Publications

Estimating individual treatment effect on disability progression in multiple sclerosis using deep learning
Jean-Pierre R. Falet
Joshua Durso-finley
Brennan Nichyporuk
Julien Schroeter
Francesca Bovis
Maria-Pia Sormani
Doina Precup
Tal Arbel
Douglas Lorne Arnold
Disability progression in multiple sclerosis remains resistant to treatment. The absence of a suitable biomarker to allow for phase 2 clinic… (voir plus)al trials presents a high barrier for drug development. We propose to enable short proof-of-concept trials by increasing statistical power using a deep-learning predictive enrichment strategy. Specifically, a multi-headed multilayer perceptron is used to estimate the conditional average treatment effect (CATE) using baseline clinical and imaging features, and patients predicted to be most responsive are preferentially randomized into a trial. Leveraging data from six randomized clinical trials ( n  = 3,830), we first pre-trained the model on the subset of relapsing-remitting MS patients ( n  = 2,520), then fine-tuned it on a subset of primary progressive MS (PPMS) patients ( n  = 695). In a separate held-out test set of PPMS patients randomized to anti-CD20 antibodies or placebo ( n  = 297), the average treatment effect was larger for the 50% (HR, 0.492; 95% CI, 0.266-0.912; p  = 0.0218) and 30% (HR, 0.361; 95% CI, 0.165-0.79; p  = 0.008) predicted to be most responsive, compared to 0.743 (95% CI, 0.482-1.15; p  = 0.179) for the entire group. The same model could also identify responders to laquinimod in another held-out test set of PPMS patients ( n  = 318). Finally, we show that using this model for predictive enrichment results in important increases in power.
2022-09-25
Nature Communications (publié)
doi.org
FedShuffle: Recipes for Better Use of Local Work in Federated Learning
Samuel Horváth
Maziar Sanjabi
Lin Xiao
Peter Richtárik
Michael G. Rabbat
The practice of applying several local updates before aggregation across clients has been empirically shown to be a successful approach to o… (voir plus)vercoming the communication bottleneck in Federated Learning (FL). Such methods are usually implemented by having clients perform one or more epochs of local training per round while randomly reshuffling their finite dataset in each epoch. Data imbalance, where clients have different numbers of local training samples, is ubiquitous in FL applications, resulting in different clients performing different numbers of local updates in each round. In this work, we propose a general recipe, FedShuffle, that better utilizes the local updates in FL, especially in this regime encompassing random reshuffling and heterogeneity. FedShuffle is the first local update method with theoretical convergence guarantees that incorporates random reshuffling, data imbalance, and client sampling — features that are essential in large-scale cross-device FL. We present a comprehensive theoretical analysis of FedShuffle and show, both theoretically and empirically, that it does not suffer from the objective function mismatch that is present in FL methods that assume homogeneous updates in heterogeneous FL setups, such as FedAvg (McMahan et al., 2017). In addition, by combining the ingredients above, FedShuffle improves upon FedNova (Wang et al., 2020), which was previously proposed to solve this mismatch. Similar to Mime (Karimireddy et al., 2020), we show that FedShuffle with momentum variance reduction (Cutkosky & Orabona, 2019) improves upon non-local methods under a Hessian similarity assumption.
2022-09-25
TMLR (accepté)
doi.org
openreview.net
Social belonging: brain structure and function is linked to membership in sports teams, religious groups, and social clubs
Carolin Kieckhaefer
Leonhard Schilbach
Danilo Bzdok
Human behavior across the life span is driven by the psychological need to belong, right from kindergarten to bingo nights. Being part of so… (voir plus)cial groups constitutes a backbone for communal life and confers many benefits for the physical and mental health. Capitalizing on the neuroimaging and behavioral data from ∼40,000 participants from the UK Biobank population cohort, we used structural and functional analyses to explore how social participation is reflected in the human brain. Across 3 different types of social groups, structural analyses point toward the variance in ventromedial prefrontal cortex, fusiform gyrus, and anterior cingulate cortex as structural substrates tightly linked to social participation. Functional connectivity analyses not only emphasized the importance of default mode and limbic network but also showed differences for sports teams and religious groups as compared to social clubs. Taken together, our findings establish the structural and functional integrity of the default mode network as a neural signature of social belonging.
2022-09-25
Cerebral Cortex (inconnu)
doi.org
Tackling bias in AI health datasets through the STANDING Together initiative
Shaswath Ganapathi
Johannes Palmer
J. Alderman
Melanie Calvert
Cyrus Espinoza
Jacqui Gath
Marzyeh Ghassemi
Katherine Heller
Francis McKay
Alan Karthikesalingam
S. Kuku
Maxine E. Mackintosh
Sinduja Manohar
Bilal Mateen
Rubeta Matin
Melissa D. McCradden
Lauren Oakden-Rayner
Johan Ordish
Russell Pearson
S. Pfohl … (voir 8 de plus)
Negar Rostamzadeh
Elizabeth Sapey
Neil J. Sebire
Viknesh Sounderajah
Charlotte Summers
Darren E. Treanor
Alastair Denniston
Xiaoxuan Liu
2022-09-25
Nature Network Boston (publié)
doi.org
The 5-year longitudinal diagnostic profile and health services utilization of patients treated with electroconvulsive therapy in Quebec: a population-based study
Simon Lafrenière
Fatemeh Gholi-Zadeh-Kharrat
Caroline Sirois
Victoria Massamba
Louis Rochette
Camille Brousseau-Paradis
Simon Patry
Christian Gagné
Morgane Lemasson
Geneviève Gariépy
Chantal Mérette
Elham Rahme
Alain Lesage
2022-09-25
Social Psychiatry and Psychiatric Epidemiology (publié)
doi.org
OSSEM: One-Shot Speaker Adaptive Speech Enhancement Using Meta Learning
Cheng Yu
Szu-wei Fu
Tsun-An Hsieh
Yu Tsao
Mirco Ravanelli
Although deep learning (DL) has achieved notable progress in speech enhancement (SE), further research is still required for a DL-based SE s… (voir plus)ystem to adapt effectively and efficiently to particular speakers. In this study, we propose a novel meta-learning-based speaker-adaptive SE approach (called OSSEM) that aims to achieve SE model adaptation in a one-shot manner. OSSEM consists of a modified transformer SE network and a speaker-specific masking (SSM) network. In practice, the SSM network takes an enrolled speaker embedding extracted using ECAPA-TDNN to adjust the input noisy feature through masking. To evaluate OSSEM, we designed a modified Voice Bank-DEMAND dataset, in which one utterance from the testing set was used for model adaptation, and the remaining utterances were used for testing the performance. Moreover, we set restrictions allowing the enhancement process to be conducted in real time, and thus designed OSSEM to be a causal SE system. Experimental results first show that OSSEM can effectively adapt a pretrained SE model to a particular speaker with only one utterance, thus yielding improved SE results. Meanwhile, OSSEM exhibits a competitive performance compared to state-of-the-art causal SE systems.
2022-09-17
Interspeech 2022 (publié)
doi.org
arxiv.org
SoundChoice: Grapheme-to-Phoneme Models with Semantic Disambiguation
Artem Ploujnikov
Mirco Ravanelli
End-to-end speech synthesis models directly convert the input characters into an audio representation (e.g., spectrograms). Despite their im… (voir plus)pressive performance, such models have difficulty disambiguating the pronunciations of identically spelled words. To mitigate this issue, a separate Grapheme-to-Phoneme (G2P) model can be employed to convert the characters into phonemes before synthesizing the audio. This paper proposes SoundChoice, a novel G2P architecture that processes entire sentences rather than operating at the word level. The proposed architecture takes advantage of a weighted homograph loss (that improves disambiguation), exploits curriculum learning (that gradually switches from word-level to sentence-level G2P), and integrates word embeddings from BERT (for further performance improvement). Moreover, the model inherits the best practices in speech recognition, including multi-task learning with Connectionist Temporal Classification (CTC) and beam search with an embedded language model. As a result, SoundChoice achieves a Phoneme Error Rate (PER) of 2.65% on whole-sentence transcription using data from LibriSpeech and Wikipedia. Index Terms grapheme-to-phoneme, speech synthesis, text-tospeech, phonetics, pronunciation, disambiguation.
2022-09-17
Interspeech 2022 (publié)
doi.org
arxiv.org
Intervertebral Disc Labeling With Learning Shape Information, A Look Once Approach
Reza Azad
Moein Heidari
Julien Cohen-Adad
Ehsan Adeli
Dorit Merhof
Accurate and automatic segmentation of intervertebral discs from medical images is a critical task for the assessment of spine-related disea… (voir plus)ses such as osteoporosis, vertebral fractures, and intervertebral disc herniation. To date, various approaches have been developed in the literature which routinely relies on detecting the discs as the primary step. A disadvantage of many cohort studies is that the localization algorithm also yields false-positive detections. In this study, we aim to alleviate this problem by proposing a novel U-Net-based structure to predict a set of candidates for intervertebral disc locations. In our design, we integrate the image shape information (image gradients) to encourage the model to learn rich and generic geometrical information. This additional signal guides the model to selectively emphasize the contextual representation and suppress the less discriminative features. On the post-processing side, to further decrease the false positive rate, we propose a permutation invariant 'look once' model, which accelerates the candidate recovery procedure. In comparison with previous studies, our proposed approach does not need to perform the selection in an iterative fashion. The proposed method was evaluated on the spine generic public multi-center dataset and demonstrated superior performance compared to previous work. We have provided the implementation code in https://github.com/rezazad68/intervertebral-lookonce
2022-09-15
Predictive Intelligence in Medicine (publié)
doi.org
arxiv.org
Open Design and Validation of a Reproducible Videogame Controller for MRI and MEG
Harel Yann
Cyr André
Boyle Julie
Pinsard Basile
Bernard Jeremy
Fourcade Marie-France
Aggarwal Himanshu
Ponce Ana Fernanda
Thirion Bertrand
Jerbi Karim
Bellec Pierre

Playing video games in a neuroimaging environment is both scientifically promising and technically challenging. Primary among these chall… (voir plus)enges is the need to use scanner-compatible devices to register player inputs, which limits the type of games that can be comfortably played in a scanner and often reduces the ecological validity of video game tasks. In this paper, we introduce an MRI- and MEG-compatible video game controller that is made exclusively of 3D-printed and commercially available parts, and we release the design files and documentations in the goal of making its production accessible to any research team with minimal engineering resources. In line with the open science philosophy, we made this work accessible under an Open Source Hardware license that aims to promote accessibility and reproducibility. Additionally, we validated the responsiveness and scanner-compatibility of our controller by comparing it to a reference, non-MRI compatible controller, and by assessing the quality of the data recorded with and without the use of the said controller. The analysis of response latencies showed reliable button press accuracies. A higher latency was detected on button releases, both for long and short button presses although this effect was small enough as not to affect gameplay in most situations. Analysis of subject motion during fMRI recordings of various tasks showed that the use of our controller didn’t increase the amount of motion produced. We hope that this tool will stimulate further neuroimaging studies of video games tasks by improving both their accessibility and their validity.

2022-09-15
PsyArXiv (prépublication)
doi.org
The BigScience ROOTS Corpus: A 1.6TB Composite Multilingual Dataset
Hugo Laurençon
Lucile Saulnier
Thomas Wang
Christopher Akiki
Albert Villanova del Moral
Teven Le Scao
Leandro Von Werra
Chenghao Mou
Eduardo González Ponferrada
Huu Nguyen
Jörg Frohberg
Mario Šaško
Quentin Lhoest
Angelina McMillan-Major
Gérard Dupont
Stella Biderman
Anna Rogers
Loubna Ben allal
Francesco De Toni
Giada Pistilli … (voir 34 de plus)
Olivier Nguyen
Somaieh Nikpoor
Maraim Masoud
Pierre Colombo
Javier de la Rosa
Paulo Villegas
Tristan Thrush
Shayne Longpre
Sebastian Nagel
Leon Weber
Manuel Romero Muñoz
Jian Zhu
Daniel Van Strien
Zaid Alyafeai
Khalid Almubarak
Vu Minh Chien
Itziar Gonzalez-Dios
Aitor Soroa
Kyle Lo
Manan Dey
Pedro Ortiz Suarez
Aaron Gokaslan
Shamik Bose
David Ifeoluwa Adelani
Long Phan
Hieu Tran
Ian Yu
Suhas Pai
Jenny Chim
Violette Lepercq
Suzana Ilic
Margaret Mitchell
Sasha Luccioni
Yacine Jernite
As language models grow ever larger, the need for large-scale high-quality text datasets has never been more pressing, especially in multili… (voir plus)ngual settings. The BigScience workshop, a 1-year international and multidisciplinary initiative, was formed with the goal of researching and training large language models as a values-driven undertaking, putting issues of ethics, harm, and governance in the foreground. This paper documents the data creation and curation efforts undertaken by BigScience to assemble the Responsible Open-science Open-collaboration Text Sources (ROOTS) corpus, a 1.6TB dataset spanning 59 languages that was used to train the 176-billion-parameter BigScience Large Open-science Open-access Multilingual (BLOOM) language model. We further release a large initial subset of the corpus and analyses thereof, and hope to empower large-scale monolingual and multilingual modeling projects with both the data and the processing tools, as well as stimulate research around this large multilingual corpus.
2022-09-15
NeurIPS.cc/2022/Track/Datasets_and_Benchmarks (accepté)
doi.org
openreview.net
Towards Better Evaluation for Dynamic Link Prediction
Farimah Poursafaei
Andy Huang
Shenyang Huang
Kellin Pelrine
Reihaneh Rabbany
Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In th… (voir plus)is work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization-based baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings which highlights that the negative edges used in the current evaluation are easy. To sample more challenging negative edges, we introduce two novel negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.
2022-09-15
NeurIPS.cc/2022/Track/Datasets_and_Benchmarks (accepté)
doi.org
openreview.net
Accurate machine learning prediction of sexual orientation based on brain morphology and intrinsic functional connectivity
Benjamin Clemens
Jeremy Lefort-Besnard
Christoph Ritter
Elke Smith
Mikhail Votinov
Birgit Derntl
Ute Habel
Danilo Bzdok
Sexual orientation in humans represents a multilevel construct that is grounded in both neurobiological and environmental factors. Here, we… (voir plus) bring to bear a machine learning approach to predict sexual orientation from gray matter volumes (GMVs) or resting-state functional connectivity (RSFC) in a cohort of 45 heterosexual and 41 homosexual participants.  In both brain assessments, we used penalized logistic regression models and nonparametric permutation.  We found an average accuracy of 62% (±6.72) for predicting sexual orientation based on GMV and an average predictive accuracy of 92% (±9.89) using RSFC. Regions in the precentral gyrus, precuneus and the prefrontal cortex were significantly informative for distinguishing heterosexual from homosexual participants in both the GMV and RSFC settings.  These results indicate that, aside from self-reports, RSFC offers neurobiological information valuable for highly accurate prediction of sexual orientation. We demonstrate for the first time that sexual orientation is reflected in specific patterns of RSFC, which enable personalized, brain-based predictions of this highly complex human trait. While these results are preliminary, our neurobiologically based prediction framework illustrates the great value and potential of RSFC for revealing biologically meaningful and generalizable predictive patterns in the human brain.
2022-09-13
Cerebral Cortex (inconnu)
doi.org