Publications

Bridging biodiversity and ecosystem services through useful plant species
Nina Obiar
Isaac Eckert
Janelle Baker
Daniel Moerman
Laura J. Pollock
2025-03-28
PLANTS, PEOPLE, PLANET (published)
doi.org
Genetic Analysis of Polyunsaturated Fatty Acids Biosynthesis Pathway Determines Four Distinct Thraustochytrid Types
Sou‐Yu Cheng
Yi‐Jing Chen
Hsiu-Chin Lin
Hsin‐Yang Chang
Ming‐Der Huang
ABSTRACT Thraustochytrids, diverse marine unicellular protists encompassing over 10 recognised genera, are renowned for synthesising polyuns… (see more)aturated fatty acids (PUFAs), with content and composition varying substantially across genera. While PUFAs are known to be produced via PUFA synthase (PUFA‐S) and/or elongase/desaturase (ELO/DES) pathways, the distinctions in genes involved remain unexplored. This study analysed PUFA biosynthetic genes in 19 thraustochytrid strains across six genera, categorising them into four types. Type I exclusively utilises the ELO/DES pathway, Type II employs both PUFA‐S and complete ELO/DES pathways, while Types III and IV primarily rely on PUFA‐S, with Type III lacking the canonical Δ9 desaturase and Type IV missing most desaturase and elongase enzymes. Notably, the Δ9 desaturase and ATP‐citrate lyase (ACLY) are exclusive to Types I and II, while β‐carotene hydroxylase (CrtZ) is absent in these types. ACLY absence suggests alternative acetyl‐CoA supply pathways in Types III and IV, whereas CrtZ absence implies either a lack of specific xanthophylls or alternative biosynthetic pathways in Types I and II. Synteny analysis revealed conserved genomic organisation of PUFA biosynthetic genes, indicating a shared evolutionary trajectory. This study provides insights into the genetic diversity underlying PUFA biosynthesis in thraustochytrids, while proposing putative evolutionary pathways for the four lineages.
2025-03-28
Environmental Microbiology (published)
doi.org
Scenario Dreamer: Vectorized Latent Diffusion for Generating Driving Simulation Environments
Luke Rowe
Roger Girgis
Anthony Gosselin
Liam Paull
Chris Pal
Felix Heide
2025-03-28
ArXiv (preprint)
arxiv.org
arxiv.org
Conditional Diffusion Models are Medical Image Classifiers that Provide Explainability and Uncertainty for Free
Gian Mario Favero
Parham Saremi
Emily Kaczmarek
Brennan Nichyporuk
Tal Arbel
2025-03-27
MIDL.io/2025/Conference (published)
doi.org
openreview.net
debug-gym: A Text-Based Environment for Interactive Debugging
Xingdi Yuan
Morgane M Moss
Charbel Feghali
Chinmay Singh
Darya Moldavskaya
Drew MacPhee
Lucas Caccia
Matheus Pereira
Minseon Kim
Alessandro Sordoni
Marc-Alexandre Côté
2025-03-27
ArXiv (preprint)
arxiv.org
arxiv.org
debug-gym: A Text-Based Environment for Interactive Debugging
Xingdi Yuan
Morgane M Moss
Charbel Feghali
Chinmay Singh
Darya Moldavskaya
Drew MacPhee
Lucas Caccia
Matheus Pereira
Minseon Kim
Alessandro Sordoni
Marc-Alexandre Côté
2025-03-27
ArXiv (preprint)
arxiv.org
arxiv.org
How do language models learn facts? Dynamics, curricula and hallucinations
Nicolas Zucchet
Jorg Bornschein
Stephanie Chan
Andrew Lampinen
Razvan Pascanu
Soham De
2025-03-27
ArXiv (preprint)
arxiv.org
arxiv.org
PRISM: High-Resolution&Precise Counterfactual Medical Image Generation using Language-guided Stable Diffusion
Amar Kumar
Anita Kriz
Mohammad Havaei
Tal Arbel
Developing reliable and generalizable deep learning systems for medical imaging faces significant obstacles due to spurious correlations, da… (see more)ta imbalances, and limited text annotations in datasets. Addressing these challenges requires architectures robust to the unique complexities posed by medical imaging data. The rapid advancements in vision-language foundation models within the natural image domain prompt the question of how they can be adapted for medical imaging tasks. In this work, we present PRISM, a framework that leverages foundation models to generate high-resolution, language-guided medical image counterfactuals using Stable Diffusion. Our approach demonstrates unprecedented precision in selectively modifying spurious correlations (the medical devices) and disease features, enabling the removal and addition of specific attributes while preserving other image characteristics. Through extensive evaluation, we show how PRISM advances counterfactual generation and enables the development of more robust downstream classifiers for clinically deployable solutions. To facilitate broader adoption and research, we make our code publicly available at https://github.com/Amarkr1/PRISM.
2025-03-27
MIDL.io/2025/Conference (published)
doi.org
openreview.net
StarFlow: Generating Structured Workflow Outputs From Sketch Images
Patrice Bechard
Chao Wang
Amirhossein Abaskohi
Juan A. Rodriguez
Chris Pal
David Vazquez
Spandana Gella
Sai Rajeswar
Perouz Taslakian
2025-03-27
ArXiv (preprint)
arxiv.org
arxiv.org
StarFlow: Generating Structured Workflow Outputs From Sketch Images
Patrice Bechard
Chao Wang
Amirhossein Abaskohi
Juan A. Rodriguez
Chris Pal
David Vazquez
Spandana Gella
Sai Rajeswar
Perouz Taslakian
2025-03-27
ArXiv (preprint)
arxiv.org
arxiv.org
Assessing SAM for Tree Crown Instance Segmentation from Drone Imagery
Mélisande Teng
Arthur Ouaknine
Etienne Lalibert'e
Yoshua Bengio
David Rolnick
Hugo Larochelle
2025-03-26
ArXiv (preprint)
arxiv.org
arxiv.org
A data-driven approach to model spatial dose characteristics for catheter placement of high dose-rate brachytherapy for prostate cancer.
Björn Morén
Hossein Jafarzadeh
Shirin A. Enger
2025-03-26
Computers in Biology and Medicine (published)
doi.org