Publications

Evaluating and Enhancing Segmentation Model Robustness with Metamorphic Testing
Seif Mzoughi
Mohamed Elshafeia
Foutse Khomh
2025-04-02
ArXiv (preprint)
doi.org
arxiv.org
Spinal Cord Tract Integrity in Degenerative Cervical Myelopathy
Newton Cho
Abdul Al-Shawwa
W. Bradley Jacobs
Nathan Evaniew
Jacques Bouchard
Steve Casha
Stephan duPlessis
Peter Lewkonia
Fred Nicholls
Alex Soroceanu
Ganesh Swamy
Kenneth C. Thomas
Michael M. H. Yang
Julien Cohen-Adad
David W. Cadotte
Degenerative cervical myelopathy (DCM) is the most common cause of spinal dysfunction globally. Despite surgical intervention, motor dysfunc… (see more)tion may persist in many patients. The purpose of this study was to comprehensively examine specific spinal cord tract changes in patients with DCM, to better understand potential substrates for compensatory recovery of function. Cervical spinal cord MRI scans with diffusion tensor imaging were performed in patients with DCM and in healthy volunteers. Spinal Cord Toolbox was used to register the PAM50 template, which includes a probabilistic atlas of the white matter tracts of the spinal cord, to the imaging data. Fractional anisotropy (FA) was extracted for each tract at C3 above the level of maximal compression and compared between patients with DCM and healthy volunteers and between patients with mild vs moderate to severe DCM. We included 25 patients with DCM (13 mild and 12 moderate to severe) and 6 healthy volunteers. FA was significantly reduced in DCM subjects relative to healthy volunteers for the lateral corticospinal tract (mild DCM vs healthy ∆ = −0.13, P = .018; moderate to severe DCM vs healthy ∆ = −0.11, P = .047), fasciculus gracilis (mild DCM vs healthy ∆ = −0.16, P = .010; moderate to severe DCM vs healthy ∆ = −0.13, P = .039), and fasciculus cuneatus (mild DCM vs healthy ∆ = −0.16, P = .007; moderate to severe DCM vs healthy ∆ = −0.15, P = .012). There were no differences in FA for all tracts between mild and moderate-to-severe DCM subjects. Patients with DCM had altered diffusion tensor imaging signal in their lateral corticospinal tract, fasciculus gracilis, and fasciculus cuneatus in comparison with healthy volunteers. These findings indicate that DCM is characterized by injury to these structures, which suggests that other tracts within the cord could potentially act as substrates for compensatory motor recovery.
2025-04-02
Neurosurgery (unknown)
doi.org
Towards Assessing Deep Learning Test Input Generators
Seif Mzoughi
Ahmed Haj Yahmed
Mohamed Elshafei
Foutse Khomh
Diego Elias Costa
2025-04-02
ArXiv (preprint)
doi.org
arxiv.org
Why do LLMs attend to the first token?
Federico Barbero
'Alvaro Arroyo
Xiangming Gu
Christos Perivolaropoulos
Michael M. Bronstein
Petar Veličković
Razvan Pascanu
2025-04-02
ArXiv (preprint)
doi.org
arxiv.org
DeepSeek-R1 Thoughtology: Let's think about LLM Reasoning
Sara Vera Marjanovi'c
Arkil Patel
Vaibhav Adlakha
Milad Aghajohari
Parishad BehnamGhader
Mehar Bhatia
Aditi Khandelwal
Austin Kraft
Benno Krojer
Xing Han Lu
Xing Han Lu
Nicholas Meade
Dongchan Shin
Amirhossein Kazemnejad
Gaurav Kamath
Marius Mosbach
Karolina Stanczak
Siva Reddy
Large Reasoning Models like DeepSeek-R1 mark a fundamental shift in how LLMs approach complex problems. Instead of directly producing an ans… (see more)wer for a given input, DeepSeek-R1 creates detailed multi-step reasoning chains, seemingly"thinking"about a problem before providing an answer. This reasoning process is publicly available to the user, creating endless opportunities for studying the reasoning behaviour of the model and opening up the field of Thoughtology. Starting from a taxonomy of DeepSeek-R1's basic building blocks of reasoning, our analyses on DeepSeek-R1 investigate the impact and controllability of thought length, management of long or confusing contexts, cultural and safety concerns, and the status of DeepSeek-R1 vis-\`a-vis cognitive phenomena, such as human-like language processing and world modelling. Our findings paint a nuanced picture. Notably, we show DeepSeek-R1 has a 'sweet spot' of reasoning, where extra inference time can impair model performance. Furthermore, we find a tendency for DeepSeek-R1 to persistently ruminate on previously explored problem formulations, obstructing further exploration. We also note strong safety vulnerabilities of DeepSeek-R1 compared to its non-reasoning counterpart, which can also compromise safety-aligned LLMs.
2025-04-01
ArXiv (preprint)
arxiv.org
arxiv.org
Predicting pathogen evolution and immune evasion in the age of artificial intelligence
D.J. Hamelin
M. Scicluna
I. Saadie
F. Mostefai
J.C. Grenier
C. Baron
E. Caron
J.G. Hussin
The genomic diversification of viral pathogens during viral epidemics and pandemics represents a major adaptive route for infectious agents … (see more)to circumvent therapeutic and public health initiatives. Historically, strategies to address viral evolution have relied on responding to emerging variants after their detection, leading to delays in effective public health responses. Because of this, a long-standing yet challenging objective has been to forecast viral evolution by predicting potentially harmful viral mutations prior to their emergence. The promises of artificial intelligence (AI) coupled with the exponential growth of viral data collection infrastructures spurred by the COVID-19 pandemic, have resulted in a research ecosystem highly conducive to this objective. Due to the COVID-19 pandemic accelerating the development of pandemic mitigation and preparedness strategies, many of the methods discussed here were designed in the context of SARS-CoV-2 evolution. However, most of these pipelines were intentionally designed to be adaptable across RNA viruses, with several strategies already applied to multiple viral species. In this review, we explore recent breakthroughs that have facilitated the forecasting of viral evolution in the context of an ongoing pandemic, with particular emphasis on deep learning architectures, including the promising potential of language models (LM). The approaches discussed here employ strategies that leverage genomic, epidemiologic, immunologic and biological information.
2025-04-01
Computational and Structural Biotechnology Journal (published)
doi.org
A Truncated Newton Method for Optimal Transport
Mete Kemertas
Amir-massoud Farahmand
Allan D. Jepson
2025-04-01
ArXiv (preprint)
doi.org
arxiv.org
Addressing Missing Modality Challenges in MRI Images: A Comprehensive Review
Reza Azad
Mohammad Dehghanmanshadi
Nika Khosravi
Julien Cohen-Adad
Dorit Merhof
2025-03-31
Computational Visual Media (published)
doi.org
Does Generative AI speak Nigerian-Pidgin?: Issues about Representativeness and Bias for Multilingualism in LLMs
David Ifeoluwa Adelani
A. Seza Doğruöz
Iyanuoluwa Shode
Aremu Anuoluwapo
2025-03-31
Findings of the Association for Computational Linguistics: NAACL 2025 (published)
doi.org
arxiv.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.
2025-03-31
Environmental Microbiology (published)
doi.org
An interpretable and reliable framework for alloy discovery in thermomechanical processing
Sushant Sinha
Xiaoping Ma
Kashif Rehman
Narges Armanfard
Stephen Yue
2025-03-31
Materials Today Communications (published)
doi.org
LLMs for Literature Review: Are we there yet?
Shubham Agarwal
Gaurav Sahu
Abhay Puri
Issam Hadj Laradji
Krishnamurthy Dj Dvijotham
Jason Stanley
Laurent Charlin
Christopher Pal
Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially du… (see more)e to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Further, we demonstrate that our planning-based approach achieves higher-quality reviews by minimizing hallucinated references in the generated review by 18-26% compared to existing simpler LLM-based generation methods.
2025-03-31
TMLR (accepted)
doi.org
openreview.net