Publications

Deep interpretability for GWAS
Deepak Sharma
Audrey Durand
Marc-Andr Legault
Louis-Philippe Lemieux Perreault
Audrey Lemaon
Marie-Pierre Dub
Joelle Pineau
Genome-Wide Association Studies are typically conducted using linear models to find genetic variants associated with common diseases. In the… (see more)se studies, association testing is done on a variant-by-variant basis, possibly missing out on non-linear interaction effects between variants. Deep networks can be used to model these interactions, but they are difficult to train and interpret on large genetic datasets. We propose a method that uses the gradient based deep interpretability technique named DeepLIFT to show that known diabetes genetic risk factors can be identified using deep models along with possibly novel associations.
2019-12-31
arXiv (preprint)
doi.org
arxiv.org
Differentiable Causal Discovery from Interventional Data
Philippe Brouillard
Sébastien Lachapelle
Alexandre Lacoste
Simon Lacoste-Julien
Alexandre Drouin
Learning a causal directed acyclic graph from data is a challenging task that involves solving a combinatorial problem for which the solutio… (see more)n is not always identifiable. A new line of work reformulates this problem as a continuous constrained optimization one, which is solved via the augmented Lagrangian method. However, most methods based on this idea do not make use of interventional data, which can significantly alleviate identifiability issues. This work constitutes a new step in this direction by proposing a theoretically-grounded method based on neural networks that can leverage interventional data. We illustrate the flexibility of the continuous-constrained framework by taking advantage of expressive neural architectures such as normalizing flows. We show that our approach compares favorably to the state of the art in a variety of settings, including perfect and imperfect interventions for which the targeted nodes may even be unknown.
2019-12-31
NeurIPS (published)
doi.org
arxiv.org
A Distributional Analysis of Sampling-Based Reinforcement Learning Algorithms
Philip Amortila
Doina Precup
Prakash Panangaden
Bellemare Marc-Emmanuel
We present a distributional approach to theoretical analyses of reinforcement learning algorithms for constant step-sizes. We demonstrate it… (see more)s effectiveness by presenting simple and unified proofs of convergence for a variety of commonly-used methods. We show that value-based methods such as TD(
2019-12-31
AISTATS (published)
doi.org
proceedings.mlr.press
Divergent protein-coding genes and brain size in primates
Malesys Bourgeron Dumas
Guillaume Dumas
Simon Malesys
Thomas Bourgeron
17 The human brain differs from that of other primates, but the genetic basis of these differences 18 remains unclear. We investigated the e… (see more)volutionary pressures acting on almost all human 19 protein-coding genes ( N =11,667; 1:1 orthologs in primates) on the basis of their divergence 20 from those of early hominins, such as Neanderthals, and non-human primates. We confirm 21 that genes encoding brain-related proteins are among the most strongly conserved protein- 22 coding genes in the human genome. Combining our evolutionary pressure metrics for the 23 protein-coding genome with recent datasets, we found that this conservation applied to genes 24 functionally associated with the synapse and expressed in brain structures such as the 25 prefrontal cortex and the cerebellum. Conversely, several of the protein-coding genes that 26 diverge most in hominins relative to other primates are associated with brain-associated 27 diseases, such as micro/macrocephaly, dyslexia, and autism. We also showed that cerebellum 28 granule neurons express a set of divergent protein-coding genes that may have contributed to 29 the emergence of fine motor skills and social cognition in humans. This resource is available 30 from http://neanderthal.pasteur.fr and can be used to estimate evolutionary constraints acting 31 on a set of genes and to explore their relative contributions to human traits. 32
2019-12-31
(published)
www.semanticscholar.org
On Efficiency in Hierarchical Reinforcement Learning
Zheng Wen
Doina Precup
Morteza Ibrahimi
Andre Barreto
Benjamin Van Roy
Satinder Singh
Hierarchical Reinforcement Learning (HRL) approaches promise to provide more efficient solutions to sequential decision making problems, bo… (see more)th in terms of statistical as well as computational efficiency. While this has been demonstrated empirically over time in a variety of tasks, theoretical results quantifying the ben-efits of such methods are still few and far between. In this paper, we discuss the kind of structure in a Markov decision process which gives rise to efficient HRL methods. Specifically, we formalize the intuition that HRL can exploit well repeating "subMDPs", with similar reward and transition structure. We show that, under reasonable assumptions, a model-based Thompson sampling-style HRL algorithm that exploits this structure is statistically efficient, as established through a finite-time regret bound. We also establish conditions under which planning with structure-induced options is near-optimal and computationally efficient.
2019-12-31
Advances in Neural Information Processing Systems 33 (NeurIPS 2020) (published)
dblp.uni-trier.de
Efficient Planning under Partial Observability with Unnormalized Q Functions and Spectral Learning
Tianyu Li
Bogdan Mazoure
Doina Precup
Guillaume Rabusseau
2019-12-31
International Conference on Artificial Intelligence and Statistics (published)
doi.org
proceedings.mlr.press
Electric Vehicles Equilibrium Model that Considers Queue Delay and Mixed Traffic
Nurit Oliker
Miguel F. Anjos
Margarida Carvalho
Emma Frejinger
Bernard Gendron
This study develops an equilibrium model for electric vehicles (EVs) that considers both queue delays in charging stations and flow dependen… (see more)t travel times. This is a user equilibrium model that accounts for travel, charging and queuing time in the path choice modelling of EVs and the complementary traffic. Waiting and service times in charging stations are represented by an m/m/k queuing system. The model considers multiple vehicle and driver classes, expressing different battery capacity, initial charge state and range anxiety level. Feasible paths are found for multiple classes given their limited travel range. A numerical application exemplifies the limitations of EVs assignment and their impact on flow distribution.
2019-12-31
(published)
www.semanticscholar.org
AN ENSEMBLE APPROACH FOR DETECTING MACHINE FAILURE FROM SOUND Technical
Faruk Ahmed
Phong Cao Nguyen
Aaron Courville
We develop an ensemble-based approach for our submission to the anomaly detection challenge at DCASE 2020. The main members of our ensemble … (see more)are auto-encoders (with reconstruction error as the signal), classifiers (with negative predictive confidence as the signal), mismatch of the time-shifted signal with its Fourier-phase-shifted version, and a Gaussian mixture model on a set of common short-term features extracted from the waveform. The scores are passed through an exponential non-linearity and weighted to provide the final score, where the weighting and scaling hyper-parameters are learned on the development set. Our ensemble improves over the baseline on the development set.
2019-12-31
(published)
www.semanticscholar.org
An Equivalence between Loss Functions and Non-Uniform Sampling in Experience Replay
Scott Fujimoto
David Meger
Doina Precup
Prioritized Experience Replay (PER) is a deep reinforcement learning technique in which agents learn from transitions sampled with non-unifo… (see more)rm probability proportionate to their temporal-difference error. We show that any loss function evaluated with non-uniformly sampled data can be transformed into another uniformly sampled loss function with the same expected gradient. Surprisingly, we find in some environments PER can be replaced entirely by this new loss function without impact to empirical performance. Furthermore, this relationship suggests a new branch of improvements to PER by correcting its uniformly sampled loss function equivalent. We demonstrate the effectiveness of our proposed modifications to PER and the equivalent loss function in several MuJoCo and Atari environments.
2019-12-31
Advances in Neural Information Processing Systems 33 (NeurIPS 2020) (published)
doi.org
arxiv.org
Equivariant Maps for Hierarchical Structures
Renhao Wang
Marjan Albooyeh
Siamak Ravanbakhsh
2019-12-31
Advances in Neural Information Processing Systems 33 (NeurIPS 2020) (published)
dblp.uni-trier.de
Expressiveness and Learning of Hidden Quantum Markov Models
Sandesh M. Adhikary
Siddarth Srinivasan
Geoff Gordon
Byron Boots
Extending classical probabilistic reasoning using the quantum mechanical view of probability has been of recent interest, particularly in th… (see more)e development of hidden quantum Markov models (HQMMs) to model stochastic processes. However, there has been little progress in characterizing the expressiveness of such models and learning them from data. We tackle these problems by showing that HQMMs are a special subclass of the general class of observable operator models (OOMs) that do not suffer from the \emph{negative probability problem} by design. We also provide a feasible retraction-based learning algorithm for HQMMs using constrained gradient descent on the Stiefel manifold of model parameters. We demonstrate that this approach is faster and scales to larger models than previous learning algorithms.
2019-12-31
AISTATS (published)
proceedings.mlr.press
proceedings.mlr.press
Fairness in Kidney Exchange Programs through Optimal Solutions Enumeration
Golnoosh Farnadi
Behrouz Babaki
Margarida Carvalho
Not all patients who need kidney transplant can find a donor with compatible characteristics. Kidney exchange programs (KEPs) seek to match … (see more)such incompatible patient-donor pairs together, usually with the objective of maximizing the total number of transplants. We propose a randomized policy for selecting an optimal solution in which patients’ equity of opportunity to receive a transplant is promoted. Our approach gives rise to the problem of enumerating all optimal solutions, which we tackle using a hybrid of constraint programming and linear programming. We empirically demonstrate the advantages of our proposed method over the common practice of using the first optimal solution obtained by a solver.
2019-12-31
(published)
www.semanticscholar.org