Publications

PERFUMES: pipeline to extract RNA functional motifs and exposed structures
Arnaud Chol
Roman Sarrazin-Gendron
Éric Lécuyer
Jérôme Waldispühl
Abstract Motivation Up to 75% of the human genome encodes RNAs. The function of many non-coding RNAs relies on their ability to fold into 3D… (see more) structures. Specifically, nucleotides inside secondary structure loops form non-canonical base pairs that help stabilize complex local 3D structures. These RNA 3D motifs can promote specific interactions with other molecules or serve as catalytic sites. Results We introduce PERFUMES, a computational pipeline to identify 3D motifs that can be associated with observable features. Given a set of RNA sequences with associated binary experimental measurements, PERFUMES searches for RNA 3D motifs using BayesPairing2 and extracts those that are over-represented in the set of positive sequences. It also conducts a thermodynamics analysis of the structural context that can support the interpretation of the predictions. We illustrate PERFUMES’ usage on the SNRPA protein binding site, for which the tool retrieved both previously known binder motifs and new ones. Availability and implementation PERFUMES is an open-source Python package (https://jwgitlab.cs.mcgill.ca/arnaud_chol/perfumes).
The Effects of a Digital Game Simulator versus a Traditional Intervention on Paramedics’ Neonatal Resuscitation Performance
Georg M. Schmölzer
Unsupervised Discovery of Steerable Factors When Graph Deep Generative Models Are Entangled
Chengpeng Wang
Weili Nie
Hanchen Wang
Zhuoxinran Li
Bolei Zhou
Asymmetric stimulus representations bias visual perceptual learning
Pooya Laamerad
Asmara Awada
Christopher C. Pack
The primate visual cortex contains various regions that exhibit specialization for different stimulus properties, such as motion, shape, and… (see more) color. Within each region, there is often further specialization, such that particular stimulus features, such as horizontal and vertical orientations, are over-represented. These asymmetries are associated with well-known perceptual biases, but little is known about how they influence visual learning. Most theories would predict that learning is optimal, in the sense that it is unaffected by these asymmetries. However, other approaches to learning would result in specific patterns of perceptual biases. To distinguish between these possibilities, we trained human observers to discriminate between expanding and contracting motion patterns, which have a highly asymmetrical representation in the visual cortex. Observers exhibited biased percepts of these stimuli, and these biases were affected by training in ways that were often suboptimal. We simulated different neural network models and found that a learning rule that involved only adjustments to decision criteria, rather than connection weights, could account for our data. These results suggest that cortical asymmetries influence visual perception and that human observers often rely on suboptimal strategies for learning.
A comparison of RL-based and PID controllers for 6-DOF swimming robots: hybrid underwater object tracking
Faraz Lotfi
Khalil Virji
Nicholas Dudek
Protocol for fever control using external cooling in mechanically ventilated patients with septic shock: SEPSISCOOL II randomised controlled trial
Armelle Guénégou-Arnoux
Juliette Murris
Stéphane Bechet
Camille Jung
Johann Auchabie
Julien Dupeyrat
Nadia Anguel
Pierre Asfar
Julio Badie
Dorothée Carpentier
Benjamin Chousterman
Jeremy Bourenne
Agathe Delbove
Jérôme Devaquet
Nicolas Deye
Anne-Florence Dureau
Jean-Baptiste Lascarrou
Stephane Legriel
Christophe Guitton … (see 14 more)
Caroline Jannière-Nartey
Jean-Pierre Quenot
Jean-Claude Lacherade
Julien Maizel
Armand Mekontso Dessap
Bruno Mourvillier
Philippe Petua
Gaetan Plantefeve
Jean-Christophe Richard
Alexandre Robert
Clément Saccheri
Ly Van Phach Vong
Sandrine Katsahian
Frédérique Schortgen
Trait‐matching models predict pairwise interactions across regions, not food web properties
Dominique Caron
Ulrich Brose
Miguel Lurgi
F. Guillaume Blanchet
Dominique Gravel
Efficient Data-Driven MPC for Demand Response of Commercial Buildings
Marie-Christine Par'e
Vasken Dermardiros
Model predictive control (MPC) has been shown to significantly improve the energy efficiency of buildings while maintaining thermal comfort.… (see more) Data-driven approaches based on neural networks have been proposed to facilitate system modelling. However, such approaches are generally nonconvex and result in computationally intractable optimization problems. In this work, we design a readily implementable energy management method for small commercial buildings. We then leverage our approach to formulate a real-time demand bidding strategy. We propose a data-driven and mixed-integer convex MPC which is solved via derivative-free optimization given a limited computational time of 5 minutes to respect operational constraints. We consider rooftop unit heating, ventilation, and air conditioning systems with discrete controls to accurately model the operation of most commercial buildings. Our approach uses an input convex recurrent neural network to model the thermal dynamics. We apply our approach in several demand response (DR) settings, including a demand bidding, a time-of-use, and a critical peak rebate program. Controller performance is evaluated on a state-of-the-art building simulation. The proposed approach improves thermal comfort while reducing energy consumption and cost through DR participation, when compared to other data-driven approaches or a set-point controller.
Graphylo: A deep learning approach for predicting regulatory DNA and RNA sites from whole-genome multiple alignments
Dongjoon Lim
Changhyun Baek
Human-Centered AI
Jean-Louis Denis
Maria Luciana Axente
Atsuo Kishimoto
Neighbor-Aware Calibration of Segmentation Networks with Penalty-Based Constraints
Balamurali Murugesan
Bingyuan Liu
Ismail Ben Ayed
Jose Dolz
Ensuring reliable confidence scores from deep neural networks is of paramount significance in critical decision-making systems, particularly… (see more) in real-world domains such as healthcare. Recent literature on calibrating deep segmentation networks has resulted in substantial progress. Nevertheless, these approaches are strongly inspired by the advancements in classification tasks, and thus their uncertainty is usually modeled by leveraging the information of individual pixels, disregarding the local structure of the object of interest. Indeed, only the recent Spatially Varying Label Smoothing (SVLS) approach considers pixel spatial relationships across classes, by softening the pixel label assignments with a discrete spatial Gaussian kernel. In this work, we first present a constrained optimization perspective of SVLS and demonstrate that it enforces an implicit constraint on soft class proportions of surrounding pixels. Furthermore, our analysis shows that SVLS lacks a mechanism to balance the contribution of the constraint with the primary objective, potentially hindering the optimization process. Based on these observations, we propose NACL (Neighbor Aware CaLibration), a principled and simple solution based on equality constraints on the logit values, which enables to control explicitly both the enforced constraint and the weight of the penalty, offering more flexibility. Comprehensive experiments on a wide variety of well-known segmentation benchmarks demonstrate the superior calibration performance of the proposed approach, without affecting its discriminative power. Furthermore, ablation studies empirically show the model agnostic nature of our approach, which can be used to train a wide span of deep segmentation networks.
Marc Bellemare
Bellemare Marc-Emmanuel