Publications

GP.2 Deep learning prediction of response to disease modifying therapy in primary progressive multiple sclerosis
JR Falet
Joshua D. Durso-Finley
Brennan Nichyporuk
Julien Schroeter
Francesca Bovis
M Sormani
D Precup
Tal Arbel
DL Arnold
Background: Only one disease modifying therapy (DMT), ocrelizumab, was found to slow disability progression in primary progressive multiple … (see more)sclerosis (PPMS). Modeling the conditional average treatment effect (CATE) using deep learning could identify individuals more responsive to DMTs, allowing for predictive enrichment to increase the power of future clinical trials. Methods: Baseline clinical and MRI data were acquired as part of three placebo-controlled randomized clinical trials: ORATORIO (ocrelizumab), OLYMPUS (rituximab) and ARPEGGIO (laquinimod). Data from ORATORIO and OLYMPUS was separated into a training (70%) and testing (30%) set, while ARPEGGIO served as additional validation. An ensemble of multitask multilayer perceptrons was trained to predict the rate of disability progression on both treatment and placebo to estimate CATE. Results: The model could separate individuals based on their predicted treatment effect. The top 25% of individuals predicted to respond most have a larger effect size (HR 0.442, p=0.0497) than the entire group (HR 0.787, p=0.292). The model could also identify responders to laquinimod. A simulated study where the 50% most responsive individuals are randomized would require 6-times less participants to detect a significant effect. Conclusions: Individuals with PPMS who respond favourably to DMTs can be identified using deep learning based on their baseline clinical and imaging characteristics.
2022-06-23
Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques (published)
doi.org
Neural Networks as Paths through the Space of Representations
Richard D Lange
Jordan Kyle Matelsky
Xinyue Wang
Devin Kwok
David Rolnick
Konrad Paul Kording
2022-06-21
ArXiv (preprint)
doi.org
openreview.net
Relationship Between Arterial Stiffness Index, Pulse Pressure, and Magnetic Resonance Imaging Markers of White Matter Integrity: A UK Biobank Study
Atef Badji
Julien Cohen-Adad
Hélène Girouard
Alzheimer’s disease and dementia in general constitute one of the major public health problems of the 21st century. Research in arterial s… (see more)tiffness and pulse pressure (PP) play an important role in the quest to reduce the risk of developing dementia through controlling modifiable risk factors. The aim of the study is to investigate the association between peripheral PP, arterial stiffness index (ASI) and brain integrity, and to discover if ASI is a better predictor of white matter integrity than peripheral PP. 17,984 participants 63.09 ± 7.31 from the UK Biobank were used for this study. ASI was estimated using infrared light (photoplethysmography) and peripheral PP was calculated by subtracting the diastolic from the systolic brachial blood pressure value. Measure of fractional anisotropy (FA) was obtained from diffusion imaging to estimate white matter microstructural integrity. White matter hyperintensities were segmented from the combined T1 and T2-weighted FLAIR images as a measure of irreversible white matter damage. An important finding is that peripheral PP better predicts white matter integrity when compared to ASI. This finding is consistent until 75 years old. Interestingly, no significant relationship is found between either peripheral PP or ASI and white matter integrity after 75 years old. These results suggest that ASI from plethysmography should not be used to estimate cerebrovascular integrity in older adults and further question the relationship between arterial stiffness, blood pressure, and white matter damage after the age of 75 years old.
2022-06-20
Frontiers in Aging Neuroscience (published)
doi.org
Healthsheet: Development of a Transparency Artifact for Health Datasets
Negar Rostamzadeh
Diana Mincu
Subhrajit Roy
Andrew J Smart
Lauren Wilcox
Mahima Pushkarna
Jessica Schrouff
Razvan Amironesei
Nyalleng Moorosi
Katherine Heller
2022-06-19
2022 ACM Conference on Fairness, Accountability, and Transparency (published)
doi.org
arxiv.org
Uniform Priors for Data-Efficient Learning
Samarth Sinha
Karsten Roth
Anirudh Goyal
Marzyeh Ghassemi
Zeynep Akata
Hugo Larochelle
Animesh Garg
Few or zero-shot adaptation to novel tasks is important for the scalability and deployment of machine learning models. It is therefore cruci… (see more)al to find properties that encourage more transferable features in deep networks for generalization. In this paper, we show that models that learn uniformly distributed features from the training data, are able to perform better transfer learning at test-time. Motivated by this, we evaluate our method: uniformity regularization (UR) on its ability to facilitate adaptation to unseen tasks and data on six distinct domains: Few-Learning with Images, Few-shot Learning with Language, Deep Metric Learning, 0-Shot Domain Adaptation, Out-of-Distribution classification, and Neural Radiance Fields. Across all experiments, we show that using UR, we are able to learn robust vision systems which consistently offer benefits over baselines trained without uniformity regularization and are able to achieve state-of-the-art performance in Deep Metric Learning, Few-shot learning with images and language.
2022-06-18
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) (published)
doi.org
From YouTube to the brain: Transfer learning can improve brain-imaging predictions with deep learning
Nahiyan Malik
Danilo Bzdok
2022-06-17
Neural Networks (accepted)
doi.org
Kubric: A scalable dataset generator
Klaus Greff
Francois Belletti
Lucas Beyer
Carl Doersch
Yilun Du
Daniel Duckworth
David J Fleet
Dan Gnanapragasam
Florian Golemo
Charles Herrmann
Thomas Kipf
Abhijit Kundu
Dmitry Lagun
Issam Hadj Laradji
Hsueh-Ti Liu
Henning Meyer
Yishu Miao
D. Nowrouzezahrai
Cengiz Oztireli
Etienne Pot … (see 14 more)
Noha Radwan
Daniel Rebain
Sara Sabour
Mehdi S. M. Sajjadi
Matan Sela
Vincent Sitzmann
Austin Stone
Deqing Sun
Suhani Vora
Ziyu Wang
Tianhao Wu
Kwang Moo Yi
Fangcheng Zhong
Andrea Tagliasacchi
Data is the driving force of machine learning, with the amount and quality of training data often being more important for the performance o… (see more)f a system than architecture and training details. But collecting, processing and annotating real data at scale is difficult, expensive, and frequently raises additional privacy, fairness and legal concerns. Synthetic data is a powerful tool with the potential to address these shortcomings: 1) it is cheap 2) supports rich ground-truth annotations 3) offers full control over data and 4) can circumvent or mitigate problems regarding bias, privacy and licensing. Unfortunately, software tools for effective data generation are less mature than those for architecture design and training, which leads to fragmented generation efforts. To address these problems we introduce Kubric, an open-source Python framework that interfaces with PyBullet and Blender to generate photo-realistic scenes, with rich annotations, and seamlessly scales to large jobs distributed over thousands of machines, and generating TBs of data. We demonstrate the effectiveness of Kubric by presenting a series of 13 different generated datasets for tasks ranging from studying 3D NeRF models to optical flow estimation. We release Kubric, the used assets, all of the generation code, as well as the rendered datasets for reuse and modification.
2022-06-17
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org
arxiv.org
Matching Feature Sets for Few-Shot Image Classification
Arman Afrasiyabi
Hugo Larochelle
Jean‐François Lalonde
Christian Gagné
In image classification, it is common practice to train deep networks to extract a single feature vector per input image. Few-shot classific… (see more)ation methods also mostly follow this trend. In this work, we depart from this established direction and instead propose to extract sets of feature vectors for each image. We argue that a set-based representation intrinsically builds a richer representation of images from the base classes, which can subsequently better transfer to the few-shot classes. To do so, we propose to adapt existing feature extractors to instead produce sets of feature vectors from images. Our approach, dubbed SetFeat, embeds shallow self-attention mechanisms inside existing encoder architectures. The attention modules are lightweight, and as such our method results in encoders that have approximately the same number of parameters as their original versions. During training and inference, a set-to-set matching metric is used to perform image classification. The effectiveness of our proposed architecture and metrics is demonstrated via thorough experiments on standard few-shot datasets-namely miniImageNet, tieredImageNet, and CUB-in both the 1- and 5-shot scenarios. In all cases but one, our method outperforms the state-of-the-art.
2022-06-17
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org
arxiv.org
Medial Spectral Coordinates for 3D Shape Analysis
Morteza Rezanejad
Mohammad Khodadad
Hamidreza Mahyar
Hervé Lombaert
Michael Gruninger
Dirk B. Walther
Kaleem Siddiqi
In recent years there has been a resurgence of interest in our community in the shape analysis of 3D objects repre-sented by surface meshes,… (see more) their voxelized interiors, or surface point clouds. In part, this interest has been stimulated by the increased availability of RGBD cameras, and by applications of computer vision to autonomous driving, medical imaging, and robotics. In these settings, spectral co-ordinates have shown promise for shape representation due to their ability to incorporate both local and global shape properties in a manner that is qualitatively invariant to iso-metric transformations. Yet, surprisingly, such coordinates have thus far typically considered only local surface positional or derivative information. In the present article, we propose to equip spectral coordinates with medial (object width) information, so as to enrich them. The key idea is to couple surface points that share a medial ball, via the weights of the adjacency matrix. We develop a spectral feature using this idea, and the algorithms to compute it. The incorporation of object width and medial coupling has direct benefits, as illustrated by our experiments on object classification, object part segmentation, and surface point correspondence.
2022-06-17
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org
arxiv.org
Multi-label Iterated Learning for Image Classification with Label Ambiguity
Sai Rajeswar
Pau Rodríguez
Soumye Singhal
David Vázquez
Aaron Courville
Transfer learning from large-scale pre-trained models has become essential for many computer vision tasks. Recent studies have shown that da… (see more)tasets like ImageNet are weakly labeled since images with multiple object classes present are assigned a single label. This ambiguity biases models towards a single prediction, which could result in the suppression of classes that tend to co-occur in the data. Inspired by language emergence literature, we propose multi-label iterated learning (MILe) to incorporate the inductive biases of multi-label learning from single labels using the framework of iterated learning. MILe is a simple yet effective procedure that builds a multi-label description of the image by propagating binary predictions through successive generations of teacher and student networks with a learning bottleneck. Experiments show that our approach exhibits systematic benefits on ImageNet accuracy as well as ReaL F1 score, which indicates that MILe deals better with label ambiguity than the standard training procedure, even when fine-tuning from self-supervised weights. We also show that MILe is effective reducing label noise, achieving state-of-the-art performance on real-world large-scale noisy data such as WebVision. Furthermore, MILe improves performance in class incremental settings such as IIRC and it is robust to distribution shifts. Code: https://github.com/rajeswar18/MILe
2022-06-17
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org
arxiv.org
Probing Representation Forgetting in Supervised and Unsupervised Continual Learning
MohammadReza Davari
Nader Asadi
Sudhir Mudur
Rahaf Aljundi
Eugene Belilovsky
Continual Learning research typically focuses on tackling the phenomenon of catastrophic forgetting in neural networks. Catastrophic forgett… (see more)ing is associated with an abrupt loss of knowledge previously learned by a model when the task, or more broadly the data distribution, being trained on changes. In supervised learning problems this forgetting, resulting from a change in the model's representation, is typically measured or observed by evaluating the decrease in old task performance. However, a model's representation can change without losing knowledge about prior tasks. In this work we consider the concept of representation forgetting, observed by using the difference in performance of an optimal linear classifier before and after a new task is introduced. Using this tool we revisit a number of standard continual learning benchmarks and observe that, through this lens, model representations trained without any explicit control for forgetting often experience small representation forgetting and can sometimes be comparable to methods which explicitly control for forgetting, especially in longer task sequences. We also show that representation forgetting can lead to new insights on the effect of model capacity and loss function used in continual learning. Based on our results, we show that a simple yet competitive approach is to learn representations continually with standard supervised contrastive learning while constructing prototypes of class samples when queried on old samples.
2022-06-17
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org
arxiv.org
Revisiting Learnable Affines for Batch Norm in Few-Shot Transfer Learning
Moslem Yazdanpanah
Aamer Abdul Rahman
Muawiz Sajjad Chaudhary
Christian Desrosiers
Mohammad Havaei
Eugene Belilovsky
S Ebrahimi Kahou
Batch normalization is a staple of computer vision models, including those employed in few-shot learning. Batch nor-malization layers in con… (see more)volutional neural networks are composed of a normalization step, followed by a shift and scale of these normalized features applied via the per-channel trainable affine parameters
2022-06-17
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org