Publications

A community effort in SARS-CoV-2 drug discovery.
Johannes Schimunek
Philipp Seidl
Katarina Elez
Tim Hempel
Tuan Le
Frank Noé
Simon Olsson
Lluís Raich
Robin Winter
Hatice Gokcan
Filipp Gusev
Evgeny M. Gutkin
Olexandr Isayev
Maria G. Kurnikova
Chamali H. Narangoda
Roman Zubatyuk
Ivan P. Bosko
Konstantin V. Furs
Anna D. Karpenko
Yury V. Kornoushenko … (see 133 more)
Mikita Shuldau
Artsemi Yushkevich
Mohammed B. Benabderrahmane
Patrick Bousquet‐Melou
Ronan Bureau
Beatrice Charton
Bertrand C. Cirou
Gérard Gil
William J. Allen
Suman Sirimulla
Stanley Watowich
Nick Antonopoulos
Nikolaos Epitropakis
Agamemnon Krasoulis
Vassilis Pitsikalis
Stavros Theodorakis
Igor Kozlovskii
Anton Maliutin
Alexander Medvedev
Petr Popov
Mark Zaretckii
Hamid Eghbal‐Zadeh
Christina Halmich
Sepp Hochreiter
Andreas Mayr
Peter Ruch
Michael Widrich
Francois Berenger
Ashutosh Kumar
Yoshihiro Yamanishi
Kam Y. J. Zhang
Emmanuel Bengio
Yoshua Bengio
Moksh J. Jain
Maksym Korablyov
Cheng-Hao Liu
Gilles Marcou
Marcous Gilles
Enrico Glaab
Kelly Barnsley
Suhasini M. Iyengar
Mary Jo Ondrechen
V. Joachim Haupt
Florian Kaiser
Michael Schroeder
Luisa Pugliese
Simone Albani
Christina Athanasiou
Andrea Beccari
Paolo Carloni
Giulia D'Arrigo
Eleonora Gianquinto
Jonas Goßen
Anton Hanke
Benjamin P. Joseph
Daria B. Kokh
Sandra Kovachka
Candida Manelfi
Goutam Mukherjee
Abraham Muñiz‐Chicharro
Francesco Musiani
Ariane Nunes‐Alves
Giulia Paiardi
Giulia Rossetti
S. Kashif Sadiq
Francesca Spyrakis
Carmine Talarico
Alexandros Tsengenes
Rebecca C. Wade
Conner Copeland
Jeremiah Gaiser
Daniel R. Olson
Amitava Roy
Vishwesh Venkatraman
Travis J. Wheeler
Haribabu Arthanari
Klara Blaschitz
Marco Cespugli
Vedat Durmaz
Konstantin Fackeldey
Patrick D. Fischer
Christoph Gorgulla
Christian Gruber
Karl Gruber
Michael Hetmann
Jamie E. Kinney
Krishna M. Padmanabha Das
Shreya Pandita
Amit Singh
Georg Steinkellner
Guilhem Tesseyre
Gerhard Wagner
Zi‐Fu Wang
Ryan J. Yust
Dmitry S. Druzhilovskiy
Dmitry A. Filimonov
Pavel V. Pogodin
Vladimir Poroikov
Anastassia V. Rudik
Leonid A. Stolbov
Alexander V. Veselovsky
Maria De Rosa
Giada De Simone
Maria R. Gulotta
Jessica Lombino
Nedra Mekni
Ugo Perricone
Arturo Casini
Amanda Embree
D. Benjamin Gordon
David Lei
Katelin Pratt
Christopher A. Voigt
Kuang‐Yu Chen
Yves Jacob
Tim Krischuns
Pierre Lafaye
Agnès Zettor
M. Luis Rodríguez
Kris M. White
Daren Fearon
Frank Von Delft
Martin A. Walsh
Dragos Horvath
Charles L. Brooks
Babak Falsafi
Bryan Ford
Adolfo García‐Sastre
Sang Yup Lee
Nadia Naffakh
Alexandre Varnek
Günter Klambauer
Thomas M. Hermans
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availabili… (see more)ty of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against Covid-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.
2023-11-14
Molecular informatics (published)
doi.org
Language Model-In-The-Loop: Data Optimal Approach to Learn-To-Recommend Actions in Text Games
Arjun Vaithilingam Sudhakar
Prasanna Parthasarathi
Janarthanan Rajendran
Sarath Chandar
2023-11-13
ArXiv (preprint)
doi.org
arxiv.org
Bridging the Gap Between Offline and Online Reinforcement Learning Evaluation Methodologies
Shiva Kanth Sujit
Pedro Braga
Jorg Bornschein
Samira Ebrahimi Kahou
Reinforcement learning (RL) has shown great promise with algorithms learning in environments with large state and action spaces purely from … (see more)scalar reward signals. A crucial challenge for current deep RL algorithms is that they require a tremendous amount of environment interactions for learning. This can be infeasible in situations where such interactions are expensive, such as in robotics. Offline RL algorithms try to address this issue by bootstrapping the learning process from existing logged data without needing to interact with the environment from the very beginning. While online RL algorithms are typically evaluated as a function of the number of environment interactions, there isn't a single established protocol for evaluating offline RL methods. In this paper, we propose a sequential approach to evaluate offline RL algorithms as a function of the training set size and thus by their data efficiency. Sequential evaluation provides valuable insights into the data efficiency of the learning process and the robustness of algorithms to distribution changes in the dataset while also harmonizing the visualization of the offline and online learning phases. Our approach is generally applicable and easy to implement. We compare several existing offline RL algorithms using this approach and present insights from a variety of tasks and offline datasets.
2023-11-10
TMLR (accepted)
doi.org
openreview.net
CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides
Guillaume Gaud
Sooraj R. Achar
François X. P. Bourassa
John S. Davies
Teri Hatzihristidis
Seeyoung Choi
Taisuke Kondo
Selamawit Gossa
Jan Lee
Paul Juneau
Naomi Taylor
Christian S. Hinrichs
Dorian B. McGavern
Paul François
Grégoire Altan-Bonnet
Paul E. Love
2023-11-09
Nature Immunology (published)
doi.org
Stochastic Mirror Descent: Convergence Analysis and Adaptive Variants via the Mirror Stochastic Polyak Stepsize
Ryan D'Orazio
Nicolas Loizou
Issam Hadj Laradji
Ioannis Mitliagkas
We investigate the convergence of stochastic mirror descent (SMD) under interpolation in relatively smooth and smooth convex optimization. I… (see more)n relatively smooth convex optimization we provide new convergence guarantees for SMD with a constant stepsize. For smooth convex optimization we propose a new adaptive stepsize scheme --- the mirror stochastic Polyak stepsize (mSPS). Notably, our convergence results in both settings do not make bounded gradient assumptions or bounded variance assumptions, and we show convergence to a neighborhood that vanishes under interpolation. Consequently, these results correspond to the first convergence guarantees under interpolation for the exponentiated gradient algorithm for fixed or adaptive stepsizes. mSPS generalizes the recently proposed stochastic Polyak stepsize (SPS) (Loizou et al. 2021) to mirror descent and remains both practical and efficient for modern machine learning applications while inheriting the benefits of mirror descent. We complement our results with experiments across various supervised learning tasks and different instances of SMD, demonstrating the effectiveness of mSPS.
2023-11-08
TMLR (accepted)
openreview.net
openreview.net
Capture the Flag: Uncovering Data Insights with Large Language Models
Issam Hadj Laradji
Perouz Taslakian
Sai Rajeswar
Valentina Zantedeschi
Alexandre Lacoste
Nicolas Chapados
David Vazquez
Chris Pal
Alexandre Drouin
2023-11-07
NeurIPS.cc/2023/Workshop/FMDM (published)
doi.org
openreview.net
Multi-resolution Time-Series Transformer for Long-term Forecasting
Yitian Zhang
Liheng Ma
Soumyasundar Pal
Yingxue Zhang
Mark Coates
2023-11-07
ArXiv (preprint)
doi.org
arxiv.org
The Unsolved Challenges of LLMs as Generalist Web Agents: A Case Study
Rim Assouel
Tom Marty
Massimo Caccia
Issam Hadj Laradji
Alexandre Drouin
Sai Rajeswar
Hector Palacios
Quentin Cappart
David Vazquez
Nicolas Chapados
Maxime Gasse
Alexandre Lacoste
2023-11-07
NeurIPS.cc/2023/Workshop/FMDM (published)
openreview.net
openreview.net
30×30 biodiversity gains rely on national coordination
Isaac Eckert
Andrea Brown
Dominique Caron
Federico Riva
Laura J. Pollock
2023-11-06
Nature Communications (published)
doi.org
Coordination among leaf and fine root traits across a strong natural soil fertility gradient
Xavier Guilbeault-Mayers
Hans Lambers
Étienne Laliberté
2023-11-05
bioRxiv (preprint)
doi.org
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles
Renata Mutalova
Roman Sarrazin-Gendron
Parham Ghasemloo Gheidari
Eddie Cai
Gabriel Richard
Sébastien Caisse
Rob Knight
Mathieu Blanchette
Attila Szantner
Jérôme Waldispühl
2023-11-05
International Conference on Climate Informatics (published)
doi.org
The feature landscape of visual cortex
Rudi Tong
Ronan da Silva
Dongyan Lin
Arna Ghosh
James Wilsenach
Erica Cianfarano
Pouya Bashivan
Blake Richards
Stuart Trenholm
Understanding computations in the visual system requires a characterization of the distinct feature preferences of neurons in different visu… (see more)al cortical areas. However, we know little about how feature preferences of neurons within a given area relate to that area’s role within the global organization of visual cortex. To address this, we recorded from thousands of neurons across six visual cortical areas in mouse and leveraged generative AI methods combined with closed-loop neuronal recordings to identify each neuron’s visual feature preference. First, we discovered that the mouse’s visual system is globally organized to encode features in a manner invariant to the types of image transformations induced by self-motion. Second, we found differences in the visual feature preferences of each area and that these differences generalized across animals. Finally, we observed that a given area’s collection of preferred stimuli (‘own-stimuli’) drive neurons from the same area more effectively through their dynamic range compared to preferred stimuli from other areas (‘other-stimuli’). As a result, feature preferences of neurons within an area are organized to maximally encode differences among own-stimuli while remaining insensitive to differences among other-stimuli. These results reveal how visual areas work together to efficiently encode information about the external world.
2023-11-05
bioRxiv (preprint)
doi.org