Publications

Virtual Cells: Predict, Explain, Discover
Emmanuel Noutahi
Jason Hartford
Prudencio Tossou
Shawn Whitfield
Ali Denton
Cas Wognum
Kristina Ulicna
Michael Craig
Jonathan Hsu
Michael Cuccarese
Emmanuel Bengio
Dominique Beaini
Christopher Gibson
Daniel Cohen
Berton Earnshaw
2025-05-01
arXiv (publié)
doi.org
arxiv.org
When to retrain a machine learning model
Florence Regol
Leo Schwinn
Kyle Sprague
Mark Coates
Thomas Markovich
A significant challenge in maintaining real-world machine learning models is responding to the continuous and unpredictable evolution of dat… (voir plus)a. Most practitioners are faced with the difficult question: when should I retrain or update my machine learning model? This seemingly straightforward problem is particularly challenging for three reasons: 1) decisions must be made based on very limited information - we usually have access to only a few examples, 2) the nature, extent, and impact of the distribution shift are unknown, and 3) it involves specifying a cost ratio between retraining and poor performance, which can be hard to characterize. Existing works address certain aspects of this problem, but none offer a comprehensive solution. Distribution shift detection falls short as it cannot account for the cost trade-off; the scarcity of the data, paired with its unusual structure, makes it a poor fit for existing offline reinforcement learning methods, and the online learning formulation overlooks key practical considerations. To address this, we present a principled formulation of the retraining problem and propose an uncertainty-based method that makes decisions by continually forecasting the evolution of model performance evaluated with a bounded metric. Our experiments, addressing classification tasks, show that the method consistently outperforms existing baselines on 7 datasets. We thoroughly assess its robustness to varying cost trade-off values and mis-specified cost trade-offs.
2025-05-01
ICML.cc/2025/Conference (poster)
openreview.net
openreview.net
Caffeine induces age-dependent increases in brain complexity and criticality during sleep
Philipp Thölke
Maxine Arcand-Lavigne
Tarek Lajnef
Sonia Frenette
Julie Carrier
Karim Jerbi
2025-04-30
Communications Biology (publié)
doi.org
ImmunoStruct: a multimodal neural network framework for immunogenicity prediction from peptide-MHC sequence, structure, and biochemical properties
Kevin Bijan Givechian
João Felipe Rocha
Edward Yang
Chen Liu
Kerrie Greene
Rex Ying
Etienne Caron
Akiko Iwasaki
Smita Krishnaswamy
2025-04-30
bioRxiv (prépublication)
doi.org
JPerfEvo: A Tool for Tracking Method-Level Performance Changes in Java Projects
Kaveh Shahedi
Maxime Lamothe
Foutse Khomh
Heng Li
Performance regressions and improvements are common phenomena in software development, occurring periodically as software evolves and mature… (voir plus)s. When developers introduce new changes to a program’s codebase, unforeseen performance variations may arise. Identifying these changes at the method level, however, can be challenging due to the complexity and scale of modern codebases. In this work, we present JPerfEvo, a tool designed to automate the evaluation of the method-level performance impact of each code commit (i.e., the performance variations between the two versions before and after a commit). Leveraging the Java Microbenchmark Harness (JMH) module for benchmarking the modified methods, JPerfEvo instruments their execution and applies robust statistical evaluations to detect performance changes. The tool can classify these changes as performance improvements, regressions, or neutral (i.e., no change), with the change magnitude. We evaluated JPerfEvo on three popular and mature open-source Java projects, demonstrating its effectiveness in identifying performance changes throughout their development histories.
2025-04-28
IEEE Working Conference on Mining Software Repositories (publié)
doi.org
Proceedings of 1st Workshop on Advancing Artificial Intelligence through Theory of Mind
Mouad Abrini
Omri Abend
Dina M. Acklin
Henny Admoni
Gregor Aichinger
Nitay Alon
Zahra Ashktorab
Ashish Atreja
Moises Auron
Alexander Aufreiter
Raghav Awasthi
Soumya Banerjee
Joseph Barnby
Rhea Basappa
Severin Bergsmann
Djallel Bouneffouf
Patrick Callaghan
Marc Cavazza
Thierry Chaminade
Sonia Chernova … (voir 88 de plus)
Mohamed Chetouan
Moumita Choudhury
Axel Cleeremans
J. Cywinski
Fabio Cuzzolin
Hokin Deng
N'yoma Diamond
C. D. Pasquasio
Guillaume Dumas
Max J. van Duijn
Mahapatra Dwarikanath
Qingying Gao
Ashok Goel
Rebecca R. Goldstein
Matthew C. Gombolay
Gabriel Enrique Gonzalez
Amar Halilovic
Tobias Halmdienst
Mahimul Islam
Julian Jara-Ettinger
Natalie Kastel
Renana Keydar
Ashish K. Khanna
Mahdi Khoramshahi
Jihyun Kim
Mihyeon Kim
Youngbin Kim
Senka Krivic
Nikita Krasnytskyi
Arun Kumar
Junehyoung Kwon
EunJu Lee
Shane Lee
Peter R. Lewis 0001
Xue Li
Yijiang Li
Michal Lewandowski
Nathan Lloyd
Matthew B. Luebbers
Dezhi Luo
Haiyun Lyu
Dwarikanath Mahapatra
Kamal Maheshwari
Mallika Mainali
P. Mathur
Patrick Mederitsch
Shuwa Miura
Manuel Preston de Miranda
Reuth Mirsky
Shreya Mishra
Nina M. Moorman
Katelyn Morrison
John Muchovej
Bernhard Nessler
Felix Nessler
Hieu Minh Jord Nguyen
Abby Ortego
F. Papay
Antoine Pasquali
Hamed Rahimi
C. Raghu
Amanda L. Royka
Stefan Sarkadi
Jaelle Scheuerman
Simon Schmid
Paul Schrater
Anik Sen
Zahra Sheikhbahaee
Ke Shi
Reid G. Simmons
Nishant Singh
Mason O. Smith
Ramira van der Meulen
Anthia Solaki
Haoran Sun
Viktor Szolga
Matthew E. Taylor
Travis Taylor
Sanne van Waveren
Juan David Vargas
R. Verbrugge
Eitan Wagner
Justin D. Weisz
Ximing Wen
William Yeoh
Wenlong Zhang
Michelle Zhao
Shlomo Zilberstein
2025-04-28
ArXiv (prépublication)
arxiv.org
arxiv.org
Solving Combinatorial Pricing Problems using Embedded Dynamic Programming Models
Quang Minh Bui
Margarida Carvalho
José Neto
The combinatorial pricing problem (CPP) is a bilevel problem in which the leader maximizes their revenue by imposing tolls on certain items … (voir plus)that they can control. Based on the tolls set by the leader, the follower selects a subset of items corresponding to an optimal solution of a combinatorial optimization problem. To accomplish the leader's goal, the tolls need to be sufficiently low to discourage the follower from choosing the items offered by the competitors. In this paper, we derive a single-level reformulation for the CPP by rewriting the follower's problem as a longest path problem using a dynamic programming model, and then taking its dual and applying strong duality. We proceed to solve the reformulation in a dynamic fashion with a cutting plane method. We apply this methodology to 2 distinct dynamic programming models, namely, a novel formulation designated as selection diagram and the well-known decision diagram. We also produce numerical results to evaluate their performances across 3 different specializations of the CPP and a closely related problem that is the knapsack interdiction problem. Our results showcase the potential of the 2 proposed reformulations over the natural value function approach, expanding the set of tools to solve combinatorial bilevel programs.
2025-04-28
INFORMS Journal on Computing (publié)
doi.org
arxiv.org
How Programmers Interact with Multimodal Software Documentation
Deeksha M. Arya
Jin Guo
Martin P. Robillard
There is a wide variety of online documentation to learn about a given software technology, and prior research has reported that programmers… (voir plus) must invest time and effort to identify one that best suits their need. We evaluated five modalities to present information that enable a software document to cater to the different presentation needs of programmers. We developed a prototype tutorial with these modalities on three topics in Java, namely, regular expressions, inheritance, and exception handling. We investigated how people interact with the modalities in the tutorial given a programming topic and a type of task. We conducted a survey study with 56 respondents and confirm that although text content is most useful for solving conceptual tasks, code examples support deeper comprehension of the underlying concepts. Furthermore, we report that respondents' contradicting preferences for the modalities suggest the need to have multiple alternatives in a software tutorial.
2025-04-27
2025 IEEE/ACM 18th International Conference on Cooperative and Human Aspects of Software Engineering (CHASE) (publié)
doi.org
RLeXplore: Accelerating Research in Intrinsically-Motivated Reinforcement Learning
Mingqi Yuan
Roger Creus Castanyer
Bin Li
Xin Jin
Glen Berseth
Wenjun Zeng
2025-04-24
TMLR (accepté)
doi.org
openreview.net
What makes a good public EV charging station? A revealed preference study
Steven Lamontagne
Margarida Carvalho
Emma Frejinger
Ribal Atallah
2025-04-24
ArXiv (prépublication)
arxiv.org
arxiv.org
What makes a good public EV charging station? A revealed preference study
Steven Lamontagne
Margarida Carvalho
Emma Frejinger
Ribal Atallah
To determine the optimal locations for electric vehicle charging stations, optimisation models need to predict which charging stations users… (voir plus) will select. We estimate discrete choice models to predict the usage of charging stations using only readily available information for charging network operators. Our parameter values are estimated from a unique, revealed preferences dataset of charging sessions in Montreal, Quebec. We find that user distance to stations, proximity to home areas, and the number of outlets at each station are significant factors for predicting station usage. Additionally, amenities near charging stations have a neutral effect overall, with some users demonstrating strong preference or aversion for these locations. High variability among the preferences of users highlight the importance of models which incorporate panel effects. Moreover, integrating mixed logit models within the optimization of charging station network design yields high-quality solutions, even when evaluated under other model specifications.
2025-04-24
ArXiv (prépublication)
arxiv.org
arxiv.org
Algorithmic Fairness Through the Lens of Metrics and Evaluation (AFME) 2024
Miriam Rateike
Awa Dieng
Jamelle Watson-Daniels
Ferdinando Fioretto
Golnoosh Farnadi
2025-04-23
Proceedings of the Algorithmic Fairness Through the Lens of Metrics and Evaluation (publié)
proceedings.mlr.press