Publications

PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information
Faizy Ahsan
Zichao Yan
Doina Precup
Mathieu Blanchette
Abstract Motivation The computational prediction of regulatory function associated with a genomic sequence is of utter importance in -omics … (see more)study, which facilitates our understanding of the underlying mechanisms underpinning the vast gene regulatory network. Prominent examples in this area include the binding prediction of transcription factors in DNA regulatory regions, and predicting RNA–protein interaction in the context of post-transcriptional gene expression. However, existing computational methods have suffered from high false-positive rates and have seldom used any evolutionary information, despite the vast amount of available orthologous data across multitudes of extant and ancestral genomes, which readily present an opportunity to improve the accuracy of existing computational methods. Results In this study, we present a novel probabilistic approach called PhyloPGM that leverages previously trained TFBS or RNA–RBP binding predictors by aggregating their predictions from various orthologous regions, in order to boost the overall prediction accuracy on human sequences. Throughout our experiments, PhyloPGM has shown significant improvement over baselines such as the sequence-based RNA–RBP binding predictor RNATracker and the sequence-based TFBS predictor that is known as FactorNet. PhyloPGM is simple in principle, easy to implement and yet, yields impressive results. Availability and implementation The PhyloPGM package is available at https://github.com/BlanchetteLab/PhyloPGM Supplementary information Supplementary data are available at Bioinformatics online.
2022-06-27
Bioinformatics (published)
doi.org
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.
2022-06-24
Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques (published)
doi.org
Augmenting Human Selves Through Artificial Agents – Lessons From the Brain
Georg Northoff
Maia Fraser
John Griffiths
Dimitris A. Pinotsis
Prakash Panangaden
Rosalyn Moran
Karl Friston
Much of current artificial intelligence (AI) and the drive toward artificial general intelligence (AGI) focuses on developing machines for f… (see more)unctional tasks that humans accomplish. These may be narrowly specified tasks as in AI, or more general tasks as in AGI – but typically these tasks do not target higher-level human cognitive abilities, such as consciousness or morality; these are left to the realm of so-called “strong AI” or “artificial consciousness.” In this paper, we focus on how a machine can augment humans rather than do what they do, and we extend this beyond AGI-style tasks to augmenting peculiarly personal human capacities, such as wellbeing and morality. We base this proposal on associating such capacities with the “self,” which we define as the “environment-agent nexus”; namely, a fine-tuned interaction of brain with environment in all its relevant variables. We consider richly adaptive architectures that have the potential to implement this interaction by taking lessons from the brain. In particular, we suggest conjoining the free energy principle (FEP) with the dynamic temporo-spatial (TSD) view of neuro-mental processes. Our proposed integration of FEP and TSD – in the implementation of artificial agents – offers a novel, expressive, and explainable way for artificial agents to adapt to different environmental contexts. The targeted applications are broad: from adaptive intelligence augmenting agents (IA’s) that assist psychiatric self-regulation to environmental disaster prediction and personal assistants. This reflects the central role of the mind and moral decision-making in most of what we do as humans.
2022-06-23
Frontiers in Computational Neuroscience (published)
doi.org
Dynamic compression and expansion in a classifying recurrent network
Matthew Farrell
Maxwell J. Farrell
Stefano Recanatesi
Timothy Moore
Guillaume Lajoie
Eric Todd SheaBrown
Recordings of neural circuits in the brain reveal extraordinary dynamical richness and high variability. At the same time, dimensionality re… (see more)duction techniques generally uncover low-dimensional structures underlying these dynamics when tasks are performed. In general, it is still an open question what determines the dimensionality of activity in neural circuits, and what the functional role of this dimensionality in task learning is. In this work we probe these issues using a recurrent artificial neural network (RNN) model trained by stochastic gradient descent to discriminate inputs. The RNN family of models has recently shown promise in revealing principles behind brain function. Through simulations and mathematical analysis, we show how the dimensionality of RNN activity depends on the task parameters and evolves over time and over stages of learning. We find that common solutions produced by the network naturally compress dimensionality, while variability-inducing chaos can expand it. We show how chaotic networks balance these two factors to solve the discrimination task with high accuracy and good generalization properties. These findings shed light on mechanisms by which artificial neural networks solve tasks while forming compact representations that may generalize well.
2022-06-22
Nature Machine Intelligence (published)
doi.org
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
2022-06-21
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
2022-06-20
2022 ACM Conference on Fairness, Accountability, and Transparency (published)
doi.org
arxiv.org
Only Tails Matter: Average-Case Universality and Robustness in the Convex Regime
Leonardo Cunha
Gauthier Gidel
Fabian Pedregosa
Damien Scieur
Courtney Paquette
2022-06-20
ArXiv (preprint)
doi.org
openreview.net
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.
2022-06-19
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) (published)
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
Derek 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.
2022-06-18
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.
2022-06-18
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.
2022-06-18
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 Rodriguez
Soumye Singhal
David Vazquez
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
2022-06-18
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (published)
doi.org
arxiv.org