Publications

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… (see more)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.
2025-04-27
IEEE Working Conference on Mining Software Repositories (published)
doi.org
Performance Smells in ML and Non-ML Python Projects: A Comparative Study
Franccois Belias
Leuson Da Silva
Foutse Khomh
Cyrine Zid
2025-04-27
ArXiv (preprint)
doi.org
arxiv.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 … (see 88 more)
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
2025-04-27
ArXiv (preprint)
doi.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 … (see more)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.
2025-04-27
INFORMS Journal on Computing (published)
doi.org
arxiv.org
How Programmers Interact with Multimodal Software Documentation
Deeksha M. Arya
Jin L.C. 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… (see more) 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.
2025-04-26
2025 IEEE/ACM 18th International Conference on Cooperative and Human Aspects of Software Engineering (CHASE) (published)
doi.org
A Learning-Based Framework for Fair and Scalable Solution Generation in Kidney Exchange Problems
William St-Arnaud
Margarida Carvalho
Golnoosh Farnadi
2025-04-26
TMLR (accepted)
openreview.net
openreview.net
AIFM-ed Curriculum Framework for Postgraduate Family Medicine Education on Artificial Intelligence: Mixed Methods Study
Raymond Tolentino
Fanny Hersson-Edery
Mark Yaffe
Samira Abbasgholizadeh-Rahimi
As health care moves to a more digital environment, there is a growing need to train future family doctors on the clinical uses of artificia… (see more)l intelligence (AI). However, family medicine training in AI has often been inconsistent or lacking. The aim of the study is to develop a curriculum framework for family medicine postgraduate education on AI called “Artificial Intelligence Training in Postgraduate Family Medicine Education” (AIFM-ed). First, we conducted a comprehensive scoping review on existing AI education frameworks guided by the methodological framework developed by Arksey and O’Malley and Joanna Briggs Institute methodological framework for scoping reviews. We adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) checklist for reporting the results. Next, 2 national expert panels were conducted. Panelists included family medicine educators and residents knowledgeable in AI from family medicine residency programs across Canada. Participants were purposively sampled, and panels were held via Zoom, recorded, and transcribed. Data were analyzed using content analysis. We followed the Standards for Reporting Qualitative Research for panels. An integration of the scoping review results and 2 panel discussions of 14 participants led to the development of the AIFM-ed curriculum framework for AI training in postgraduate family medicine education with five key elements: (1) need and purpose of the curriculum, (2) learning objectives, (3) curriculum content, (4) organization of curriculum content, and (5) implementation aspects of the curriculum. Using the results of this study, we developed the AIFM-ed curriculum framework for AI training in postgraduate family medicine education. This framework serves as a structured guide for integrating AI competencies into medical education, ensuring that future family physicians are equipped with the necessary skills to use AI effectively in their clinical practice. Future research should focus on the validation and implementation of the AIFM-ed framework within family medicine education. Institutions also are encouraged to consider adapting the AIFM-ed framework within their own programs, tailoring it to meet the specific needs of their trainees and health care environments.
2025-04-24
JMIR Medical Education (published)
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
Transactions on Machine Learning Research (accepted)
doi.org
openreview.net
A Survey on Model MoErging: Recycling and Routing Among Specialized Experts for Collaborative Learning
Prateek Yadav
Colin Raffel
Mohammed Muqeeth
Lucas Caccia
Haokun Liu
Tianlong Chen
Mohit Bansal
Leshem Choshen
Alessandro Sordoni
The availability of performant pre-trained models has led to a proliferation of fine-tuned expert models that are specialized to a particula… (see more)r domain or task. Model MoErging methods aim to recycle expert models to create an aggregate system with improved performance or generalization. A key component of MoErging methods is the creation of a router that decides which expert model(s) to use for a particular input or application. The promise, effectiveness, and large design space of MoErging has spurred the development of many new methods over the past few years. This rapid pace of development has made it challenging to compare different MoErging methods, which are rarely compared to one another and are often validated in different experimental setups. To remedy such gaps, we present a comprehensive survey of MoErging methods that includes a novel taxonomy for cataloging key design choices and clarifying suitable applications for each method. Apart from surveying MoErging research, we inventory software tools and applications that make use of MoErging. We additionally discuss related fields of study such as model merging, multitask learning, and mixture-of-experts models. Taken as a whole, our survey provides a unified overview of existing MoErging methods and creates a solid foundation for future work in this burgeoning field.
2025-04-24
TMLR (accepted)
doi.org
openreview.net
3DMolFormer: A Dual-Channel Framework for Structure-Based Drug Discovery
Xiuyuan Hu
Guoqing Liu
Can (Sam) Chen
Yang Zhao
Hao Zhang
Xue Liu
Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challeng… (see more)e in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer .
2025-04-22
International Conference on Learning Representations (Accept (Poster))
doi.org
openreview.net
Accelerating Training with Neuron Interaction and Nowcasting Networks
Boris Knyazev
Abhinav Moudgil
Guillaume Lajoie
Eugene Belilovsky
Simon Lacoste-Julien
Neural network training can be accelerated when a learnable update rule is used in lieu of classic adaptive optimizers (e.g. Adam). However,… (see more) learnable update rules can be costly and unstable to train and use. Recently, Jang et al. (2023) proposed a simpler approach to accelerate training based on weight nowcaster networks (WNNs). In their approach, Adam is used for most of the optimization steps and periodically, only every few steps, a WNN nowcasts (predicts near future) parameters. We improve WNNs by proposing neuron interaction and nowcasting (NiNo) networks. In contrast to WNNs, NiNo leverages neuron connectivity and graph neural networks to more accurately nowcast parameters. We further show that in some networks, such as Transformers, modeling neuron connectivity accurately is challenging. We address this and other limitations, which allows NiNo to accelerate Adam training by up to 50% in vision and language tasks.
2025-04-22
International Conference on Learning Representations (Accept (Poster))
doi.org
openreview.net
AdaFisher: Adaptive Second Order Optimization via Fisher Information
Damien Martins Gomes
Yanlei Zhang
Eugene Belilovsky
Guy Wolf
Mahdi S. Hosseini
First-order optimization methods are currently the mainstream in training deep neural networks (DNNs). Optimizers like Adam incorporate limi… (see more)ted curvature information by employing the diagonal matrix preconditioning of the stochastic gradient during the training. Despite their widespread, second-order optimization algorithms exhibit superior convergence properties compared to their first-order counterparts e.g. Adam and SGD. However, their practicality in training DNNs is still limited due to increased per-iteration computations compared to the first-order methods. We present \emph{AdaFisher}--an adaptive second-order optimizer that leverages a \emph{diagonal block-Kronecker} approximation of the Fisher information matrix for adaptive gradient preconditioning. AdaFisher aims to bridge the gap between enhanced \emph{convergence/generalization} capabilities and computational efficiency in second-order optimization framework for training DNNs. Despite the slow pace of second-order optimizers, we showcase that AdaFisher can be reliably adopted for image classification, language modeling and stands out for its stability and robustness in hyper-parameter tuning. We demonstrate that AdaFisher \textbf{outperforms the SOTA optimizers} in terms of both accuracy and convergence speed. Code is available from https://github.com/AtlasAnalyticsLab/AdaFisher.
2025-04-22
International Conference on Learning Representations (Accept (Poster))
doi.org
openreview.net