ALESSIO RAGNO

PhD Graduate

PhD program:: XXXVII


supervisor: Roberto Capobianco
co-supervisor: Daniele Nardi

Thesis title: Topology-based Explanations For Neural Networks

Neural networks have driven significant advancements across various tasks and domains. However, they are often seen as black boxes due to their complex nature. This aspect hinders the understanding of the reasoning behind their predictions, posing serious challenges for their applications. This thesis addresses these challenges by contributing to the field of eXplainable AI, with a specific focus on improving the interpretability of deep neural networks. The proposed solution takes a topology-based approach, either by learning interpretable representations with self-explainable neural networks or by analyzing the organization of the models' inner layers. The core contributions involve introducing novel techniques that enhance the interpretability of these networks by leveraging an analysis of their internal workings. Specifically, the contributions are threefold. First, we introduce novel neural network architectures that integrate the use of prototypes to enhance model interpretability across several domains like graphs and reinforcement learning. Second, this study delves into the application of logic for interpreting neural network behaviors. Finally, this research explores the study of neural network representations in different scientific fields, such as chemistry, biology, and linguistics. In summary, this thesis advances the field of Explainable AI by proposing topology-based techniques to enhance the interpretability of deep neural networks. By applying these techniques to various applications, the thesis aims to encourage the collaboration between AI research and other scientific fields.

Research products

11573/1732570 - 2025 - Essential oils as antimicrobials against Acinetobacter baumannii. Experimental and literature data to definite predictive quantitative composition–activity relationship models using machine learning algorithms
Astolfi, Roberta; Oliva, Alessandra; Raffo, Antonio; Sapienza, Filippo; Ragno, Alessio; Proia, Eleonora; Mastroianni, Claudio M; Luceri, Cristina; Bozovic, Mijat; Mladenovic, Milan; Papa, Rosanna; Bottoni, Patrizia; Mazzinelli, Elena; Nocca, Giuseppina; Ragno, Rino - 01a Articolo in rivista
paper: JOURNAL OF CHEMICAL INFORMATION AND MODELING (AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, USA, DC, 20036) pp. - - issn: 1549-9596 - wos: WOS:001403553800001 (0) - scopus: 2-s2.0-85215935824 (0)

11573/1710609 - 2024 - Nuovi approcci metodologici applicati a Cencelle (Tarquinia, VT). New methodological approaches applied to Cencelle (Tarquinia, VT)
Annoscia, Giorgia Maria; Astolfi, Roberta; Bellini, Ilaria; Cavallero, Serena; Chiovoloni, Claudia; D’Amelio, Stefano; Di Fazio, Melania; Gabrielli, Simona; Moschetto, Francesco; Perugini, Eleonora; Pombi, Marco; Ragno, Alessio; Ragno, Rino; Rondón, Silvia; Sapienza, Filippo - 01a Articolo in rivista
paper: SPOLIA (Fregene (RM) : Teresa Nocita) pp. - - issn: 1824-727X - wos: (0) - scopus: (0)

11573/1729677 - 2024 - Identifying Candidates for Protein-Protein Interaction: A Focus on NKp46’s Ligands
Borghini, A.; Di Valerio, F.; Ragno, A.; Capobianco, R. - 04b Atto di convegno in volume
conference: 1st Workshop on Explainable Artificial Intelligence for the Medical Domain, EXPLIMED 2024 (Santiago de Compostela; Spain)
book: Proceedings of the First Workshop on Explainable Artificial Intelligence for the Medical Domain (EXPLIMED 2024) - ()

11573/1722615 - 2024 - Transparent Explainable Logic Layers
Ragno, Alessio; Plantevit, Marc; Robardet, Celine; Capobianco, Roberto - 04b Atto di convegno in volume
conference: European Conference on Artificial Intelligence (ECAI 2024) (Santiago de Compostela; Spain)
book: ECAI 2024 - 27th European Conference on Artificial Intelligence, 19–24 October 2024, Santiago de Compostela, Spain – Including 13th Conference on Prestigious Applications of Intelligent Systems (PAIS 2024) - (978-1-64368-548-9)

11573/1696769 - 2023 - Understanding Deep RL agent decisions: a novel interpretable approach with trainable prototypes
Borzillo, Caterina; Ragno, Alessio; Capobianco, Roberto - 04b Atto di convegno in volume
conference: XAI.it 2023: Italian Workshop on Explainable Artificial Intelligence 2023 (Rome)
book: CEUR Workshop Proceedings Vol-3518 - ()

11573/1690926 - 2023 - Memory Replay For Continual Learning With Spiking Neural Networks
Proietti, Michela; Ragno, Alessio; Capobianco, Roberto - 04b Atto di convegno in volume
conference: 2023 IEEE 33rd International Workshop on Machine Learning for Signal Processing (MLSP) (Rome; Italy)
book: Proceedings of the 2023 IEEE 33rd International Workshop on Machine Learning for Signal Processing (MLSP) - (979-8-3503-2411-2; 979-8-3503-2412-9)

11573/1691190 - 2023 - Explainable AI in drug discovery: self-interpretable graph neural network for molecular property prediction using concept whitening
Proietti, Michela; Ragno, Alessio; Rosa, Biagio La; Ragno, Rino; Capobianco, Roberto - 01a Articolo in rivista
paper: MACHINE LEARNING (Springer Nature Hingham, MA: Kluwer Academic Publishers) pp. 2013-2044 - issn: 0885-6125 - wos: WOS:001091343300001 (2) - scopus: 2-s2.0-85175337233 (3)

11573/1659035 - 2022 - Ligand-based and structure-based studies to develop predictive models for {SARS}-{CoV}-2 main protease inhibitors through the 3d-qsar.com portal
Proia, Eleonora; Ragno, Alessio; Antonini, Lorenzo; Sabatino, Manuela; Mladenović, Milan; Capobianco, Roberto; Ragno, Rino - 01a Articolo in rivista
paper: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (-SPRINGER, VAN GODEWIJCKSTRAAT 30, DORDRECHT, NETHERLANDS, 3311 GZ -Kluwer Academic Publishers:Journals Department, PO Box 322, 3300 AH Dordrecht Netherlands:011 31 78 6576050, EMAIL: frontoffice@wkap.nl, kluweronline@wkap.nl, INTERNET: http://www.kluwerlaw.com, Fax: 011 31 78 6576254) pp. 483-505 - issn: 0920-654X - wos: WOS:000812582700001 (7) - scopus: 2-s2.0-85132189914 (8)

11573/1680634 - 2022 - Explainable AI in drug design: self-interpretable graph neural network for molecular property prediction using concept whitening
Proietti, Michela; Ragno, Alessio; Capobianco, Roberto - 04f Poster
conference: 3rd Molecules Medicinal Chemistry Symposium: Shaping Medicinal Chemistry for the New Decade (Rome; Italy)
book: 2022 - ()

11573/1681948 - 2022 - Py-Graph: An Easy-To-Use Interface for Building Graph-Based QSAR Models
Ragno, Alessio; Capobianco, Roberto; Ragno, Rino - 04f Poster
conference: 23rd European Symposium on Quantitative Structure-Activity Relationship (Heidelberg, Germany)
book: 2022 - ()

11573/1662081 - 2022 - Prototype-based Interpretable Graph Neural Networks
Ragno, Alessio; La Rosa, Biagio; Capobianco, Roberto - 01a Articolo in rivista
paper: IEEE TRANSACTIONS ON ARTIFICIAL INTELLIGENCE (Piscataway NJ: IEEE) pp. 1486-1495 - issn: 2691-4581 - wos: WOS:000893639106029 (6) - scopus: 2-s2.0-85142856655 (8)

11573/1583175 - 2021 - Machine learning data augmentation as a tool to enhance quantitative composition–activity relationships of complex mixtures. A new application to dissect the role of main chemical components in bioactive essential oils
Ragno, A.; Baldisserotto, A.; Antonini, L.; Sabatino, M.; Sapienza, F.; Baldini, E.; Buzzi, R.; Vertuani, S.; Manfredini, S. - 01a Articolo in rivista
paper: MOLECULES (Basel: MDPI Berlin: Springer, 1996-) pp. 1-12 - issn: 1420-3049 - wos: WOS:000714423500001 (5) - scopus: 2-s2.0-85117456880 (4)

11573/1635487 - 2021 - Semi-Supervised GCN for learning Molecular Structure-Activity Relationships
Ragno, Alessio; Savoia, Dylan; Capobianco, Roberto - 04f Poster
conference: ELLIS Machine Learning for Molecules Workshop (Online)
book: 2021 - ()

11573/1645783 - 2021 - Molecule Generation from Input-Attribution over Graph Convolutional Networks
Savoia, Dylan; Ragno, Alessio; Capobianco, Roberto - 04f Poster
conference: ELLIS Machine Learning for Molecules Workshop (Online)
book: 2021 - ()

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