Publications

SCIseg: Automatic Segmentation of T2-weighted Hyperintense Lesions in Spinal Cord Injury
Enamundram Naga Karthik
Jan Valošek
Andrew C. Smith
Dario Pfyffer
Simon Schading-Sassenhausen
Lynn Farner
Kenneth A. Weber
Patrick Freund
Julien Cohen-Adad
Background: Quantitative MRI biomarkers in spinal cord injury (SCI) can help understand the extent of the focal injury. However, due to the … (see more)lack of automatic segmentation methods, these biomarkers are derived manually, which is a time-consuming process prone to intra- and inter-rater variability, thus limiting large multi-site studies and translation to clinical workflows. Purpose: To develop a deep learning tool for the automatic segmentation of T2-weighted hyperintense lesions and the spinal cord in SCI patients. Material and Methods: This retrospective study included a cohort of SCI patients from three sites enrolled between July 2002 and February 2023 who underwent clinical MRI examination. A deep learning model, SCIseg, was trained on T2-weighted images with heterogeneous image resolutions (isotropic, anisotropic), and orientations (axial, sagittal) acquired using scanners from different manufacturers (Siemens, Philips, GE) and different field strengths (1T, 1.5T, 3T) for the automatic segmentation of SCI lesions and the spinal cord. The proposed method was visually and quantitatively compared with other open-source baseline methods. Quantitative biomarkers (lesion volume, lesion length, and maximal axial damage ratio) computed from manual ground-truth lesion masks and automatic SCIseg predictions were correlated with clinical scores (pinprick, light touch, and lower extremity motor scores). A between-group comparison was performed using the Wilcoxon signed-rank test. Results: MRI data from 191 SCI patients (mean age, 48.1 years {+/-} 17.9 [SD]; 142 males) were used for training. Compared to existing methods, SCIseg achieved the best segmentation performance for both the cord and lesions and generalized well to both traumatic and non-traumatic SCI patients. SCIseg is open-source and accessible through the Spinal Cord Toolbox. Conclusion: Automatic segmentation of intramedullary lesions commonly seen in traumatic SCI replaces the tedious manual annotation process and enables the extraction of relevant lesion morphometrics in large cohorts. The proposed model generalizes across lesion etiologies (traumatic, ischemic), scanner manufacturers and heterogeneous image resolutions.
2024-01-03
medRxiv (preprint)
doi.org
DIG In: Evaluating Disparities in Image Generations with Indicators for Geographic Diversity
Melissa Hall
Candace Ross
Adina Williams
Nicolas Carion
Michal Drozdzal
Adriana Romero Soriano
The unprecedented photorealistic results achieved by recent text-to-image generative systems and their increasing use as plug-and-play conte… (see more)nt creation solutions make it crucial to understand their potential biases. In this work, we introduce three indicators to evaluate the realism, diversity and prompt-generation consistency of text-to-image generative systems when prompted to generate objects from across the world. Our indicators complement qualitative analysis of the broader impact of such systems by enabling automatic and efficient benchmarking of geographic disparities, an important step towards building responsible visual content creation systems. We use our proposed indicators to analyze potential geographic biases in state-of-the-art visual content creation systems and find that: (1) models have less realism and diversity of generations when prompting for Africa and West Asia than Europe, (2) prompting with geographic information comes at a cost to prompt-consistency and diversity of generated images, and (3) models exhibit more region-level disparities for some objects than others. Perhaps most interestingly, our indicators suggest that progress in image generation quality has come at the cost of real-world geographic representation. Our comprehensive evaluation constitutes a crucial step towards ensuring a positive experience of visual content creation for everyone. Code is available at https://github.com/facebookresearch/DIG-In/.
2024-01-02
TMLR (accepted)
doi.org
openreview.net
Influence of scanning plane on Human Spinal Cord functional Magnetic Resonance echo planar imaging
Marta Moraschi
Silvia Tommasin
Laura Maugeri
Mauro Dinuzzo
Julien Cohen-Adad
Marco Masullo
Fabio Mangini
Lorenzo Giovannelli
Daniele Mascali
Tommaso Gili
Valerio Pisani
Ugo Md Nocentini
Federico Giove
Michela Fratini
BACKGROUND: Functional Magnetic Resonance Imaging (fMRI) is based on the Blood Oxygenation Level Dependent contrast and has been exploited f… (see more)or the indirect study of the neuronal activity within both the brain and the spinal cord. However, the interpretation of spinal cord fMRI (scfMRI) is still controversial and its diffusion is rather limited because of technical limitations. Overcoming these limitations would have a beneficial effect for the assessment and follow-up of spinal injuries and neurodegenerative diseases. PURPOSE: This study was aimed at systematically verify whether sagittal scanning in scfMRI using EPI readout is a viable alternative to the more common axial scanning, and at optimizing a pipeline for EPI-based scfMRI data analysis, based on Spinal Cord Toolbox (SCT). METHODS: Forty-five healthy subjects underwent MRI acquisition in a Philips Achieva 3T MRI scanner. T2*-weighted fMRI data were acquired using a GE-EPI sequence along sagittal and axial planes during an isometric motor task. Differences on benchmarks were assessed via paired two-sample t-test at p=0.05. RESULTS: We investigated the impact of the acquisition strategy by means of various metrics such as Temporal Signal to Noise Ratio (tSNR), Dice Coefficient to assess geometric distortions, Reproducibility and Sensitivity. tSNR was higher in axial than in sagittal scans, as well as reproducibility within the whole cord mask (t=7.4, p0.01) and within the GM mask (t=4.2, p0.01). The other benchmarks, associated with distortion and functional response, showed no differenc
2024-01-02
ArXiv (preprint)
arxiv.org
arxiv.org
More than one way to skin a dose volume: the impact of dose-surface map calculation approach on study reproducibility.
Haley Patrick
John Kildea
2024-01-02
Physics in Medicine and Biology (published)
doi.org
Uncertainty Resolution in Misinformation Detection
Yury Orlovskiy
Camille Thibault
Anne Imouza
Jean-François Godbout
Reihaneh Rabbany
Kellin Pelrine
2024-01-02
ArXiv (preprint)
doi.org
arxiv.org
Adaptation Odyssey in LLMs: Why Does Additional Pretraining Sometimes Fail to Improve?
Firat Oncel
Matthias Bethge
Beyza Ermis
Mirco Ravanelli
Cem Subakan
cCaugatay Yildiz
2024-01-01
EMNLP (published)
arxiv.org
arxiv.org
An Addendum to NeBula: Towards Extending TEAM CoSTAR’s Solution to Larger Scale Environments
Benjamin Morrell
Kyohei Otsu
Ali Agha
David D. Fan
Sung-Kyun Kim
Muhammad Fadhil Ginting
Xianmei Lei
Jeffrey Edlund
Seyed Fakoorian
Amanda Bouman
Fernando Chavez
Taeyeon Kim
Gustavo J. Correa
Maira Saboia
Angel Santamaria-Navarro
Brett Lopez
Boseong Kim
Chanyoung Jung
Mamoru Sobue
Oriana Claudia Peltzer … (see 69 more)
Joshua Ott
Robert Trybula
Thomas Touma
Marcel Kaufmann
Tiago Stegun Vaquero
Torkom Pailevanian
Matteo Palieri
Yun Chang
Andrzej Reinke
Matthew Anderson
Frederik E.T. Schöller
Patrick Spieler
Lillian Clark
Avak Archanian
Kenny Chen
Hovhannes Melikyan
Anushri Dixit
Harrison Delecki
Daniel Pastor
Barry Ridge
Nicolas Marchal
Jose Uribe
Sharmita Dey
Kamak Ebadi
Kyle Coble
Alexander Nikitas Dimopoulos
Vivek Thangavelu
Vivek Shankar Vardharajan
Nicholas Palomo
Antoni Rosinol
Arghya Chatterjee
Christoforos Kanellakis
Bjorn Lindqvist
Micah Corah
Kyle Strickland
Ryan Stonebraker
Michael Milano
Christopher E. Denniston
Sami Sahnoune
Thomas Claudet
Seungwook Lee
Gautam Salhotra
Edward Terry
Rithvik Musuku
Robin Schmid
Tony Tran
Ara Kourchians
Justin Schachter
Hector Azpurua
Levi Resende
Arash Kalantari
Jeremy Nash
Josh Lee
Christopher Patterson
Jen Blank
Kartik Patath
Yuki Kubo
Ryan Alimo
Yasin Almalioglu
Aaron Curtis
Jacqueline Sly
Tesla Wells
Nhut T. Ho
Mykel Kochenderfer
Giovanni Beltrame
George Nikolakopoulos
David Shim
Luca Carlone
Joel Burdick
This paper presents an appendix to the original NeBula autonomy solution [Agha et al., 2021] developed by the TEAM CoSTAR (Collaborative Sub… (see more)Terranean Autonomous Robots), participating in the DARPA Subterranean Challenge. Specifically, this paper presents extensions to NeBula’s hardware, software, and algorithmic components that focus on increasing the range and scale of the exploration environment. From the algorithmic perspective, we discuss the following extensions to the original NeBula framework: (i) large-scale geometric and semantic environment mapping; (ii) an adaptive positioning system; (iii) probabilistic traversability analysis and local planning; (iv) large-scale POMDPbased global motion planning and exploration behavior; (v) large-scale networking and decentralized reasoning; (vi) communication-aware mission planning; and (vii) multi-modal ground-aerial exploration solutions. We demonstrate the application and deployment of the presented systems and solutions in various large-scale underground environments, including limestone mine exploration scenarios as well as deployment in the DARPA Subterranean challenge.
2024-01-01
IEEE Transactions on Field Robotics (published)
doi.org
Affirmative Safety: An Approach to Risk Management for Advanced Ai
Akash Wasil
Joshua Clymer
David Scott Krueger
Emily Dardaman
Simeon Campos
Evan Murphy
2024-01-01
SSRN Electronic Journal (published)
doi.org
AIoT Smart Home via Autonomous LLM Agents
Dmitriy Rivkin
Francois Hogan
Amal Feriani
Abhisek Konar
Adam Sigal
Xue (Steve) Liu
Gregory Dudek
2024-01-01
IEEE Internet of Things Journal (published)
doi.org
AmbieGen at the SBFT 2024 Tool Competition - CPS-UAV Track
Dmytro Humeniuk
Foutse Khomh
2024-01-01
SBFT@ICSE (published)
doi.org
AmbieGenVAE at the SBFT 2024 Tool Competition - Cyber-Physical Systems Track
Dmytro Humeniuk
Foutse Khomh
2024-01-01
SBFT@ICSE (published)
doi.org
An Analysis of Quantile Temporal-Difference Learning
Mark Rowland
Remi Munos
Mohammad Gheshlaghi Azar
Yunhao Tang
Georg Ostrovski
Anna Harutyunyan
K. Tuyls
Marc Gendron-Bellemare
Will Dabney
We analyse quantile temporal-difference learning (QTD), a distributional reinforcement learning algorithm that has proven to be a key compon… (see more)ent in several successful large-scale applications of reinforcement learning. Despite these empirical successes, a theoretical understanding of QTD has proven elusive until now. Unlike classical TD learning, which can be analysed with standard stochastic approximation tools, QTD updates do not approximate contraction mappings, are highly non-linear, and may have multiple fixed points. The core result of this paper is a proof of convergence to the fixed points of a related family of dynamic programming procedures with probability 1, putting QTD on firm theoretical footing. The proof establishes connections between QTD and non-linear differential inclusions through stochastic approximation theory and non-smooth analysis.
arxiv.org