Publications

2025
1. Exploring Query-to-Reference Mapping Challenges for Automated Single-Cell Atlas-Based Diagnostics
  
  Francesco Craighero, Davide Maspero, Laura Jiménez-Gracia, Sergio Aguilar-Fernández, Maria Boulougouri, Juan C. Nieto, Holger Heyn
  
  In Learning Meaningful Representations of Life (LMRL) Workshop at ICLR 2025
  
  2025
  
  URL
2. Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation
  
  Mohan Vamsi Nallapareddy, Francesco Craighero, Lina Worpenberg, Felix Naef, Cedric Gobet, Pierre Vandergheynst
  
  bioRxiv
  
  2025
  
  DOI
2024
1. Beyond Fine-Tuning: LoRA Modules Boost Near-OOD Detection and LLM Security
  
  Etienne Salimbeni, Francesco Craighero, Renata Khasanova, Milos Vasic, Pierre Vandergheynst
  
  In ICLR 2024 Workshop on Secure and Trustworthy Large Language Models
  
  2024
  
  URL
2. Beyond Fine-Tuning: LoRA Modules Boost Near-OOD Detection and LLM Security
  
  Etienne Salimbeni, Francesco Craighero, Renata Khasanova, Milos Vasic, Pierre Vandergheynst
  
  In 7th Deep Learning Security and Privacy Workshop (DLSP 2024)
  
  2024
  
  Best Extended Abstract Award
  
  URL
3. Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations
  
  Mohan Vamsi Nallapareddy, Francesco Craighero, Cédric Gobet, Felix Naef, Pierre Vandergheynst
  
  In Proceedings of the 19th Machine Learning in Computational Biology meeting
  
  2024
  
  Spotlight
  
  URL
2023
1. LACE 2.0: An Interactive R Tool for the Inference and Visualization of Longitudinal Cancer Evolution
  
  Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi
  
  BMC Bioinformatics
  
  2023
  
  DOI
2. Three Perspectives on Anomaly Detection in Deep Learning
  
  Francesco Craighero
  
  2023
  
  URL
3. Unity is strength: Improving the detection of adversarial examples with ensemble approaches
  
  Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
  
  Neurocomputing
  
  2023
  
  DOI
4. Interpretable Inflammation Landscape of Circulating Immune cells
  
  Laura Jiménez-Gracia, Davide Maspero, Sergio Aguilar-Fernández, Francesco Craighero, Sara Ruiz, Domenica Marchese, Ginevra Caratu, Marc Elosua-Bayes, Mohamed Abdalfatah, Angela Sanzo-Machuca, others
  
  bioRxiv
  
  2023
  
  DOI
2021
1. On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples
  
  Jeaneth Machicao, Francesco Craighero, Davide Maspero, Fabrizio Angaroni, Chiara Damiani, Alex Graudenzi, Marco Antoniotti, Odemir M Bruno
  
  CURRENT GENOMICS
  
  2021
  
  DOI
2. Combining Multi-Target Regression Deep Neural Networks and Kinetic Modeling to Predict Relative Fluxes in Reaction Systems
  
  Lucrezia Patruno, Francesco Craighero, Davide Maspero, Alex Graudenzi, Chiara Damiani
  
  Information and Computation
  
  2021
  
  DOI
2020
1. A review of computational strategies for denoising and imputation of single-cell transcriptomic data
  
  Lucrezia Patruno, Davide Maspero, Francesco Craighero, Fabrizio Angaroni, Marco Antoniotti, Alex Graudenzi
  
  Briefings in Bioinformatics
  
  2020
  
  DOI
2. Understanding Deep Learning with Activation Pattern Diagrams
  
  Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti
  
  In Proceedings of the Italian Workshop on Explainable Artificial Intelligence co-located with 19th International Conference of the Italian Association for Artificial Intelligence, XAI.it@AIxIA 2020, Online Event, November 25-26, 2020
  
  2020
  
  URL
3. Investigating the Compositional Structure of Deep Neural Networks
  
  Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
  
  In Machine Learning, Optimization, and Data Science
  
  2020
  
  DOI

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