Publications

NeoRS: A Neonatal Resting State fMRI Data Preprocessing Pipeline
Vicente Enguix
Jeanette Kenley
David Luck
Julien Cohen-Adad
Gregory Anton Lodygensky
Resting state functional MRI (rsfMRI) has been shown to be a promising tool to study intrinsic brain functional connectivity and assess its … (see more)integrity in cerebral development. In neonates, where functional MRI is limited to very few paradigms, rsfMRI was shown to be a relevant tool to explore regional interactions of brain networks. However, to identify the resting state networks, data needs to be carefully processed to reduce artifacts compromising the interpretation of results. Because of the non-collaborative nature of the neonates, the differences in brain size and the reversed contrast compared to adults due to myelination, neonates can’t be processed with the existing adult pipelines, as they are not adapted. Therefore, we developed NeoRS, a rsfMRI pipeline for neonates. The pipeline relies on popular neuroimaging tools (FSL, AFNI, and SPM) and is optimized for the neonatal brain. The main processing steps include image registration to an atlas, skull stripping, tissue segmentation, slice timing and head motion correction and regression of confounds which compromise functional data interpretation. To address the specificity of neonatal brain imaging, particular attention was given to registration including neonatal atlas type and parameters, such as brain size variations, and contrast differences compared to adults. Furthermore, head motion was scrutinized, and motion management optimized, as it is a major issue when processing neonatal rsfMRI data. The pipeline includes quality control using visual assessment checkpoints. To assess the effectiveness of NeoRS processing steps we used the neonatal data from the Baby Connectome Project dataset including a total of 10 neonates. NeoRS was designed to work on both multi-band and single-band acquisitions and is applicable on smaller datasets. NeoRS also includes popular functional connectivity analysis features such as seed-to-seed or seed-to-voxel correlations. Language, default mode, dorsal attention, visual, ventral attention, motor and fronto-parietal networks were evaluated. Topology found the different analyzed networks were in agreement with previously published studies in the neonate. NeoRS is coded in Matlab and allows parallel computing to reduce computational times; it is open-source and available on GitHub (https://github.com/venguix/NeoRS). NeoRS allows robust image processing of the neonatal rsfMRI data that can be readily customized to different datasets.
2022-06-17
Frontiers in Neuroinformatics (published)
doi.org
arxiv.org
Survival Modelling for Data From Combined Cohorts: Opening the Door to Meta Survival Analyses and Survival Analysis Using Electronic Health Records
James H. McVittie
Ana F. Best
David B. Wolfson
David A. Stephens
Julian Wolfson
David Buckeridge
Shahinaz M. Gadalla
Non‐parametric estimation of the survival function using observed failure time data depends on the underlying data generating mechanism, i… (see more)ncluding the ways in which the data may be censored and/or truncated. For data arising from a single source or collected from a single cohort, a wide range of estimators have been proposed and compared in the literature. Often, however, it may be possible, and indeed advantageous, to combine and then analyse survival data that have been collected under different study designs. We review non‐parametric survival analysis for data obtained by combining the most common types of cohort. We have two main goals: (i) to clarify the differences in the model assumptions and (ii) to provide a single lens through which some of the proposed estimators may be viewed. Our discussion is relevant to the meta‐analysis of survival data obtained from different types of study, and to the modern era of electronic health records.
2022-06-16
International Statistical Review (published)
doi.org
Popular and Scientific Discourse on Autism: Representational Cross-Cultural Analysis of Epistemic Communities to Inform Policy and Practice
Christophe Gauld
Julien Maquet
Jean‐Arthur Micoulaud‐Franchi
Guillaume Dumas
Background Social media provide a window onto the circulation of ideas in everyday folk psychiatry, revealing the themes and issues discusse… (see more)d both by the public and by various scientific communities. Objective This study explores the trends in health information about autism spectrum disorder within popular and scientific communities through the systematic semantic exploration of big data gathered from Twitter and PubMed. Methods First, we performed a natural language processing by text-mining analysis and with unsupervised (machine learning) topic modeling on a sample of the last 10,000 tweets in English posted with the term #autism (January 2021). We built a network of words to visualize the main dimensions representing these data. Second, we performed precisely the same analysis with all the articles using the term “autism” in PubMed without time restriction. Lastly, we compared the results of the 2 databases. Results We retrieved 121,556 terms related to autism in 10,000 tweets and 5.7x109 terms in 57,121 biomedical scientific articles. The 4 main dimensions extracted from Twitter were as follows: integration and social support, understanding and mental health, child welfare, and daily challenges and difficulties. The 4 main dimensions extracted from PubMed were as follows: diagnostic and skills, research challenges, clinical and therapeutical challenges, and neuropsychology and behavior. Conclusions This study provides the first systematic and rigorous comparison between 2 corpora of interests, in terms of lay representations and scientific research, regarding the significant increase in information available on autism spectrum disorder and of the difficulty to connect fragments of knowledge from the general population. The results suggest a clear distinction between the focus of topics used in the social media and that of scientific communities. This distinction highlights the importance of knowledge mobilization and exchange to better align research priorities with personal concerns and to address dimensions of well-being, adaptation, and resilience. Health care professionals and researchers can use these dimensions as a framework in their consultations to engage in discussions on issues that matter to beneficiaries and develop clinical approaches and research policies in line with these interests. Finally, our study can inform policy makers on the health and social needs and concerns of individuals with autism and their caregivers, especially to define health indicators based on important issues for beneficiaries.
2022-06-15
Journal of Medical Internet Research (published)
doi.org
Conditions for indexability of restless bandits and an
$\mathcal{O}\!\left(K^3\right)$
algorithm to compute Whittle index
Nima Akbarzadeh
Aditya Mahajan
Abstract Restless bandits are a class of sequential resource allocation problems concerned with allocating one or more resources among sever… (see more)al alternative processes where the evolution of the processes depends on the resources allocated to them. Such models capture the fundamental trade-offs between exploration and exploitation. In 1988, Whittle developed an index heuristic for restless bandit problems which has emerged as a popular solution approach because of its simplicity and strong empirical performance. The Whittle index heuristic is applicable if the model satisfies a technical condition known as indexability. In this paper, we present two general sufficient conditions for indexability and identify simpler-to-verify refinements of these conditions. We then revisit a previously proposed algorithm called the adaptive greedy algorithm which is known to compute the Whittle index for a sub-class of restless bandits. We show that a generalization of the adaptive greedy algorithm computes the Whittle index for all indexable restless bandits. We present an efficient implementation of this algorithm which can compute the Whittle index of a restless bandit with K states in
2022-06-14
Advances in Applied Probability (published)
doi.org
arxiv.org
Clustering units in neural networks: upstream vs downstream information
Richard D Lange
David Rolnick
Konrad Paul Kording
It has been hypothesized that some form of"modular"structure in artificial neural networks should be useful for learning, compositionality, … (see more)and generalization. However, defining and quantifying modularity remains an open problem. We cast the problem of detecting functional modules into the problem of detecting clusters of similar-functioning units. This begs the question of what makes two units functionally similar. For this, we consider two broad families of methods: those that define similarity based on how units respond to structured variations in inputs ("upstream"), and those based on how variations in hidden unit activations affect outputs ("downstream"). We conduct an empirical study quantifying modularity of hidden layer representations of simple feedforward, fully connected networks, across a range of hyperparameters. For each model, we quantify pairwise associations between hidden units in each layer using a variety of both upstream and downstream measures, then cluster them by maximizing their"modularity score"using established tools from network science. We find two surprising results: first, dropout dramatically increased modularity, while other forms of weight regularization had more modest effects. Second, although we observe that there is usually good agreement about clusters within both upstream methods and downstream methods, there is little agreement about the cluster assignments across these two families of methods. This has important implications for representation-learning, as it suggests that finding modular representations that reflect structure in inputs (e.g. disentanglement) may be a distinct goal from learning modular representations that reflect structure in outputs (e.g. compositionality).
2022-06-13
TMLR (accepted)
doi.org
openreview.net
Studying the Practices of Deploying Machine Learning Projects on Docker
Moses Openja
Forough Majidi
Foutse Khomh
Bhagya Chembakottu
Heng Li
2022-06-13
The International Conference on Evaluation and Assessment in Software Engineering 2022 (published)
doi.org
arxiv.org
A Unified Approach to Reinforcement Learning, Quantal Response Equilibria, and Two-Player Zero-Sum Games
Samuel Sokota
Ryan D’orazio
J. Z. Kolter
Nicolas Loizou
Marc Lanctot
Ioannis Mitliagkas
Noam Brown
Christian Kroer
This work studies an algorithm, which we call magnetic mirror descent, that is inspired by mirror descent and the non-Euclidean proximal gra… (see more)dient algorithm. Our contribution is demonstrating the virtues of magnetic mirror descent as both an equilibrium solver and as an approach to reinforcement learning in two-player zero-sum games. These virtues include: 1) Being the first quantal response equilibria solver to achieve linear convergence for extensive-form games with first order feedback; 2) Being the first standard reinforcement learning algorithm to achieve empirically competitive results with CFR in tabular settings; 3) Achieving favorable performance in 3x3 Dark Hex and Phantom Tic-Tac-Toe as a self-play deep reinforcement learning algorithm.
2022-06-12
ArXiv (preprint)
doi.org
arxiv.org
Leveraging Integer Linear Programming to Learn Optimal Fair Rule Lists
Ulrich Aivodji
Julien Ferry
Sébastien Gambs
Marie-José Huguet
Mohamed
Siala
2022-06-10
Integration of Constraint Programming, Artificial Intelligence, and Operations Research (published)
doi.org
On Neural Architecture Inductive Biases for Relational Tasks
Giancarlo Kerg
Sarthak Mittal
David Rolnick
Yoshua Bengio
Blake Richards
Guillaume Lajoie
Current deep learning approaches have shown good in-distribution generalization performance, but struggle with out-of-distribution generaliz… (see more)ation. This is especially true in the case of tasks involving abstract relations like recognizing rules in sequences, as we find in many intelligence tests. Recent work has explored how forcing relational representations to remain distinct from sensory representations, as it seems to be the case in the brain, can help artificial systems. Building on this work, we further explore and formalize the advantages afforded by 'partitioned' representations of relations and sensory details, and how this inductive bias can help recompose learned relational structure in newly encountered settings. We introduce a simple architecture based on similarity scores which we name Compositional Relational Network (CoRelNet). Using this model, we investigate a series of inductive biases that ensure abstract relations are learned and represented distinctly from sensory data, and explore their effects on out-of-distribution generalization for a series of relational psychophysics tasks. We find that simple architectural choices can outperform existing models in out-of-distribution generalization. Together, these results show that partitioning relational representations from other information streams may be a simple way to augment existing network architectures' robustness when performing out-of-distribution relational computations.
2022-06-09
ArXiv (preprint)
doi.org
arxiv.org
Few-shot Question Generation for Personalized Feedback in Intelligent Tutoring Systems
Devang Kulshreshtha
Muhammad Shayan
Robert Belfer
Siva Reddy
Iulian V. Serban
Ekaterina Kochmar
2022-06-08
ArXiv (preprint)
doi.org
arxiv.org
Sequential Density Estimation via NCWFAs Sequential Density Estimation via Nonlinear Continuous Weighted Finite Automata
Tianyu Li
Bogdan Mazoure
Guillaume Rabusseau
Weighted finite automata (WFAs) have been widely applied in many fields. One of the classic problems for WFAs is probability distribution es… (see more)timation over sequences of discrete symbols. Although WFAs have been extended to deal with continuous input data, namely continuous WFAs (CWFAs), it is still unclear how to approximate density functions over sequences of continuous random variables using WFA-based models, due to the limitation on the expressiveness of the model as well as the tractability of approximating density functions via CWFAs. In this paper, we propose a nonlinear extension to the CWFA model to first improve its expressiveness, we refer to it as the nonlinear continuous WFAs (NCWFAs). Then we leverage the so-called RNADE method, which is a well-known density estimator based on neural networks, and propose the RNADE-NCWFA model. The RNADE-NCWFA model computes a density function by design. We show that this model is strictly more expressive than the Gaussian HMM model, which CWFA cannot approximate. Empirically, we conduct a synthetic experiment using Gaussian HMM generated data. We focus on evaluating the model's ability to estimate densities for sequences of varying lengths (longer length than the training data). We observe that our model performs the best among the compared baseline methods.
2022-06-08
ArXiv (preprint)
doi.org
arxiv.org
Interacting brains revisited: A cross‐brain network neuroscience perspective
Christian Gerloff
Kerstin Konrad
Danilo Bzdok
Christina Büsing
Vanessa Reindl
2022-06-06
Human Brain Mapping (published)
doi.org