Publications

Is Meta-training Really Necessary for Molecular Few-Shot Learning ?
Philippe Formont
Hugo Jeannin
Pablo Piantanida
Ismail Ben Ayed
Few-shot learning has recently attracted significant interest in drug discovery, with a recent, fast-growing literature mostly involving con… (voir plus)voluted meta-learning strategies. We revisit the more straightforward fine-tuning approach for molecular data, and propose a regularized quadratic-probe loss based on the the Mahalanobis distance. We design a dedicated block-coordinate descent optimizer, which avoid the degenerate solutions of our loss. Interestingly, our simple fine-tuning approach achieves highly competitive performances in comparison to state-of-the-art methods, while being applicable to black-box settings and removing the need for specific episodic pre-training strategies. Furthermore, we introduce a new benchmark to assess the robustness of the competing methods to domain shifts. In this setting, our fine-tuning baseline obtains consistently better results than meta-learning methods.
2024-04-02
ArXiv (prépublication)
doi.org
arxiv.org
Advanced MRI metrics improve the prediction of baseline disease severity for individuals with degenerative cervical myelopathy
Abdul Al-Shawwa
Kalum Ost
David Anderson
Newton Cho
Nathan Evaniew
W. Bradley Jacobs
Allan R. Martin
Ranjeet Gaekwad
Saswati Tripathy
Jacques Bouchard
Steven Casha
Roger Cho
Stephen duPlessis
Peter Lewkonia
Fred Nicholls
Paul T. Salo
Alex Soroceanu
Ganesh Swamy
Kenneth C. Thomas
Michael M.H. Yang … (voir 2 de plus)
Julien Cohen-Adad
David W. Cadotte
2024-04-01
The spine journal (publié)
doi.org
Co-developing longitudinal patient registries for phenylketonuria and mucopolysaccharidoses in Canada
John Adams
Kim Angel
John J. Mitchell
Pranesh Chakraborty
Beth K. Potter
Michal Inbar-Feigenberg
Sylvia Stockler
Monica Lamoureux
Alison H. Howie
Alex Pace
Nancy J. Butcher
Cheryl Rockman-Greenberg
Robin Hayeems
Anne-Marie Laberge
Thierry Lacaze-Masmonteil
Jeff Round
Martin Offringa
Maryam Oksoui
Andreas Schulze
Kathy N. Speechley … (voir 3 de plus)
Kednapa Thavorn
Yannis Trakadis
Kumanan Wilson
2024-04-01
Molecular Genetics and Metabolism (publié)
doi.org
Increasing schedule reliability in the multiple depot vehicle scheduling problem with stochastic travel time
L'ea Ricard
Guy Desaulniers
Andrea Lodi
Louis-Martin Rousseau
2024-04-01
Omega (publié)
doi.org
Machine Learning Robustness: A Primer
Houssem Ben Braiek
Foutse Khomh
This chapter explores the foundational concept of robustness in Machine Learning (ML) and its integral role in establishing trustworthiness … (voir plus)in Artificial Intelligence (AI) systems. The discussion begins with a detailed definition of robustness, portraying it as the ability of ML models to maintain stable performance across varied and unexpected environmental conditions. ML robustness is dissected through several lenses: its complementarity with generalizability; its status as a requirement for trustworthy AI; its adversarial vs non-adversarial aspects; its quantitative metrics; and its indicators such as reproducibility and explainability. The chapter delves into the factors that impede robustness, such as data bias, model complexity, and the pitfalls of underspecified ML pipelines. It surveys key techniques for robustness assessment from a broad perspective, including adversarial attacks, encompassing both digital and physical realms. It covers non-adversarial data shifts and nuances of Deep Learning (DL) software testing methodologies. The discussion progresses to explore amelioration strategies for bolstering robustness, starting with data-centric approaches like debiasing and augmentation. Further examination includes a variety of model-centric methods such as transfer learning, adversarial training, and randomized smoothing. Lastly, post-training methods are discussed, including ensemble techniques, pruning, and model repairs, emerging as cost-effective strategies to make models more resilient against the unpredictable. This chapter underscores the ongoing challenges and limitations in estimating and achieving ML robustness by existing approaches. It offers insights and directions for future research on this crucial concept, as a prerequisite for trustworthy AI systems.
2024-04-01
ArXiv (prépublication)
doi.org
arxiv.org
Self-supervised anomaly detection in computer vision and beyond: A survey and outlook.
Hadi Hojjati
Thi Kieu Khanh Ho
Narges Armanfard
2024-04-01
Neural Networks (publié)
doi.org
arxiv.org
CtRL-Sim: Reactive and Controllable Driving Agents with Offline Reinforcement Learning
Luke Rowe
Roger Girgis
Anthony Gosselin
Bruno Carrez
Florian Golemo
Felix Heide
Liam Paull
Chris Pal
Evaluating autonomous vehicle stacks (AVs) in simulation typically involves replaying driving logs from real-world recorded traffic. However… (voir plus), agents replayed from offline data do not react to the actions of the AV, and their behaviour cannot be easily controlled to simulate counterfactual scenarios. Existing approaches have attempted to address these shortcomings by proposing methods that rely on heuristics or learned generative models of real-world data but these approaches either lack realism or necessitate costly iterative sampling procedures to control the generated behaviours. In this work, we take an alternative approach and propose CtRL-Sim, a method that leverages return-conditioned offline reinforcement learning within a physics-enhanced Nocturne simulator to efficiently generate reactive and controllable traffic agents. Specifically, we process real-world driving data through the Nocturne simulator to generate a diverse offline reinforcement learning dataset, annotated with various reward terms. With this dataset, we train a return-conditioned multi-agent behaviour model that allows for fine-grained manipulation of agent behaviours by modifying the desired returns for the various reward components. This capability enables the generation of a wide range of driving behaviours beyond the scope of the initial dataset, including those representing adversarial behaviours. We demonstrate that CtRL-Sim can efficiently generate diverse and realistic safety-critical scenarios while providing fine-grained control over agent behaviours. Further, we show that fine-tuning our model on simulated safety-critical scenarios generated by our model enhances this controllability.
2024-03-29
ArXiv (prépublication)
doi.org
arxiv.org
Scaling up ridge regression for brain encoding in a massive individual fMRI dataset
Sana Ahmadi
Pierre (Louis) Bellec
Tristan Glatard
2024-03-28
ArXiv (prépublication)
doi.org
arxiv.org
Fast burst fraction transients convey information independent of the firing rate
Richard Naud
Xingyun Wang
Zachary Friedenberger
Alexandre Payeur
Jiyun N. Shin
Jean-Claude Béïque
Blake Richards
Moritz Drüke
Matthew E. Larkum
Guy Doron
Theories of attention and learning have hypothesized a central role for high-frequency bursting in cognitive functions, but experimental rep… (voir plus)orts of burst-mediated representations in vivo have been limited. Here we used a novel demultiplexing approach by considering a conjunctive burst code. We studied this code in vivo while animals learned to report direct electrical stimulation of the somatosensory cortex and found two acquired yet independent representations. One code, the event rate, showed a sparse and succint stiumulus representation and a small modulation upon detection errors. The other code, the burst fraction, correlated more globally with stimulation and more promptly responded to detection errors. Bursting modulation was potent and its time course evolved, even in cells that were considered unresponsive based on the firing rate. During the later stages of training, this modulation in bursting happened earlier, gradually aligning temporally with the representation in event rate. The alignment of bursting and event rate modulation sharpened the firing rate response, and was strongly associated behavioral accuracy. Thus a fine-grained separation of spike timing patterns reveals two signals that accompany stimulus representations: an error signal that can be essential to guide learning and a sharpening signal that could implement attention mechanisms.
2024-03-27
bioRxiv (prépublication)
doi.org
Application-Driven Innovation in Machine Learning
David Rolnick
Alan Aspuru-Guzik
Sara Beery
Bistra N. Dilkina
Priya L. Donti
Marzyeh Ghassemi
Hannah Kerner
Claire Monteleoni
Esther Rolf
Milind Tambe
Adam White
As applications of machine learning proliferate, innovative algorithms inspired by specific real-world challenges have become increasingly i… (voir plus)mportant. Such work offers the potential for significant impact not merely in domains of application but also in machine learning itself. In this paper, we describe the paradigm of application-driven research in machine learning, contrasting it with the more standard paradigm of methods-driven research. We illustrate the benefits of application-driven machine learning and how this approach can productively synergize with methods-driven work. Despite these benefits, we find that reviewing, hiring, and teaching practices in machine learning often hold back application-driven innovation. We outline how these processes may be improved.
2024-03-26
ArXiv (prépublication)
doi.org
arxiv.org
Improving Text-to-Image Consistency via Automatic Prompt Optimization
Oscar Mañas
Pietro Astolfi
Melissa Hall
Candace Ross
Jack Urbanek
Adina Williams
Aishwarya Agrawal
Adriana Romero Soriano
Michal Drozdzal
2024-03-26
ArXiv (prépublication)
doi.org
arxiv.org
Predicting Species Occurrence Patterns from Partial Observations
Hager Radi
Mélisande Teng
David Rolnick
To address the interlinked biodiversity and climate crises, we need an understanding of where species occur and how these patterns are chang… (voir plus)ing. However, observational data on most species remains very limited, and the amount of data available varies greatly between taxonomic groups. We introduce the problem of predicting species occurrence patterns given (a) satellite imagery, and (b) known information on the occurrence of other species. To evaluate algorithms on this task, we introduce SatButterfly, a dataset of satellite images, environmental data and observational data for butterflies, which is designed to pair with the existing SatBird dataset of bird observational data. To address this task, we propose a general model, R-Tran, for predicting species occurrence patterns that enables the use of partial observational data wherever found. We find that R-Tran outperforms other methods in predicting species encounter rates with partial information both within a taxon (birds) and across taxa (birds and butterflies). Our approach opens new perspectives to leveraging insights from species with abundant data to other species with scarce data, by modelling the ecosystems in which they co-occur.
2024-03-26
ArXiv (prépublication)
doi.org
arxiv.org