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Department of Computer Science and Technology

  • Professor of Computational Biology

I am Full Professor at the department of Computer Science and Technology of the University of Cambridge and I am a member of the Artificial Intelligence group. I am a member of the Cambridge Centre for AI in Medicine.

Background: PhD in Complex Systems and Non Linear Dynamics (School of Informatics, dept of Engineering of the University of Firenze, Italy) and PhD in (Theoretical) Genetics (University of Pavia, Italy). More information is on my personal homepage

Other Affliations: Fellow and member of the Council of Clare Hall College, member of Ellis, the European Lab for Learning & Intelligent Systems, I am member of the Academia Europaea; I am listed in www.topitalianscientists.org/Top_italian_scientists_VIA-Academy.aspx

I am happy to receive enquiries for PhD applications. I have successfully completed the equality and diversity essentials.

Committees : Student complaints; Postdoc mentoring

 

Research

My research interest focuses on developing Artificial Intelligence and Computational Biology models to understand diseases complexity and address personalised and precision medicine. Current focus is on Graph Neural Network modeling to build predictive models based on the integration of multi scale, multi omics and multi physics data; integrate deep learning and mechanistic approaches; explainability and interpretability in medicine; exploiting short and long range communications in the human body, between cells and tissues and predict emerging mechanistic properties at systemic medicine level. Develop an AI-based medical digital twin to increase self-awareness; Develop an AI personal decision support system to increase social awareness.

Teaching

Current: Geometric Deep learning

Past: Bioinformatics Algorithms

Current Agenda (March):

Member of the committee to assess Pasteur Institutes (France)

 

 

 

Current and Past Postdoctoral students

  • Francesco di Giovanni
  • Tiago Azevedo
  • Helena Andres Terre
  • Nikola Simidjievski
  • Zohreh Shams
  • Alessandro di Stefano
  • Gianluca Ascolani
  • Julien Mozziconacci
  • Eric Yu-En Lu

Current and Past PhD students

  • Jonas Jurg
  • Iulia Duta
  • Adrian Bazaga (with Gos Mickeim)
  • Simon Mathis
  • Chaitanya Joshi
  • Alex Norcliffe
  • David Buterez
  • Dobrik Georgiev
  • Jacob Moss
  • Pietro Barbiero
  • Giulio De Angeli (with MariaGrazia Spillantini)
  • Cristian Bodnar
  • Alexander Campbell
  • Paris Flood
  • Felix Opolka
  • Ramon Viñas Torné
  • Junwei Yang
  • Paul Scherer
  • Jacob Deasy
  • Catalina Cangea
  • Benjamin Day
  • Emma Rocheteau
  • Tiago Azevedo
  • Simeon Spasov
  • Duo Wang
  • Jin Zhu
  • Petar Velickovic
  • Helena Andres Terre
  • Giovanna maria Dimitri
  • Pablo Spivakovsky-Gonzalez
  • Thomas Brouwer
  • Maxwell Conway
  • Hui Xiao
  • Annalisa Occhipinti
  • Naruemon (Ploy) Pratanwanich
  • Yoli Shavit
  • Claudio Angione
  • Mohammad Ali Moni
  • Syed Haider
  • Stephan Kitchovitch
  • Yuedong Song
  • Ian Leung
  • Viet Anh Nguyen
  • Anilkumar Sorathiya
  • Richard Van der Wath

Publications

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
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  • 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
  • Bella, G. and Lio, P., 2009. Formal Analysis of the Genetic Toggle COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY, PROCEEDINGS, v. 5688
  • Sorathiyar, A., Lio, P. and Sguanci, L., 2009. Mathematical Model of HIV Superinfection and Comparative Drug Therapy ARTIFICIAL IMMUNE SYSTEMS, PROCEEDINGS, v. 5666
  • Xie, SK., Lio, P. and Lawniczak, AT., 2009. A Case Study of ICA with Multi-scale PCA of Simulated Traffic Data ARTIFICIAL NEURAL NETWORKS - ICANN 2009, PT II, v. 5769
  • Giampaolo Bella, GB. and Lio, P., 2009. Analysing the microRNA-17-92/Myc/E2F/RB Compound Toggle Switch by Theorem Proving Proc. of the 9th Workshop on Network Tools and Applications in Biology (Nettab’09), v. Liberodiscrivere (2009)
  • Nguyen, VA. and Lio, P., 2009. Measuring similarity between gene expression profiles: a Bayesian approach BMC GENOMICS, v. 10
    Doi: 10.1186/1471-2164-10-S3-S14
  • Hui, P., Xu, K., Li, VOK., Crowcroft, J., Latora, V. and Lio, P., 2009. Selfishness, Altruism and Message Spreading in Mobile Social Networks IEEE INFOCOM 2009 - IEEE CONFERENCE ON COMPUTER COMMUNICATIONS WORKSHOPS,
  • Lu, Y-E., Roberts, SGB., Cheng, TMK., Dunbar, R., Liò, P. and Crowcroft, J., 2009. On optimising personal network size to manage information flow. CIKM-CNIKM,
  • Lu, Y-E., Roberts, SGB., Liò, P., Dunbar, R. and Crowcroft, J., 2009. Size Matters: Variation in Personal Network Size, Personality and Effect on Information Transmission. CSE (4),
    Doi: 10.1109/CSE.2009.179
  • Xie, SK., Lio, P. and Lawniczak, AT., 2009. A Comparative Study of Noise Effect on Wavelet Based De-noising Methods IEEE TIC-STH 09: 2009 IEEE TORONTO INTERNATIONAL CONFERENCE: SCIENCE AND TECHNOLOGY FOR HUMANITY,
  • Lu, YE., Lio, P. and Hand, S., 2008. Beta Random Projection BIO-INSPIRED COMPUTING AND COMMUNICATION, v. 5151
  • Schwarz, E., Leweke, FM., Bahn, S. and Lio, P., 2008. Combining molecular and physiological data of complex disorders BIOINFORMATICS RESEARCH AND DEVELOPMENT, PROCEEDINGS, v. 13
  • Allen, SM., Conti, M., Crowcroft, J., Dunbar, R., Lio, P., Mendes, JF., Molva, R., Passarella, A., Stavrakakis, I. and Whitaker, RM., 2008. Social Networking for Pervasive Adaptation SASOW 2008: SECOND IEEE INTERNATIONAL CONFERENCE ON SELF-ADAPTIVE AND SELF-ORGANIZING SYSTEMS WORKSHOPS, PROCEEDINGS,
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  • Lu, XF., Hui, P., Lio, P. and Xiong, Z., 2008. Identity Privacy Protection by Delayed Transmission in Pocket Switched Networks EUC 2008: PROCEEDINGS OF THE 5TH INTERNATIONAL CONFERENCE ON EMBEDDED AND UBIQUITOUS COMPUTING, VOL 2, WORKSHOPS,
  • van der Wath, RC. and Lio, P., 2008. A Stochastic Single Cell Based Model of BrdU Measured Hematopoietic Stem Cell Kinetics COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY, PROCEEDINGS, v. 5307
  • 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,
  • 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
  • Lee, U., Magistretti, E., Gerla, M., Bellavista, P., Lio, P. and Lee, KW., 2008. Bio-Inspired Multi-agent Collaboration for Urban Monitoring Applications BIO-INSPIRED COMPUTING AND COMMUNICATION, v. 5151
  • van der Wath, RC. and Lio, P., 2008. A Stochastic Multi-agent Model of Stem Cell Proliferation CELLULAR AUTOMATA, PROCEEDINGS, v. 5191
  • Kershenbaum, A., Pappas, V., Lee, KW., Lio, P., Sadler, B. and Verma, D., 2008. A biologically-inspired MANET architecture - art. no. 698106 DEFENSE TRANSFORMATION AND NET-CENTRIC SYSTEMS 2008, v. 6981
  • Koukolikova-Nicola, Z., Lio, P. and Bagnoli, F., 2008. Inference on missing values in genetic networks using high-throughput data EVOLUTIONARY COMPUTATION, MACHINE LEARNING AND DATA MINING IN BIOINFORMATICS, PROCEEDINGS, v. 4973
  • Leung, IXY., Gibbs, G., Bagnoli, F., Sorathiya, A. and Lio, P., 2008. Contact Network Modeling of Flu Epidemics CELLULAR AUTOMATA, PROCEEDINGS, v. 5191
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  • Angelini, C., Cutillo, L., De Feis, I., Lio, P. and van der Wath, R., 2008. Combining experimental evidences from replicates and nearby species data for annotating novel genomes COLLECTIVE DYNAMICS: TOPICS ON COMPETITION AND COOPERATION IN THE BIOSCIENCES, v. 1028
  • Lio, P., Angelini, C., DeFeis, I., Nguyen, V., Cutillo, L. and va der Wath, R., 2008. Statistical issues for combining replicates and nearby species data and different omics Proceedings The Art and Science of Statistical Bioinformatics The 27th Leeds Annual Statistical Research Workshop 15th - 17th July 2008,
  • van der Wath, RC., van der Wath, E., Carapelli, A., Nardi, F., Frati, F., Milanesi, L. and Lio, P., 2008. Bayesian phylogeny on grid BIOINFORMATICS RESEARCH AND DEVELOPMENT, PROCEEDINGS, v. 13
  • Xie, SK., Lawniczak, AT. and Lio, P., 2008. Parametric & non-parametric analysis of mean treatment effects of number of packets in transit in data network model 2008 CANADIAN CONFERENCE ON ELECTRICAL AND COMPUTER ENGINEERING, VOLS 1-4,
  • 2008. Bio-Inspired Computing and Communication, First Workshop on Bio-Inspired Design of Networks, BIOWIRE 2007, Cambridge, UK, April 2-5, 2007, Revised Selected Papers BIOWIRE, v. 5151
  • Lu, XF., Wicker, F., Lio', P. and Towsley, D., 2008. Security Estimation Model with Directional Antennas 2008 IEEE MILITARY COMMUNICATIONS CONFERENCE: MILCOM 2008, VOLS 1-7,
  • Allen, SM., Conti, M., Crowcroft, J., Dunbar, R., Liò, P., Mendes, JFF., Molva, R., Passarella, A., Stavrakakis, I. and Whitaker, RM., 2008. Social Networking for Pervasive Adaptation. SASO Workshops,
  • Milanesi, L., Lio, P. and Breton, V., 2007. Bioinformatics Challenges in Life Science IST-Africa 2007 Conference Proceedings, Paul Cunningham and Miriam Cunningham (Eds), IIMC International Information Management Corporation, 2007, ISBN: 1-905824-04-1,
  • Lu, YE., Hand, S. and Lio, P., 2007. Keyword searching in structured overlays via content distance addressing Databases, Information Systems, and Peer-to-Peer Computing, v. 4125
  • Lu, YE., Lio, P. and Hand, S., 2007. Beta random projection ISM WORKSHOPS 2007: NINTH IEEE INTERNATIONAL SYMPOSIUM ON MULTIMEDIA - WORKSHOPS, PROCEEDINGS,
    Doi: 10.1109/ISM.Workshops.2007.61
  • Sguanci, L., Bagnoli, F. and Lio, P., 2007. Modeling HIV quasispecies evolutionary dynamics BMC EVOLUTIONARY BIOLOGY, v. 7
    Doi: 10.1186/1471-2148-7-S2-S5
  • Angelini, C., Cutillo, L., De Feis, I., Van der Wath, R. and Lio, P., 2007. Identifying regulatory sites using neighborhood species Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings, v. 4447
  • Lawniczak, AT., Lio, P., Xie, S. and Xu, JY., 2007. Wavelet spectral analysis of packet traffic near phase transition point from free flow to congestion in data network model 2007 CANADIAN CONFERENCE ON ELECTRICAL AND COMPUTER ENGINEERING, VOLS 1-3,
  • Fani, R., Brilli, M., Fondi, M. and Lio, P., 2007. The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case BMC EVOLUTIONARY BIOLOGY, v. 7
    Doi: 10.1186/1471-2148-7-S2-S4
  • Carapelli, A., Lio, P., Nardi, F., van der Wath, E. and Frati, F., 2007. Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea BMC EVOLUTIONARY BIOLOGY, v. 7
    Doi: 10.1186/1471-2148-7-S2-S8
  • Sguanci, L., Lio, P. and Bagnoli, F., 2006. Modeling evolutionary dynamics of HIV infection COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY, PROCEEDINGS, v. 4210
  • Fani, R., Caramelli, D. and Lio, P., 2006. It happened... From prebiotic chemistry to human evolution Rivista di biologia,
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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,
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    Doi: 10.1016/j.gene.2004.11.033
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    Doi: 10.1016/S0378-1119(03)00666-8
  • 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
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  • 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
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    Doi: 10.1016/j.is.2024.102465
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  • Longa, A., Azzolin, S., Santin, G., Cencetti, G., Lio, P., Lepri, B. and Passerini, A., 2025. Explaining the Explainers in Graph Neural Networks: a Comparative Study ACM Computing Surveys, v. 57
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    Doi: http://doi.org/10.1192/bjo.2025.32
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  • Theses / dissertations

  • Georgiev, D., 2025 (No publication date). Neural algorithmic reasoning in a bottle(neck)
    Doi: http://doi.org/10.17863/CAM.115714
  • 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

  • Joshi, CK. and Liò, P., 2025. gRNAde: A Geometric Deep Learning Pipeline for 3D RNA Inverse Design.
    Doi: 10.1007/978-1-0716-4079-1_8
  • 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
  • Vignani, R., Scali, M. and Liò, P., 2021. Molecular Markers and Genomics for Food and Beverages Characterization
    Doi: 10.1007/978-981-15-9364-2_43-1
  • 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
  • Liò, P., Brilli, M. and Fani, R., 2007. Phylogenetics and Computational Biology of Multigene Families
    Doi: 10.1007/978-3-540-35306-5_9
  • Li��, P. and Bishop, MJ., 2006 (Published online). Nucleic Acid and Protein Sequence Analysis and Bioinformatics
    Doi: 10.1002/3527600906.mcb.200400067
  • 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
  • Contact Details

    Room: 
    FC20
    Office phone: 
    (01223) 7-63604
    Email: 

    pl219at@cam.ac.uk