Publications

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… (voir plus)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 (publié)
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 (publié)
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… (voir plus)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 (accepté)
doi.org
openreview.net
Multiple-model coding scheme for electrical signal compression
Corentin Presvôts
Michel Kieffer
Thibault Prevost
Patrick Panciatici
Zuxing Li
Pablo Piantanida
2025-03-31
Signal Processing (publié)
doi.org
Negative Language Transfer Identification in the English Writing of Chinese and Farsi Native Speakers
Mohammad Karimiabdolmaleki
Leticia Farias Wanderley
Maria Cutumisu
Mohsen Rezazadeh
Carrie Demmans Epp
2025-03-31
International Journal of Artificial Intelligence in Education (publié)
doi.org
Online Interior-point Methods for Time-varying Equality-constrained Optimization
Jean-Luc Lupien
Iman Shames
Antoine Lesage-Landry
2025-03-31
IEEE Transactions on Automatic Control (publié)
doi.org
arxiv.org
Scaling Language-Free Visual Representation Learning
David Fan
Shengbang Tong
Jiachen Zhu
Koustuv Sinha
Zhuang Liu
Xinlei Chen
Michael G. Rabbat
Nicolas Ballas
Yann Lecun
Amir Bar
Saining Xie
2025-03-31
ArXiv (prépublication)
doi.org
arxiv.org
A Systematic Review of the Empirical Use of the CCHS-MH (Canadian Community Health Survey–Mental Health) Survey
Maria Cutumisu
2025-03-31
Proceedings of the 2025 AERA Annual Meeting (publié)
doi.org
On the Analysis and Distillation of Emergent Outlier Properties in Pre-trained Language Models
Tianyang Zhao
Kunwar Yashraj Singh
Srikar Appalaraju
Peng Tang
Ying Nian Wu
Li Erran Li
Li
Rishabh Agarwal
Nino Vieillard
Yongchao Zhou
Piotr Stańczyk
Sabela Ramos Garea
Matthieu Geist
Rohan Anil
Andrew M. Dai
Melvin Orhan Firat
Dmitry Lepikhin
Alexandre Passos
Siamak Shakeri
Emanuel Taropa … (voir 478 de plus)
Paige Bailey
Zhifeng Chen
Eric Chu
Jonathan H. Clark
Laurent El
Yanping Huang
K. Meier-Hellstern
Gaurav Mishra
Erica Moreira
Mark Omernick
Kevin Robinson
Sebastian Ruder
Yi Tay
Kefan Xiao
Yuanzhong Xu
Yujing Zhang
Gustavo Hernández Abrego
Junwhan Ahn
Jacob Austin
Paul R. Barham
Jan Botha
James Bradbury
Siddhartha Brahma
Kevin Brooks
M. Catasta
Yong Cheng
Colin Cherry
Christopher A. Choquette-Choo
Aakanksha Chowdhery
Clé-ment Crepy
Shachi Dave
Mostafa Dehghani
Sunipa Dev
Jacob Devlin
Mark Díaz
Nan Du
Ethan Dyer
Vladimir Feinberg
Fangxiaoyu Feng
Vlad Fienber
Markus Freitag
Xavier Garcia
Sebastian Gehrmann
Lucas Gonzalez
Guy Gur-Ari
Steven Hand
Hadi Hashemi
Le Hou
Joshua Howland
Andrea Hu
Jeffrey Hui
Jeremy Hur-witz
Michael Acheson Isard
Abe Ittycheriah
Matthew Jagiel-ski
Wenhao Jia
Kathleen Kenealy
M. Krikun
Sneha Kudugunta 0001
Chang Lan
Kather-ine Lee
Benjamin Lee
Music Eric Li
Wei Li
YaGuang Li
Li Jian
Hyeontaek Li
Hanzhao Lim
Zhongtao Lin
Liu Frederick
Marcello Liu
Aroma Maggioni
Mahendru Joshua
Vedant Maynez
Maysam Misra
Moussalem Zachary
John Nado
E. Nham
Andrew Ni
Alicia Nys-trom
Marie Parrish
M. Pellat
Polacek Alex
Reiner Polozov
Siyuan Pope
Emily Qiao
Reif Bryan
Parker Richter
Alex Riley
Castro Ros
Aurko Roy
Brennan Saeta
Rajkumar Samuel
Renee Shelby
Ambrose Slone
Daniel Smilkov
David R. So
Daniel Sohn
Simon Tokumine
Dasha Valter
Haim-ing Bao
Mo Bavarian
Jeff Belgum
Ir-wan Bello
Jake Berdine
Gabriel Bernadett-Shapiro
Christopher Berner
Lenny Bogdonoff
Oleg Boiko
Madelaine Boyd
Anna-Luisa Brakman
Greg Brock-man
Tim Brooks
M. Brundage
Kevin Button
Trevor Cai
Rosie Campbell
Andrew Cann
Brittany Carey
Chelsea Carlson
Rory Carmichael
Brooke Chan
Che Chang
Fotis Chantzis
Derek Chen
Sully Chen
Ruby Chen
Jason Chen
Mark Chen
Benjamin Chess
Chester Cho
Hyung Casey Chu
Won Chung
Dave Cummings
Jeremiah Currier
Yunxing Dai
Tarun Goel
Gabriel Gogineni
Rapha Goh
Jonathan Gontijo-Lopes
Morgan Gordon
Scott Grafstein
Ryan Gray
Joshua Greene
Shixiang Shane Gross
Yufei Gu
Chris Guo
Jesse Hallacy
Jeff Han
Harris Yuchen
Mike He
Johannes Heaton
C. Heidecke
Alan Hesse
Wade Hickey
Peter Hickey
Hoeschele Brandon
Kenny Houghton
Shengli Hsu
Xin Hu
Joost Hu
Shantanu Huizinga
Shawn Jain
Jain Joanne
Angela Jang
Roger Jiang
Haozhun Jiang
Denny Jin
Shino Jin
Billie Jomoto
Hee-woo Jonn
Tomer Jun
Łukasz Kaftan
Ali Kaiser
Ingmar Ka-mali
Kanitscheider
Nitish Shirish
Keskar Tabarak
Logan Khan
J. Kilpatrick
Kim Christina
Yongjik Kim
Jan Hendrik Kim
Jamie Kirch-ner
Matt Kiros
Daniel Knight
Kokotajlo Łukasz
A. Kondraciuk
Aris Kondrich
Kyle Kon-stantinidis
Gretchen Kosic
Vishal Krueger
Michael Kuo
Ikai Lampe
Teddy Lan
Jan Lee
Jade Leike
Daniel Leung
Chak Ming Levy
Li Rachel
Molly Lim
Stephanie Lin
Mateusz Lin
Theresa Litwin
Ryan Lopez
Patricia Lowe
Lue Anna
Kim Makanju
S. Malfacini
Todor Manning
Yaniv Markov
Bianca Markovski
Katie Martin
Andrew Mayer
Bob Mayne
Scott Mayer McGrew
Christine McKinney
Paul McLeavey
McMillan Jake
David McNeil
Aalok Medina
Jacob Mehta
Luke Menick
Andrey Metz
Pamela Mishchenko
Vinnie Mishkin
Evan Monaco
Daniel Morikawa
Tong Mossing
Mira Mu
Oleg Murati
David Murk
Ashvin Mély
Reiichiro Nair
Rajeev Nakano
Nayak Arvind
Richard Neelakantan
Hyeonwoo Ngo
Noh Long
Cullen Ouyang
Jakub O’Keefe
Alex Pachocki
J. Paino
Ashley Palermo
Pantuliano
Carl Ross
Bob Rotsted
Henri Roussez
Nick Ry-der
Mario Saltarelli
Ted Sanders
Shibani Santurkar
Girish Sastry
Heather Schmidt
David Schnurr
John Schulman
Daniel Selsam
Kyla Sheppard
Toki Sherbakov
Jessica Shieh
Sarah Shoker
Pranav Shyam
Szymon Sidor
Eric Sigler
Maddie Simens
Jordan Sitkin
Katarina Slama
Ian Sohl
Benjamin D. Sokolowsky
Yang Song
Natalie Staudacher
Clemens Winter
Samuel Wolrich
Hannah Wong
Lauren Workman
Sherwin Wu
Michael Wu
Kai Xiao
Tao Xu
Sarah Yoo
Kevin Yu
Qim-ing Yuan
Wojciech Zaremba
Rowan G. Zellers
Chong Zhang
Marvin Zhang
Tianhao Shengjia Zhao
Ouyang Long
Jeff Wu
Xu Jiang
Diogo Almeida
C. Wainwright
Pamela Mishkin
Sandhini Agarwal
Alex Ray
Jacob Hilton
Fraser Kelton
Luke Miller
Amanda Askell
Peter Welinder
Paul F. Christiano
Jan Leike
Ryan Lowe. 2022
Adam Paszke
Sam Gross
Francisco Massa
Adam Lerer
Gregory Chanan
Trevor Killeen
Ze-Bin Lin
Natalia Gimelshein
L. Antiga
Alban Desmaison
Andreas Köpf
Edward Yang
Zachary DeVito
Martin Raison
A. Tejani
Sasank Chilamkurthy
Benoit Steiner
Giovanni Puccetti
Anna Rogers
Aleksandr Drozd
Felice
Dell’Orletta. 2022. Outlier
Alec Radford
Jong Wook Kim
Chris Hallacy
Aditya Ramesh
Gabriel Goh
Girish Sas-try
J. Clark
Rewon Child
David Luan
Victor Sanh
Alex Webson
Colin Raffel
Stephen H. Bach
Lintang A. Sutawika
Zaid Alyafeai
Antoine Chaffin
Arnaud Stiegler
Arun Raja
Manan Dey
Saiful Bari
Canwen Xu
Urmish Thakker
Shanya Sharma Sharma
Eliza Szczechla
Taewoon Kim 0002
Gunjan Chhablani
Ni-hal Nayak
Debajyoti Datta
Mike Jonathan Chang
Tian-Jian Jiang
Han Wang
Matteo Manica
Sheng Shen
Zheng-Xin Yong
Harshit Pandey
Rachel Bawden
Thomas Wang
Trishala Neeraj
Jos Rozen
Abheesht Sharma
Thibault Févry
Jason Alan Fries
Ryan Teehan
Teven Le Scao
Stella Biderman
Leo Gao
Thomas Wolf 0008
A. M. R. 2022
Multi-task
Richard Socher
Alex Perelygin
Jean Wu
Jason Chuang
Christopher D Manning
Andrew Ng
Christopher Potts
Recursive
Aarohi Srivastava
Abhinav Rastogi
Abhishek Rao
Abu Awal
Md. Shoeb
Abubakar Abid
Adam Fisch
Adam R. Brown
Adam Santoro
Aditya Gupta
Adrià Garriga-Alonso
Agnieszka Kluska
Aitor Lewkowycz
Akshat Agarwal
Alethea Power
Alex Warstadt
Alexander W. Kocurek
Ali Safaya
Ali Tazarv
Alice Xiang
Alicia Parrish
Allen Nie
Aman Hussain
Amanda Dsouza
Ameet Rahane
Anantharaman S. Iyer
Anders Johan Andreassen
Andrea Madotto
Andrea Santilli
Andreas Stuhlmüller
Andrew La
Andrew Lampinen
Andy Zou
Angela Jiang
Angelica Chen
Anh Vuong
Animesh Gupta
Anna Gottardi
Antonio Norelli
Anu Venkatesh
Arash Gholamidavoodi
Arfa Tabassum
Arul Menezes
Arun Kirubara-jan
Asher Mullokandov
Ashish Sabharwal
Austin Herrick
Avia Efrat
Aykut Erdem
Ayla Karaka¸s
Ryan Roberts
Bao Sheng Loe
Barret Zoph
Bartłomiej Bojanowski
Batuhan Özyurt
Behnam Hedayatnia
Behnam Neyshabur
Benjamin Inden
Benno Stein
Berk Ekmekci
Bill Yuchen
Blake Lin
Bryan Howald
Cameron Orinion
Cameron Diao
Catherine Dour
Cedrick Stinson
César Argueta
Chandan Ferri
Charles Singh
Chenlin Rathkopf
Chitta Meng
C. Baral
Chris Wu
Chris Callison-Burch
Christopher Waites
Christo-pher D Voigt
Cindy Potts
E. RamirezClara
Clemencia Rivera
Colin Siro
Court-ney Raffel
Cristina Ashcraft
Damien Garbacea
Sileo Dan
Dan Garrette
Dan Hendrycks
Dan Kilman
C. Roth
C. Daniel Freeman
Daniel Khashabi
Daniel Levy
Daniel Moseguí González
Danielle Perszyk
Danny Hernandez
Danqi Chen
2025-03-31
Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers) (publié)
doi.org
Trade‐off of different deep learning‐based auto‐segmentation approaches for treatment planning of pediatric craniospinal irradiation autocontouring of OARs for pediatric CSI
Alana Thibodeau‐Antonacci
Marija Popovic
Ozgur Ates
Chia‐Ho Hua
James Schneider
Sonia Skamene
Carolyn Freeman
S. Enger
James Man Git Tsui
As auto‐segmentation tools become integral to radiotherapy, more commercial products emerge. However, they may not always suit our needs. … (voir plus)One notable example is the use of adult‐trained commercial software for the contouring of organs at risk (OARs) of pediatric patients.
2025-03-31
Medical Physics (Lancaster) (publié)
doi.org
NoProp: Training Neural Networks without Back-propagation or Forward-propagation
Qinyu Li
Yee Whye Teh
Razvan Pascanu
2025-03-30
ArXiv (prépublication)
doi.org
arxiv.org
Sharpening the dark matter signature in gravitational waveforms. II. Numerical simulations
Bradley J. Kavanagh
Theophanes K. Karydas
Gianfranco Bertone
Pierfrancesco Di Cintio
Mario Pasquato
Future gravitational wave observatories can probe dark matter by detecting the dephasing in the waveform of binary black hole mergers induce… (voir plus)d by dark matter overdensities. Such a detection hinges on the accurate modeling of the dynamical friction, induced by dark matter on the secondary compact object in intermediate and extreme mass ratio inspirals. In this paper, we introduce nbodyimri, a new publicly available code designed for simulating binary systems within cold dark matter spikes. Leveraging higher particle counts and finer time steps, we validate the applicability of the standard dynamical friction formalism and provide an accurate determination of the maximum impact parameter of particles which can effectively scatter with a compact object, across various mass ratios. We also show that in addition to feedback due to dynamical friction, the dark matter also evolves through a stirring effect driven by the time-dependent potential of the binary. We introduce a simple semianalytical scheme to account for this effect and demonstrate that including stirring tends to slow the rate of dark matter depletion and therefore enhances the impact of dark matter on the dynamics of the binary.
2025-03-30
Physical Review D (publié)
doi.org