Publications

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.
2023-06-29
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
2023-06-28
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
2023-06-27
NeuroImage : Clinical (published)
doi.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 the distortions in the images of background sources and to reconstruct the mass de… (see more)nsity in the 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 (RIM) to simultaneously reconstruct 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.
2023-06-26
The Astrophysical Journal (published)
doi.org
arxiv.org
Adaptive Discrete Communication Bottlenecks with Dynamic Vector Quantization for Heterogeneous Representational Coarseness
Dianbo Liu
Alex Lamb
Xu Ji
Pascal Junior Tikeng Notsawo
Michael Mozer
Yoshua Bengio
Kenji Kawaguchi
Vector Quantization (VQ) is a method for discretizing latent representations and has become a major part of the deep learning toolkit. It ha… (see more)s been theoretically and empirically shown that discretization of representations leads to improved generalization, including in reinforcement learning where discretization can be used to bottleneck multi-agent communication to promote agent specialization and robustness. The discretization tightness of most VQ-based methods is defined by the number of discrete codes in the representation vector and the codebook size, which are fixed as hyperparameters. In this work, we propose learning to dynamically select discretization tightness conditioned on inputs, based on the hypothesis that data naturally contains variations in complexity that call for different levels of representational coarseness which is observed in many heterogeneous data sets. We show that dynamically varying tightness in communication bottlenecks can improve model performance on visual reasoning and reinforcement learning tasks with heterogeneity in representations.
2023-06-25
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 R. 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.
2023-06-25
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.
2023-06-25
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org
Signed Laplacian Graph Neural Networks
Yu Li
Meng Qu
Jian Tang
Yi Chang
This paper studies learning meaningful node representations for signed graphs, where both positive and negative links exist. This problem ha… (see more)s been widely studied by meticulously designing expressive signed graph neural networks, as well as capturing the structural information of the signed graph through traditional structure decomposition methods, e.g., spectral graph theory. In this paper, we propose a novel signed graph representation learning framework, called Signed Laplacian Graph Neural Network (SLGNN), which combines the advantages of both. Specifically, based on spectral graph theory and graph signal processing, we first design different low-pass and high-pass graph convolution filters to extract low-frequency and high-frequency information on positive and negative links, respectively, and then combine them into a unified message passing framework. To effectively model signed graphs, we further propose a self-gating mechanism to estimate the impacts of low-frequency and high-frequency information during message passing. We mathematically establish the relationship between the aggregation process in SLGNN and signed Laplacian regularization in signed graphs, and theoretically analyze the expressiveness of SLGNN. Experimental results demonstrate that SLGNN outperforms various competitive baselines and achieves state-of-the-art performance.
2023-06-25
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org
The Effect of Diversity in Meta-Learning
Ramnath Kumar
Tristan Deleu
Yoshua Bengio
Recent studies show that task distribution plays a vital role in the meta-learner's performance. Conventional wisdom is that task diversity … (see more)should improve the performance of meta-learning. In this work, we find evidence to the contrary; (i) our experiments draw into question the efficacy of our learned models: similar manifolds can be learned with a subset of the data (lower task diversity). This finding questions the advantage of providing more data to the model, and (ii) adding diversity to the task distribution (higher task diversity) sometimes hinders the model and does not lead to a significant improvement in performance as previously believed. To strengthen our findings, we provide both empirical and theoretical evidence.
2023-06-25
Proceedings of the AAAI Conference on Artificial Intelligence (published)
doi.org
openreview.net
Partial Ordered Statistics Decoding with Enhanced Error Patterns
Marwan Jalaleddine
Huayi Zhou
Jiajie Li
Warren J. Gross
Guessing Random Additive Noise Decoding (GRAND) excels at decoding high-rate codes but struggles to decode low-rate codes with reasonable co… (see more)mplexity. Ordered Statistics Decoding (OSD) specifically excels in decoding short codes irrespective of rates; however, OSD necessitates the use of Gaussian elimination which introduces additional time, space and computational complexity. Partial Ordered Statistics Decoding (POSD) was proposed to reduce the time, space, and computational complexity of OSD; however, the current partition-based POSD has poor decoding performance since it does not generate test error patterns across partitions. In this paper, we propose to improve the decoding performance of POSD by incorporating test error patterns inspired by GRAND methods. This work offers a trade-off between performance and complexity compared to existing decoders such as GRAND and OSD. We enhance POSD by optimizing the scheduling of Test Error Patterns (TEPs) and show that our technique can be applied to any code in a standard form. At a target BER 10−4 with eBCH (128,64) the enhanced error patterns achieve more than 0.6 dB gain in performance compared to the POSD with partition-based error patterns. Moreover, at a target frame error rate of 10−5, POSD uses 10× less binary operations compared to GRAND when decoding eBCH (128,64) and RLC(128,64) codes. With BCH (127,29) and RLC(128,32), at a target frame error rate of 10−2, POSD with enhanced error patterns with a maximum number of queries (MQ) of 104 achieves up to a 2 dB gain to its GRAND equivalent which is using 107 maximum number of queries.
2023-06-24
2023 IEEE International Symposium on Information Theory (ISIT) (published)
doi.org
CeBed: A Benchmark for Deep Data-Driven OFDM Channel Estimation
Amal Feriani
Di Wu
Steve Liu
Gregory Dudek
2023-06-22
ArXiv (preprint)
doi.org
arxiv.org
Goal-conditioned GFlowNets for Controllable Multi-Objective Molecular Design
Julien Roy
Pierre-Luc Bacon
Christopher Pal
Emmanuel Bengio
In recent years, in-silico molecular design has received much attention from the machine learning community. When designing a new compound f… (see more)or pharmaceutical applications, there are usually multiple properties of such molecules that need to be optimised: binding energy to the target, synthesizability, toxicity, EC50, and so on. While previous approaches have employed a scalarization scheme to turn the multi-objective problem into a preference-conditioned single objective, it has been established that this kind of reduction may produce solutions that tend to slide towards the extreme points of the objective space when presented with a problem that exhibits a concave Pareto front. In this work we experiment with an alternative formulation of goal-conditioned molecular generation to obtain a more controllable conditional model that can uniformly explore solutions along the entire Pareto front.
2023-06-22
ICML.cc/2023/Workshop/DeployableGenerativeAI (published)
doi.org
openreview.net