Publications

Spinal cord evaluation in multiple sclerosis: clinical and radiological associations, present and future
B Mark Keegan
Martina Absinta
Julien Cohen-Adad
Eoin P Flanagan
Roland G Henry
Eric C Klawiter
Shannon Kolind
Stephen Krieger
Cornelia Laule
John A Lincoln
Steven Messina
Jiwon Oh
Nico Papinutto
Seth Aaron Smith
Anthony Traboulsee
2024-11-05
Brain Communications (published)
doi.org
Towards Optimizing SQL Generation via LLM Routing
Mohammadhossein Malekpour
Nour Shaheen
Foutse Khomh
Amine Mhedhbi
Text-to-SQL enables users to interact with databases through natural language, simplifying access to structured data. Although highly capabl… (see more)e large language models (LLMs) achieve strong accuracy for complex queries, they incur unnecessary latency and dollar cost for simpler ones. In this paper, we introduce the first LLM routing approach for Text-to-SQL, which dynamically selects the most cost-effective LLM capable of generating accurate SQL for each query. We present two routing strategies (score- and classification-based) that achieve accuracy comparable to the most capable LLM while reducing costs. We design the routers for ease of training and efficient inference. In our experiments, we highlight a practical and explainable accuracy-cost trade-off on the BIRD dataset.
2024-11-05
ArXiv (preprint)
doi.org
arxiv.org
Temporal Residual Jacobians For Rig-free Motion Transfer
Sanjeev Muralikrishnan
Niladri Dutt
Siddhartha Chaudhuri
Noam Aigerman
Vladimir Kim
Matthew Fisher
Niloy J. Mitra
We introduce Temporal Residual Jacobians as a novel representation to enable data-driven motion transfer. Our approach does not assume acces… (see more)s to any rigging or intermediate shape keyframes, produces geometrically and temporally consistent motions, and can be used to transfer long motion sequences. Central to our approach are two coupled neural networks that individually predict local geometric and temporal changes that are subsequently integrated, spatially and temporally, to produce the final animated meshes. The two networks are jointly trained, complement each other in producing spatial and temporal signals, and are supervised directly with 3D positional information. During inference, in the absence of keyframes, our method essentially solves a motion extrapolation problem. We test our setup on diverse meshes (synthetic and scanned shapes) to demonstrate its superiority in generating realistic and natural-looking animations on unseen body shapes against SoTA alternatives. Supplemental video and code are available at https://temporaljacobians.github.io/ .
2024-11-04
Lecture Notes in Computer Science (published)
doi.org
arxiv.org
Efficient Assignment with Time Constraints for Heterogeneous DSP Systems.
Jiajie Li
Christophe Dubach
Warren J. Gross
High-level synthesis (HLS) produces hardware au-tomatically by scheduling and assigning resources based on an input control/data-flow graph.… (see more) One particular aspect of HLS for the digital signal processing (DSP) architecture is the het-erogeneous assignment problem (HAP) which maps operations into different types of functional units available in the electronic design automation tools to build efficient implementations. An optimal solution to this assignment problem can be found by formulating the problem as integer linear programming (ILP) and using a solver. However, given the slow nature of this process, heuristics tend to be used instead leading to sub-optimal designs. This paper revisits the classical ILP formulation of the HAP with time constraints for the DSP architecture by identifying redundant constraints. This paper proves theoretically, and demonstrates experimentally, that removing these constraints does not affect the obtained solution. This technique achieves speedups of more than 100 × in terms of runtime and reductions of more than 50 × in terms of memory usage of the solver. Also, this work proposes an updated heuristic that keeps reducing the latency of a path instead of finding a new critical path after giving a new node assignment. Runtime reductions (more than another 10×) due to reduced numbers of critical path searches are observed while returning similar results.
2024-11-03
IEEE Workshop on Signal Processing Systems (published)
doi.org
Crystal Design Amidst Noisy DFT Signals: A Reinforcement Learning Approach
Prashant Govindarajan
Mathieu Reymond
Santiago Miret
Mariano Phielipp
A. Chandar
2024-11-02
NeurIPS.cc/2024/Workshop/AI4Mat (published)
openreview.net
openreview.net
ImmunoStruct: Integration of protein sequence, structure, and biochemical properties for immunogenicity prediction and interpretation
Kevin Bijan Givechian
João Felipe Rocha
Edward Yang
Chen Liu
Kerrie Greene
Rex Ying
Etienne Caron
Akiko Iwasaki
Smita Krishnaswamy
2024-11-02
bioRxiv (preprint)
doi.org
Enhancing Neural Network Interpretability with Feature-Aligned Sparse Autoencoders
Luke Marks
Alasdair Paren
David M. Krueger
Fazl Barez
Sparse Autoencoders (SAEs) have shown promise in improving the interpretability of neural network activations, but can learn features that a… (see more)re not features of the input, limiting their effectiveness. We propose \textsc{Mutual Feature Regularization} \textbf{(MFR)}, a regularization technique for improving feature learning by encouraging SAEs trained in parallel to learn similar features. We motivate \textsc{MFR} by showing that features learned by multiple SAEs are more likely to correlate with features of the input. By training on synthetic data with known features of the input, we show that \textsc{MFR} can help SAEs learn those features, as we can directly compare the features learned by the SAE with the input features for the synthetic data. We then scale \textsc{MFR} to SAEs that are trained to denoise electroencephalography (EEG) data and SAEs that are trained to reconstruct GPT-2 Small activations. We show that \textsc{MFR} can improve the reconstruction loss of SAEs by up to 21.21\% on GPT-2 Small, and 6.67\% on EEG data. Our results suggest that the similarity between features learned by different SAEs can be leveraged to improve SAE training, thereby enhancing performance and the usefulness of SAEs for model interpretability.
2024-11-01
ArXiv (preprint)
doi.org
openreview.net
AI-EDI-SPACE: A Co-designed Dataset for Evaluating the Quality of Public Spaces
S. Gowaikar
Hugo Berard
Rashid A. Mushkani
Emmanuel Beaudry Marchand
Toumadher Ammar
Shin Koseki
Advancements in AI heavily rely on large-scale datasets meticulously curated and annotated for training. However, concerns persist regarding… (see more) the transparency and context of data collection methodologies, especially when sourced through crowdsourcing platforms. Crowdsourcing often employs low-wage workers with poor working conditions and lacks consideration for the representativeness of annotators, leading to algorithms that fail to represent diverse views and perpetuate biases against certain groups. To address these limitations, we propose a methodology involving a co-design model that actively engages stakeholders at key stages, integrating principles of Equity, Diversity, and Inclusion (EDI) to ensure diverse viewpoints. We apply this methodology to develop a dataset and AI model for evaluating public space quality using street view images, demonstrating its effectiveness in capturing diverse perspectives and fostering higher-quality data.
2024-10-31
arXiv (published)
doi.org
arxiv.org
Association Between Circulating Vitamin K Levels, Gut Microbiome, and Type 1 Diabetes: A Mendelian Randomization Study
Samuel De La Barrera
Benjamin De La Barrera
Marc-André Legault
Isabel Gamache
Despoina Manousaki
Background/Objectives: Nutritional deficiencies have been proposed as possible etiological causes for autoimmune diseases, among which type … (see more)1 diabetes (T1D). Vitamin K (VK) has potentially positive effects on type 2 diabetes, but its role on T1D in humans remains largely unknown. We aimed to examine the presence of a causal association between VK and T1D using a Mendelian randomization (MR) approach. Methods: Genetic variants from a genome-wide association study (GWAS) for VK (N = 2138 Europeans) were used as instruments in our two-sample MR study to investigate whether circulating VK levels are causally associated with the risk of T1D in a large European T1D GWAS cohort (18,942 cases/520,580 controls). Through a multivariable MR (MVMR), the effects of both VK and specific gut microbiota on T1D were investigated given that the gut microbiome synthesizes VK. Results: We found that changes in levels of circulating VK did not affect T1D risk in our univariate two-sample MR, but this study had limited power to detect small effects of VK (OR for T1D of less than 0.8). However, our MVMR indicated a suggestive association of VK with the risk of T1D adjusting for two different gut microbiome populations. Conclusions: In conclusion, VK levels are unlikely to significantly affect the risk of T1D, but small effects cannot be excluded, and the role of gut microbiome in this association should be further investigated.
2024-10-31
Nutrients (published)
doi.org
Community-based reconstruction and simulation of a full-scale model of the rat hippocampus CA1 region
Armando Romani
Alberto Antonietti
Davide Bella
Julian Budd
Elisabetta Giacalone
Kerem Kurban
Sára Sáray
Marwan Abdellah
Alexis Arnaudon
Elvis Boci
Cristina Colangelo
Jean-Denis Courcol
Thomas Delemontex
András Ecker
Joanne Falck
Cyrille Favreau
Michael Gevaert
Juan B. Hernando
Joni Herttuainen
Genrich Ivaska … (see 28 more)
Lida Kanari
Anna-Kristin Kaufmann
James Gonzalo King
Pramod Kumbhar
Sigrun Lange
Huanxiang Lu
Carmen Alina Lupascu
Rosanna Migliore
Fabien Petitjean
Judit Planas
Pranav Rai
Srikanth Ramaswamy
Michael W. Reimann
Juan Luis Riquelme
Nadir Román Guerrero
Ying Shi
Vishal Sood
Mohameth François Sy
Werner Van Geit
Liesbeth Vanherpe
Tamás F. Freund
Audrey Mercer
Eilif Muller
Felix Schürmann
Alex M. Thomson
Michele Migliore
Szabolcs Káli
Henry Markram
The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive fun… (see more)ctions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to integrate information obtained from diverse experimental approaches. To address this challenge, we present a community-based, full-scale in silico model of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system. We tested and validated each model component and the final network model, and made input data, assumptions, and strategies explicit and transparent. The unique flexibility of the model allows scientists to potentially address a range of scientific questions. In this article, we describe the methods used to set up simulations to reproduce in vitro and in vivo experiments. Among several applications in the article, we focus on theta rhythm, a prominent hippocampal oscillation associated with various behavioral correlates and use our computer model to reproduce experimental findings. Finally, we make data, code, and model available through the hippocampushub.eu portal, which also provides an extensive set of analyses of the model and a user-friendly interface to facilitate adoption and usage. This community-based model represents a valuable tool for integrating diverse experimental data and provides a foundation for further research into the complex workings of the hippocampal CA1 region.
2024-10-31
PLoS Biology (published)
doi.org
Evaluating Generative AI Systems is a Social Science Measurement Challenge
Hanna Wallach
Meera Desai
Nicholas Pangakis
A. Feder Cooper
Angelina Wang
Solon Barocas
Alexandra Chouldechova
Chad Atalla
Su Lin Blodgett
Emily Corvi
P. A. Dow
Jean Garcia-Gathright
A.R. Olteanu
Stefanie Reed
Emily Sheng
Dan Vann
Jennifer Wortman Vaughan
Matthew Vogel
Hannah Washington
Abigail Z. Jacobs … (see 1 more)
Microsoft Research
Across academia, industry, and government, there is an increasing awareness that the measurement tasks involved in evaluating generative AI … (see more)(GenAI) systems are especially difficult. We argue that these measurement tasks are highly reminiscent of measurement tasks found throughout the social sciences. With this in mind, we present a framework, grounded in measurement theory from the social sciences, for measuring concepts related to the capabilities, impacts, opportunities, and risks of GenAI systems. The framework distinguishes between four levels: the background concept, the systematized concept, the measurement instrument(s), and the instance-level measurements themselves. This four-level approach differs from the way measurement is typically done in ML, where researchers and practitioners appear to jump straight from background concepts to measurement instruments, with little to no explicit systematization in between. As well as surfacing assumptions, thereby making it easier to understand exactly what the resulting measurements do and do not mean, this framework has two important implications for evaluating evaluations: First, it can enable stakeholders from different worlds to participate in conceptual debates, broadening the expertise involved in evaluating GenAI systems. Second, it brings rigor to operational debates by offering a set of lenses for interrogating the validity of measurement instruments and their resulting measurements.
2024-10-31
arXiv (published)
doi.org
arxiv.org
Evaluating the effectiveness of the Smart About Meds (SAM) mobile application among patients discharged from hospital: protocol of a randomised controlled trial
Robyn Tamblyn
Bettina Habib
David L Buckeridge
Daniala L Weir
Elizaveta Frolova
Rolan Alattar
Jessica Rogozinsky
Caroline Beauchamp
Rosalba Pupo
Susan J Bartlett
Emily McDonald
NCT05371548.
2024-10-31
BMJ Open (published)
doi.org