Publications

Exploring the roles of artificial intelligence in surgical education: A scoping review.
Elif Bilgic
Andrew Gorgy
Alison Yang
Michelle Cwintal
Hamed Ranjbar
Kalin Kahla
Dheeksha Reddy
Kexin Li
Helin Ozturk
Eric Zimmermann
Andrea Quaiattini
Samira Abbasgholizadeh-Rahimi
Dan Poenaru
Jason M. Harley
2021-11-30
American Journal of Surgery (published)
doi.org
Hypo- and hyper- sensory processing heterogeneity in Autism Spectrum Disorder
Aline Lefebvre
Julian Tillmann
Freddy Cliquet
Frederique Amsellem
Anna Maruani
Claire Leblond
Anita Beggiato
David Germanaud
Anouck Amestoy
Myriam Ly‐Le Moal
Daniel Umbricht
Christopher Chattam
Lorraine Murtagh
Manuel Bouvard
Marion Leboyer
Tony Charman
Thomas Bourgeron
Richard Delorme
Guillaume Dumas
Background. Sensory processing atypicalities are part of the core symptoms of autism spectrum disorder (ASD) and could result from an excita… (voir plus)tion/inhibition imbalance. Yet, the convergence level of phenotypic sensory processing atypicalities with genetic alterations in GABA-ergic and glutamatergic pathways remains poorly understood. This study aimed to characterize the distribution of hypo/hyper-sensory profile among individuals with ASD and investigate the role of deleterious mutations in GABAergic and glutamatergic pathways related genes in sensory processing atypicalities. Method. From the Short Sensory Profile (SSP) questionnaire, we defined and explored a score – the differential Short Sensory Profile (dSSP) - as a normalized and centralized hypo/hypersensitivity ratio for 1136 participants (533 with ASD, 210 first-degree relatives, and 267 controls) from two independent study samples (PARIS and LEAP). We also performed an unsupervised item-based clustering analysis on SSP items scores to validate this new categorization in terms of hypo and hyper sensitivity. We then explored the link between the dSSP score and the burden of deleterious mutations in a subset of individuals for which whole-genome sequencing data were available. Results. We observed a mean dSSP score difference between ASD and controls, driven mostly by a high dSSP score variability among groups (PARIS: p0.0001, η2 = 0.0001, LEAP: p0.0001, Cohen’s d=3.67). First-degree relatives were with an intermediate distribution variability prof
2021-11-30
(publié)
doi.org
Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators
Alexander Tong
Guy Wolf
Smita Krishnaswamy
Anomaly detection is of great interest in fields where abnormalities need to be identified and corrected (e.g., medicine and finance). Deep … (voir plus)learning methods for this task often rely on autoencoder reconstruction error, sometimes in conjunction with other penalties. We show that this approach exhibits intrinsic biases that lead to undesirable results. Reconstruction-based methods can sometimes show low error on simple-to-reconstruct points that are not part of the training data, for example the all black image. Instead, we introduce a new unsupervised Lipschitz anomaly discriminator (LAD) that does not suffer from these biases. Our anomaly discriminator is trained, similar to the discriminator of a GAN, to detect the difference between the training data and corruptions of the training data. We show that this procedure successfully detects unseen anomalies with guarantees on those that have a certain Wasserstein distance from the data or corrupted training set. These additions allow us to show improved performance on MNIST, CIFAR10, and health record data. Further, LAD does not require decoding back to the original data space, which makes anomaly detection possible in domains where it is difficult to define a decoder, such as in irregular graph structured data. Empirically, we show this framework leads to improved performance on image, health record, and graph data.
2021-11-28
Journal of Signal Processing Systems (publié)
doi.org
Processing visual ambiguity in fractal patterns: Pareidolia as a sign of creativity
Antoine Bellemare
Yann Harel
Jordan O’Byrne
Genevieve A. Mageau
Arne Dietrich
Karim Jerbi
2021-11-28
iScience (published)
doi.org
Medial Spectral Coordinates for 3D Shape Analysis
Morteza Rezanejad
Mohammad Khodadad
H. Mahyar
Hervé Lombaert
M. Gruninger
Dirk. B. Walther
Kaleem Siddiqi
In recent years there has been a resurgence of interest in our community in the shape analysis of 3D objects repre-sented by surface meshes,… (voir plus) their voxelized interiors, or surface point clouds. In part, this interest has been stimulated by the increased availability of RGBD cameras, and by applications of computer vision to autonomous driving, medical imaging, and robotics. In these settings, spectral co-ordinates have shown promise for shape representation due to their ability to incorporate both local and global shape properties in a manner that is qualitatively invariant to iso-metric transformations. Yet, surprisingly, such coordinates have thus far typically considered only local surface positional or derivative information. In the present article, we propose to equip spectral coordinates with medial (object width) information, so as to enrich them. The key idea is to couple surface points that share a medial ball, via the weights of the adjacency matrix. We develop a spectral feature using this idea, and the algorithms to compute it. The incorporation of object width and medial coupling has direct benefits, as illustrated by our experiments on object classification, object part segmentation, and surface point correspondence.
2021-11-26
ArXiv (preprint)
doi.org
arxiv.org
Multi-label Iterated Learning for Image Classification with Label Ambiguity
Sai Rajeswar
Pau Rodriguez
Soumye Singhal
David Vazquez
Aaron Courville
Transfer learning from large-scale pre-trained models has become essential for many computer vision tasks. Recent studies have shown that da… (voir plus)tasets like ImageNet are weakly labeled since images with multiple object classes present are assigned a single label. This ambiguity biases models towards a single prediction, which could result in the suppression of classes that tend to co-occur in the data. Inspired by language emergence literature, we propose multi-label iterated learning (MILe) to incorporate the inductive biases of multi-label learning from single labels using the framework of iterated learning. MILe is a simple yet effective procedure that builds a multi-label description of the image by propagating binary predictions through successive generations of teacher and student networks with a learning bottleneck. Experiments show that our approach exhibits systematic benefits on ImageNet accuracy as well as ReaL F1 score, which indicates that MILe deals better with label ambiguity than the standard training procedure, even when fine-tuning from self-supervised weights. We also show that MILe is effective reducing label noise, achieving state-of-the-art performance on real-world large-scale noisy data such as WebVision. Furthermore, MILe improves performance in class incremental settings such as IIRC and it is robust to distribution shifts. Code: https://github.com/rajeswar18/MILe
2021-11-23
ArXiv (preprint)
doi.org
arxiv.org
The meaning of significant mean group differences for biomarker discovery
Eva Loth
Jumana Ahmad
Christopher H. Chatham
Beatriz López
Ben Carter
Daisy Crawley
Beth Oakley
Hannah Hayward
Jennifer Cooke
Antonia San José Cáceres
Danilo Bzdok
Emily J. H. Jones
Tony Charman
Christian Beckmann
Thomas Bourgeron
Roberto Toro
Jan K. Buitelaar
Declan Murphy
Guillaume Dumas
2021-11-18
PLoS Computational Biology (publié)
doi.org
Splitting, Renaming, Removing: A Study of Common Cleaning Activities in Jupyter Notebooks
Helen Dong
Shurui Zhou
Jin Guo
Christian Kästner
Data scientists commonly use computational notebooks because they provide a good environment for testing multiple models. However, once the … (voir plus)scientist completes the code and finds the ideal model, he or she will have to dedicate time to clean up the code in order for others to easily understand it. In this paper, we perform a qualitative study on how scientists clean their code in hopes of being able to suggest a tool to automate this process. Our end goal is for tool builders to address possible gaps and provide additional aid to data scientists, who then can focus more on their actual work rather than the routine and tedious cleaning work. By sampling notebooks from GitHub and analyzing changes between subsequent commits, we identified common cleaning activities, such as changes to markdown (e.g., adding headers sections or descriptions) or comments (both deleting dead code and adding descriptions) as well as reordering cells. We also find that common cleaning activities differ depending on the intended purpose of the notebook. Our results provide a valuable foundation for tool builders and notebook users, as many identified cleaning activities could benefit from codification of best practices and dedicated tool support, possibly tailored depending on intended use.
2021-11-15
2021 36th IEEE/ACM International Conference on Automated Software Engineering Workshops (ASEW) (publié)
doi.org
Subtle Bugs Everywhere: Generating Documentation for Data Wrangling Code
Chenyang Yang
Shurui Zhou
Jin Guo
Christian Kästner
Data scientists reportedly spend a significant amount of their time in their daily routines on data wrangling, i.e. cleaning data and extrac… (voir plus)ting features. However, data wrangling code is often repetitive and error-prone to write. Moreover, it is easy to introduce subtle bugs when reusing and adopting existing code, which results in reduced model quality. To support data scientists with data wrangling, we present a technique to generate documentation for data wrangling code. We use (1) program synthesis techniques to automatically summarize data transformations and (2) test case selection techniques to purposefully select representative examples from the data based on execution information collected with tailored dynamic program analysis. We demonstrate that a JupyterLab extension with our technique can provide on-demand documentation for many cells in popular notebooks and find in a user study that users with our plugin are faster and more effective at finding realistic bugs in data wrangling code.
2021-11-15
2021 36th IEEE/ACM International Conference on Automated Software Engineering (ASE) (publié)
doi.org
ZERO: Playing Mathematical Programming Games
Gabriele Dragotto
S. Sankaranarayanan
Margarida Carvalho
Andrea Lodi
2021-11-15
ArXiv (prépublication)
arxiv.org
arxiv.org
OSSEM: one-shot speaker adaptive speech enhancement using meta learning
Cheng Yu
Szu‐wei Fu
Tsun-An Hsieh
Yu-shan 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.
2021-11-10
ArXiv (preprint)
doi.org
arxiv.org
The Cut and Play Algorithm: Computing Nash Equilibria via Outer Approximations
Margarida Carvalho
Gabriele Dragotto
Andrea Lodi
Sriram Sankaranarayanan
We introduce the Cut-and-Play, an efficient algorithm for computing equilibria in simultaneous non-cooperative games where players solve non… (voir plus)convex and possibly unbounded optimization problems. Our algorithm exploits an intrinsic relationship between the equilibria of the original nonconvex game and the ones of a convexified counterpart. In practice, Cut-and-Play formulates a series of convex approximations of the original game and refines them with techniques from integer programming, for instance, cutting planes and branching operations. We test our algorithm on two families of challenging nonconvex games involving discrete decisions and bilevel programs, and we empirically demonstrate that it efficiently computes equilibria and outperforms existing game-specific algorithms.
2021-11-10
ArXiv (prépublication)
arxiv.org
arxiv.org