Saez-Rodriguez Group

Systems Biomedicine

Francesco Carli

Francesco Carli has a multidisciplinary background in economics, maths, and data science. He completed his B.Sc. in Economics and Social Sciences at Bocconi University in Milan, Italy, followed by an MSc in Stochastics and Data Science at the University of Turin. During his master’s, he collaborated with Biorek s.r.l., a startup incubated by San Raffaele Hospital, where he developed machine learning models to detect and characterize renal cancer using genetic biomarkers. In 2019, he received the “Best Project Prize” at the Milan Critical Care Datathon, a 24-hour international challenge organized by MIT Critical Data, Humanitas Research Hospital, and Politecnico di Milano. This achievement led to a research collaboration with the MIT Critical Data Lab, where he worked with Prof. Leo Celi to design AI-based tools for enhancing clinical decision-making in intensive care units. Afterward, he contributed to the DTeam2Vec project at the University of Turin, applying graph-based deep learning techniques to model collaborative dynamics in online communities. Francesco then pursued a Ph.D. at Scuola Normale Superiore in Pisa, where he focused on developing machine-learning models to explore drug-biosystem interactions across multiple biological scales.

Research Interests

Francesco’s research focuses on enhancing tasks in computational biology by leveraging the reasoning and agentic capabilities of large language models (LLMs). He is particularly interested in exploring how LLMs can be integrated with classical modeling techniques to harness their complementary strengths, aiming to improve interpretability, robustness, and generalizability in biological data analysis.

Professional Career

2025-present Research Software Engineer, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI) and OpenTargets
2021 Research Assistant, Departement of Computer Science, University of Turin, Italy
2019-2020 Data Scientist, Biorek S.r.l., San Raffaele Hospital, Milano, Italy

Education

2021-2025 PhD in Artificial Intelligence, Joint National PhD program at Scuola Normale Superiore and University of Pisa, Italy
2016-2020 M.Sc. in Stochastics and Data Science, University of Turin, Turin, Italy
2013-2016 B.Sc. in Economics, Bocconi University, Milano, Italy