Joseph Paul Cohen

{COMPANYNAME}11K: An Unsupervised Representation Learning Dataset for Arrhythmia Subtype Discovery

Guillaume Androz

Pierre Fecteau

2019-09-24

(published)

On summarized validation curves and generalization

Mohammad Hashir

2019-09-24

(published)

Torchmeta: A Meta-Learning library for PyTorch

The constant introduction of standardized benchmarks in the literature has helped accelerating the recent advances in meta-learning research… (see more). They offer a way to get a fair comparison between different algorithms, and the wide range of datasets available allows full control over the complexity of this evaluation. However, for a large majority of code available online, the data pipeline is often specific to one dataset, and testing on another dataset requires significant rework. We introduce Torchmeta, a library built on top of PyTorch that enables seamless and consistent evaluation of meta-learning algorithms on multiple datasets, by providing data-loaders for most of the standard benchmarks in few-shot classification and regression, with a new meta-dataset abstraction. It also features some extensions for PyTorch to simplify the development of models compatible with meta-learning algorithms. The code is available here: this https URL

2019-09-13

ArXiv (preprint)

GradMask: Reduce Overfitting by Regularizing Saliency

Becks Simpson

Francis Dutil

With too few samples or too many model parameters, overfitting can inhibit the ability to generalise predictions to new data. Within medical… (see more) imaging, this can occur when features are incorrectly assigned importance such as distinct hospital specific artifacts, leading to poor performance on a new dataset from a different institution without those features, which is undesirable. Most regularization methods do not explicitly penalize the incorrect association of these features to the target class and hence fail to address this issue. We propose a regularization method, GradMask, which penalizes saliency maps inferred from the classifier gradients when they are not consistent with the lesion segmentation. This prevents non-tumor related features to contribute to the classification of unhealthy samples. We demonstrate that this method can improve test accuracy between 1-3% compared to the baseline without GradMask, showing that it has an impact on reducing overfitting.

2019-04-14

Medical Imaging with Deep Learning (accepted)

doi.org

Adversarial Domain Adaptation for Stable Brain-Machine Interfaces

Ali Farshchian

Juan A. Gallego

Lee Miller

Sara Solla

Brain-Machine Interfaces (BMIs) have recently emerged as a clinically viable option to restore voluntary movements after paralysis. These de… (see more)vices are based on the ability to extract information about movement intent from neural signals recorded using multi-electrode arrays chronically implanted in the motor cortices of the brain. However, the inherent loss and turnover of recorded neurons requires repeated recalibrations of the interface, which can potentially alter the day-to-day user experience. The resulting need for continued user adaptation interferes with the natural, subconscious use of the BMI. Here, we introduce a new computational approach that decodes movement intent from a low-dimensional latent representation of the neural data. We implement various domain adaptation methods to stabilize the interface over significantly long times. This includes Canonical Correlation Analysis used to align the latent variables across days; this method requires prior point-to-point correspondence of the time series across domains. Alternatively, we match the empirical probability distributions of the latent variables across days through the minimization of their Kullback-Leibler divergence. These two methods provide a significant and comparable improvement in the performance of the interface. However, implementation of an Adversarial Domain Adaptation Network trained to match the empirical probability distribution of the residuals of the reconstructed neural signals outperforms the two methods based on latent variables, while requiring remarkably few data points to solve the domain adaptation problem.

2018-12-31

ICLR.cc/2019/Conference (poster)

A Survey of Mobile Computing for the Visually Impaired

Martin Weiss

Margaux Luck

Roger Girgis

Christopher Pal

The number of visually impaired or blind (VIB) people in the world is estimated at several hundred million. Based on a series of interviews … (see more)with the VIB and developers of assistive technology, this paper provides a survey of machine-learning based mobile applications and identifies the most relevant applications. We discuss the functionality of these apps, how they align with the needs and requirements of the VIB users, and how they can be improved with techniques such as federated learning and model compression. As a result of this study we identify promising future directions of research in mobile perception, micro-navigation, and content-summarization.

2018-11-24

ArXiv (preprint)

Towards the Latent Transcriptome

Assya Trofimov

Francis Dutil

Claude Perreault

S. Lemieux

In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, in a reference-free fashion. We report th… (see more)at our model captures information of both DNA sequence similarity as well as DNA sequence abundance in the embedding latent space. We confirm the quality of these vectors by comparing them to known gene sub-structures and report that the latent space recovers exon information from raw RNA-Seq data from acute myeloid leukemia patients. Furthermore we show that this latent space allows the detection of genomic abnormalities such as translocations as well as patient-specific mutations, making this representation space both useful for visualization as well as analysis.

2018-09-26

ArXiv (preprint)

Towards Gene Expression Convolutions using Gene Interaction Graphs

We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the… (see more) data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep model similar to the spatial bias imposed by convolutions on an image. We explore the usage of Graph Convolutional Neural Networks coupled with dropout and gene embeddings to utilize the graph information. We find this approach provides an advantage for particular tasks in a low data regime but is very dependent on the quality of the graph used. We conclude that more work should be done in this direction. We design experiments that show why existing methods fail to capture signal that is present in the data when features are added which clearly isolates the problem that needs to be addressed.

2018-06-17

ArXiv (preprint)

Learning to rank for censored survival data

Margaux Luck

Tristan Sylvain

Heloise Cardinal

Andrea Lodi

Survival analysis is a type of semi-supervised ranking task where the target output (the survival time) is often right-censored. Utilizing t… (see more)his information is a challenge because it is not obvious how to correctly incorporate these censored examples into a model. We study how three categories of loss functions, namely partial likelihood methods, rank methods, and our classification method based on a Wasserstein metric (WM) and the non-parametric Kaplan Meier estimate of the probability density to impute the labels of censored examples, can take advantage of this information. The proposed method allows us to have a model that predict the probability distribution of an event. If a clinician had access to the detailed probability of an event over time this would help in treatment planning. For example, determining if the risk of kidney graft rejection is constant or peaked after some time. Also, we demonstrate that this approach directly optimizes the expected C-index which is the most common evaluation metric for ranking survival models.

2018-06-05

ArXiv (preprint)

Graph Priors for Deep Neural Networks

In this work we explore how gene-gene interaction graphs can be used as a prior for the representation of a model to construct features base… (see more)d on known interactions between genes. Most existing machine learning work on graphs focuses on building models when data is confined to a graph structure. In this work we focus on using the information from a graph to build better representations in our models. We use the percolate task, determining if a path exists across a grid for a set of node values, as a proxy for gene pathways. We create variants of the percolate task to explore where existing methods fail. We test the limits of existing methods in order to determine what can be improved when applying these methods to a real task. This leads us to propose new methods based on Graph Convolutional Networks (GCN) that use pooling and dropout to deal with noise in the graph prior.

2018-02-11

International Conference on Machine Learning (published)

BigBrain: 1D convolutional neural networks for automated sementation of cortical layers

Konrad Wagstyl

Claude Lepage

Karl Zilles

Sebastian Bludau

G. Cucurul

Alan C. Evans

Paul C Fletcher

Adriana Romero

Stéphanie Larocque

Thomas Funck

Katrin Amunts