Damiano Sgarbossa

I am a recent PhD graduate in Computational Biology working at the interface between deep learning and biology.

About me

I obtained my PhD in Computational Biology from the École Polytechnique Fédérale de Lausanne (EPFL), where my research focused on understanding how large language models trained on protein sequences capture and leverage coevolutionary information. Originally from Italy, I earned my Master of Science in Physics from the University of Padova, where my thesis applied statistical physics methods to study the stability of large ecosystems. This early work sparked my interest in using quantitative approaches to explore complex biological systems.

I am passionate about problems at the intersection of deep learning and biology, with a particular focus on applying generative AI to protein design, structural biology, and chemistry. I am also deeply interested in the interpretability of large neural networks, representation learning, and generative diffusion models.

public_defense_phd_crop.mp4

My PhD public defense presentation

An accessible presentation in which I explain my PhD work to a non-technical audience of colleagues, friends and family.

This presentation was registered on June the 27th 2025 during the public defense of my PhD thesis.

Selected projects

RAG-ESM

RAG-ESM: Improving pretrained protein language models via sequence retrieval

[Paper] [Code]

ProtMamba

ProtMamba: a homology-aware but alignment-free protein state space model

[Paper] [Code] [Video]

DiffPALM

Pairing interacting protein sequences using masked language modeling

[Paper] [Code] [Video]

See all my projects

Timeline

19 Aug 2025 The "RAG-ESM" paper is published by PRX Life

27 Jun 2025 I obtained my PhD in Computational Biology at EPFL

13 Jun 2025 The "ProtMamba" paper is published by Bioinformatics

26 May 2025 I successfully passed the oral exam (private defense)

26 Jul 2024 I obtained the "Best Paper Award" at the ICML AccMLBio Workshop

24 Jun 2024 The "DiffPALM" paper is published by PNAS

23 May 2024 I landed in NYC where I worked as an AI Research Intern at Absci for the next 3 months

03 Feb 2023 The "Iterative masking" paper is published by eLife

22 Oct 2022 The "Phylogeny" paper is published by Nature Communications

22 Jul 2022 I obtained the "Contributed Talk Award" at the ICML Workshop on computational biology

24 Mar 2022 I passed the candidacy exam of the doctoral school, the first step to obtain my PhD

01 Apr 2021 I officially started my PhD journey at EPFL in Anne-Florence Bitbol Lab

27 Oct 2020 I graduated in Physics (MSc) at the University of Padova

02 Sep 2019 I started my Erasmus semester abroad at Heidelberg University (Germany)

27 Sep 2018 I graduated in Physics (BSc) at the University of Padova

Other interests

When I'm not working, I'm usually outside. I am a big sports addict, I love climbing, skiing, running, and surfing. I am constantly on the lookout for a new challenge, and recently I've become obsessed with photography and scuba diving.

My adventurous spirit also fuels my passion for travelling, I love immersing myself in new experiences and getting to know different cultures.

Here is a small selection of pictures that I particularly like.

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