I am a postdoctoral researcher at IBISC (FR), in the AROBAS team. I am working on a Graph Neural Network (GNN) to integrate multi-omics data to predict the stages of Parkinson’s disease.

🔗 Some links

🆔 ORCID 0000-0002-4079-5501

💼 LinkedIn Nicolas Buton

𝕏 Twitter @NicolasButon1

🦊 GitLab nbuton

🐱 GitHub nbuton

📫 Contact

📨 Professional out of lab’ nicolas<dot>buton44<at>gmail.com

👤 Work colleagues

👤 Postdoc advisor Blaise Hanczar

👤 Postdoc advisor Farida Zehraoui

👤 Postdoc advisor Victoria Bourgeais

👤 PhD Inria supervisor Francois.Coste

👤 PhD Inria supervisor Yann Le Cunff

👤 PhD thesis director Olivier Dameron

You can find my CV below partitioned into several categories.

📰 Publications

Nicolas Buton, François Coste, Yann Le Cunff, Predicting enzymatic function of protein sequences with attention. Bioinformatics, 2023

🗣️ Talks

GDR BIM - GT MASIM - 2022 Thematic meetings (ML & Sampling) (https://gt-masim.cnrs.fr/actions/thematic-meetings-ml-sampling/)

🪧 Poster

2022 | Poster presentation at JOBIM

🏫 Teaching

2021-2022 | ST1: Apprentissages Statistiques (TP), Master 1 – Univ. Rennes 1

  • Supervisor: Yann Le Cunff

2020-2021 | ST1: Apprentissages Statistiques (TP), Master 1 – Univ. Rennes 1

  • Supervisor: Yann Le Cunff

2020-2021 | Jury stage, Master 1 – Univ. Rennes 1

  • Supervisor: Annabelle Monnier

🎓 Education

2020–2023 | PhD in bioinformatics

  • IRISA/University of Rennes - DYLISS team

2018–2020 | Master degree in computer science specialized in machine learning with the highest honor

  • Données, Apprentissage, Connaissances (DAC), Sorbonne University

2017–2018 | Bachelor degree in computer science (7th/110)

  • University of Rennes 1

2018 | Toeic listening and reading - 900/990

  • Centre d’Examen à l’ESSCA 49000 ANGERS

2015–2017 | CPGE scientifique MPSI-MP, Preparation for national competitive entrance exams to leading French “grandes écoles”, specialising in mathematics and physics

  • Lycée Dupuy de Lôme Lorient

2012–2015 | Science baccalaureate grades with honors

  • Lycée Alcide D’Orbigny

2013 | Aeronautical Initiation Certificate (B.I.A. in french)

  • Aéroport Nantes Atlantique

🧑‍💻 WORK EXPERIENCE

2020-2023 | PhD student | INRIA - DYLISS team, Rennes, France

  • Title: Transformer models for interpretable and multilevel prediction of protein functions from sequence.
  • Abstract: Automatic annotation of protein sequences is on the rise to manage the increasing number of experimentally unannotated sequences. First, we investigated the application of the Transformer for enzymatic function prediction. The EnzBert model improves macro-F1 from 41% to 54% compared to the previous state-of-the-art. Furthermore, a comparison of interpretability methods shows that an attention-based approach achieves an F-Gain score of 96.05%, surpassing classical methods (91.44%). Second, the integration of Gene Ontology into function prediction models was explored. Two approaches were tested: integration in the labeling process and the use of hyperbolic embeddings. The results confirm both the effectiveness of the True Path Rule and the superiority of hyperbolic embeddings (mean WFmax: 0.36) compared to the Euclidean model (0.34) in low dimensions (32). They maintain greater consistency with the Gene Ontology (correctly ordered relations: 99.25%-99.28% vs. 78.48%-91.41% for the Euclidean model)

2020 | Intern | INRIA - DYLISS team, Rennes, France

  • Study of the state of the art in protein characterization and create neural network inspired by the states of the art in NLP architecture, to characterize ptotein. And use domain knoledge to check and improve the network.

2019 | Intern | MONDECA, Paris, France

  • Study of the state of the art in Natural Language Processing with deep learning. Implementation and test of Transformer network and LSTM with pytorch framework. In order to do multiple task like commonsense reasoning, semantic textual similarity, stance detection, open information extraction and entity linking.

2018 | Intern | INRIA - LACODAM team, Rennes, France

  • Unsupervised learning for Intrusion Detection System (IDS), creation of auto encoder with Tensorflow and test of differents architecture and hyperparameters.

2016 | Individual |Nantes

  • Individual tutoring in math for high school students

🥼 Services

2023 | Vice treasurer in Nicomaque PhD association

2022 | Organisation of “Journée au vert”

2022 | JOBIM2022 Francophone conference

  • Volunteer at the JOBIM conference, creating badges, registering, welcoming and guiding participants around the conference site.

💬 Science popularisation

2023 | Volunteer for the recording of a conference on ethics in academia

2022 | Organisation of PhD popularisation film festival Sciences en Cour[t]s

2021 | Team member in Sciences en Cour[t]s PhD popularisation film festival

🏅 Programming competition

2023 | TRACS

2022 | TRACS

  • CentraleSupélec, 91190 Gif-sur-Yvette, France
  • First place in TRACS competition of Data science, cybersecurity, and cryptography

2021 | TRACS

2021 | Google Hash Code

2020 | TRACS

2019 | Les entrep’

  • Paris, France
  • Entrepreneurship competition with certificate.

2018 | Prologin, the French National Computer Science Contest

  • Paris, France
  • Finalist of the national competition of computer science

2018 | 24H du code

  • La Mans, France
  • Winner of the 6th edition

2018 | Google Hash Code

2018 | Google Code Jam

🚀 Projects

2019 | Master 1 project - PLDAC

  • UPMC, Paris, France
  • Brain Computer Interface(BCI)

2016-2017 | TIPE (Work project in CPGE)

  • Lycée Dupuy de Lôme, Lorient, France
  • Game theory / neural network / min-max / alpha-beta

🖥️ Skills

Programming languages

Python3 (advanced)

BASH | Java | R | C | PHP | SQL | JavaScript | Prolog | clips | whyml

Tools

LaTeX | Markdown | Git

Languages

  • French (native speaker)
  • English (good working knowledge)
  • Spanish (notions)

Hobbies

🏃‍♂️ Running

🚴‍♂️ Biking

  • 2015 | 3 days | 381km | Sainte-Pazanne > Sainte-Foy Triaize > Sainte-Pazanne
  • 2016 | 4 days | 370km | Saint-Jean-de-Boiseau > Avrillé > Saumur > Saint Florent-le-Vieil > Sant-Jean-de-Boiseau
  • 2017 | 4 days | 348km | La Montagne > Redon > Sulniac > La Turbale > Sainte-Pazanne
  • 2018 | 3 days | 182km | La Rochelle > Saint-Laurent-de-la-Prée > Royan > Around Île de Ré
  • 2019 | 3 days | 222km | Saumur > Tours > Blois > Orléan
  • 2020 | 4 days | 273km | Morlaix > Perros-Guirec > Paimpol > Saint Brieuc > Saint Malo
  • 2021 | 3 days | 197m | Angers > Château-Gontier > Laval > Mayenne > Laval
  • 2023 | 4 days | 210km | Saint-Jean-de-Boiseau > Saint-Brevin-les-Pins > Bourgneuf-en-Retz > La Barre-de-Monts > Les Sables-d’Olonne

🥾 Hiking

  • 2023 | 6 days | 70km | Jura
  • 2023 | 2 days | 80km | Belle-île
  • 2022 | 4 days | 20km | Alps
  • 2020 | Pyrenees

🛩️ Aero modelling

  • At a club from 2008 to 2012

🏸 Badminton

  • At a club in 2015 and 2022

🎾 Tennis

  • At a club from 2007 to 2012

🤾 Handball

  • At a club from 2005 to 2007

🏀 Basketball

  • At a club from 2003 to 2005