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Francesco Carli

Bioinformatician

Biography

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

Contact Information