W., 2021 (Accepted for publication). iBitter-Fuse: A Novel Sequence-Based Bitter Peptide Predictor by Fusing Multi-View Features. International Journal of Molecular Sciences, v. 22
Doi: 10.3390/ijms22168958
Viñas, R., Andrés-Terré, H., Liò, P. and Bryson, K., 2021 (Accepted for publication). Adversarial generation of gene expression data. Bioinformatics,
Doi: 10.1093/bioinformatics/btab035
Bardozzo, F., Lió, P. and Tagliaferri, R., 2021. Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks. Bioinform., v. 37
Azevedo, T., Dimitri, GM., Lió, P. and Gamazon, ER., 2021. Multilayer modelling of the human transcriptome and biological mechanisms of complex diseases and traits. NPJ Syst Biol Appl, v. 7
Doi: 10.1038/s41540-021-00186-6
Zhu, M., Lió, P. and Moss, J., 2021. Modular Neural Ordinary Differential Equations. CoRR, v. abs/2109.07359
Bodnar, C., Cangea, C. and Liò, P., 2021. Deep Graph Mapper: Seeing Graphs Through the Neural Lens. Frontiers Big Data, v. 4
Islam, MR., Moni, MA., Islam, MM., Rashed-Al-Mahfuz, M., Islam, MS., Hasan, MK., Hossain, MS., Ahmad, M., Uddin, S., Azad, A., Alyami, SA., Ahad, MAR. and Lio, P., 2021. Emotion Recognition from EEG Signal Focusing on Deep Learning and Shallow Learning Techniques IEEE Access, v. 9
Doi: 10.1109/ACCESS.2021.3091487
Zhu, M., Lio, P. and Moss, J., 2021. Modular Neural Ordinary Differential Equations
COVID-19 Host Genetics Initiative, , 2021. Mapping the human genetic architecture of COVID-19. Nature, v. 600
Doi: 10.1038/s41586-021-03767-x
Weber, JM., Lindenmeyer, CP., Liò, P. and Lapkin, AA., 2021. Teaching sustainability as complex systems approach: a sustainable development goals workshop International Journal of Sustainability in Higher Education, v. 22
Doi: 10.1108/IJSHE-06-2020-0209
Deasy, J., Simidjievski, N. and Liò, P., 2021. Heavy-tailed denoising score matching. CoRR, v. abs/2112.09788
Tangherloni, A., Ricciuti, F., Besozzi, D., Liò, P. and Cvejic, A., 2021. Analysis of single-cell RNA sequencing data based on autoencoders. BMC Bioinformatics, v. 22
Doi: 10.1186/s12859-021-04150-3
Ma, Z., Xuan, J., Wang, YG., Li, M. and Liò, P., 2021. tion Processing Systems vol 33 ed H Larochelle, M Ranzato, R Hadsell, M F Balcan and H Lin (New York: Curran Associates) pp 16421–33. ... Journal of Statistical Mechanics: Theory and Experiment, v. 2021
Doi: 10.1088/1742-5468/ac3ae4
Castiglione, F., Deb, D., Srivastava, AP., Liò, P. and Liso, A., 2021. From Infection to Immunity: Understanding the Response to SARS-CoV2 Through In-Silico Modeling. Front Immunol, v. 12
Doi: 10.3389/fimmu.2021.646972
van Der Schaar, M., Alaa, AM., Floto, A., Gimson, A., Scholtes, S., Wood, A., McKinney, E., Jarrett, D., Lio, P. and Ercole, A., 2021. How artificial intelligence and machine learning can help healthcare systems respond to COVID-19 Machine Learning, v. 110
Doi: 10.1007/s10994-020-05928-x
Iuliano, A., Occhipinti, A., Angelini, C., De Feis, I. and Liò, P., 2021. Cosmonet: An r package for survival analysis using screening-network methods Mathematics, v. 9
Doi: 10.3390/math9243262
Roberts, M., Driggs, D., Thorpe, M., Gilbey, J., Yeung, M., Ursprung, S., Aviles-Rivero, AI., Etmann, C., McCague, C., Beer, L., Weir-McCall, JR., Teng, Z., Gkrania-Klotsas, E., Ruggiero, A., Korhonen, A., Jefferson, E., Ako, E., Langs, G., Gozaliasl, G., Yang, G., Prosch, H., Preller, J., Stanczuk, J., Tang, J., Hofmanninger, J., Babar, J., Sánchez, LE., Thillai, M., Gonzalez, PM., Teare, P., Zhu, X., Patel, M., Cafolla, C., Azadbakht, H., Jacob, J., Lowe, J., Zhang, K., Bradley, K., Wassin, M., Holzer, M., Ji, K., Ortet, MD., Ai, T., Walton, N., Lio, P., Stranks, S., Shadbahr, T., Lin, W., Zha, Y., Niu, Z., Rudd, JHF., Sala, E. and Schönlieb, CB., 2021. Common pitfalls and recommendations for using machine learning to detect and prognosticate for COVID-19 using chest radiographs and CT scans Nature Machine Intelligence, v. 3
Doi: 10.1038/s42256-021-00307-0
Yang, J., Li, X-X., Liu, F., Nie, D., Liò, P., Qi, H. and Shen, D., 2021. Fast T2w/FLAIR MRI Acquisition by Optimal Sampling of Information Complementary to Pre-acquired T1w MRI. CoRR, v. abs/2111.06400
Vecchio, AD., Deac, A., Liò, P. and Veličković, P., 2021. Neural message passing for joint paratope-epitope prediction
Amor, A., Lio', P., Singh, V., Torné, RV. and Terre, HA., 2021. Graph Representation Learning on Tissue-Specific Multi-Omics
Lu, X., Wang, F., Jiang, C. and Lio, P., 2021. A universal malicious documents static detection framework based on feature generalization Applied Sciences (Switzerland), v. 11
Doi: 10.3390/app112412134
Dimitri, GM., Beqiri, E., Czosnyka, M., Ercole, A., Smielewski, P., Lio, P. and CENTER-TBI High Resolution Substudy Participants and Investigators, , 2021. Analysis of Cardio-Cerebral Crosstalk Events in an Adult Cohort from the CENTER-TBI Study. Acta Neurochir Suppl, v. 131
Doi: 10.1007/978-3-030-59436-7_9
Moss, J., Opolka, FL., Dumitrascu, B. and Lió, P., 2021. Approximate Latent Force Model Inference. CoRR, v. abs/2109.11851
Barbiero, P., Ciravegna, G., Giannini, F., Lió, P., Gori, M. and Melacci, S., 2021. Entropy-based Logic Explanations of Neural Networks In Proceedings of the AAAI Conference on Artificial Intelligence, v. 36
Magister, LC., Kazhdan, D., Singh, V. and Liò, P., 2021. GCExplainer: Human-in-the-Loop Concept-based Explanations for Graph
Neural Networks
Stärk, H., Beaini, D., Corso, G., Tossou, P., Dallago, C., Günnemann, S. and Liò, P., 2021. 3D Infomax improves GNNs for Molecular Property Prediction 39th International Conference on Machine Learning (ICML 2022),
King, J., Torné, RV., Campbell, A. and Liò, P., 2021. An investigation of pre-upsampling generative modelling and Generative Adversarial Networks in audio super resolution. CoRR, v. abs/2109.14994
Bodnar, C., Frasca, F., Otter, N., Wang, YG., Liò, P., Montúfar, G. and Bronstein, M., 2021. Weisfeiler and Lehman Go Cellular: CW Networks Advances in Neural Information Processing Systems, v. 4
Chen, Y., Schönlieb, C-B., Liò, P., Leiner, T., Dragotti, PL., Wang, G., Rueckert, D., Firmin, DN. and Yang, G., 2021. AI-based Reconstruction for Fast MRI - A Systematic Review and Meta-analysis. CoRR, v. abs/2112.12744
Day, B., Viñas, R., Simidjievski, N. and Liò, P., 2021. Attentional Meta-learners for Few-shot Polythetic Classification
Opolka, FL., Zhi, Y-C., Liò, P. and Dong, X., 2021. Adaptive Gaussian Processes on Graphs via Spectral Graph Wavelets
Lu, X., Fu, S., Jiang, C. and Lió, P., 2021. A Fine-Grained IoT Data Access Control Scheme Combining Attribute-Based Encryption and Blockchain. Secur. Commun. Networks, v. 2021
Fanfani, V., Vinas Torne, R., Lio', P. and Stracquadanio, G., 2021. Discovering cancer driver genes and pathways using stochastic block model graph neural networks
Doi: 10.1101/2021.06.29.450342
Pirazzini, C., Azevedo, T., Baldelli, L., Bartoletti-Stella, A., Calandra-Buonaura, G., Dal Molin, A., Dimitri, GM., Doykov, I., Gómez-Garre, P., Hägg, S., Hällqvist, J., Halsband, C., Heywood, W., Jesús, S., Jylhävä, J., Kwiatkowska, KM., Labrador-Espinosa, MA., Licari, C., Maturo, MG., Mengozzi, G., Meoni, G., Milazzo, M., Periñán-Tocino, MT., Ravaioli, F., Sala, C., Sambati, L., Schade, S., Schreglmann, S., Spasov, S., Tenori, L., Williams, D., Xumerle, L., Zago, E., Bhatia, KP., Capellari, S., Cortelli, P., Garagnani, P., Houlden, H., Liò, P., Luchinat, C., Delledonne, M., Mills, K., Mir, P., Mollenhauer, B., Nardini, C., Pedersen, NL., Provini, F., Strom, S., Trenkwalder, C., Turano, P., Bacalini, MG., Franceschi, C. and PROPAG-AGEING Consortium, , 2021. A geroscience approach for Parkinson's disease: Conceptual framework and design of PROPAG-AGEING project. Mech Ageing Dev, v. 194
Doi: 10.1016/j.mad.2020.111426
Ciravegna, G., Barbiero, P., Giannini, F., Gori, M., Lió, P., Maggini, M. and Melacci, S., 2021. Logic Explained Networks Artificial Intelligence, 103822, 2022,
Nain, Z., Rana, HK., Liò, P., Islam, SMS., Summers, MA. and Moni, MA., 2021. Pathogenetic profiling of COVID-19 and SARS-like viruses. Briefings Bioinform., v. 22
Caccuri, F., D'Ursi, P., Uggeri, M., Bugatti, A., Mazzuca, P., Zani, A., Filippini, F., Salmona, M., Ribatti, D., Slevin, M., Orro, A., Lu, W., Liò, P., Gallo, RC. and Caruso, A., 2021. Evolution toward beta common chain receptor usage links the matrix proteins of HIV-1 and its ancestors to human erythropoietin. Proc Natl Acad Sci U S A, v. 118
Doi: 10.1073/pnas.2021366118
D'Agostino, D., Liò, P., Aldinucci, M. and Merelli, I., 2021. Advantages of using graph databases to explore chromatin conformation capture experiments. BMC Bioinformatics, v. 22
Doi: 10.1186/s12859-020-03937-0
Lipov, A. and Liò, P., 2021. A Multiscale Graph Convolutional Network Using Hierarchical Clustering Advances in Intelligent Systems and Computing, v. 1364 AISC
Doi: 10.1007/978-3-030-73103-8_35
Viñas, R., Azevedo, T., Gamazon, ER. and Liò, P., 2021. Deep Learning Enables Fast and Accurate Imputation of Gene Expression. Front Genet, v. 12
Doi: 10.3389/fgene.2021.624128
Jamasb, AR., Day, B., Cangea, C., Liò, P. and Blundell, TL., 2021. Deep Learning for Protein-Protein Interaction Site Prediction. Methods Mol Biol, v. 2361
Doi: 10.1007/978-1-0716-1641-3_16
Zhou, B., Liu, X., Liu, Y., Huang, Y., Liò, P. and Wang, Y., 2021. Spectral Transform Forms Scalable Transformer
Chen, K., Xu, H., Lei, Y., Lio, P., Li, Y., Guo, H. and Ali Moni, M., 2021. Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance. Brief Bioinform, v. 22
Doi: 10.1093/bib/bbab100
Georgiev, D., Barbiero, P., Kazhdan, D., Veličković, P. and Liò, P., 2021. Algorithmic Concept-based Explainable Reasoning
Lu, X., Fu, S., Jiang, C. and Lio, P., 2021. A Fine-Grained IoT Data Access Control Scheme Combining Attribute-Based Encryption and Blockchain Security and Communication Networks, v. 2021
Doi: 10.1155/2021/5308206
Bagnoli, F., Lorini, D. and Lió, P., 2021. Modeling Social Groups, Policies and Cognitive Behavior in COVID-19 Epidemic Phases. Basic Scenarios Substantia, v. 4
Doi: 10.13128/Substantia-914
Yang, J., Li, X-X., Liu, F., Nie, D., Lio, P., Qi, H. and Shen, D., 2021. Fast T2w/FLAIR MRI Acquisition by Optimal Sampling of Information
Complementary to Pre-acquired T1w MRI
Beaini, D., Passaro, S., Letourneau, V., Hamilton, WL., Corso, G. and Lio, P., 2021. Directional Graph Networks INTERNATIONAL CONFERENCE ON MACHINE LEARNING, VOL 139, v. 139
Zheng, X., Zhou, B., Gao, J., Wang, YG., Lio, P., Li, M. and Montufar, G., 2021. How Framelets Enhance Graph Neural Networks INTERNATIONAL CONFERENCE ON MACHINE LEARNING, VOL 139, v. 139
Day, B., Norcliffe, A., Moss, J. and Liò, P., 2021. Meta-learning using privileged information for dynamics
Qendro, L., Campbell, A., Liò, P. and Mascolo, C., 2021. High Frequency EEG Artifact Detection with Uncertainty via Early Exit
Paradigm
Barbiero, P., Viñas Torné, R. and Lió, P., 2021. Graph Representation Forecasting of Patient's Medical Conditions: Toward a Digital Twin. Front Genet, v. 12
Doi: 10.3389/fgene.2021.652907
Shankar, V., Tibshirani, R. and Zare, RN., 2021. MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data. Bioinformatics,
Doi: 10.1093/bioinformatics/btab282
Zhu, J., Tan, C., Yang, J., Yang, G. and Lio', P., 2021. Arbitrary Scale Super-Resolution for Medical Images. Int J Neural Syst, v. 31
Doi: 10.1142/S0129065721500374
Rocheteau, E., Liò, P. and Hyland, S., 2021. Temporal pointwise convolutional networks for length of stay prediction in the intensive care unit ACM CHIL 2021 - Proceedings of the 2021 ACM Conference on Health, Inference, and Learning,
Doi: 10.1145/3450439.3451860
Baldelli, L., Schade, S., Jesús, S., Schreglmann, SR., Sambati, L., Gómez-Garre, P., Halsband, C., Calandra-Buonaura, G., Adarmes-Gómez, AD., Sixel-Döring, F., Zenesini, C., Pirazzini, C., Garagnani, P., Bacalini, MG., Bhatia, KP., Cortelli, P., Mollenhauer, B., Franceschi, C., PROPAG-AGEING consortium, , Mir, P., Trenkwalder, C. and Provini, F., 2021. Heterogeneity of prodromal Parkinson symptoms in siblings of Parkinson disease patients. NPJ Parkinsons Dis, v. 7
Doi: 10.1038/s41531-021-00219-1
Scata, M., Di Stefano, A., La Corte, A. and Lio, P., 2021. A Multiplex Social Contagion Dynamics Model to Shape and Discriminate D2D Content Dissemination IEEE Transactions on Cognitive Communications and Networking, v. 7
Doi: 10.1109/TCCN.2020.3027697
Rashed-Al-Mahfuz, M., Moni, MA., Lio', P., Islam, SMS., Berkovsky, S., Khushi, M. and Quinn, JMW., 2021. Deep convolutional neural networks based ECG beats classification to diagnose cardiovascular conditions. Biomed Eng Lett, v. 11
Doi: 10.1007/s13534-021-00185-w
Zhu, J., Tan, C., Yang, J., Yang, G. and Lio', P., 2021. MIASSR: An Approach for Medical Image Arbitrary Scale Super-Resolution
Bardozzo, F., Lió, P. and Tagliaferri, R., 2021. Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks. Bioinformatics, v. 37
Doi: 10.1093/bioinformatics/btaa966
Deasy, J., Simidjievski, N. and Liò, P., 2021. Heavy-tailed denoising score matching
Zubić, N. and Liò, P., 2021. An Effective Loss Function for Generating 3D Models from Single 2D Image Without Rendering IFIP Advances in Information and Communication Technology, v. 627
Doi: 10.1007/978-3-030-79150-6_25
Zhou, B., Liu, X., Liu, Y., Huang, Y., Liò, P. and Wang, Y., 2021. Spectral Transform Forms Scalable Transformer. CoRR, v. abs/2111.07602
Deasy, J., Liò, P. and Ercole, A., 2020 (Published online). Dynamic survival prediction in intensive care units from heterogeneous time series without the need for variable selection or curation Scientific Reports, v. 10
Doi: 10.1038/s41598-020-79142-z
Trębacz, M., Shams, Z., Jamnik, M., Scherer, P., Simidjievski, N., Terre, HA. and Liò, P., 2020 (Published online). Using ontology embeddings for structural inductive bias in gene
expression data analysis arxiv,
Azevedo, T., Passamonti, L., Liò, P. and Toschi, N., 2020. Towards a predictive spatio-temporal representation of brain data
Azevedo, T., Dimitri, GM., Lio, P. and Gamazon, E., 2020. Multilayer modelling and analysis of the human transcriptome
Doi: 10.1101/2020.05.21.109082
Glass, S., Spasov, S. and Liò, P., 2020. RicciNets: Curvature-guided Pruning of High-performance Neural Networks
Using Ricci Flow
Deasy, J., Liò, P. and Ercole, A., 2020. Dynamic survival prediction in intensive care units from heterogeneous time series without the need for variable selection or curation. Sci Rep, v. 10
Doi: 10.1038/s41598-020-79142-z
Nain, Z., Rana, HK., Liò, P., Islam, SMS., Summers, MA. and Moni, MA., 2020. Pathogenetic profiling of COVID-19 and SARS-like viruses. Briefings in Bioinformatics,
Doi: 10.1093/bib/bbaa173
Rocheteau, E., Liò, P. and Hyland, S., 2020. Predicting Length of Stay in the Intensive Care Unit with Temporal
Pointwise Convolutional Networks
Azevedo, T., Campbell, A., Romero-Garcia, R., Passamonti, L., Bethlehem, RAI., Liò, P. and Toschi, N., 2020. A Deep Graph Neural Network Architecture for Modelling Spatio-temporal Dynamics in resting-state functional MRI Data
Doi: 10.1101/2020.11.08.370288
Corso, G., Cavalleri, L., Beaini, D., Liò, P. and Velickovic, P., 2020. Principal neighbourhood aggregation for graph nets Advances in Neural Information Processing Systems, v. 2020-December
John, MS., Nagoth, JA., Ramasamy, KP., Ballarini, P., Mozzicafreddo, M., Mancini, A., Telatin, A., Liò, P., Giuli, G., Natalello, A., Miceli, C. and Pucciarelli, S., 2020. Horizontal gene transfer and silver nanoparticles production in a new Marinomonas strain isolated from the Antarctic psychrophilic ciliate Euplotes focardii. Scientific Reports, v. 10
Doi: 10.1038/s41598-020-66878-x
Christensen, CN., Ward, EN., Lio, P. and Kaminski, CF., 2020. ML-SIM: A deep neural network for reconstruction of structured
illumination microscopy images
Rakowski, AG., Veličković, P., Dall'Ara, E. and Liò, P., 2020. ChronoMID-Cross-modal neural networks for 3-D temporal medical imaging data. PLoS One, v. 15
Doi: 10.1371/journal.pone.0228962
Ahamad, MM., Aktar, S., Rashed-Al-Mahfuz, M., Uddin, S., Liò, P., Xu, H., Summers, MA., Quinn, JMW. and Moni, MA., 2020. A machine learning model to identify early stage symptoms of SARS-Cov-2 infected patients. Expert Systems with Applications, v. 160
Doi: 10.1016/j.eswa.2020.113661
Norcliffe, A., Bodnar, C., Day, B., Simidjievski, N. and Liò, P., 2020. On second order behaviour in augmented neural ODEs Advances in Neural Information Processing Systems, v. 2020-December
Rollins, CPE., Garrison, JR., Arribas, M., Seyedsalehi, A., Li, Z., Chan, RCK., Yang, J., Wang, D., Liò, P., Yan, C., Yi, Z-H., Cachia, A., Upthegrove, R., Deakin, B., Simons, JS., Murray, GK. and Suckling, J., 2020. Evidence in cortical folding patterns for prenatal predispositions to hallucinations in schizophrenia. Transl Psychiatry, v. 10
Doi: 10.1038/s41398-020-01075-y
Lu, X., Liao, Y., Lio, P. and Pan, H., 2020. An Asynchronous Federated Learning Mechanism for Edge Network Computing Jisuanji Yanjiu yu Fazhan/Computer Research and Development, v. 57
Doi: 10.7544/issn1000-1239.2020.20190754
Scherer, P. and Lio, P., 2020. Learning distributed representations of graphs with Geo2DR
Lu, X., Wang, X., Lio, P. and Hui, P., 2020. DADIM: A distance adjustment dynamic influence map model Future Generation Computer Systems, v. 112
Doi: 10.1016/j.future.2020.06.020
Tan, C., Zhu, J. and Lio’, P., 2020. Arbitrary scale super-resolution for brain MRI images IFIP Advances in Information and Communication Technology, v. 583 IFIP
Doi: 10.1007/978-3-030-49161-1_15
Rollins, CPE., Garrison, J., Arribas, M., Seyedsalehi, A., Li, Z., Chan, RCK., Yang, J., Wang, D., Lio, P., Yan, C., Yi, Z-H., Cachia, A., Upthegrove, R., Deakin, B., Simons, J., Murray, G. and Suckling, J., 2020. The neurodevelopment of anomalous perception: Evidence in cortical folding patterns for prenatal predispositions to hallucinations in schizophrenia
Doi: 10.1101/2020.06.04.20122424
Flood, PDL., Viñas, R. and Liò, P., 2020. Investigating Estimated Kolmogorov Complexity as a Means of
Regularization for Link Prediction
Cangea, C., Velickovic, P. and Liò, P., 2020. XFlow: Cross-Modal Deep Neural Networks for Audiovisual Classification. IEEE Trans. Neural Networks Learn. Syst., v. 31
Doi: 10.1109/TNNLS.2019.2945992
Di Stefano, A., Scatá, M., Attanasio, B., La Corte, A., Lió, P. and Das, SK., 2020. A Novel Methodology for designing Policies in Mobile Crowdsensing Systems Pervasive and Mobile Computing, v. 67
Doi: 10.1016/j.pmcj.2020.101230
Jamasb, A., Viñas, R., Ma, E., Harris, C., Huang, K., Hall, D., Lió, P. and Blundell, T., 2020. Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures and Interaction Networks
Doi: 10.1101/2020.07.15.204701
Spasov, SE. and Liò, P., 2020. Dynamic neural network channel execution for efficient training 30th British Machine Vision Conference 2019, BMVC 2019,
Spasov, S., Stefano, AD., Lio, P. and Tang, J., 2020. GRADE: Graph Dynamic Embedding
Wichitwechkarn, V., Day, B., Bodnar, C., Wales, M. and Liò, P., 2020. The Role of Isomorphism Classes in Multi-Relational Datasets
Müller, TT. and Lio, P., 2020. PECLIDES Neuro: A Personalisable Clinical Decision Support System for Neurological Diseases. Front Artif Intell, v. 3
Doi: 10.3389/frai.2020.00023
Stankevičiūtė, K., Azevedo, T., Campbell, A., Bethlehem, R. and Liò, P., 2020. Population Graph GNNs for Brain Age Prediction
Doi: 10.1101/2020.06.26.172171
Kazhdan, D., Dimanov, B., Jamnik, M., Liò, P. and Weller, A., 2020. Now You See Me (CME): Concept-based Model Extraction. CoRR, v. abs/2010.13233
Del Prete, E., Facchiano, A. and Liò, P., 2020. Bioinformatics methodologies for coeliac disease and its comorbidities. Brief Bioinform, v. 21
Doi: 10.1093/bib/bby109
Deasy, J., Simidjievski, N. and Liò, P., 2020. Constraining variational inference with geometric Jensen-Shannon divergence Advances in Neural Information Processing Systems, v. 2020-December
Day, B., Cangea, C., Jamasb, AR. and Liò, P., 2020. Message Passing Neural Processes
Lu, X., Liao, Y., Lio, P. and Hui, P., 2020. Privacy-preserving asynchronous federated learning mechanism for edge network computing IEEE Access, v. 8
Doi: 10.1109/ACCESS.2020.2978082
Kazhdan, D., Shams, Z. and Lio, P., 2020. MARLeME: A Multi-Agent Reinforcement Learning Model Extraction Library Proceedings of the International Joint Conference on Neural Networks,
Doi: 10.1109/IJCNN48605.2020.9207564
Wang, D., Jamnik, M. and Lio, P., 2020. ABSTRACT DIAGRAMMATIC REASONING WITH MULTIPLEX GRAPH NETWORKS 8th International Conference on Learning Representations, ICLR 2020,
Maria, ED., Despeyroux, J., Felty, A., Liò, P., Olarte, C. and Bahrami, A., 2020. Computational Logic for Biomedicine and Neurosciences
Zhao, Y., Wang, D., Bates, D., Mullins, R., Jamnik, M. and Lio, P., 2020. Learned Low Precision Graph Neural Networks
Rana, HK., Akhtar, MR., Islam, MB., Ahmed, MB., Lió, P., Huq, F., Quinn, JMW. and Moni, MA., 2020. Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. Sci Rep, v. 10
Doi: 10.1038/s41598-020-57916-9
Yeghikyan, G., Opolka, FL., Nanni, M., Lepri, B. and Lio', P., 2020. Learning Mobility Flows from Urban Features with Spatial Interaction
Models and Neural Networks
Bodnar, C., Day, B. and Lió, P., 2020. Proximal distilled evolutionary reinforcement learning AAAI 2020 - 34th AAAI Conference on Artificial Intelligence,
Scherer, P., Trȩbacz, M., Simidjievski, N., Shams, Z., Terre, HA., Liò, P. and Jamnik, M., 2020. Incorporating network based protein complex discovery into automated
model construction
Merelli, I., Liò, P., Kotenko, I. and D'Agostino, D., 2020. Latest advances in parallel, distributed, and network-based processing Concurrency and Computation: Practice and Experience, v. 32
Doi: 10.1002/cpe.5683
Karavias, V., Day, B. and Liò, P., 2020. Uncertainty in Neural Relational Inference Trajectory Reconstruction
Moss, J. and Lió, P., 2020. Gene Regulatory Network Inference with Latent Force Models
Lu, X., Zhang, S., Hui, P. and Lio, P., 2020. Continuous authentication by free-text keystroke based on CNN and RNN Computers and Security, v. 96
Doi: 10.1016/j.cose.2020.101861
Campbell, A. and Liò, P., 2020. tvGP-VAE: Tensor-variate Gaussian Process Prior Variational Autoencoder
Georgiev, D. and Liò, P., 2020. Neural Bipartite Matching
Stefano, AD., Scatà, M., Attanasio, B., Corte, AL., Lió, P. and Das, SK., 2020. A Novel Methodology for designing Policies in Mobile Crowdsensing Systems. Pervasive Mob. Comput., v. 67
Doi: 10.1016/j.pmcj.2020.101230
Buterez, D., Bica, I., Tariq, I., Andrés-Terré, H. and Liò, P., 2020. CellVGAE: An unsupervised scRNA-seq analysis workflow with graph attention networks
Doi: 10.1101/2020.12.20.423645
Lu, X., Zhou, X., Wang, W., Lio, P. and Hui, P., 2020. Domain-oriented topic discovery based on features extraction and topic clustering IEEE Access, v. 8
Doi: 10.1109/ACCESS.2020.2994516
Barbiero, P., Viñas Torné, R. and Lió, P., 2020. Graph representation forecasting of patient’s medical conditions: towards a digital twin
Doi: 10.1101/2020.09.19.20197764
Bica, I., Andrés-Terré, H., Cvejic, A. and Liò, P., 2020. Unsupervised generative and graph representation learning for modelling cell differentiation. Sci Rep, v. 10
Doi: 10.1038/s41598-020-66166-8
Viñas, R., Azevedo, T., Gamazon, E. and Liò, P., 2020. Gene Expression Imputation with Generative Adversarial Imputation Nets
Doi: 10.1101/2020.06.09.141689
Prokhorov, V., Pilehvar, MT., Kartsaklis, D., Lio, P. and Collier, N., 2019 (Published online). Unseen Word Representation by Aligning Heterogeneous Lexical Semantic Spaces Proceedings of the AAAI Conference on Artificial Intelligence, v. 33
Doi: 10.1609/aaai.v33i01.33016900
Müller, T. and Lió, P., 2019 (Published online). Personalisable Clinical Decision Support System. ERCIM News, v. 116
Tangherloni, A., Spolaor, S., Rundo, L., Nobile, MS., Cazzaniga, P., Mauri, G., Liò, P., Merelli, I. and Besozzi, D., 2019 (Published online). GenHap: a novel computational method based on genetic algorithms for haplotype assembly. BMC Bioinformatics, v. 20
Doi: 10.1186/s12859-019-2691-y
Ascolani, G. and Liò, P., 2019 (Published online). Modeling breast cancer progression to bone: how driver mutation order and metabolism matter. BMC Medical Genomics, v. 12
Doi: 10.1186/s12920-019-0541-4
Maj, C., Azevedo, T., Giansanti, V., Borisov, O., Dimitri, GM., Spasov, S., Alzheimer’s Disease Neuroimaging Initiative, , Lió, P. and Merelli, I., 2019 (Accepted for publication). Integration of Machine Learning Methods to Dissect Genetically Imputed Transcriptomic Profiles in Alzheimer's Disease. Frontiers in Genetics, v. 10
Doi: 10.3389/fgene.2019.00726
Ganggayah, MD., Taib, NA., Har, YC., Lio, P. and Dhillon, SK., 2019 (Accepted for publication). Predicting factors for survival of breast cancer patients using machine learning techniques. BMC Medical Informatics and Decision Making, v. 19
Doi: 10.1186/s12911-019-0801-4
Rana, HK., Akhtar, MR., Ahmed, MB., Liò, P., Quinn, JMW., Huq, F. and Moni, MA., 2019. Genetic effects of welding fumes on the progression of neurodegenerative diseases. Neurotoxicology, v. 71
Doi: 10.1016/j.neuro.2018.12.002
Rana, HK., Akhtar, MR., Islam, MB., Ahmed, MB., Liò, P., Quinn, JMW., Huq, F. and Moni, MA., 2019. Genetic effects of welding fumes on the development of respiratory system diseases. Comput Biol Med, v. 108
Doi: 10.1016/j.compbiomed.2019.04.004
Spasov, S., Passamonti, L., Duggento, A., Liò, P., Toschi, N. and Alzheimer's Disease Neuroimaging Initiative, , 2019. A parameter-efficient deep learning approach to predict conversion from mild cognitive impairment to Alzheimer's disease. Neuroimage, v. 189
Doi: 10.1016/j.neuroimage.2019.01.031
Tangherloni, A., Spolaor, S., Rundo, L., Nobile, MS., Cazzaniga, P., Mauri, G., Liò, P., Merelli, I. and Besozzi, D., 2019. GenHap: a novel computational method based on genetic algorithms for haplotype assembly. BMC Bioinform., v. 20-S
Parmar, V. and Lió, P., 2019. Multi-omic network regression: Methodology, tool and case study Studies in Computational Intelligence, v. 813
Doi: 10.1007/978-3-030-05414-4_49
Xiaofeng, L., Fangshuo, J., Xiao, Z., Shengwei, Y., Jing, S. and Lio, P., 2019. ASSCA: API sequence and statistics features combined architecture for malware detection Computer Networks, v. 157
Doi: 10.1016/j.comnet.2019.04.007
Deac, A., Huang, Y-H., Veličković, P., Liò, P. and Tang, J., 2019. Drug-Drug Adverse Effect Prediction with Graph Co-Attention
Deasy, J., Ercole, A. and Liò, P., 2019. Impact of novel aggregation methods for flexible, time-sensitive EHR
prediction without variable selection or cleaning
Di Stefano, A., Scatà, M., Vijayakumar, S., Angione, C., La Corte, A. and Liò, P., 2019. Social dynamics modeling of chrono-nutrition. PLoS Comput Biol, v. 15
Doi: 10.1371/journal.pcbi.1006714
Scherer, P., Andres-Terre, H., Lio, P. and Jamnik, M., 2019. Decoupling feature propagation from the design of graph auto-encoders
Vignani, R., Liò, P. and Scali, M., 2019. How to integrate wet lab and bioinformatics procedures for wine DNA admixture analysis and compositional profiling: Case studies and perspectives. PLoS One, v. 14
Doi: 10.1371/journal.pone.0211962
Azevedo, T., Passamonti, L., Lió, P. and Toschi, N., 2019. A machine learning tool for interpreting differences in cognition using brain features
Doi: 10.1101/558403
Yang, J., Wang, D., Rollins, C., Leming, M., Liò, P., Suckling, J., Murray, G., Garrison, J. and Cachia, A., 2019. Volumetric Segmentation and Characterisation of the Paracingulate Sulcus on MRI Scans
Doi: 10.1101/859496
Zhu, J., Yang, G. and Lio, P., 2019. Lesion focused super-resolution Progress in Biomedical Optics and Imaging - Proceedings of SPIE, v. 10949
Doi: 10.1117/12.2512576
Weber, J., Lio’, P. and Lapkin, A., 2019. Identification of Strategic Molecules for Future Circular Supply Chains Using Large Reaction Networks
Doi: 10.26434/chemrxiv.8488934.v1
Smith, HL., Stevens, A., Minogue, B., Sneddon, S., Shaw, L., Wood, L., Adeniyi, T., Xiao, H., Lio, P., Kimber, SJ. and Brison, DR., 2019. Systems based analysis of human embryos and gene networks involved in cell lineage allocation. BMC Genomics, v. 20
Doi: 10.1186/s12864-019-5558-8
Wang, D., Jamnik, M. and Lio, P., 2019. Unsupervised and interpretable scene discovery with
Discrete-Attend-Infer-Repeat
Andrés-Terré, H. and Lió, P., 2019. Perturbation theory approach to study the latent space degeneracy of
Variational Autoencoders
Bartoszek, K. and Liò, P., 2019. Modelling trait-dependent speciation with approximate Bayesian computation Acta Physica Polonica B, Proceedings Supplement, v. 12
Doi: 10.5506/APhysPolBSupp.12.25
Singh, V. and Lio', P., 2019. Towards Probabilistic Generative Models Harnessing Graph Neural Networks
for Disease-Gene Prediction
Cangea, C., Velickovic, P. and Lio, P., 2019. XFlow: Cross-Modal Deep Neural Networks for Audiovisual Classification. IEEE Trans Neural Netw Learn Syst,
Doi: 10.1109/TNNLS.2019.2945992
Pernice, S., Follia, L., Balbo, G., Milanesi, L., Sartini, G., Totis, N., Lió, P., Merelli, I., Cordero, F. and Beccuti, M., 2019. Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: A Methodological and Computational Practice Fundamenta Informaticae, v. 171
Doi: 10.3233/FI-2020-1888
Luzhnica, E., Day, B. and Lio', P., 2019. Clique pooling for graph classification
Simidjievski, N., Bodnar, C., Tariq, I., Scherer, P., Andres-Terre, H., Shams, Z., Jamnik, M. and Liò, P., 2019. Variational autoencoders for cancer data integration: design principles and computational practice
Doi: 10.1101/719542
Simidjievski, N., Bodnar, C., Tariq, I., Scherer, P., Andres Terre, H., Shams, Z., Jamnik, M. and Liò, P., 2019. Variational Autoencoders for Cancer Data Integration: Design Principles and Computational Practice. Front Genet, v. 10
Doi: 10.3389/fgene.2019.01205
Weber, JM., Lió, P. and Lapkin, AA., 2019. Identification of strategic molecules for future circular supply chains using large reaction networks Reaction Chemistry and Engineering, v. 4
Doi: 10.1039/c9re00213h
Akter, T., Shahriare Satu, M., Khan, MI., Ali, MH., Uddin, S., Lio, P., Quinn, JMW. and Moni, MA., 2019. Machine Learning-Based Models for Early Stage Detection of Autism Spectrum Disorders IEEE Access, v. 7
Doi: 10.1109/ACCESS.2019.2952609
Benmounah, Z., Meshoul, S., Batouche, M. and Lio, P., 2018 (Accepted for publication). Parallel swarm intelligence strategies for large-scale clustering based on MapReduce with application to epigenetics of aging Applied Soft Computing, v. 69
Doi: 10.1016/j.asoc.2018.04.012
Veličković, P., Casanova, A., Liò, P., Cucurull, G., Romero, A. and Bengio, Y., 2018. Graph attention networks 6th International Conference on Learning Representations, ICLR 2018 - Conference Track Proceedings,
Liberis, E., Velickovic, P., Sormanni, P., Vendruscolo, M. and Liò, P., 2018. Parapred: antibody paratope prediction using convolutional and recurrent neural networks. Bioinformatics, v. 34
Doi: 10.1093/bioinformatics/bty305
Sheehan, C., Day, B. and Liò, P., 2018. Introducing Curvature to the Label Space
Vijayakumar, S., Conway, M., Lió, P. and Angione, C., 2018. Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling. Briefings in Bioinformatics, v. 19
Doi: 10.1093/bib/bbx053
Karazija, L., Veličković, P. and Liò, P., 2018. Automatic inference of cross-modal connection topologies for X-CNNs Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 10878 LNCS
Doi: 10.1007/978-3-319-92537-0_7
Cangea, C., Veličković, P., Jovanović, N., Kipf, T. and Liò, P., 2018. Towards Sparse Hierarchical Graph Classifiers
Haider, S., Yao, CQ., Sabine, VS., Grzadkowski, M., Stimper, V., Starmans, MHW., Wang, J., Nguyen, F., Moon, NC., Lin, X., Drake, C., Crozier, CA., Brookes, CL., van de Velde, CJH., Hasenburg, A., Kieback, DG., Markopoulos, CJ., Dirix, LY., Seynaeve, C., Rea, DW., Kasprzyk, A., Lambin, P., Lio', P., Bartlett, JMS. and Boutros, PC., 2018. Pathway-based subnetworks enable cross-disease biomarker discovery. Nat Commun, v. 9
Doi: 10.1038/s41467-018-07021-3
Karazija, L., Velickovic, P. and Liò, P., 2018. Automatic Inference of Cross-modal Connection Topologies for X-CNNs. CoRR, v. abs/1805.00987
He, P., Nakano, T., Mao, Y., Lio, P., Liu, Q. and Yang, K., 2018. Stochastic Channel Switching of Frequency-Encoded Signals in Molecular Communication Networks IEEE Communications Letters, v. 22
Doi: 10.1109/LCOMM.2017.2768537
Dimitri, GM., Agrawal, S., Young, A., Donnelly, J., Liu, X., Smielewski, P., Hutchinson, P., Czosnyka, M., Lio, P. and Haubrich, C., 2018. Simultaneous Transients of Intracranial Pressure and Heart Rate in Traumatic Brain Injury: Methods of Analysis. Acta Neurochirurgica: Supplementum, v. 126
Doi: 10.1007/978-3-319-65798-1_31
Cangea, C., Grauslys, A., Liò, P. and Falciani, F., 2018. Structure-Based Networks for Drug Validation
Tordini, F., Aldinucci, M., Viviani, P., Merelli, I. and Liò, P., 2018. Scientific Workflows on Clouds with Heterogeneous and Preemptible Instances Advances in Parallel Computing, v. 32
Doi: 10.3233/978-1-61499-843-3-605
Barsacchi, M., Terre, HA. and Lió, P., 2018. GEESE: Metabolically driven latent space learning for gene expression data
Doi: 10.1101/365643
Scatà, M., Di Stefano, A., La Corte, A. and Liò, P., 2018. Quantifying the propagation of distress and mental disorders in social networks. Sci Rep, v. 8
Doi: 10.1038/s41598-018-23260-2
Iuliano, A., Occhipinti, A., Angelini, C., De Feis, I. and Liò, P., 2018. Combining Pathway Identification and Breast Cancer Survival Prediction via Screening-Network Methods. Front Genet, v. 9
Doi: 10.3389/fgene.2018.00206
Mancini, A., Eyassu, F., Conway, M., Occhipinti, A., Liò, P., Angione, C. and Pucciarelli, S., 2018. CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design. BMC Bioinformatics, v. 19
Doi: 10.1186/s12859-018-2422-9
Xiao, H., Bartoszek, K. and Lio', P., 2018. Multi-omic analysis of signalling factors in inflammatory comorbidities. BMC Bioinformatics, v. 19
Doi: 10.1186/s12859-018-2413-x
Bardozzo, F., Lió, P. and Tagliaferri, R., 2018. A study on multi-omic oscillations in Escherichia coli metabolic networks. BMC Bioinformatics, v. 19
Doi: 10.1186/s12859-018-2175-5
Saggese, I., Bona, E., Conway, M., Favero, F., Ladetto, M., Liò, P., Manzini, G. and Mignone, F., 2018. STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow. BMC Bioinformatics, v. 19
Doi: 10.1186/s12859-018-2174-6
Bartocci, E., Lio, P. and Paoletti, N., 2018. Guest Editors' Introduction to the Special Section on the 14th International Conference on Computational Methods in Systems Biology (CMSB 2016) IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 15
Doi: 10.1109/TCBB.2018.2816979
He, P., Nakano, T., Mao, Y., Liò, P., Liu, Q. and Yang, K., 2018. Stochastic Channel Switching of Frequency-Encoded Signals in Molecular Communication Networks. IEEE Commun. Lett., v. 22
Doi: 10.1109/LCOMM.2017.2768537
Felicetti, L., Femminella, M., Reali, G. and Liò, P., 2018. Applications of molecular communications to medicine: a survey. CoRR, v. abs/1808.04242
Martins, DP., Barros, M., Pierobon, M., Kandhavelu, M., Lio, P. and Balasubramaniam, S., 2017 (Accepted for publication). Computational Models for Trapping Ebola Virus Using Engineered Bacteria IEEE/ACM Transactions on Computational Biology and Bioinformatics, v. 15
Doi: 10.1109/TCBB.2018.2836430
Peychev, M., Veličković, P. and Liò, P., 2017. Quantifying the Effects of Enforcing Disentanglement on Variational
Autoencoders
Bianchi, L. and Liò, P., 2017. Opportunities for community awareness platforms in personal genomics and bioinformatics education. Brief Bioinform, v. 18
Doi: 10.1093/bib/bbw078
Tordini, F., Drocco, M., Misale, C., Milanesi, L., Liò, P., Merelli, I., Torquati, M. and Aldinucci, M., 2017. NuChart-II: The road to a fast and scalable tool for Hi-C data analysis International Journal of High Performance Computing Applications, v. 31
Doi: 10.1177/1094342016668567
Brouwer, T. and Lio', P., 2017. Prior and Likelihood Choices for Bayesian Matrix Factorisation on Small
Datasets
Ascolani, G. and Lió, P., 2017. Modelling the order of driver mutations and metabolic mutations as
structures in cancer dynamics
Oshota, O., Conway, M., Fookes, M., Schreiber, F., Chaudhuri, R., Yu, L., Morgan, F., Clare, S., Choudhary, J., Thomson, N., Lio, P., Maskell, D., Mastroeni, P. and Grant, AJ., 2017. Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice PLoS ONE, v. 12
Doi: 10.1371/journal.pone.0181365
Barandalla, M., Shi, H., Xiao, H., Colleoni, S., Galli, C., Lio, P., Trotter, M. and Lazzari, G., 2017. Global gene expression profiling and senescence biomarker analysis of hESC exposed to H2O2 induced non-cytotoxic oxidative stress. Stem Cell Res Ther, v. 8
Doi: 10.1186/s13287-017-0602-6
Brouwer, T., Frellsen, J. and Lió, P., 2017. Comparative Study of Inference Methods for Bayesian Nonnegative Matrix Factorisation Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 10534 LNAI
Doi: 10.1007/978-3-319-71249-9_31
Prokhorov, V., Pilehvar, MT., Kartsaklis, D., Lió, P. and Collier, N., 2017. Learning Rare Word Representations using Semantic Bridging
Liberis, E., Veličković, P., Sormanni, P., Vendruscolo, M. and Liò, P., 2017. Paratope Prediction using Convolutional and Recurrent Neural Networks
Doi: 10.1101/185488
Kashaf, SS., Angione, C. and Lió, P., 2017. Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. BMC Syst Biol, v. 11
Doi: 10.1186/s12918-017-0395-3
Moni, MA. and Lio', P., 2017. Genetic Profiling and Comorbidities of Zika Infection. J Infect Dis, v. 216
Doi: 10.1093/infdis/jix327
Dimitri, GM., Agrawal, S., Young, A., Donnelly, J., Liu, X., Smielewski, P., Hutchinson, P., Czosnyka, M., Lió, P. and Haubrich, C., 2017. A multiplex network approach for the analysis of intracranial pressure and heart rate data in traumatic brain injured patients. Appl Netw Sci, v. 2
Doi: 10.1007/s41109-017-0050-3
Bianchi, L. and Liò, P., 2017. Opportunities for community awareness platforms in personal genomics and bioinformatics education. Briefings in Bioinformatics, v. 18
Doi: 10.1093/bib/bbw078
Athanasiadis, EI., Botthof, JG., Andres, H., Ferreira, L., Lio, P. and Cvejic, A., 2017. Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis. Nat Commun, v. 8
Doi: 10.1038/s41467-017-02305-6
Reali, G. and Lio, P., 2016 (Published online). Simulation Tools for Molecular Communications IEEE TCSIM Newsletter,
Veličković, P., Wang, D., Lane, ND. and Liò, P., 2016 (Accepted for publication). X-CNN: Cross-modal Convolutional Neural Networks for Sparse Datasets SSCI 2016: 1-8,
Shavit, Y., Walker, BJ. and Lio', P., 2016. Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration. Bioinformatics, v. 32
Doi: 10.1093/bioinformatics/btv736
Shavit, Y., Merelli, I., Milanesi, L. and Lio', P., 2016. How computer science can help in understanding the 3D genome architecture. Brief Bioinform, v. 17
Doi: 10.1093/bib/bbv085
Bartocci, E. and Lió, P., 2016. Computational Modeling, Formal Analysis, and Tools for Systems Biology. PLoS Comput Biol, v. 12
Doi: 10.1371/journal.pcbi.1004591
Sansom, C., Castiglione, F. and Lio, P., 2016. Metabolic disorders: how can systems modelling help? Lancet Diabetes Endocrinol, v. 4
Doi: 10.1016/S2213-8587(16)00047-4
Angione, C., Conway, M. and Lió, P., 2016. Multiplex methods provide effective integration of multi-omic data in genome-scale models. BMC Bioinformatics, v. 17 Suppl 4
Doi: 10.1186/s12859-016-0912-1
Schwarz, E., Izmailov, R., Liò, P. and Meyer-Lindenberg, A., 2016. Protein Interaction Networks Link Schizophrenia Risk Loci to Synaptic Function. Schizophr Bull, v. 42
Doi: 10.1093/schbul/sbw035
Brouwer, T., Frellsen, J. and Lio', P., 2016. Fast Bayesian Non-Negative Matrix Factorisation and Tri-Factorisation CoRR abs/1610.08127 (2016),
Conway, M., Angione, C. and Liò, P., 2016. Iterative multi level calibration of metabolic networks Current Bioinformatics, v. 11
Doi: 10.2174/1574893611666151203222505
Scatà, M., Di Stefano, A., Liò, P. and La Corte, A., 2016. The Impact of Heterogeneity and Awareness in Modeling Epidemic Spreading on Multiplex Networks. Scientific Reports, v. 6
Doi: 10.1038/srep37105
Veličković, P. and Liò, P., 2016. Muxstep: an open-source C ++ multiplex HMM library for making inferences on multiple data types. Bioinformatics, v. 32
Doi: 10.1093/bioinformatics/btw196
Veličković, P. and Lió, P., 2016. Molecular multiplex network inference using Gaussian mixture hidden Markov models Journal of Complex Networks, v. 4
Doi: 10.1093/comnet/cnv029
Angione, C. and Lió, P., 2016. Erratum: Predictive analytics of environmental adaptability in multi-omic network models. Sci Rep, v. 6
Doi: 10.1038/srep26266
Tordini, F., Aldinucci, M., Milanesi, L., Liò, P. and Merelli, I., 2016. The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer. Front Genet, v. 7
Doi: 10.3389/fgene.2016.00194
Castellani, GC., Menichetti, G., Garagnani, P., Giulia Bacalini, M., Pirazzini, C., Franceschi, C., Collino, S., Sala, C., Remondini, D., Giampieri, E., Mosca, E., Bersanelli, M., Vitali, S., Valle, IFD., Liò, P. and Milanesi, L., 2016. Systems medicine of inflammaging. Brief Bioinform, v. 17
Doi: 10.1093/bib/bbv062
Scatà, M., Di Stefano, A., La Corte, A., Liò, P., Catania, E., Guardo, E. and Pagano, S., 2016. Combining evolutionary game theory and network theory to analyze human cooperation patterns Chaos, Solitons and Fractals, v. 91
Doi: 10.1016/j.chaos.2016.04.018
Narula, P., Piratla, V., Bansal, A., Azad, S. and Lio, P., 2016. Parameter estimation of tuberculosis transmission model using Ensemble Kalman filter across Indian states and union territories Infection, Disease and Health, v. 21
Doi: 10.1016/j.idh.2016.11.001
Lu, X., Lio, P. and Hui, P., 2016. Distance-Based Opportunistic Mobile Data Offloading. Sensors (Basel), v. 16
Doi: 10.3390/s16060878
Felicetti, L., Femminella, M., Reali, G. and Liò, P., 2016. Applications of molecular communications to medicine: A survey Nano Communication Networks, v. 7
Doi: 10.1016/j.nancom.2015.08.004
Iuliano, A., Occhipinti, A., Angelini, C., De Feis, I. and Lió, P., 2016. Cancer Markers Selection Using Network-Based Cox Regression: A Methodological and Computational Practice. Front Physiol, v. 7
Doi: 10.3389/fphys.2016.00208
Capobianco, E. and Lio, P., 2016. Electronic Health Systems: Golden Mine for Precision Medicine The journal of precision medicine,
Haider, S., Lipinszki, Z., Przewloka, MR., Ladak, Y., D'Avino, PP., Kimata, Y., Lio', P. and Glover, DM., 2015. DAPPER: a data-mining resource for protein-protein interactions. BioData Min, v. 8
Doi: 10.1186/s13040-015-0063-3
Moni, MA. and Liò, P., 2015. How to build personalized multi-omics comorbidity profiles. Front Cell Dev Biol, v. 3
Doi: 10.3389/fcell.2015.00028
Fondi, M. and Liò, P., 2015. Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology. Microbiol Res, v. 171
Doi: 10.1016/j.micres.2015.01.003
Angione, C., Costanza, J., Carapezza, G., Lió, P. and Nicosia, G., 2015. Analysis and design of molecular machines Theoretical Computer Science, v. 599
Doi: 10.1016/j.tcs.2015.01.030
Merelli, I., Tordini, F., Drocco, M., Aldinucci, M., Liò, P. and Milanesi, L., 2015. Integrating multi-omic features exploiting Chromosome Conformation Capture data. Front Genet, v. 6
Doi: 10.3389/fgene.2015.00040
Liò, P., Miglino, O., Nicosia, G., Nolfi, S. and Pavone, M., 2015. Advances in artificial life: Synthesis and simulation of living systems: Editorial Artificial Life, v. 21
Doi: 10.1162/ARTL_e_00189
Bosi, E., Donati, B., Galardini, M., Brunetti, S., Sagot, M-F., Lió, P., Crescenzi, P., Fani, R. and Fondi, M., 2015. MeDuSa: a multi-draft based scaffolder. Bioinformatics, v. 31
Doi: 10.1093/bioinformatics/btv171
Di Stefano, A., Scatà, M., La Corte, A., Liò, P., Catania, E., Guardo, E. and Pagano, S., 2015. Quantifying the Role of Homophily in Human Cooperation Using Multiplex Evolutionary Game Theory. PLoS One, v. 10
Doi: 10.1371/journal.pone.0140646
Narula, P., Sihota, P., Azad, S. and Lio, P., 2015. Analyzing seasonality of tuberculosis across Indian states and union territories. J Epidemiol Glob Health, v. 5
Doi: 10.1016/j.jegh.2015.02.004
Angione, C. and Lió, P., 2015. Predictive analytics of environmental adaptability in multi-omic network models. Sci Rep, v. 5
Doi: 10.1038/srep15147
Capobianco, E. and Liò, P., 2015. Comorbidity networks: Beyond disease correlations Journal of Complex Networks, v. 3
Doi: 10.1093/comnet/cnu048
Liò, P., Miglino, O., Nicosia, G., Nolfi, S. and Pavone, M., 2015. Advances in Artificial Life: Synthesis and Simulation of Living Systems: Editorial. Artif Life, v. 21
Doi: 10.1162/ARTL_e_00189
Angione, C., Pratanwanich, N. and Lió, P., 2015. A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation. ACS Synth Biol, v. 4
Doi: 10.1021/sb5003407
Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, MH., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, AJ., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, JW., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, RJ., Dassi, E., Di Genova, A., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, RC., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, JM., Goodstein, D., Gray, K., Guerra-Assunção, JA., Haggarty, B., Han, D-J., Han, BW., Harris, T., Harshbarger, J., Hastings, RK., Hayes, RD., Hoede, C., Hu, S., Hu, Z-L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J-H., Letellier, T., Li, C-Y., Lio, P., Liu, C-J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, AM., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, AA., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, DM., Steinbach, D., Stone, K., Stupka, E., Teague, JW., Dayem Ullah, AZ., Wang, J., Ware, D., Wong-Erasmus, M., Youens-Clark, K., Zadissa, A., Zhang, S-J. and Kasprzyk, A., 2015. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res, v. 43
Doi: 10.1093/nar/gkv350
Ascolani, G., Occhipinti, A. and Liò, P., 2015. Modelling circulating tumour cells for personalised survival prediction in metastatic breast cancer. PLoS Comput Biol, v. 11
Doi: 10.1371/journal.pcbi.1004199
Fondi, M., Maida, I., Perrin, E., Mellera, A., Mocali, S., Parrilli, E., Tutino, ML., Liò, P. and Fani, R., 2015. Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. Environ Microbiol, v. 17
Doi: 10.1111/1462-2920.12513
Moni, MA., Xu, H. and Liò, P., 2015. CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks. Bioinformatics, v. 31
Doi: 10.1093/bioinformatics/btu731
Narula, P., Azad, S. and Lio, P., 2015. Bayesian Melding Approach to Estimate the Reproduction Number for Tuberculosis Transmission in Indian States and Union Territories. Asia Pac J Public Health, v. 27
Doi: 10.1177/1010539515595068
Taffi, M., Taffi, M., Paoletti, N., Liò, P., Pucciarelli, S. and Marini, M., 2015. Bioaccumulation modelling and sensitivity analysis for discovering key players in contaminated food webs: The case study of PCBs in the Adriatic Sea Ecological Modelling, v. 306
Doi: 10.1016/j.ecolmodel.2014.11.030
Angione, C., Costanza, J., Carapezza, G., Lió, P. and Nicosia, G., 2015. Multi-Target Analysis and Design of Mitochondrial Metabolism. PLoS One, v. 10
Doi: 10.1371/journal.pone.0133825
Xu, H., Moni, MA. and Liò, P., 2015. Network regularised Cox regression and multiplex network models to predict disease comorbidities and survival of cancer. Comput Biol Chem, v. 59 Pt B
Doi: 10.1016/j.compbiolchem.2015.08.010
Nardi, F., Liò, P., Carapelli, A. and Frati, F., 2014. MtPAN(3): site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola. Mol Phylogenet Evol, v. 75
Doi: 10.1016/j.ympev.2014.02.001
Shavit, Y. and Lio', P., 2014. Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data. Mol Biosyst, v. 10
Doi: 10.1039/c4mb00142g
Pratanwanich, N. and Lió, P., 2014. Pathway-based Bayesian inference of drug-disease interactions. Mol Biosyst, v. 10
Doi: 10.1039/c4mb00014e
Lu, X., Qu, Z., Lio, P., Hui, P., Li, Q., Lu, P. and Bie, R., 2014. Directional communication with movement prediction in mobile wireless sensor networks Personal and Ubiquitous Computing,
Doi: 10.1007/s00779-014-0793-0
Raju, HB., Englander, Z., Capobianco, E., Tsinoremas, NF. and Lerch, JK., 2014. Identification of potential therapeutic targets in a model of neuropathic pain. Front Genet, v. 5
Doi: 10.3389/fgene.2014.00131
Felicetti, L., Femminella, M., Reali, G. and Liò, P., 2014. A molecular communication system in blood vessels for tumor detection Proceedings of the 1st ACM International Conference on Nanoscale Computing and Communication, NANOCOM 2014,
Doi: 10.1145/2619955.2619978
Nardi, F., Liò, P., Carapelli, A. and Frati, F., 2014. MtPAN<sup>3</sup>: Site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola Molecular Phylogenetics and Evolution, v. 75
Doi: 10.1016/j.ympev.2014.02.001
Lió, P., 2014. Computing longevity: Insights from controls Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8738 LNBI
Doi: 10.1007/978-3-319-10398-3_4
Capobianco, E. and Lió, P., 2014. Advances in translational biomedicine from systems approaches. Front Genet, v. 5
Doi: 10.3389/fgene.2014.00273
Pratanwanich, N. and Lio, P., 2014. Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation. Comput Biol Chem, v. 53 Pt A
Doi: 10.1016/j.compbiolchem.2014.08.019
Petrov, V., Balasubramaniam, S., Lale, R., Moltchanov, D., Lio', P. and Koucheryavy, Y., 2014. Forward and Reverse coding for chromosome transfer in bacterial nanonetworks Nano Communication Networks,
Azad, S. and Lio, P., 2014. Emerging trends of malaria-dengue geographical coupling in the Southeast Asia region. J Vector Borne Dis, v. 51
Taffi, M., Paoletti, N., Liò, P., Tesei, L., Pucciarelli, S. and Marini, M., 2014. Estimation and Modelling of PCBs Bioaccumulation in the Adriatic Sea
Ecosystem
Taffi, M., Paoletti, N., Angione, C., Pucciarelli, S., Marini, M. and Liò, P., 2014. Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis. Front Genet, v. 5
Doi: 10.3389/fgene.2014.00319
Moni, MA. and Liò, P., 2014. Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. BMC Bioinformatics, v. 15
Doi: 10.1186/1471-2105-15-333
Fondi, M., Orlandini, V., Perrin, E., Maida, I., Bosi, E., Papaleo, MC., Michaud, L., Lo Giudice, A., de Pascale, D., Tutino, ML., Liò, P. and Fani, R., 2014. Draft genomes of three Antarctic Psychrobacter strains producing antimicrobial compounds against Burkholderia cepacia complex, opportunistic human pathogens. Mar Genomics, v. 13
Doi: 10.1016/j.margen.2013.12.009
Pratanwanich, N. and Lio, P., 2014. Exploring the complexity of pathway-drug relationships using latent Dirichlet allocation Computational Biology and Chemistry,
Doi: 10.1016/j.compbiolchem.2014.08.019
Petrov, V., Balasubramaniam, S., Lale, R., Moltchanov, D., Lio', P. and Koucheryavy, Y., 2014. Forward and Reverse coding for chromosome transfer in bacterial nanonetworks Nano Communication Networks, v. 5
Doi: 10.1016/j.nancom.2014.04.003
Moni, MA. and Liò, P., 2014. comoR: a software for disease comorbidity risk assessment. J Clin Bioinforma, v. 4
Doi: 10.1186/2043-9113-4-8
Lu, X., Qu, Z., Lio, P., Hui, P., Li, Q., Lu, P. and Bie, R., 2014. Directional communication with movement prediction in mobile wireless sensor networks Personal and Ubiquitous Computing, v. 18
Doi: 10.1007/s00779-014-0793-0
Shavit, Y., Hamey, FK. and Lio, P., 2014. FisHiCal: an R package for iterative FISH-based calibration of Hi-C data. Bioinformatics, v. 30
Doi: 10.1093/bioinformatics/btu491
Taffi, M., Paoletti, N., Liò, P., Pucciarelli, S. and Marini, M., 2014. Bioaccumulation modelling and sensitivity analysis for discovering key players in contaminated food webs: The case study of PCBs in the Adriatic Sea Ecological Modelling, v. 306
Doi: 10.1016/j.ecolmodel.2014.11.030
Merelli, I., Liò, P. and Milanesi, L., 2013 (Published online). Describing the genes social networks relying on chromosome conformation capture data EMBnet.journal, v. 19
Doi: 10.14806/ej.19.b.735
Lio, P., 2013 (No publication date). Physio-Environmental Sensing and Live Modeling interactive Journal of Medical Research (i-JMR), v. 2
Doi: 10.2196/ijmr.2092.
Angione, C., Costanza, J., Carapezza, G., Lió, P. and Nicosia, G., 2013. A design automation framework for computational bioenergetics in biological networks. Mol Biosyst, v. 9
Doi: 10.1039/c3mb25558a
Jacovella, L. and Lio, P., 2013. Speeding up the transition to collective awareness 2013 IEEE International Conference on Communications Workshops, ICC 2013,
Doi: 10.1109/ICCW.2013.6649232
Lu, X., Hui, P. and Lio, P., 2013. Offloading Mobile Data from Cellular Networks Through Peer-to-Peer WiFi Communication: A Subscribe-and-Send Architecture CHINA COMMUNICATIONS, v. 10
Merelli, I., Liò, P. and Milanesi, L., 2013. NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations PLoS ONE, v. 8
Doi: 10.1371/journal.pone.0075146
Di Stefano, A., La Corte, A., Leotta, M., Lió, P. and Scatá, M., 2013. It measures like me: An IoTs algorithm in WSNs based on heuristics behavior and clustering methods Ad Hoc Networks, v. 11
Doi: 10.1016/j.adhoc.2013.04.011
Xie, S., Lawnizak, AT., Lio, P. and Krishnan, S., 2013. Feature Extraction by Multi-Scale Principal Component Analysis and Classification in Spectral Domain Engineering, v. 05
Doi: 10.4236/eng.2013.510b056
Angione, C., Carapezza, G., Costanza, J., Lió, P. and Nicosia, G., 2013. Design and strain selection criteria for bacterial communication networks Nano Communication Networks,
Taffi, M., Paoletti, N., Liò, P., Tesei, L., Merelli, E. and Marini, M., 2013. A systems biology and ecology framework for POPs bioaccumulation in marine ecosystems Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 8130 LNBI
Castiglione, F., Tieri, P., De Graaf, A., Franceschi, C., Liò, P., Van Ommen, B., Mazzà, C., Tuchel, A., Bernaschi, M., Samson, C., Colombo, T., Castellani, GC., Capri, M., Garagnani, P., Salvioli, S., Nguyen, VA., Bobeldijk-Pastorova, I., Krishnan, S., Cappozzo, A., Sacchetti, M., Morettini, M. and Ernst, M., 2013. The onset of type 2 diabetes: proposal for a multi-scale model. JMIR Res Protoc, v. 2
Doi: 10.2196/resprot.2854
Moni, MA., Mariani, S., Poli, G., Lio, P. and Vicenzi, E., 2013. Differential impacts of R5 vs. X4 HIV-1 on the transcriptome of primary CD4<sub>+</sub> T cells RETROVIROLOGY, v. 10
Doi: 10.1186/1742-4690-10-S1-P114
Di Stefano, A., La Corte, A., Leotta, M., Lió, P. and Scatá, M., 2013. It measures like me: An IoTs algorithm in WSNs based on heuristics behavior and clustering methods Ad Hoc Networks,
Vicenzi, E., Liò, P. and Poli, G., 2013. The puzzling role of CXCR4 in human immunodeficiency virus infection. Theranostics, v. 3
Doi: 10.7150/thno.5392
Castiglione, F., Diaz, V., Gaggioli, A., Lio, P., Mazza, C., Merelli, E., Meskers, CGM., Pappalardo, F. and von Ammon, R., 2013. Physio-Environmental Sensing and Live Modeling JOURNAL OF MEDICAL INTERNET RESEARCH, v. 15
Doi: 10.2196/ijmr.2092
Angione, C., Carapezza, G., Costanza, J., Lió, P. and Nicosia, G., 2013. Design and strain selection criteria for bacterial communication networks Nano Communication Networks, v. 4
Doi: 10.1016/j.nancom.2013.08.001
Balasubramaniam, S. and Lio', P., 2013. Multi-hop conjugation based bacteria nanonetworks. IEEE Trans Nanobioscience, v. 12
Doi: 10.1109/TNB.2013.2239657
Brilli, M., Liò, P., Lacroix, V. and Sagot, M-F., 2013. Short and long-term genome stability analysis of prokaryotic genomes. BMC Genomics, v. 14
Doi: 10.1186/1471-2164-14-309
Angione, C., Carapezza, G., Costanza, J., Lió, P. and Nicosia, G., 2013. Pareto optimality in organelle energy metabolism analysis. IEEE/ACM Trans Comput Biol Bioinform, v. 10
Doi: 10.1109/TCBB.2013.95
Shavit, Y. and Lio', P., 2013. CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks. Bioinformatics, v. 29
Doi: 10.1093/bioinformatics/btt120
Carapezza, G., Umeton, R., Costanza, J., Angione, C., Stracquadanio, G., Papini, A., Lió, P. and Nicosia, G., 2013. Efficient behavior of photosynthetic organelles via Pareto optimality, identifiability, and sensitivity analysis. ACS Synth Biol, v. 2
Doi: 10.1021/sb300102k
Lu, X., Lio, P., Hui, P. and Jin, H., 2013. A Location Prediction Algorithm for Mobile Communications Using Directional Antennas INTERNATIONAL JOURNAL OF DISTRIBUTED SENSOR NETWORKS,
Doi: 10.1155/2013/418606
Angione, C., Carapezza, G., Costanza, J., Lio, P. and Nicosia, G., 2013. Pareto Optimality in Organelle Energy Metabolism Analysis. IEEE/ACM Trans Comput Biol Bioinform,
Balasubramaniam, S., Ben-Yehuda, S., Pautot, S., Jesorka, A., Lio', P. and Koucheryavy, Y., 2013. A review of experimental opportunities for molecular communication Nano Communication Networks, v. 4
Doi: 10.1016/j.nancom.2013.02.002
Moni, MA., Liò, P. and Milanesi, L., 2013. Comparing viral (HIV) and bacterial (staphylococcus aureus) infection of the bone tissue BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms,
Angione, C., Carapezza, G., Costanza, J., Lio, P. and Nicosia, G., 2013. Rational design of organelle compartments in cells EMBnet. journal, v. 18
Liò, P., 2013. Pathways to P4 medicine BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms,
Angione, C., Costanza, J., Carapezza, G., Lió, P. and Nicosia, G., 2013. Pareto epsilon-dominance and identifiable solutions for BioCAD modeling Proceedings - Design Automation Conference,
Doi: 10.1145/2463209.2488787
Capobianco, E. and Lio', P., 2013. Comorbidity: a multidimensional approach Trends in Molecular Medicine,
Angione, C., Carapezza, G., Costanza, J., Lio, P. and Nicosia, G., 2013. Multi objective design for bacterial communication networks 2013 IEEE International Conference on Communications Workshops, ICC 2013,
Doi: 10.1109/ICCW.2013.6649345
Laise, P., Fanelli, D., Lio, P. and Arcangeli, A., 2012 (No publication date). Modeling TGF-β signaling pathway in epithelial-mesenchymal transition AIP Advances, v. Special Topic: Physics of Cancer
Lu, X., Pan, H. and Lio, P., 2012. High Delivery Performance Opportunistic Routing Scheme for Delay Tolerant Networks CHINA COMMUNICATIONS, v. 9
Paoletti, N., Liò, P., Merelli, E. and Viceconti, M., 2012. Multilevel computational modeling and quantitative analysis of bone remodeling. IEEE/ACM Trans Comput Biol Bioinform, v. 9
Doi: 10.1109/TCBB.2012.51
Liò, P., Angelini, C., De Feis, I. and Nguyen, V-A., 2012. Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species. PLoS One, v. 7
Doi: 10.1371/journal.pone.0042489
Peng, C., Jin, X., Wong, KC., Shi, M. and Liò, P., 2012. Correction: Collective Human Mobility Pattern from Taxi Trips in Urban Area. PLoS One, v. 7
Doi: 10.1371/annotation/f0d48839-ed4b-4cb2-822a-d449a6b4fa5d
Angione, C., Liò, P. and Nicosia, G., 2012. How to Compute with Metabolism in Bacteria? ERCIM News, v. 2012
Liò, P., Merelli, E. and Paoletti, N., 2012. Disease processes as hybrid dynamical systems EPTCS 92, 2012, pp. 152-166,
Haider, S., Cordeddu, L., Robinson, E., Movassagh, M., Siggens, L., Vujic, A., Choy, M-K., Goddard, M., Lio, P. and Foo, R., 2012. The landscape of DNA repeat elements in human heart failure. Genome Biol, v. 13
Doi: 10.1186/gb-2012-13-10-r90
Bartocci, E., Liò, P., Merelli, E. and Paoletti, N., 2012. Multiple Verification in Complex Biological Systems: The Bone Remodelling Case Study. Trans. Comp. Sys. Biology, v. 14
Doi: 10.1007/978-3-642-35524-0_3
Costanza, J., Carapezza, G., Angione, C., Lió, P. and Nicosia, G., 2012. Robust design of microbial strains. Bioinformatics, v. 28
Doi: 10.1093/bioinformatics/bts590
Massaro, E., Bagnoli, F., Guazzini, A. and Lió, P., 2012. Information dynamics algorithm for detecting communities in networks Communications in Nonlinear Science and Numerical Simulation,
Liò, P., Paoletti, N., Moni, MA., Atwell, K., Merelli, E. and Viceconti, M., 2012. Modelling osteomyelitis. BMC Bioinformatics, v. 13 Suppl 14
Doi: 10.1186/1471-2105-13-S14-S12
Nazri, A. and Lio, P., 2012. Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context. PLoS One, v. 7
Doi: 10.1371/journal.pone.0028713
Costanza, J., Carapezza, G., Angione, C., Liò, P. and Nicosia, G., 2012. Multi-objective optimisation, sensitivity and robustness analysis in FBA modelling Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 7605 LNBI
Doi: 10.1007/978-3-642-33636-2_9
Xie, S., Lawniczak, AT., Krishnan, S. and Lio, P., 2012. Wavelet Kernel Principal Component Analysis in Noisy Multiscale Data Classification ISRN Computational Mathematics, v. 2012
Doi: 10.5402/2012/197352
Lio', P. and Balasubramaniam, S., 2012. Opportunistic routing through conjugation in bacteria communication nanonetwork Nano Communication Networks, v. 3
Doi: 10.1016/j.nancom.2011.10.003
Peng, C., Jin, X., Wong, K-C., Shi, M. and Liò, P., 2012. Collective human mobility pattern from taxi trips in urban area. PLoS One, v. 7
Doi: 10.1371/journal.pone.0034487
Laise, P., Fanelli, D., Lio, P. and Arcangeli, A., 2012. Modeling TGF-beta signaling pathway in epithelial-mesenchymal transition AIP ADV, v. 2
Doi: 10.1063/1.3697962
Massaro, E., Bagnoli, F., Guazzini, A. and Lió, P., 2012. Information dynamics algorithm for detecting communities in networks Communications in Nonlinear Science and Numerical Simulation, v. 17
Doi: 10.1016/j.cnsns.2012.03.023
Umeton, R., Stracquadanio, G., Papini, A., Costanza, J., Liò, P. and Nicosia, G., 2012. Identification of sensitive enzymes in the photosynthetic carbon metabolism. Adv Exp Med Biol, v. 736
Doi: 10.1007/978-1-4419-7210-1_26
Lu, XF., Towsley, D., Lio, P. and Xiong, Z., 2012. An adaptive directional MAC protocol for ad hoc networks using directional antennas Science China Information Sciences, v. 55
Doi: 10.1007/s11432-012-4550-6
Leung, IXY., Chan, S-Y., Hui, P. and Lio', P., 2011. Intra-City Urban Network and Traffic Flow Analysis from GPS Mobility
Trace
Yoneki, E., Crowcroft, J., Lio', P., Walton, N., Vojnovic, M. and Whitaker, R., 2011. Message from the Workshop on the Future of Social Networking COMPUT COMMUN REV, v. 41
Doi: 10.1145/2002250.2002254
Movassagh, M., Choy, MK., Knowles, DA., Cordeddu, L., Haider, S., Down, T., Siggens, L., Vujic, A., Simeoni, I., Penkett, C., Goddard, M., Lio, P., Bennett, MR. and Foo, RSY., 2011. Distinct epigenomic features in end-stage failing human hearts Circulation, v. 124
Doi: 10.1161/CIRCULATIONAHA.111.040071
Song, Y. and Liò, P., 2011. Epileptic EEG detection via a novel pattern recognition framework 5th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2011,
Doi: 10.1109/icbbe.2011.5780179
Lio, P., Emanuela Merelli, , Nicola Paoletti, NP. and Marco Viceconti, MV., 2011. A Combined Process Algebraic and Stochastic Approach to Bone Remodeling Electronic Notes in Theoretical Computer Science, v. 277
Bagnoli, F. and Lio, P., 2011. HOW THE MUTATIONAL-SELECTION INTERPLAY ORGANIZES THE FITNESS LANDSCAPE J NONLINEAR MATH PHY, v. 18
Doi: 10.1142/S1402925111001532
Hebenstreit, D., Gu, M., Haider, S., Turner, DJ., Liò, P. and Teichmann, SA., 2011. EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res, v. 39
Doi: 10.1093/nar/gkq1226
Aldinucci, M., Bracciali, A., Liò, P., Sorathiya, A. and Torquati, M., 2011. StochKit-FF: Efficient systems biology on multicore architectures Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 6586 LNCS
Doi: 10.1007/978-3-642-21878-1_21
Balocco, C. and Lio, P., 2011. Assessing ventilation system performance in isolation rooms ENERG BUILDINGS, v. 43
Doi: 10.1016/j.enbuild.2010.09.020
Lio, P. and Verma, D., 2011. Preface Biologically Inspired Networking and Sensing: Algorithms and Architectures,
Doi: 10.4018/978-1-61350-092-7
Umeton, R., Stracquadanio, G., Sorathiya, A., Papini, A., Liò, P. and Nicosia, G., 2011. Design of robust metabolic pathways Proceedings - Design Automation Conference,
Doi: 10.1145/2024724.2024892
Schwarz, E., Whitfield, P., Nahnsen, S., Wang, L., Major, H., Leweke, FM., Koethe, D., Lio, P. and Bahn, S., 2011. Alterations of primary fatty acid amides in serum of patients with severe mental illness. Front Biosci (Elite Ed), v. 3
Doi: 10.2741/e246
Movassagh, M., Choy, M-K., Knowles, DA., Cordeddu, L., Haider, S., Down, T., Siggens, L., Vujic, A., Simeoni, I., Penkett, C., Goddard, M., Lio, P., Bennett, MR. and Foo, RS-Y., 2011. Distinct epigenomic features in end-stage failing human hearts. Circulation, v. 124
Doi: 10.1161/CIRCULATIONAHA.111.040071
Paoletti, N., Liò, P., Merelli, E. and Viceconti, M., 2011. Osteoporosis: A multiscale modeling viewpoint Proceedings of the 9th International Conference on Computational Methods in Systems Biology, CMSB'11,
Doi: 10.1145/2037509.2037536
Lu, X., Hui, P. and Lio, P., 2011. Evolving model of opportunistic routing in delay tolerant networks Proceedings - 2011 7th International Conference on Mobile Ad-hoc and Sensor Networks, MSN 2011,
Doi: 10.1109/MSN.2011.35
Khoo, WM. and Lió, P., 2011. Unity in diversity: Phylogenetic-inspired techniques for reverse engineering and detection of malware families Proceedings - 1st SysSec Workshop, SysSec 2011,
Doi: 10.1109/SysSec.2011.24
Lio, P. and Verma, D., 2011. Biologically inspired networking and sensing: Algorithms and architectures Biologically Inspired Networking and Sensing: Algorithms and Architectures,
Doi: 10.4018/978-1-61350-092-7
Lu, X., Xin, Y. and Lio, P., 2011. ADMAC: An adaptive directional MAC protocol for mobile ad hoc networks Proceedings - 2011 4th IEEE International Conference on Broadband Network and Multimedia Technology, IC-BNMT 2011,
Doi: 10.1109/ICBNMT.2011.6155982
Gilks, WR., Nye, TMW. and Lio, P., 2011. A Variance-Components Model for Distance-Matrix Phylogenetic Reconstruction STAT APPL GENET MOL, v. 10
Doi: 10.2202/1544-6115.1574
Giampieri, E., Remondini, D., de Oliveira, L., Castellani, G. and Lió, P., 2011. Stochastic analysis of a miRNA-protein toggle switch. Mol Biosyst, v. 7
Doi: 10.1039/c1mb05086a
Lio, P. and Sasitharan Balasubramaniam, SB., 2011. Opportunistic routing through conjugation in bacteria communication nanonetwork Nano Communication Networks, v. 2
Doi: 10.1016/j.nancom.2011.10.003
Balasubramaniam, S., Leibnitz, K., Lio', P., Botvich, D. and Murata, M., 2011. Biological Principles for Future Internet Architecture Design IEEE COMMUN MAG, v. 49
Liò, P., Merelli, E., Paoletti, N. and Viceconti, M., 2011. A combined process algebraic and stochastic approach to bone remodeling Electronic Notes in Theoretical Computer Science, v. 277
Doi: 10.1016/j.entcs.2011.09.034
Van Der Wath, RC., Van Der Wath, EC. and Lió, P., 2011. Parallel hematopoietic stem cell division rate estimation using an agent-based model on the grid Proceedings - 19th International Euromicro Conference on Parallel, Distributed, and Network-Based Processing, PDP 2011,
Doi: 10.1109/PDP.2011.65
Kitchovitch, S. and Liò, P., 2011. Community structure in social networks: applications for epidemiological modelling. PLoS One, v. 6
Doi: 10.1371/journal.pone.0022220
Xie, S., Lawniczak, AT., Song, Y. and Liò, P., 2010. Feature extraction via dynamic PCA for epilepsy diagnosis and epileptic seizure detection Proceedings of the 2010 IEEE International Workshop on Machine Learning for Signal Processing, MLSP 2010,
Doi: 10.1109/MLSP.2010.5588995
Botta, M., Haider, S., Leung, IXY., Lio, P. and Mozziconacci, J., 2010. Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide. Mol Syst Biol, v. 6
Doi: 10.1038/msb.2010.79
Liò, P. and Verma, DC., 2010. Biologically inspired networking [Guest Editorial]. IEEE Netw., v. 24
Doi: 10.1109/MNET.2010.5464220
Balocco, C. and Lio, P., 2010. Modelling infection spreading control in a Hospital isolation room Journal of Biomedical Science and Engineering, v. 3
Doi: 10.4236/jbise.2010.37089
Aldinucci, M., Bracciali, A. and Lio, P., 2010. Formal Synthetic Immunology Ercim News, v. 82
Sorathiya, A., Bracciali, A. and Liò, P., 2010. Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy. BMC Bioinformatics, v. 11 Suppl 1
Doi: 10.1186/1471-2105-11-S1-S67
Lio, P. and Verma, D., 2010. Guest Editorial: Biologically inspired networking IEEE Network, v. 24
Doi: 10.1109/MNET.2010.5464220
Angelini, C., De Feis, I., Nguyen, VA., Van Der Wath, R. and Liò, P., 2010. Combining replicates and nearby species data: A Bayesian approach Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 6160 LNBI
Doi: 10.1007/978-3-642-14571-1_14
Lio, P., Guazzini, A., Passarella, A. and Conti, M., 2010. Modeling perisaccadic time perception Journal of Biomedical Science and Engineering, v. 3
Doi: 10.4236/jbise.2010.312147
Lu, XF., Wicker, FD., Towsley, D., Xiong, Z. and Lio, P., 2010. Detection Probability Estimation of Directional Antennas and Omni-Directional Antennas WIRELESS PERS COMMUN, v. 55
Doi: 10.1007/s11277-009-9785-1
Pappas, V., Verma, DC. and Lio, P., 2010. Morphogenesis in computer networks 33rd IEEE Sarnoff Symposium 2010, Conference Proceedings,
Doi: 10.1109/SARNOF.2010.5469776
Lio, P. and Song, Y., 2010. A new approach for epileptic seizure detection: sample entropy based feature extraction and extreme learning machine Journal of Biomedical Science and Engineering, v. 3
Doi: 10.4236/jbise.2010.36078
Xie, S., Lawniczak, AT. and Liò, P., 2010. Features extraction via wavelet kernel PCA for data classification Proceedings of the 2010 IEEE International Workshop on Machine Learning for Signal Processing, MLSP 2010,
Doi: 10.1109/MLSP.2010.5588766
Sorathiya, A., Bracciali, A. and Lio, P., 2010. An integrated modelling approach for R5-X4 mutation and HAART therapy assessment SWARM INTELL-US, v. 4
Doi: 10.1007/s11721-010-0046-4
Lio, P. and Verma, D., 2010. Biologically Inspired Networking IEEE NETWORK, v. 24
Sorathiya, A., Bracciali, A. and Liò, P., 2010. An integrated modelling approach for R5-X4 mutation and HAART therapy assessment Swarm Intelligence,
Song, Y., Azad, S. and Lio, P., 2010. A new approach for epileptic seizure detection using extreme learning machine BIOSIGNALS 2010 - Proceedings of the 3rd International Conference on Bio-inpsired Systems and Signal Processing, Proceedings,
Stracquadanio, G., Umeton, R., Papini, A., Lio, P. and Nicosia, G., 2010. Analysis and optimization of C<inf>3</inf> photosynthetic carbon metabolism 10th IEEE International Conference on Bioinformatics and Bioengineering 2010, BIBE 2010,
Doi: 10.1109/BIBE.2010.17
Cheng, TMK., Lu, Y-E., Guest, PC., Rahmoune, H., Harris, LW., Wang, L., Ma, D., Stelzhammer, V., Umrania, Y., Wayland, MT., Lió, P. and Bahn, S., 2010. Identification of targeted analyte clusters for studies of schizophrenia. Mol Cell Proteomics, v. 9
Doi: 10.1074/mcp.M900372-MCP200
Guazzini, A., Lió, P., Bagnoli, F., Passarella, A. and Conti, M., 2010. Cognitive network dynamics in chatlines Procedia Computer Science, v. 1
Doi: 10.1016/j.procs.2010.04.265
Kitchovitch, S. and Liò, P., 2010. Risk perception and disease spread on social networks Procedia Computer Science, v. 1
Doi: 10.1016/j.procs.2010.04.264
Lio, P., 2009 (Published online). Modeling space and clocks constraints in visual information processing Frontiers in Neuroinformatics, v. 3
Doi: 10.3389/conf.neuro.11.2009.08.137
Leung, IXY., Hui, P., Lio, P. and Crowcroft, J., 2009. Towards real-time community detection in large networks PHYS REV E, v. 79
Doi: 10.1103/PhysRevE.79.066107
Bianchi, L. and Lio, P., 2009. La legge e il DNA Le Scienze, Italian Edition Scientific American,
Lee, U., Magistretti, E., Gerla, M., Bellavista, P., Lio, P. and Lee, KW., 2009. Bio-inspired multi-agent data harvesting in a proactive urban monitoring environment AD HOC NETW, v. 7
Doi: 10.1016/j.adhoc.2008.03.009
Wilson, A., Laurenti, E., Oser, G., van der Wath, RC., Blanco-Bose, W., Jaworski, M., Offner, S., Dunant, C., Eshkind, L., Bockamp, E., Lio, P., MacDonald, HR. and Trumpp, A., 2009. Hematopoietic Stem Cells Reversibly Switch from Dormancy to Self-Renewal during Homeostasis and Repair (DOI:10.1016/j.cell.2008.10.048) Cell, v. 138
Doi: 10.1016/j.cell.2009.06.020
Cheng, TMK., Lu, YE. and Lió, P., 2009. Identification of structurally important amino acids in proteins by graph-theoretic measures Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09,
Doi: 10.1145/1562090.1562092
Milanesi, L., Romano, P., Castellani, G., Remondini, D. and Lio, P., 2009. Trends in modeling Biomedical Complex Systems BMC BIOINFORMATICS, v. 10
Doi: 10.1186/1471-2105-10-S12-11
Nguyen, VA., Koukolikova-Nicola, Z., Bagnoli, F. and Lio, P., 2009. Noise and non-linearities in high-throughput data J STAT MECH-THEORY E,
Doi: 10.1088/1742-5468/2009/01/P01014
Milanesi, L., Romano, P., Castellani, G., Remondini, D. and Liò, P., 2009. Trends in modeling Biomedical Complex Systems. BMC Bioinformatics, v. 10 Suppl 12
Doi: 10.1186/1471-2105-10-S12-I1
Chan, SY., Leung, IXY. and Liò, P., 2009. Fast centrality approximation in modular networks International Conference on Information and Knowledge Management, Proceedings,
Doi: 10.1145/1651274.1651282
Lu, XF., Towsley, D., Lio, P., Wicker, F. and Xiong, Z., 2009. Minimizing Detection Probability Routing in Ad Hoc Networks Using Directional Antennas EURASIP J WIREL COMM,
Doi: 10.1155/2009/256714
Fondi, M., Emiliani, G., Liò, P., Gribaldo, S. and Fani, R., 2009. The evolution of histidine biosynthesis in archaea: insights into the his genes structure and organization in LUCA. J Mol Evol, v. 69
Doi: 10.1007/s00239-009-9286-6
Brilli, M., Fondi, M., Lio, P. and Fani, R., 2009. The Origin and Evolution of Nitrogen Fixation Genes ORIGINS LIFE EVOL B, v. 39
Schwarz, E., Leweke, FM., Bahn, S. and Liò, P., 2009. Clinical bioinformatics for complex disorders: a schizophrenia case study. BMC Bioinformatics, v. 10 Suppl 12
Doi: 10.1186/1471-2105-10-S12-S6
Wilson, A., Laurenti, E., Oser, G., van der Wath, RC., Blanco-Bose, W., Jaworski, M., Offner, S., Dunant, C., Eshkind, L., Bockamp, E., Lio, P., MacDonald, HR. and Trumpp, A., 2009. Hematopoietic Stem Cells Reversibly Switch from Dormancy to Self-Renewal during Homeostasis and Repair (vol 135, pg 1118, 2008) CELL, v. 138
Doi: 10.1016/j.cell.2009.06.020
Carla Balocco, CB., Lio, P. and Luca Sani, , 2009. Simulazione di un sistema di ventilazione per il controllo degli agenti eziologici nei reparti infettivi. Un caso reale CDA CONDIZIONAMENTO DELL'ARIA RISCALDAMENTO REFRIGERAZIONE, v. May 2009
van der Wath, RC., Wilson, A., Laurenti, E., Trumpp, A. and Liò, P., 2009. Estimating dormant and active hematopoietic stem cell kinetics through extensive modeling of bromodeoxyuridine label-retaining cell dynamics. PLoS One, v. 4
Doi: 10.1371/journal.pone.0006972
Lu, X., Wicker, F., Leung, I., Liò, P. and Xiong, Z., 2008. A location prediction algorithm for directional communication IWCMC 2008 - International Wireless Communications and Mobile Computing Conference,
Doi: 10.1109/IWCMC.2008.28
Xie, S., Lawniczak, AT. and Lió, P., 2008. Parametric & non-parametric analysis of mean treatment effects of number of packets in transit in data network model Canadian Conference on Electrical and Computer Engineering,
Doi: 10.1109/CCECE.2008.4564900
Brilli, M., Fani, R. and Liò, P., 2008. Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes. Brief Bioinform, v. 9
Doi: 10.1093/bib/bbm051
Lu, YE., Lió, P. and Hand, S., 2008. On low dimensional random projections and similarity search International Conference on Information and Knowledge Management, Proceedings,
Doi: 10.1145/1458082.1458182
Bagnoli, F., Guazzini, A. and Liò, P., 2008. Human Heuristics for Autonomous Agents CoRR, v. abs/0801.3048
Stajano, F., Bianchi, L., Liò, P. and Korff, D., 2008. Forensic genomics: Kin privacy, driftnets and other open questions Proceedings of the ACM Conference on Computer and Communications Security,
Doi: 10.1145/1456403.1456407
Wilson, A., Osee, G., van der Wath, R., Blanco-Bose, W., Laurenti, E., Dunant, C., Lio, P., MacDonald, HR. and Trumpp, A., 2008. Haematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair SWISS MED WKLY, v. 138
Lio, P. and Bishop, M., 2008. Modeling sequence evolution Methods Mol Biol., v. 452
Wilson, A., Laurenti, E., Oser, G., van der Wath, RC., Blanco-Bose, W., Jaworski, M., Offner, S., Dunant, CF., Eshkind, L., Bockamp, E., Lió, P., Macdonald, HR. and Trumpp, A., 2008. Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair. Cell, v. 135
Doi: 10.1016/j.cell.2008.10.048
Liò, P., Lawniczak, AT., Xie, S. and Xu, J., 2008. Wavelet-domain statistics of packet switching networks near traffic congestion Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 5151 LNCS
Doi: 10.1007/978-3-540-92191-2_24
Brilli, M., Mengoni, A., Fondi, M., Bazzicalupo, M., Liò, P. and Fani, R., 2008. Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. BMC Bioinformatics, v. 9
Doi: 10.1186/1471-2105-9-551
Kershenbaum, A., Pappas, V., Lee, KW., Lio, P., Sadler, B. and Verma, D., 2008. A biologically-inspired MANET architecture Proceedings of SPIE - The International Society for Optical Engineering, v. 6981
Doi: 10.1117/12.783462
Cheng, TMK., Lu, Y-E., Vendruscolo, M., Lio', P. and Blundell, TL., 2008. Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms. PLoS Comput Biol, v. 4
Doi: 10.1371/journal.pcbi.1000135
Brilli, M., Fani, R. and Lio, P., 2007. MotifScorer: using a compendium of microarrays to identify regulatory motifs BIOINFORMATICS, v. 23
Doi: 10.1093/bioinformatics/btl607
Bagnoli, F., Liò, P. and Sguanci, L., 2007. Risk perception in epidemic modeling. Phys Rev E Stat Nonlin Soft Matter Phys, v. 76
Doi: 10.1103/PhysRevE.76.061904
Caretta-Cartozo, C., De Los Rios, P., Piazza, F. and Lio, P., 2007. Bottleneck genes and community structure in the cell cycle network of S-pombe PLOS COMPUT BIOL, v. 3
Doi: 10.1371/journal.pcbi.0030103
Liò, P., 2007. Topological and dynamical properties of genetic and social networks PAMM, v. 7
Doi: 10.1002/pamm.200700842
Lawniczak, AT., Xie, S., Liò, PP. and Xu, J., 2007. Study of packet traffic fluctuations near phase transition point from free flow to congestion in data network model Canadian Conference on Electrical and Computer Engineering,
Doi: 10.1109/CCECE.2007.93
Bianchi, L. and Lio, P., 2007. Forensic DNA and bioinformatics BRIEF BIOINFORM, v. 8
Doi: 10.1093/bib/bbm006
Weston, EM., Friday, AE. and Liò, P., 2007. Biometric evidence that sexual selection has shaped the hominin face. PloS one, v. 2
Chen, F., Archambault, V., Kar, A., Lio, P., D'Avino, PP., Sinka, R., Lilley, K., Laue, ED., Deak, P., Capalbo, L. and Glover, DM., 2007. Multiple protein phosphatases are required for mitosis in Drosophila CURR BIOL, v. 17
Doi: 10.1016/j.cub.2007.01.068
Papetti, C., Lio, P., Ruber, L., Patarnello, T. and Zardoya, R., 2007. Antarctic fish mitochondrial genomes lack ND6 gene J MOL EVOL, v. 65
Doi: 10.1007/s00239-007-9030-z
Weston, EM., Friday, AE. and Liò, P., 2007. Biometric evidence that sexual selection has shaped the hominin face. PLoS One, v. 2
Doi: 10.1371/journal.pone.0000710
Caretta-Cartozo, C., De Los Rios, P., Piazza, F. and Liò, P., 2007. Bottleneck genes and community structure in the cell cycle network of S. pombe PLoS Computational Biology, v. 3
Doi: 10.1371/journal.pcbi.0030103
van der Wath, E., Moutsianas, L., van der Wath, R., Visagie, A., Milanesi, L. and Lio, P., 2007. Grid methodology for identifying co-regulated genes and transcription factor binding sites IEEE T NANOBIOSCI, v. 6
Doi: 10.1109/TNB.2007.897470
Fani, R., Caramelli, D. and Liò, P., 2006. [It happened... From prebiotic chemistry to human evolution. In Florence, the First Congress of S.I.B.E. September, 4-6, 2006]. Riv Biol, v. 99
Nye, TMW., Lio, P. and Gilks, WR., 2006. A novel algorithm and web-based tool for comparing two alternative phylogenetic trees BIOINFORMATICS, v. 22
Doi: 10.1093/bioinformatics/bti720
Ambesi-Impiombato, A., Bansal, M., Liò, P. and di Bernardo, D., 2006. Computational framework for the prediction of transcription factor binding sites by multiple data integration. BMC Neurosci, v. 7 Suppl 1
Doi: 10.1186/1471-2202-7-S1-S8
Bagnoli, F., Lio, P. and Sguanci, L., 2006. Modeling viral coevolution: HIV multi-clonal persistence and competition dynamics PHYSICA A, v. 366
Doi: 10.1016/j.physa.2005.10.055
Fani, R., Brilli, M. and Liò, P., 2006. Inference from proteobacterial operons shows piecewise organization: a reply to Price et al. J Mol Evol, v. 63
Doi: 10.1007/s00239-006-0074-2
Fani, R., Caramelli, D. and Liò, P., 2006. From prebiotic chemistry to the evolution of man: The First Conference of the S.I.B.E. (Italian Society of Evolutionary Biology) in Florence Rivista di Biologia - Biology Forum, v. 99
Fani, R., Caramelli, D. and Liò, P., 2006. From prebiotic chemistry to the evolution of man: The First Conference of the S.I.B.E. (Italian Society of Evolutionary Biology) in Florence Rivista di Biologia - Biology Forum, v. 99
Sguanci, L., Bagnoli, F. and Lio, P., 2006. Mathematical Model of HIV superinfection dynamics and R5 to X4 switch
Fani, R., Brilli, M. and Lio, P., 2005. The origin and evolution of operons: The piecewise building of the proteobacterial histidine operon J MOL EVOL, v. 60
Doi: 10.1007/s00239-004-0198-1
Piazza, F. and Lio, P., 2005. Statistical analysis of simple repeats in the human genome PHYSICA A, v. 347
Doi: 10.1016/j.physa.2004.08.038
Rustici, G., Mata, J., Kivinen, K., Lió, P., Penkett, CJ., Burns, G., Hayles, J., Brazma, A., Nurse, P. and Bähler, J., 2004. Periodic gene expression program of the fission yeast cell cycle Nature Genetics, v. 36
Doi: 10.1038/ng1377
Tadesse, MG., Vannucci, M. and Lio, P., 2004. Identification of DNA regulatory motifs using Bayesian variable selection BIOINFORMATICS, v. 20
Doi: 10.1093/bioinformatics/bth282
Rustici, G., Mata, J., Kivinen, K., Lió, P., Penkett, CJ., Burns, G., Hayles, J., Brazma, A., Nurse, P. and Bähler, J., 2004. Periodic gene expression program of the fission yeast cell cycle. Nat Genet, v. 36
Doi: 10.1038/ng1377
Lio, P. and Goldman, N., 2004. Phylogenomics and bioinformatics of SARS-CoV TRENDS MICROBIOL, v. 12
Liò, P., 2003. Dimensionality and dependence problems in statistical genomics. Brief Bioinform, v. 4
Doi: 10.1093/bib/4.2.168
Lio, P., 2003. Il genoma della Sars Le Scienze Italian Edition of Scientific American, v. June 2003
Lio, P., 2003. Wavelets in bioinformatics and computational biology: state of art and perspectives BIOINFORMATICS, v. 19
Lio, P., 2003. Statistical bioinformatic methods in microbial genome analysis BIOESSAYS, v. 25
Doi: 10.1002/bies.10231
Lio, P., 2002. Una vita per le proteine Le Scienze Italian Edition of Scientific American, v. February 2002
Skaer, N., Pistillo, D., Gibert, JM., Lio, P., Wulbeck, C. and Simpson, P., 2002. Gene duplication at the achaete-scute complex and morphological complexity of the peripheral nervous system in Diptera TRENDS GENET, v. 18
Liò, P. and Goldman, N., 2002. Modeling mitochondrial protein evolution using structural information. J Mol Evol, v. 54
Doi: 10.1007/s00239001-0052-7
Lio, P., 2002. Investigating the relationship between genome structure, composition, and ecology in prokaryotes MOL BIOL EVOL, v. 19
Lio, P. and Goldman, N., 2002. Modeling mitochondrial protein evolution using structural information J MOL EVOL, v. 54
Doi: 10.1007/s00239001-0052-7
Whelan, S., Lio, P. and Goldman, N., 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past TRENDS GENET, v. 17
Lio, P., 2001. Dal Genoma al Fisioma
Lio, P., 2001. Le nuove sfide della filogenesi molecolare Le Scienze Italian Edition of Scientific American, v. February 2001
Massingham, T., Davies, LJ. and Lio, P., 2001. Analysing gene function after duplication BIOESSAYS, v. 23
Vannucci, M. and Lio, P., 2001. Non-decimated wavelet analysis of biological sequences: applications to protein structure and genomics Sankhyā: The Indian Journal of Statistics, Series B, v. 63b2
Bogani, P., Simoni, A., Lio, P., Germinario, A. and Buiatti, M., 2001. Molecular variation in plant cell populations evolving in vitro in different physiological contexts. Genome, v. 44
Lio, P., 2000. Siamo uomini non DNA robot,
Lio, P. and Vannucci, M., 2000. Finding pathogenicity islands and gene transfer events in genome data BIOINFORMATICS, v. 16
Thomas, NS., Wilkinson, J., Lio, P., Doull, I., Morton, NE. and Holgate, ST., 2000. Investigation of the genetic factors underlying asthma and atopy in outbred UK populations Revue des Maladies Respiratoires, v. 17
Fani, R., Gallo, R. and Liò, P., 2000. Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes. J Mol Evol, v. 51
Doi: 10.1007/s002390010061
Thomas, NS., Wilkinson, J., Lio, P., Doull, I., Morton, NE. and Holgate, ST., 2000. [Genetic factors involved in asthma and atopy. Studies in British families]. Rev Mal Respir, v. 17
Thomas, NS., Wilkinson, J., Lio, P., Doull, I., Morton, NE. and Holgate, ST., 2000. Investigation of the genetic factors underlying asthma and atopy in outbred UK populations REV MAL RESPIR, v. 17
Hagelberg, E., Goldman, N., Lio, P., Whelan, S., Schiefenhovel, W., Clegg, JB. and Bowden, DK., 2000. Evidence for mitochondrial DNA recombination in a human population of island Melanesia: correction P ROY SOC LOND B BIO, v. 267
Mori, E., Liò, P., Daly, S., Damiani, G., Perito, B. and Fani, R., 1999. Molecular nature of RAPD markers from Haemophilus influenzae Rd genome. Res Microbiol, v. 150
Doi: 10.1016/s0923-2508(99)80026-6
Hagelberg, E., Goldman, N., Lió, P., Whelan, S., Schiefenhövel, W., Clegg, JB. and Bowden, DK., 1999. Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proc Biol Sci, v. 266
Doi: 10.1098/rspb.1999.0663
Liò, P. and Goldman, N., 1998. Models of molecular evolution and phylogeny. Genome Res, v. 8
Doi: 10.1101/gr.8.12.1233
Lio, P. and Ruffo, S., 1998. Searching for genomic constraints NUOVO CIMENTO D, v. 20
Liò, P., Goldman, N., Thorne, JL. and Jones3, DT., 1998. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics, v. 14
Doi: 10.1093/bioinformatics/14.8.726
Liò, P., Goldman, N., Thorne, JL. and Jones, DT., 1998. PASSML: Combining evolutionary inference and protein secondary structure prediction Bioinformatics, v. 14
Doi: 10.1093/bioinformatics/14.8.726
Liò, P. and Goldman, N., 1998. Review: Models of molecular evolution and phylogeny Genome Research, v. 8
Doi: 10.1101/gr.8.12.1233
Liò, P. and Morton, NE., 1997. Comparison of parametric and nonparametric methods to map oligogenes by linkage. Proc Natl Acad Sci U S A, v. 94
Doi: 10.1073/pnas.94.10.5344
Bogani, P., Liò, P., Intrieri, MC. and Buiatti, M., 1997. A physiological and molecular analysis of the genus Nicotiana. Mol Phylogenet Evol, v. 7
Doi: 10.1006/mpev.1996.0356
Dewar, JC., Wilkinson, J., Wheatley, A., Thomas, NS., Doull, I., Morton, N., Lio, P., Harvey, JF., Liggett, SB., Holgate, ST. and Hall, IP., 1997. The glutamine 27 beta2-adrenoceptor polymorphism is associated with elevated IgE levels in asthmatic families. J Allergy Clin Immunol, v. 100
Doi: 10.1016/s0091-6749(97)70234-3
Lio, P., 1997. Correlation methods for genomic constraints analysis Annals of Human Genetics, v. 61
Lio, P., 1997. Comparison of multipoint analyses for complex inheritance: IDDM and asthma Annals of Human Genetics, v. 61
Dewar, J., Wheatley, A., Wilkinson, J., Holgate, ST., Thomas, NS., Lio, P., Morton, NE. and Hall, IP., 1997. Association of the Gln 27 beta 2-adrenoceptor polymorphism and IgE variability in asthmatic families. Chest, v. 111
Doi: 10.1378/chest.111.6_supplement.78s
Fani, R., Tamburini, E., Mori, E., Lazcano, A., Liò, P., Barberio, C., Casalone, E., Cavalieri, D., Perito, B. and Polsinelli, M., 1997. Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes. Gene, v. 197
Doi: 10.1016/s0378-1119(97)00146-7
Liò, P., Politi, A., Ruffo, S. and Buiatti, M., 1996. Analysis of genomic patchiness of Haemophilus influenzae and Saccharomyces cerevisiae chromosomes. J Theor Biol, v. 183
Doi: 10.1006/jtbi.1996.0235
Alifano, P., Fani, R., Liò, P., Lazcano, A., Bazzicalupo, M., Carlomagno, MS. and Bruni, CB., 1996. Histidine biosynthetic pathway and genes: structure, regulation, and evolution. Microbiol Rev, v. 60
Doi: 10.1128/mr.60.1.44-69.1996
Bogani, P., Simoni, A., Lio', P., Scialpi, A. and Buiatti, M., 1996. Genome flux in tomato cell clones cultured in vitro in different physiological equilibria. II. A RAPD analysis of variability. Genome, v. 39
Doi: 10.1139/g96-107
Alifano, P., Fani, R., Lio, P., Lazcano, A., Bazzicalupo, M., Carlomagno, MS. and Bruni, CB., 1996. Histidine biosynthetic pathway and genes: Structure, regulation, and evolution MICROBIOL REV, v. 60
Liò, P., Politi, A., Buiatti, M. and Ruffo, S., 1996. High statistics block entropy measures of DNA sequences. J Theor Biol, v. 180
Doi: 10.1006/jtbi.1996.0091
Fani, R., Liò, P. and Lazcano, A., 1995. Molecular evolution of the histidine biosynthetic pathway. J Mol Evol, v. 41
Doi: 10.1007/BF00173156
VICARIO, F., VENDRAMIN, GG., ROSSI, P., LIO, P. and GIANNINI, R., 1995. ALLOZYME, CHLOROPLAST DNA AND RAPD MARKERS FOR DETERMINING GENETIC-RELATIONSHIPS BETWEEN ABIES-ALBA AND THE RELIC POPULATION OF ABIES NEBRODENSIS THEOR APPL GENET, v. 90
Bagnoli, F. and Liò, P., 1995. Selection, mutations and codon usage in a bacterial model. J Theor Biol, v. 173
Doi: 10.1006/jtbi.1995.0062
Lió, P., Ruffo, S. and Buiatti, M., 1994. Third codon G + C periodicity as a possible signal for an "internal" selective constraint. J Theor Biol, v. 171
Doi: 10.1006/jtbi.1994.1225
Fani, R., Liò, P., Chiarelli, I. and Bazzicalupo, M., 1994. The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. J Mol Evol, v. 38
Doi: 10.1007/BF00178849
Theses / dissertations
Scherer, P., 2024 (No publication date). Distributional and relational inductive biases for graph representation learning in biomedicine
Doi: 10.17863/CAM.107338
Bernstein, A., 2023 (No publication date). Immune Infiltrates in Breast Cancer: Clinical Significance from Histopathology to Prognosis
Doi: 10.17863/CAM.99938
Zhu, J., 2023 (No publication date). Deep neural networks for medical image super-resolution
Doi: 10.17863/CAM.101535
Tilly, T., 2023 (No publication date). Deep learning of regulatory sequence variation in Pulmonary Arterial Hypertension
Doi: 10.17863/CAM.100199
Bodnar, C., 2023 (No publication date). Topological Deep Learning: Graphs, Complexes, Sheaves
Doi: 10.17863/CAM.97212
Christensen, CN., 2023 (No publication date). Deep learning for image processing in optical super-resolution microscopy
Doi: 10.17863/CAM.101919
Rocheteau, E., 2023 (No publication date). Representation Learning for Patients in the Intensive Care Unit
Doi: 10.17863/CAM.96504
Deasy, J., 2022 (No publication date). Relaxing assumptions in deep probabilistic modelling
Doi: 10.17863/CAM.90966
Azevedo, T., 2022 (No publication date). Data-driven Representations in Brain Science: Modelling Approaches in Gene Expression and Neuroimaging Domains
Doi: 10.17863/CAM.86924
Spivakovsky-Gonzalez, P., 2022 (No publication date). Computational Tools for Metabolic Modeling and Gene Duplication Analysis
Doi: 10.17863/CAM.86478
Spasov, S., 2022 (No publication date). Encoding parameter and structural efficiency in deep learning
Doi: 10.17863/CAM.84834
Wang, D., 2021 (No publication date). Neural Diagrammatic Reasoning
Dimanov, B., 2021 (No publication date). Interpretable Deep Learning: Beyond Feature-Importance with Concept-based Explanations
Andres Terre, H., 2020 (No publication date). Interpreting Deep Learning for cell differentiation. Supervised and Unsupervised models viewed through the lens of information and perturbation theory.
Doi: 10.17863/CAM.54136
Book chapters
Giannini, F., Fioravanti, S., Barbiero, P., Tonda, A., Liò, P. and Di Lavore, E., 2024. Categorical Foundation of Explainable AI: A Unifying Theory
Doi: 10.1007/978-3-031-63800-8_10
Ciravegna, G., Giannini, F., Barbiero, P., Gori, M., Lio, P., Maggini, M. and Melacci, S., 2023. Learning logic explanations by neural networks
Doi: 10.3233/FAIA230157
Ciravegna, G., Giannini, F., Barbiero, P., Gori, M., Lio, P., Maggini, M. and Melacci, S., 2023. Learning logic explanations by neural networks
Doi: 10.3233/FAIA230157
De Maria, E., Despeyroux, J., Felty, A., Liò, P., Olarte, C. and Bahrami, A., 2023. Computational logic for biomedicine and neurosciences
Doi: 10.1002/9781394229086.ch6
Rocheteau, E., Bica, I., Liò, P. and Ercole, A., 2023. Dynamic Outcomes-Based Clustering of Disease Trajectory in Mechanically Ventilated Patients
Doi: 10.1007/978-3-031-36938-4_6
Magister, LC., Barbiero, P., Kazhdan, D., Siciliano, F., Ciravegna, G., Silvestri, F., Jamnik, M. and Liò, P., 2023. Concept Distillation in Graph Neural Networks
Doi: 10.1007/978-3-031-44070-0_12
Ciravegna, G., Giannini, F., Barbiero, P., Gori, M., Lio, P., Maggini, M. and Melacci, S., 2023. Chapter 25. Learning Logic Explanations by Neural Networks
Doi: 10.3233/faia230157
DE MARIA, E., DESPEYROUX, J., FELTY, A., LIÒ, P., OLARTE, C. and BAHRAMI, A., 2022. Logique calculatoire pour la biomédecine et les neurosciences
Doi: 10.51926/iste.9029.ch6
Vignani, R., Scali, M. and Liò, P., 2022. Molecular markers and genomics for food and beverages characterization
Doi: 10.1007/978-981-16-4318-7_43
Barsacchi, M., Andres-Terré, H. and Lió, P., 2022. Metabolically driven latent space learning for gene expression data
Doi: 10.1142/9781800610941_0005
Vijayakumar, S., Conway, M., Lió, P. and Angione, C., 2018. Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives.
Doi: 10.1007/978-1-4939-7528-0_18
Felicetti, L., Femminella, M., Liò, P. and Reali, G., 2017. Effect of aging, disease versus health conditions in the design of nano-communications in blood vessels
Doi: 10.1007/978-3-319-50688-3_19
Di Stefano, A., La Corte, A., Lió, P. and Scatá, M., 2016. Bio-Inspired ICT for Big Data Management in Healthcare
Doi: 10.1007/978-3-319-23742-8_1
Liu, Z., Tang, L. and Yan, J., 2015. A random early detection based active queue management algorithm in power optical communication network
Doi: 10.1201/b18592-52
Bansal, A., Azad, S. and Lio, P., 2013. Malaria incidence forecasting and its implication to intervention strategies in South East Asia Region
Doi: 10.1007/978-3-319-00395-5_110
Lio, P., Bianchi, L., Nguyen, V. and Kitchovich, S., 2013. Risk Perception, Heuristics and Epidemic Spread
Lio, P. and Verma, D., 2012. Biologically Inspired Networking and Sensing: Algorithms and Architectures Preface
Lio, P. and Brilli, M., 2010. Transcription factors and gene regulatory networks
Emiliani, G., Fondi, M., Lio, P. and Fani, R., 2010. Evolution of Metabolic Pathways and Evolution of Genomes
Brilli, M., Fani, R. and Lio, P., 2010. Bioinformatics of gene families
Brilli, M. and Lio, P., 2010. The structural and dynamical properties of biological systems
Carapelli, A., Nardi, F., Dallai, R., Boore, J., LiÒ, P. and Frati, F., 2005. Relationships between hexapods and crustaceans based on four mitochondrial genes
Doi: 10.1201/9781420037548.ch12
Carapelli, A., Nardi, F., Dallai, R., Boore, JL., Lio, P. and Frati, F., 2005. Relationships between hexapods and crustaceans based on 4 mitochondrial genes
Renato Fani, RF., Silvia Casadei, SC. and Lio, P., 2002. Origin and Evolution of nif Genes
Doi: 10.1007/0-306-47615-0_85
Liò, P., Bazzicalupo, M., Grifoni, A., Mori, E. and Fani, R., 1995. Cloning and Analysis of an Azospirillum brasilense Iteron and hslUV Operon Containing Region
Doi: 10.1007/978-3-642-79906-8_14
Internet publications
Igashov, I., Jamasb, A., Sadek, A., Sverrisson, F., Schneuing, A., Liò, P., Blundell, T., Bronstein, M. and Correia, B., 2022. Decoding Surface Fingerprints for Protein-Ligand Interactions
Doi: 10.1101/2022.04.26.489341
Zhao, Y., Wang, D., Gao, X., Mullins, R., Lio, P. and Jamnik, M., 2020. Probabilistic Dual Network Architecture Search on Graphs
Wang, D., Jamnik, M. and Lio, P., 2020. Extrapolatable Relational Reasoning With Comparators in Low-Dimensional
Manifolds
Luzhnica, E., Day, B. and Liò, P., 2019. On Graph Classification Networks, Datasets and Baselines
Viñas, R., Andrés-Terré, H., Liò, P. and Bryson, K., 2019. Adversarial generation of gene expression data
Doi: 10.1101/836254
Bica, I., Andrés-Terré, H., Cvejic, A. and Liò, P., 2019. Unsupervised generative and graph representation learning for modelling cell differentiation
Doi: 10.1101/801605
Books
Lio, P. and Zuliani, P., 2019. Automated Reasoning for Systems Biology and Medicine Preface
Aiello, LM., Cherifi, C., Cherifi, H., Lambiotte, R., Lió, P. and Rocha, LM., 2019. Preface
Aiello, LM., Cherifi, C., Cherifi, H., Lambiotte, R., Lió, P. and Rocha, LM., 2019. Preface
Bartocci, E., Lio, P. and Paoletti, N., 2016. Preface
Di Serio, C., Liò, P., Nonis, A. and Tagliaferri, R., 2015. Preface
Lio, P. and Verma, D., 2011. Biologically Inspired Networking and Sensing