Publications

Preprints

Nanog fluctuations in ES cells highlight the problem of measurement in cell biology
Rosanna C G Smith, Patrick S Stumpf, Sonya J Ridden, Aaron Sim, Sarah Filippi, Heather Harrington, Ben D MacArthur

Analog nitrogen sensing in Escherichia coli enables high fidelity information processing
Michal Komorowski, Jorg Schumacher, Volker Behrends, Tomasz Jetka, Mark H Bennett, Angelique Ale, Sarah Filippi , John W Pinney, Jake G Bundy, Martin Buck, Michael PH Stumpf

2017

Large-Scale Kernel Methods for Independence Testing
Qinyi Zhang, Sarah Filippi, Arthur Gretton, Dino Sejdinovic
To appear in Statistics and Computing

The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq
Quin F. Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes, Michael D. MooreEmail and Rory BowdenEmail
BMC Genomics

2016

A Bayesian nonparametric approach to quantifying dependence between random variables
Sarah Filippi and Chris Holmes
Bayesian analysis

Scalable exploratory Bayesian nonparametric measures of pairwise dependence via Dirichlet Process Mixtures
Sarah Filippi , Chris Holmes and Luis E. Nieto-Barajas
Electronic Journal of Statistics, 2016

Bayesian Learning of Kernel Embeddings
Seth Flaxman, Dino Sejdinovic, John P. Cunningham and Sarah Filippi
Conference on Uncertainty in Artificial Intelligence (UAI 2016 -- Accepted for plenary presentation)

Robustness of MEK-ERK dynamics and origins of cell-to-cell variability in MAPK signaling
Sarah Filippi, Chris P. Barnes, Paul D.W. Kirk, Takamasa Kudo, Katsuyuki Kunida, Siobhan S. McMahon, Takaho Tsuchiya, Takumi Wada, Shinya Kuroda and Michael P.H. Stumpf
Cell Reports, 2016

2015

Information Processing by Simple Molecular Motifs and Susceptibility to Noise
Siobhan McMahon, Oleg Lenive, Sarah Filippi and Michael P.H. Stumpf
Interface, 2015
Here is the pdf on biorxiv.

Stem and progenitor cell dysfunction in human trisomies
Binbin Liu, Sarah Filippi, Anindita Roy and Irene Roberts
EMBO reports, 2015

2014

Information theory and signal transduction systems: From molecular information processing to network inference
Siobhan S. Mc Mahon, Aaron Sim, Sarah Filippi, Robert Johnson, Juliane Liepe, Dominic Smith and Michael P.H. Stumpf
Seminar in Cell and Developmental Biology, 2014

The ecology of chronic myeloid leukemia: hematopoietic stem cell niche dynamics determine clinical outcome
Adam L. MacLean*, Sarah Filippi*, and Michael P. H. Stumpf
Proceedings of the National Academy of Sciences of USA, 2014
* joint first-authors

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
Juliane Liepe, Paul Kirk, Sarah Filippi, Tina Toni, Chris P. Barnes, Michael P. H. Stumpf>
Nature Protocols, 2014

2013

Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems
Daniel Silk*, Sarah Filippi*, Michael P. H. Stumpf
Statistical Applications in Genetics and Molecular Biology, 2013
* joint first-authors

On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo
Sarah Filippi, Chris Barnes, Julien Cornebise, Michael P. H. Stumpf
Statistical Applications in Genetics and Molecular Biology, 2013

Maximizing the Information Content of Experiments in Systems Biology
Juliane Liepe*, Sarah Filippi*, Michal Komorowski and Michael P. H. Stumpf
PLoS Computational Biology, 2013
* joint first-authors

2012

Perturbation of fetal liver hematopoietic stem and progenitor cell development by trisomy 21
Anindita Roy, Gillian Cowan, Adam J. Mead, Sarah Filippi, Georg Bohn, Aristeidis Chaidos, Oliver Tunstall, Jerry K. Y. Chan, Mahesh Choolani, Phillip Bennett, Sailesh Kumar, Deborah Atkinson, Josephine Wyatt-Ashmead, Ming Hu, Michael P. H. Stumpf, Katerina Goudevenou, David O'Connor, Stella T. Chou, Mitchell J. Weiss, Anastasios Karadimitris, Sten Eirik Jacobsen, Paresh Vyas, and Irene Roberts
Proceedings of the National Academy of Sciences of USA, 2012

Considerate approaches to constructing summary statistics for ABC model selection
Chris P. Barnes †, Sarah Filippi †, Michael P. H. Stumpf † and Thomas Thorne †
Statistics and Computing, 2012
† the authors contributed equally

2011

Optimally Sensing a Single Channel Without Prior Information: The Tiling Algorithm and Regret Bounds
Sarah Filippi, Olivier Cappe and Aurelien Garivier
Journal of Selected Topics in Signal Processing (IEEE), 2011

Parametric Bandits: The Generalized Linear Case
Sarah Filippi, Olivier Cappe, Aurelien Garivier and Csaba Szepesvari
Neural Information Processing Systems (NIPS'2010), 2011

2010

Optimism in Reinforcement Learning Based on Kullback-Leibler Divergence
Sarah Filippi, Olivier Cappe and Aurelien Garivier
ALLERTON Conference, 2010

2008

A Near Optimal Policy for Channel Allocation in Cognitive Radio
Sarah Filippi, Olivier Cappe, Fabrice Clerot, and Eric Moulines
Lecture Notes in Computer Science, Recent Advances in Reinforcement Learning, Springer, 2008

Thesis

Title: Optimistic strategies in Reinforcement Learning
Under the supervision of: Olivier Cappé and Aurélien Garivier
At: LTCI (Laboratoire Traitement et Communication de l'Information) which is a joint lab of TELECOM ParisTech and CNRS
Jury: Jean-Yves Audibert, Rémi Munos, Damien Ernst, Frédérick Garcia, Eric Moulines, Fabrice Clérot
Download the manuscript here (in french).



Last modified: March 8th, 2016