Publications

Studying the challenges of developing hardware description language programs
Fatemeh Yousefifeshki
Heng Li
Foutse Khomh
2023-07-01
Information and Software Technology (published)
doi.org
EuclidNets: An Alternative Operation for Efficient Inference of Deep Learning Models
Xinlin Li
Mariana Parazeres
Adam M. Oberman
Alireza Ghaffari
Masoud Asgharian
Vahid Nia
2023-06-30
SN Computer Science (published)
doi.org
arxiv.org
Generalization Limits of Graph Neural Networks in Identity Effects Learning
Giuseppe Alessio D'inverno
Simone Brugiapaglia
Mirco Ravanelli
Graph Neural Networks (GNNs) have emerged as a powerful tool for data-driven learning on various graph domains. They are usually based on a … (see more)message-passing mechanism and have gained increasing popularity for their intuitive formulation, which is closely linked to the Weisfeiler-Lehman (WL) test for graph isomorphism to which they have been proven equivalent in terms of expressive power. In this work, we establish new generalization properties and fundamental limits of GNNs in the context of learning so-called identity effects, i.e., the task of determining whether an object is composed of two identical components or not. Our study is motivated by the need to understand the capabilities of GNNs when performing simple cognitive tasks, with potential applications in computational linguistics and chemistry. We analyze two case studies: (i) two-letters words, for which we show that GNNs trained via stochastic gradient descent are unable to generalize to unseen letters when utilizing orthogonal encodings like one-hot representations; (ii) dicyclic graphs, i.e., graphs composed of two cycles, for which we present positive existence results leveraging the connection between GNNs and the WL test. Our theoretical analysis is supported by an extensive numerical study.
2023-06-30
ArXiv (preprint)
doi.org
arxiv.org
Reference panel-guided super-resolution inference of Hi-C data
Yanlin Zhang
Mathieu Blanchette
Abstract Motivation Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding… (see more) the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types. Results Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains. Availability and implementation https://github.com/BlanchetteLab/RefHiC.
2023-06-30
Bioinformatics (published)
doi.org
Should We Feed the Trolls? Using Marketer-Generated Content to Explain Average Toxicity and Product Usage
Marcelo Vinhal Nepomuceno
Hooman Rahemi
Tolga Cenesizoglu
Laurent Charlin
2023-06-29
Journal of Interactive Marketing (published)
doi.org
Cortico-Cerebellar neurodynamics during social interaction in Autism Spectrum Disorders
Fleur Gaudfernau
Aline Lefebvre
Denis-Alexander Engemann
Amandine Pedoux
Anna Bánki
Florence Baillin
Benjamin Landman
Frederique Amsellem
Anna Maruani
Thomas Bourgeron
Richard Delorme
Guillaume Dumas
2023-06-28
NeuroImage : Clinical (published)
doi.org
On the Identifiability of Quantized Factors
Vitória Barin Pacela
Kartik Ahuja
Simon Lacoste-Julien
Pascal Vincent
Disentanglement aims to recover meaningful latent ground-truth factors from the observed distribution solely, and is formalized through the … (see more)theory of identifiability. The identifiability of independent latent factors is proven to be impossible in the unsupervised i.i.d. setting under a general nonlinear map from factors to observations. In this work, however, we demonstrate that it is possible to recover quantized latent factors under a generic nonlinear diffeomorphism. We only assume that the latent factors have independent discontinuities in their density, without requiring the factors to be statistically independent. We introduce this novel form of identifiability, termed quantized factor identifiability, and provide a comprehensive proof of the recovery of the quantized factors.
2023-06-28
ArXiv (preprint)
arxiv.org
arxiv.org
Pixelated Reconstruction of Foreground Density and Background Surface Brightness in Gravitational Lensing Systems Using Recurrent Inference Machines
Alexandre Adam
Laurence Perreault-Levasseur
Yashar Hezaveh
Max Welling
Modeling strong gravitational lenses in order to quantify distortions in the images of background sources and to reconstruct the mass densit… (see more)y in foreground lenses has been a difficult computational challenge. As the quality of gravitational lens images increases, the task of fully exploiting the information they contain becomes computationally and algorithmically more difficult. In this work, we use a neural network based on the recurrent inference machine to reconstruct simultaneously an undistorted image of the background source and the lens mass density distribution as pixelated maps. The method iteratively reconstructs the model parameters (the image of the source and a pixelated density map) by learning the process of optimizing the likelihood given the data using the physical model (a ray-tracing simulation), regularized by a prior implicitly learned by the neural network through its training data. When compared to more traditional parametric models, the proposed method is significantly more expressive and can reconstruct complex mass distributions, which we demonstrate by using realistic lensing galaxies taken from the IllustrisTNG cosmological hydrodynamic simulation.
2023-06-27
The Astrophysical Journal (published)
doi.org
arxiv.org
Adaptive Discrete Communication Bottlenecks with Dynamic Vector Quantization
Dianbo Liu
Alex Lamb
Xu Ji
Pascal Notsawo
Michael Curtis Mozer
Yoshua Bengio
Kenji Kawaguchi
2023-06-26
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org
arxiv.org
Hypernetworks for Zero-shot Transfer in Reinforcement Learning
Sahand Rezaei-Shoshtari
Charlotte Morissette
Francois Hogan
Gregory Dudek
David Meger
In this paper, hypernetworks are trained to generate behaviors across a range of unseen task conditions, via a novel TD-based training objec… (see more)tive and data from a set of near-optimal RL solutions for training tasks. This work relates to meta RL, contextual RL, and transfer learning, with a particular focus on zero-shot performance at test time, enabled by knowledge of the task parameters (also known as context). Our technical approach is based upon viewing each RL algorithm as a mapping from the MDP specifics to the near-optimal value function and policy and seek to approximate it with a hypernetwork that can generate near-optimal value functions and policies, given the parameters of the MDP. We show that, under certain conditions, this mapping can be considered as a supervised learning problem. We empirically evaluate the effectiveness of our method for zero-shot transfer to new reward and transition dynamics on a series of continuous control tasks from DeepMind Control Suite. Our method demonstrates significant improvements over baselines from multitask and meta RL approaches.
2023-06-26
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org
arxiv.org
Latent Space Evolution under Incremental Learning with Concept Drift (Student Abstract)
Charles Bourbeau
Audrey Durand
This work investigates the evolution of latent space when deep learning models are trained incrementally in non-stationary environments that… (see more) stem from concept drift. We propose a methodology for visualizing the incurred change in latent representations. We further show that classes not targeted by concept drift can be negatively affected, suggesting that the observation of all classes during learning may regularize the latent space.
2023-06-26
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org
Signed Laplacian Graph Neural Networks
Yu Li
Meng Qu
Jian Tang
Yi Chang
2023-06-26
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org