Publications

Adaptive Integration of Categorical and Multi-relational Ontologies with EHR Data for Medical Concept Embedding
Chin Wang Cheong
Kejing Yin
William K. Cheung
Benjamin C. M. Fung
Jonathan Poon
2023-11-13
ACM Transactions on Intelligent Systems and Technology (publié)
doi.org
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 … (voir 133 de plus)
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
M. 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… (voir plus)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.
2023-11-13
Molecular Informatics (publié)
doi.org
Correlation between Preoperative MRI Parameters and Oswestry Disability Index in Patients with Lumbar Spinal Stenosis: A Retrospective Study
Radu Caprariu
Manuel D. Oprea
Dan V. Poenaru
Diana Andrei
Background and Objectives: Lumbar spinal stenosis (LSS) is a degenerative condition posing significant challenges in clinical management. De… (voir plus)spite the use of radiological parameters and patient-reported outcome measures like the Oswestry Disability Index (ODI) for evaluation, there is limited understanding of their interrelationship. This study aimed to investigate the correlation between preoperative MRI parameters and ODI scores in patients with LSS undergoing surgical treatment. Materials and Methods: A retrospective analysis was conducted on 86 patients diagnosed with LSS over a 5-year period. Preoperative MRI measurements, including the cross-sectional area of the psoas muscle, lumbar canal stenosis, neural foramina area, and facet joint osteoarthritis, were assessed. ODI scores were collected preoperatively and at a 1-year follow-up. Statistical analyses were performed using IBM SPSS Statistics software (version 26). Results: Weak to moderate correlations were observed between certain MRI parameters and ODI scores. The initial ODI score had a weak positive correlation with the severity of lumbar canal stenosis according to Schizas criteria (rho = 0.327, p = 0.010) and a moderate negative correlation with the relative cross-sectional area of the psoas muscle (rho = −0.498, p = 0.000). At 1-year follow-up, the ODI had a weak negative correlation with the relative cross-sectional area of the psoas muscle (rho = −0.284, p = 0.026). Conclusions: While the severity of LSS showed a weak correlation with initial ODI, it was not a predictor of 1-year postoperative ODI. Furthermore, although the cross-sectional area of the thecal sac, the sagittal area of the neural foramen, and the grade of facet joint osteoarthritis influence the imagistic severity, none of them correlate with ODI. These findings underscore the need for a comprehensive model that integrates multiple imaging and clinical parameters for a holistic understanding of LSS and its functional outcomes.
2023-11-13
Medicina (publié)
doi.org
Expressiveness and Learnability: A Unifying View for Evaluating Self-Supervised Learning
Yuchen Lu
Zhen Liu
Aristide Baratin
Romain Laroche
Aaron Courville
Alessandro Sordoni
2023-11-13
Transactions on Machine Learning Research (accepté)
doi.org
openreview.net
General anaesthesia reduces the uniqueness of brain connectivity across individuals and across species
Andrea I. Luppi
Daniel Golkowski
Andreas Ranft
Rudiger Ilg
Denis Jordan
Danilo Bzdok
Adrian M. Owen
Lorina Naci
Emmanuel A. Stamatakis
Enrico Amico
Bratislav Misic
The human brain is characterised by idiosyncratic patterns of spontaneous thought, rendering each brain uniquely identifiable from its neura… (voir plus)l activity. However, deep general anaesthesia suppresses subjective experience. Does it also suppress what makes each brain unique? Here we used functional MRI under the effects of the general anaesthetics sevoflurane and propofol to determine whether anaesthetic-induced unconsciousness diminishes the uniqueness of the human brain: both with respect to the brains of other individuals, and the brains of another species. We report that under anaesthesia individual brains become less self-similar and less distinguishable from each other. Loss of distinctiveness is highly organised: it co-localises with the archetypal sensory-association axis, correlating with genetic and morphometric markers of phylogenetic differences between humans and other primates. This effect is more evident at greater anaesthetic depths, reproducible across sevoflurane and propofol, and reversed upon recovery. Providing convergent evidence, we show that under anaesthesia the functional connectivity of the human brain becomes more similar to the macaque brain. Finally, anaesthesia diminishes the match between spontaneous brain activity and meta-analytic brain patterns aggregated from the NeuroSynth engine. Collectively, the present results reveal that anaesthetised human brains are not only less distinguishable from each other, but also less distinguishable from the brains of other primates, with specifically human-expanded regions being the most affected by anaesthesia.
2023-11-12
bioRxiv (prépublication)
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
2023-11-12
arXiv (prépublication)
doi.org
arxiv.org
Towards Climate Variable Prediction with Conditioned Spatio-Temporal Normalizing Flows
Christina Winkler
David Rolnick
2023-11-11
ArXiv (prépublication)
arxiv.org
arxiv.org
Bridging the Gap Between Offline and Online Reinforcement Learning Evaluation Methodologies
Shiva Kanth Sujit
Pedro Braga
Jörg Bornschein
S Ebrahimi Kahou
Reinforcement learning (RL) has shown great promise with algorithms learning in environments with large state and action spaces purely from … (voir plus)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.
2023-11-09
TMLR (accepté)
doi.org
openreview.net
DASVDD: Deep Autoencoding Support Vector Data Descriptor for Anomaly Detection
Hadi Hojjati
Narges Armanfard
Semi-supervised anomaly detection aims to detect anomalies from normal samples using a model that is trained on normal data. With recent adv… (voir plus)ancements in deep learning, researchers have designed efficient deep anomaly detection methods. Existing works commonly use neural networks to map the data into a more informative representation and then apply an anomaly detection algorithm. In this paper, we propose a method, DASVDD, that jointly learns the parameters of an autoencoder while minimizing the volume of an enclosing hyper-sphere on its latent representation. We propose an anomaly score which is a combination of autoencoder's reconstruction error and the distance from the center of the enclosing hypersphere in the latent representation. Minimizing this anomaly score aids us in learning the underlying distribution of the normal class during training. Including the reconstruction error in the anomaly score ensures that DASVDD does not suffer from the common hypersphere collapse issue since the DASVDD model does not converge to the trivial solution of mapping all inputs to a constant point in the latent representation. Experimental evaluations on several benchmark datasets show that the proposed method outperforms the commonly used state-of-the-art anomaly detection algorithms while maintaining robust performance across different anomaly classes.
2023-11-09
IEEE Transactions on Knowledge and Data Engineering (inconnu)
doi.org
arxiv.org
CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides
Guillaume Gaud
Sooraj Achar
François X. P. Bourassa
John 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
2023-11-08
Nature Immunology (inconnu)
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… (voir plus)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.
2023-11-07
TMLR (accepté)
openreview.net
openreview.net
Capture the Flag: Uncovering Data Insights with Large Language Models.
Issam H. Laradji
Perouz Taslakian
Sai Rajeswar
Valentina Zantedeschi
Alexandre Lacoste
Nicolas Chapados
David Vázquez
Christopher Pal
Alexandre Drouin
The extraction of a small number of relevant insights from vast amounts of data is a crucial component of data-driven decision-making. Howev… (voir plus)er, accomplishing this task requires considerable technical skills, domain expertise, and human labor. This study explores the potential of using Large Language Models (LLMs) to automate the discovery of insights in data, leveraging recent advances in reasoning and code generation techniques. We propose a new evaluation methodology based on a "capture the flag" principle, measuring the ability of such models to recognize meaningful and pertinent information (flags) in a dataset. We further propose two proof-of-concept agents, with different inner workings, and compare their ability to capture such flags in a real-world sales dataset. While the work reported here is preliminary, our results are sufficiently interesting to mandate future exploration by the community.
2023-11-06
NeurIPS.cc/2023/Workshop/FMDM (publié)
doi.org
openreview.net