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Hi, I am

Colas Droin

I am a researcher and data scientist.

Research

As of 2019, I’m 3rd year PhD student at the Computational Systems Biology Lab (Naef Lab) at the École Polytechnique Fédérale of Lausanne (EPFL). I work under the supervision of the theoretical physicist and now biologist Pr. Félix Naef. 

Research interests

Broadly, I am interested in developing mathematical and physical tools to better understand both single-cell and genome-wide biological phenomena. This includes using bayesian inference (Kalman filters, HMM) in conjunction with physical models under the form of deterministic or stochastic differential equations (ODE, PDE, SDE).

In the frame of my PhD, I mainly studied the synchronisation of biological oscillators, using dynamical systems and tools from non-linear physics in general. As part of subsidiaries projects, I also took interest in statistical modeling in a more general way, e.g. regression analysis, mixed-model, dimensionality reduction.

Out of personal interest, I’m also actively maintaining my knowledge of the state of the art in data science, via courses and workshops given by my university, as will with internet browsing in general. I mainly like machine learning and data visualisation.

Publications

As part of my PhD, I have several papers in preparation, but nothing out yet. All these articles should get published this year.

  • Low-dimensional Dynamics of Two Coupled Biological Oscillators. Colas Droin1, Eric R Paquet1, Felix Naef. In reviews.
  • Spatial chronobiology of the mammalian liver. TDB.
  • Phase inference tools, a review with application to biological data. Colas Droin, Felix Naef. TBD.

I am also co-author of a publication from my internship at the SBRI in 2014, in which I worked on optimizing the parameters of a neural network to improve the NLP performances of the iCub robot:

  • Corticostriatal response selection in sentence production: Insights from neural network simulation with reservoir computing. Hinaut, X., Lance, F., Droin, C., Petit, M., Pointeau, G., & Dominey, P. F. (2015). Brain and language150, 54-68.

1These authors contributed equally to this work.

Conferences (talks)

  • Characterization of the influence of the cell-cycle in the circadian clock in mammalian cells. 16/06/2017. Physics of living systems, EPFL, Lausanne, Switzerland.
  • A reconstruction of the phase dynamics of interacting cell-cycle and circadian clock. 20/07/2017. SSBSS, Cambdrige, UK.
  • Low-dimensional Dynamics of Two Coupled Biological Oscillators. 03/04/2019. CompSysBio, CNRS, Aussois, France.

Conferences (posters)

  • A reconstruction of the phase dynamics of interacting cell-cycle and circadian clock. 20/07/2017. SSBSS, Cambdrige, UK.
  • How can two biological oscillators synchronize? A study of the cell-cycle influence on the circadian clock. 04/08/2017. 3rd International SystemsX.ch Conference on Systems Biology. Zurich, Switzerland.
  • Low-dimensional Dynamics of Two Coupled Biological Oscillators. 04/06/2018. EMBO/ EMBL Symposium on Biological Oscillators: Design, Mechanism, Function. Heidelberg, Germany.
  • Deciphering the Phase Dynamics of Two Coupled Biological Oscillators. 01/10/2018. EPFL Physics days. Lausanne, Switzerland. This poster received the Physics days best poster award.
  • Exploring Circadian Zonation. 14/03/2019. VISualizing BIological data 2019 (VIZBI). Heidelberg, Germany.
  • Exploring Circadian Zonation. 10/04/2019. DDay, CHUV, Lausanne, Switzerland. This poster received the best poster award.

Teaching assistant

Courses

References

Available upon request.

Projects

Deciphering the coupling between the cell-cycle and the circadian clock

Techniques: HMM, stochastic processes, expectation-maximization

Understanding gene zonation and rhythmicity in the mouse liver

Techniques: SVD, linear mixed-model, penalized model selection

resume

WORK HISTORY

Oct 2016 – Current

PhD student in mathematical biology

Computational systems biology lab, EPFL.
  • Subject : Inference and modelling of the coupling between the circadian cycle and the cell-cycle.

  • Details : Inference of the circadian and cell-cycle phases from previously collected fluorescent signals using an HMM and characterization of the coupling between them through maximization of the likelihood of the data. Analysis of the results under different biological conditions.

Feb 2016 – Jun 2016

Master Thesis (ENS Msc)

Dante Team, ENS Lyon.
  • Subject : Data-driven characterization of social tie heterogeneities in real information cascades.

  • Details : Exploration and extraction of data in a corpus containing several billions of tweets, social network construction and analysis (SQLite, Python, R).

Feb 2015 – Jul 2015

Master Thesis (INSA master of engineering)

Dassault Systems, Velizy-Villacoublay.
  • Subject : study and development of an hybrid system for the Chemical Master Equation.

  • Details : state of the art of hybrid systems (differential-stochastic), choice of an optimal model, integration of a boolean feature, development, optimization and tests (C++, R).

May 2014 – Aug 2014

Internship

Stem Cell and Brain Institute, Lyon.
  • Subject : study of a sentences production model based on a recurrent neural network.

  • Details : model analysis, debugging and optimization (Python).

EDUCATION

Sep 2015 – Jun 2016

Msc in Physics of Complex Systems

Ecole Normale Supérieure de Lyon
  • Graduated with honors in July 2016

  • Major in computer science, minor in physics

  • Courses including (non-exhaustive list): complex networks, statistical physics, dynamical processes and networks, network algorithms for molecular biology, rule-based modeling, Randomized Algorithms, applied machine learning

Sep 2010 – Jun 2015

Engineering studies in computational and mathematical biology

Institut National des Sciences  Appliquées de Lyon
  • Graduated with honors in July 2015

  • Exchange student in the school of Computer Science of  KTH (Sweden) from august 2014 to January 2015

  • Courses including (non-exhaustive list): Courses including (non-exhaustive list) : software development, discrete mathematics, ODE, machine learning, PDE, fundamental and applied, statistics, artificial intelligence, Markov models, population genetics, cellular biology.

PERSONAL INTERESTS

SCIENCE:

  • Deterministic and statistical modelling

  • Bayesian inference

  • Physics and mathematics in general

  • Systems and circadian biology

COMPUTER SCIENCE:

  • Machine learning

  • Data visualization

  • Algorithmics

PHILOSOPHY:

  • Analytic philosophy

  • Metaphysics, epistemology

  • Ethics

  • Jungian psychology

WRITING:

  • Novels

  • Philosophy

  • Poetry

SPORT:

  • Rackets (squash, badminton, tennis)

  • Jogging

  • Ski

Coding Skills

Python

Julia

C, C++

R

Matlab

Processing

Office Skills

OS X

Windows

Latex, Beamer

Office Suite

Linux

Data Science Library Skills

Numpy/Scipy/Matplotlib

Plotly

Pandas

SciKitLearn

PyTorch

NetworkX

Design Skills

Photoshop CC

Illustrator CC

Web Skills

Python Dash

WordPress

HTML5

CSS3

Bootstrap

Languages

French

English

Spanish

contact

Let’s Socialize

Reach Me

based in Lausanne, Switzerland

Tel :

colasdroin [at] gmail.com

Freelance Available

Drop Me A Line