Publications

GPS-SSL: Guided Positive Sampling to Inject Prior Into Self-Supervised Learning
Aarash Feizi
Randall Balestriero
Arantxa Casanova
Adriana Romero Soriano
Reihaneh Rabbany
We propose Guided Positive Sampling Self-Supervised Learning (GPS-SSL), a general method to inject a priori knowledge into Self-Supervised L… (voir plus)earning (SSL) positive samples selection. Current SSL methods leverage Data-Augmentations (DA) for generating positive samples and incorporate prior knowledge - an incorrect, or too weak DA will drastically reduce the quality of the learned representation. GPS-SSL proposes instead to design a metric space where Euclidean distances become a meaningful proxy for semantic relationship. In that space, it is now possible to generate positive samples from nearest neighbor sampling. Any prior knowledge can now be embedded into that metric space independently from the employed DA. From its simplicity, GPS-SSL is applicable to any SSL method, e.g. SimCLR or BYOL. A key benefit of GPS-SSL is in reducing the pressure in tailoring strong DAs. For example GPS-SSL reaches 85.58% on Cifar10 with weak DA while the baseline only reaches 37.51%. We therefore move a step forward towards the goal of making SSL less reliant on DA. We also show that even when using strong DAs, GPS-SSL outperforms the baselines on under-studied domains. We evaluate GPS-SSL along with multiple baseline SSL methods on numerous downstream datasets from different domains when the models use strong or minimal data augmentations. We hope that GPS-SSL will open new avenues in studying how to inject a priori knowledge into SSL in a principled manner.
2024-01-03
ArXiv (prépublication)
doi.org
openreview.net
Recovering Dantzig–Wolfe Bounds by Cutting Planes
Rui Chen
Oktay Günlük
Andrea Lodi
Leveraging Dantzig–Wolfe Decomposition in the Original Variable Space for Mixed-Integer Programming Dantzig–Wolfe decomposition has been… (voir plus) extensively applied to solve large-scale mixed-integer programs with decomposable structures, leading to exact solution approaches, such as branch and price. However, these approaches would require solving the problem in an extended variable space and are not readily present in off-the-shelf solvers. In “Recovering Dantzig–Wolfe Bounds by Cutting Planes,” Chen, Günlük, and Lodi propose a computational effective approach for generating cutting planes from Dantzig–Wolfe decomposition to enhance branch and cut in the space of original variables. The proposed approach requires a relatively small number of cutting planes to recover the strength of the Dantzig–Wolfe dual bound and should be easy to implement in general-purpose mixed-integer programming solvers. The authors show that these cutting planes typically lead to a formulation with lower dual degeneracy and hence, a better computational performance than naïve approaches, such as the objective function cut.
2024-01-03
Operations Research (publié)
doi.org
arxiv.org
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 … (voir plus)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 (prépublication)
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… (voir plus)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 (accepté)
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… (voir plus)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 (prépublication)
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 (publié)
doi.org
Uncertainty Resolution in Misinformation Detection
Yury Orlovskiy
Camille Thibault
Anne Imouza
Jean-François Godbout
Reihaneh Rabbany
Kellin Pelrine
2024-01-02
ArXiv (prépublication)
doi.org
arxiv.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… (voir plus)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
Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral Entropy
Danqi Liao
Chen Liu
Benjamin W Christensen
Alexander Tong
Guillaume Huguet
Guy Wolf
Maximilian Nickel
Ian Adelstein
Smita Krishnaswamy
Entropy and mutual information in neural networks provide rich information on the learning process, but they have proven difficult to comput… (voir plus)e reliably in high dimensions. Indeed, in noisy and high-dimensional data, traditional estimates in ambient dimensions approach a fixed entropy and are prohibitively hard to compute. To address these issues, we leverage data geometry to access the underlying manifold and reliably compute these information-theoretic measures. Specifically, we define diffusion spectral entropy (DSE) in neural representations of a dataset as well as diffusion spectral mutual information (DSMI) between different variables representing data. First, we show that they form noise-resistant measures of intrinsic dimensionality and relationship strength in high-dimensional simulated data that outperform classic Shannon entropy, nonparametric estimation, and mutual information neural estimation (MINE). We then study the evolution of representations in classification networks with supervised learning, self-supervision, or overfitting. We observe that (1) DSE of neural representations increases during training; (2) DSMI with the class label increases during generalizable learning but stays stagnant during overfitting; (3) DSMI with the input signal shows differing trends: on MNIST it increases, while on CIFAR-10 and STL-10 it decreases. Finally, we show that DSE can be used to guide better network initialization and that DSMI can be used to predict downstream classification accuracy across 962 models on ImageNet.
2024-01-01
CISS (publié)
doi.org
openreview.net
BAND: Biomedical Alert News Dataset
Zihao Fu
Meiru Zhang
Zaiqiao Meng
Yannan Shen
Anya Okhmatovskaia
David Buckeridge
Nigel Collier
2024-01-01
AAAI (publié)
doi.org
arxiv.org
A benchmark of individual auto-regressive models in a massive fMRI dataset
Fraçois Paugam
Basile Pinsard
Guillaume Lajoie
Pierre (Louis) Bellec
Dense functional magnetic resonance imaging datasets open new avenues to create auto-regressive models of brain activity. Individual idiosyn… (voir plus)crasies are obscured by group models, but can be captured by purely individual models given sufficient amounts of training data. In this study, we compared several deep and shallow individual models on the temporal auto-regression of BOLD time series recorded during a natural video watching task. The best performing models were then analyzed in terms of their data requirements and scaling, subject specificity and the space-time structure of their predicted dynamics. We found the Chebnets, a type of graph convolutional neural network, to be best suited for temporal BOLD auto-regression, closely followed by linear models. Chebnets demonstrated an increase in performance with increasing amounts of data, with no complete saturation at 9 h of training data. Good generalization to other kinds of video stimuli and to resting state data marked the Chebnets’ ability to capture intrinsic brain dynamics rather than only stimulus-specific autocorrelation patterns. Significant subject specificity was found at short prediction time lags. The Chebnets were found to capture lower frequencies at longer prediction time lags, and the spatial correlations in predicted dynamics were found to match traditional functional connectivity networks. Overall, these results demonstrate that large individual fMRI datasets can be used to efficiently train purely individual auto-regressive models of brain activity, and that massive amounts of individual data are required to do so. The excellent performance of the Chebnets likely reflects their ability to combine spatial and temporal interactions on large time scales at a low complexity cost. The non-linearities of the models did not appear as a key advantage. In fact, surprisingly, linear versions of the Chebnets appeared to outperform the original nonlinear ones. Individual temporal auto-regressive models have the potential to improve the predictability of the BOLD signal. This study is based on a massive, publicly-available dataset, which can serve for future benchmarks of individual auto-regressive modeling.
2024-01-01
Imaging Neuroscience (publié)
doi.org
BETAC: Bidirectional Encoder Transformer for Assembly Code Function Name Recovery
Guillaume Breyton
Mohd Saqib
Benjamin Fung
Philippe Charland
Recovering function names from stripped binaries is a crucial and time-consuming task for software reverse engineering’ particularly in en… (voir plus)hancing network reliability, resilience, and security. This paper tackles the challenge of recovering function names in stripped binaries, a fundamental step in reverse engineering. The absence of syntactic information and the possibility of different code producing identical behavior complicate this task. To overcome these challenges, we introduce a novel model, the Bidirectional Encoder Transformer for Assembly Code (BETAC), leveraging a transformer-based architecture known for effectively processing sequential data. BETAC utilizes self-attention mechanisms and feed-forward networks to discern complex relationships within assembly code for precise function name prediction. We evaluated BETAC against various existing encoder and decoder models in diverse binary datasets, including benign and malicious codes in multiple formats. Our model demonstrated superior performance over previous techniques in certain metrics and showed resilience against code obfuscation.
2024-01-01
DRCN (publié)
doi.org