Publications

EPISeg: Automated segmentation of the spinal cord on echo planar images using open-access multi-center data
Rohan Banerjee
Merve Kaptan
Alexandra Tinnermann
Ali Khatibi
Alice Dabbagh
Christian Büchel
Christian W. Kündig
Christine S. W. Law
Csw Law
Dario Pfyffer
David J. Lythgoe
Dimitra Tsivaka
Dimitri Van De Ville
Falk Eippert
Fauziyya Muhammad
Gary H. Glover
Gergely David
Grace Haynes
Jan Haaker
Jonathan C. W. Brooks … (voir 23 de plus)
Jürgen Finsterbusch
Katherine T. Martucci
Kimberly J. Hemmerling
Mahdi Mobarak-Abadi
Mark A. Hoggarth
Matthew A. Howard
Molly G. Bright
Nawal Kinany
Olivia S. Kowalczyk
Patrick Freund
Robert L. Barry
Sean Mackey
Shahabeddin Vahdat
Simon Schading
Stephen B. McMahon
Todd Parish
Véronique Marchand-Pauvert
Yufen Chen
Zachary A. Smith
KA Weber
Kenneth A. Weber
Benjamin De Leener
Julien Cohen-Adad
Functional magnetic resonance imaging (fMRI) of the spinal cord is relevant for studying sensation, movement, and autonomic function. Prepro… (voir plus)cessing of spinal cord fMRI data involves segmentation of the spinal cord on gradient-echo echo planar imaging (EPI) images. Current automated segmentation methods do not work well on these data, due to the low spatial resolution, susceptibility artifacts causing distortions and signal drop-out, ghosting, and motion-related artifacts. Consequently, this segmentation task demands a considerable amount of manual effort which takes time and is prone to user bias. In this work, we (i) gathered a multi-center dataset of spinal cord gradient-echo EPI with ground-truth segmentations and shared it on OpenNeuro https://openneuro.org/datasets/ds005143/versions/1.3.0, and (ii) developed a deep learning-based model, EPISeg, for the automatic segmentation of the spinal cord on gradient-echo EPI data. We observe a significant improvement in terms of segmentation quality compared to other available spinal cord segmentation models. Our model is resilient to different acquisition protocols as well as commonly observed artifacts in fMRI data. The training code is available at https://github.com/sct-pipeline/fmri-segmentation/, and the model has been integrated into the Spinal Cord Toolbox as a command-line tool.
2025-09-09
Imaging neuroscience (publié)
doi.org
RL Fine-Tuning Heals OOD Forgetting in SFT
Hangzhan Jin
Sitao Luan
Sicheng Lyu
Guillaume Rabusseau
Reihaneh Rabbany
Doina Precup
Mohammad Hamdaqa
2025-09-08
ArXiv (prépublication)
arxiv.org
arxiv.org
RL Fine-Tuning Heals OOD Forgetting in SFT
Hangzhan Jin
Sitao Luan
Sicheng Lyu
Guillaume Rabusseau
Reihaneh Rabbany
Doina Precup
Mohammad Hamdaqa
The two-stage fine-tuning paradigm of Supervised Fine-Tuning (SFT) followed by Reinforcement Learning (RL) has empirically shown better reas… (voir plus)oning performance than one-stage SFT for the post-training of Large Language Models (LLMs). However, the evolution and mechanism behind the synergy of SFT and RL are still under-explored and inconclusive. In our study, we find the well-known claim"SFT memorizes, RL generalizes"is over-simplified, and discover that: (1) OOD performance peaks at the early stage of SFT and then declines (OOD forgetting), the best SFT checkpoint cannot be captured by training/test loss; (2) the subsequent RL stage does not generate fundamentally better OOD capability, instead it plays an \textbf{OOD restoration} role, recovering the lost reasoning ability during SFT; (3) The recovery ability has boundaries, \ie{} \textbf{if SFT trains for too short or too long, RL cannot recover the lost OOD ability;} (4) To uncover the underlying mechanisms behind the forgetting and restoration process, we employ SVD analysis on parameter matrices, manually edit them, and observe their impacts on model performance. Unlike the common belief that the shift of model capacity mainly results from the changes of singular values, we find that they are actually quite stable throughout fine-tuning. Instead, the OOD behavior strongly correlates with the \textbf{rotation of singular vectors}. Our findings re-identify the roles of SFT and RL in the two-stage fine-tuning and discover the rotation of singular vectors as the key mechanism. %reversing the rotations induced by SFT, which shows recovery from forgetting, whereas imposing the SFT parameter directions onto a RL-tuned model results in performance degradation. Code is available at https://github.com/xiaodanguoguo/RL_Heals_SFT
2025-09-08
ArXiv (prépublication)
arxiv.org
arxiv.org
An AI system to help scientists write expert-level empirical software
Eser Aygün
Anastasiya Belyaeva
Gheorghe Comanici
Marc Coram
Hao Cui
Jake Garrison
Renee Johnston Anton Kast
Cory Y. McLean
Peter C. Norgaard
Zahra Shamsi
David Smalling
James Thompson
Subhashini Venugopalan
Brian P Williams
Chujun He
Sarah Martinson
Martyna Plomecka
Lai Wei
Yuchen Zhou
Qian-Ze Zhu … (voir 21 de plus)
Matthew Abraham
Erica Brand
Anna Bulanova
Jeff Cardille
Chris Co
Scott Ellsworth
Grace Joseph
Malcolm Kane
Ryan K. Krueger
Johan Kartiwa
D. Liebling
Jan-Matthis Lueckmann
Paul Raccuglia
Xuefei Wang
Katherine Chou
James Manyika
Yossi Matias
J.C. Platt
Lizzie Dorfman
Shibl Mourad
Michael P. Brenner
The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. … (voir plus)To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.
2025-09-08
ArXiv (prépublication)
arxiv.org
arxiv.org
An AI system to help scientists write expert-level empirical software
Eser Aygün
Anastasiya Belyaeva
Gheorghe Comanici
Marc Coram
Hao Cui
Jake Garrison
Renee Johnston Anton Kast
Cory Y. McLean
Peter C. Norgaard
Zahra Shamsi
David Smalling
James Thompson
Subhashini Venugopalan
Brian P Williams
Chujun He
Sarah Martinson
Martyna Plomecka
Lai Wei
Yuchen Zhou
Qian-Ze Zhu … (voir 21 de plus)
Matthew Abraham
Erica Brand
Anna Bulanova
Jeff Cardille
Chris Co
Scott Ellsworth
Grace Joseph
Malcolm Kane
Ryan K. Krueger
Johan Kartiwa
D. Liebling
Jan-Matthis Lueckmann
Paul Raccuglia
Xuefei Wang
Katherine Chou
James Manyika
Yossi Matias
J.C. Platt
Lizzie Dorfman
Shibl Mourad
Michael P. Brenner
The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. … (voir plus)To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.
2025-09-08
ArXiv (prépublication)
arxiv.org
arxiv.org
Discrete Audio Tokens: More Than a Survey!
Pooneh Mousavi
Gallil Maimon
Adel Moumen
Darius Petermann
Jiatong Shi
Haibin Wu
Haici Yang
Anastasia Kuznetsova
Artem Ploujnikov
Ricard Marxer
Bhuvana Ramabhadran
Benjamin Elizalde
Loren Lugosch
Jinyu Li
Cem Subakan
Phil Woodland
Minje Kim
Hung-yi Lee
Shinji Watanabe
Yossi Adi … (voir 1 de plus)
Mirco Ravanelli
Discrete audio tokens are compact representations that aim to preserve perceptual quality, phonetic content, and speaker characteristics whi… (voir plus)le enabling efficient storage and inference, as well as competitive performance across diverse downstream tasks. They provide a practical alternative to continuous features, enabling the integration of speech and audio into modern large language models (LLMs). As interest in token-based audio processing grows, various tokenization methods have emerged, and several surveys have reviewed the latest progress in the field. However, existing studies often focus on specific domains or tasks and lack a unified comparison across various benchmarks. This paper presents a systematic review and benchmark of discrete audio tokenizers, covering three domains: speech, music, and general audio. We propose a taxonomy of tokenization approaches based on encoder-decoder, quantization techniques, training paradigm, streamability, and application domains. We evaluate tokenizers on multiple benchmarks for reconstruction, downstream performance, and acoustic language modeling, and analyze trade-offs through controlled ablation studies. Our findings highlight key limitations, practical considerations, and open challenges, providing insight and guidance for future research in this rapidly evolving area. For more information, including our main results and tokenizer database, please refer to our website: https://poonehmousavi.github.io/dates-website/.
2025-09-07
TMLR (accepté)
doi.org
openreview.net
Imagining Alternatives: Towards High-Resolution 3D Counterfactual Medical Image Generation via Language Guidance
Mohamed Mohamed
Brennan Nichyporuk
Douglas Arnold
Tal Arbel
Vision-language models have demonstrated impressive capabilities in generating 2D images under various conditions; however, the success of t… (voir plus)hese models is largely enabled by extensive, readily available pretrained foundation models. Critically, comparable pretrained models do not exist for 3D, significantly limiting progress. As a result, the potential of vision-language models to produce high-resolution 3D counterfactual medical images conditioned solely on natural language remains unexplored. Addressing this gap would enable powerful clinical and research applications, such as personalized counterfactual explanations, simulation of disease progression, and enhanced medical training by visualizing hypothetical conditions in realistic detail. Our work takes a step toward this challenge by introducing a framework capable of generating high-resolution 3D counterfactual medical images of synthesized patients guided by free-form language prompts. We adapt state-of-the-art 3D diffusion models with enhancements from Simple Diffusion and incorporate augmented conditioning to improve text alignment and image quality. To our knowledge, this is the first demonstration of a language-guided native-3D diffusion model applied to neurological imaging, where faithful three-dimensional modeling is essential. On two neurological MRI datasets, our framework simulates varying counterfactual lesion loads in Multiple Sclerosis and cognitive states in Alzheimer's disease, generating high-quality images while preserving subject fidelity. Our results lay the groundwork for prompt-driven disease progression analysis in 3D medical imaging. Project link - https://lesupermomo.github.io/imagining-alternatives/.
2025-09-07
ArXiv (prépublication)
arxiv.org
arxiv.org
Imagining Alternatives: Towards High-Resolution 3D Counterfactual Medical Image Generation via Language Guidance
Mohamed Mohamed
Brennan Nichyporuk
Douglas Arnold
Tal Arbel
Vision-language models have demonstrated impressive capabilities in generating 2D images under various conditions; however the impressive pe… (voir plus)rformance of these models in 2D is largely enabled by extensive, readily available pretrained foundation models. Critically, comparable pretrained foundation models do not exist for 3D, significantly limiting progress in this domain. As a result, the potential of vision-language models to produce high-resolution 3D counterfactual medical images conditioned solely on natural language descriptions remains completely unexplored. Addressing this gap would enable powerful clinical and research applications, such as personalized counterfactual explanations, simulation of disease progression scenarios, and enhanced medical training by visualizing hypothetical medical conditions in realistic detail. Our work takes a meaningful step toward addressing this challenge by introducing a framework capable of generating high-resolution 3D counterfactual medical images of synthesized patients guided by free-form language prompts. We adapt state-of-the-art 3D diffusion models with enhancements from Simple Diffusion and incorporate augmented conditioning to improve text alignment and image quality. To our knowledge, this represents the first demonstration of a language-guided native-3D diffusion model applied specifically to neurological imaging data, where faithful three-dimensional modeling is essential to represent the brain's three-dimensional structure. Through results on two distinct neurological MRI datasets, our framework successfully simulates varying counterfactual lesion loads in Multiple Sclerosis (MS), and cognitive states in Alzheimer's disease, generating high-quality images while preserving subject fidelity in synthetically generated medical images. Our results lay the groundwork for prompt-driven disease progression analysis within 3D medical imaging.
2025-09-07
ArXiv (prépublication)
arxiv.org
arxiv.org
Task Robustness via Re-Labelling Vision-Action Robot Data
Artur Kuramshin
Özgür Aslan
Cyrus Neary
Glen Berseth
The recent trend in scaling models for robot learning has resulted in impressive policies that can perform various manipulation tasks and ge… (voir plus)neralize to novel scenarios. However, these policies continue to struggle with following instructions, likely due to the limited linguistic and action sequence diversity in existing robotics datasets. This paper introduces
2025-09-06
robot-learning.org/CoRL/2025/Workshop/Robot_Data (publié)
openreview.net
openreview.net
Massive Extremely High-Velocity Outflow in the Quasar J164653.72+243942.2
Paola Rodríguez Hidalgo
Hyunseop 현섭 Choi 최
Patrick B. Hall
Karen M. Leighly
Liliana Flores
Mikel M. Charles
Cora DeFrancesco
J. Hlavacek-Larrondo
Laurence Perreault-Levasseur
2025-09-04
The Astrophysical Journal (publié)
doi.org
arxiv.org
Warming Up for Zeroth-Order Federated Pre-Training with Low Resource Clients
Gwen Legate
Irina Rish
Eugene Belilovsky
Federated learning enables collaborative model training across numerous edge devices without requiring participants to share data; however, … (voir plus)memory and communication constraints on these edge devices may preclude their participation in training. We consider a setting in which a subset of edge devices are below a critical memory or communication threshold required to conduct model updates. Under typical federated optimization algorithms, these devices are excluded from training which renders their data inaccessible and increases system induced bias. We are inspired by MeZO, a zeroth-order method used for memory-efficient fine-tuning. The increased variance inherent to zeroth-order gradient approximations has relegated previous zeroth-order optimizers exclusively to the domain of fine tuning; a limitation we seek to correct. We devise a federated, memory-efficient zeroth-order optimizer, ZOWarmUp that permits zeroth-order training from a random initialization. ZOWarmUp leverages differing client capabilities and careful variance reduction techniques to facilitate participation of under-represented, low-resource clients in model training. Like other federated zeroth-order methods, ZOWarmUp eliminates the need for edge devices to transmit their full gradients to the server and instead relies on only a small set of random seeds, rendering the up-link communication cost negligible. We present experiments using various datasets and model architectures to show that ZOWarmUp is a robust algorithm that can can be applied under a wide variety of circumstances. For systems with a high proportion of edge devices that would otherwise be excluded from training, this algorithm provides access to a greater volume and diversity of data, thus improving training outcomes.
2025-09-03
ArXiv (prépublication)
arxiv.org
arxiv.org
Behaviour Discovery and Attribution for Explainable Reinforcement Learning
Rishav
Somjit Nath
Vincent Michalski
Samira Ebrahimi Kahou
2025-09-02
TMLR (accepté)
openreview.net
openreview.net