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  • Ecole Normale Supérieure Paris-Saclay, AgroParisTech, Université Paris-Saclay & Université Paris-Cité
  • LinkedIn in/raphaël-rubrice

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raphaelrubrice/README.md

Hi, I'm Raphaël Rubrice !

Currently seeking an internship in generative modeling for biology and/or biomedical discovery for my Master's thesis (April–October 2026).


I'm a Master's student at the intersection of computational biology and machine learning, specializing in generative models for biological systems.


Currently following the MVA Master program at ENS Paris-Saclay & Paris-Cité University where I'm focusing on the mathematics behind ML and reinforcing my knowledge and skills to prepare for a future PhD in AI for Biology and/or Biomedical discovery.

Here are the classes I took for the first semester (Fall 2025):

  • Optimal Transport by Gabriel Peyré & Julie Delon
  • Computational Statistics by Stéphanie Allassonière
  • Geometric Data Analysis by Jean Feydy
  • Introduction to Probabilistic Graphical Models and deep generative models by Pierre Latouche & Pierre-Alexandre Mattei
  • ALTEGRAD (NLP and Graphs) by Michalis Vazirgiannis

Spring 2026 courses I will take:

  • Stochastic Calculus for Generative Modeling by Alain Durmus
  • Algorithms and Learning for Protein Science by Frédéric Cazals
  • Reinforcement Learning by D. Basu, E. Kaufmann & O. Maillard
  • Graphs in Machine Learning by Michal Valko
  • Generative Models for Imaging by B. Galerne & A. Leclaire
  • Representation Learning for Computer Vision and Medical Imaging by Pietro Gori & Loïc Le Folgoc

I previously completed an MSc in Artificial Intelligence and Computational Biology at Paris-Saclay University and AgroParisTech.

I am constantly trying to improve my data science and programming skills which makes me eager to contribute to impactful and ground-breaking projects involving AI and computational biology.

I am fascinated by these research fields (lot of work ahead to truly get there though 🤓):

  • Single-cell & spatial biology: Latent diffusion models (e.g scLDM, SquiDiff), perturbation prediction (e.g, STATE), generative models for cellular dynamics
  • Foundation models for biology: Protein language models (e.g, BoltzGen), multi-omic integration, virtual cell systems
  • Geometric & generative ML: Optimal transport (e.g, GWOT, GrALe), diffusion models, representation learning for biological data
  • AI for precision medicine: Multi-modal integration for patient stratification and biomarker discovery

💻Operating Systems I've worked with :

ubuntu logo windows8 logo apple logo

🧰📊What I use to contribute to projects :

vscode logo git logo github logo docker logo rstudio logo jupyter logo anaconda logo postgresql logo latex logo

💻📚Programming Languages :

python logo nextflow logo rstudio logo bash logo

🧪⌨️Current/Recent projects :

🤓😁Cool stuff :

  • Got accepted into ENS Paris-Saclay's MVA coursework (really excited)
  • Laureate of the PR[AI]RIE Institute Excellence Scholarship (huge support throughout the year)
  • Published in the Journal Artificial Intelligence in the Life Sciences : A machine learning framework for the prediction and analysis of bacterial antagonism in biofilms using morphological descriptors
  • Got an internship at Dassault Systèmes, the topic ? Explainable clustering for clinical data
  • Our main project of the year during IODAA got accepted for presentation at the 1st AI for Animal Science Conference at ETH Zurich (2025)
  • With a few friends from AgroParisTech, we won the AI Methodology Award at the 2025 Owkin & Servier AI Hackathon for Glioblastoma Research
  • Gave a presentation at the Micalis Institute on the work I've done on the biofilm antagonism prediction model

📫Contacts :

Email

linkedin logo


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  1. scVAE_mva2025 scVAE_mva2025 Public

    Github for the project on VAEs for single cell data for the "Introduction to Probabilistic Graphical Models and Deep Generative Models" course of the MVA.

    Jupyter Notebook

  2. blackswan-advitamaeternam/HVAE blackswan-advitamaeternam/HVAE Public

    Reproduction of HVAE (Davidson et al., UAI 2018) - von Mises-Fisher latent spaces for VAEs | Master MVA - Computational Statistics

    Jupyter Notebook 1 1

  3. ReproHackathon_G6 ReproHackathon_G6 Public

    Repository made for the ReproHackathon course of the Master 2 AMI2B program (Computational Biology) at Paris-Saclay University. The goal is to reproduce part of the results shown in : https://doi.o…

    R 2 1

  4. TELLAM TELLAM Public

    Pipeline for Transposable Elements Locus Level Analysis.

    Python

  5. lauronta/projet_fil_rouge_afz lauronta/projet_fil_rouge_afz Public

    Jupyter Notebook 3