Publications

Towards the Latent Transcriptome
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… (voir plus)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.
Universal Successor Features for Transfer Reinforcement Learning
Dylan R. Ashley
Junfeng Wen
Transfer in Reinforcement Learning (RL) refers to the idea of applying knowledge gained from previous tasks to solving related tasks. Learni… (voir plus)ng a universal value function (Schaul et al., 2015), which generalizes over goals and states, has previously been shown to be useful for transfer. However, successor features are believed to be more suitable than values for transfer (Dayan, 1993; Barreto et al.,2017), even though they cannot directly generalize to new goals. In this paper, we propose (1) Universal Successor Features (USFs) to capture the underlying dynamics of the environment while allowing generalization to unseen goals and (2) a flexible end-to-end model of USFs that can be trained by interacting with the environment. We show that learning USFs is compatible with any RL algorithm that learns state values using a temporal difference method. Our experiments in a simple gridworld and with two MuJoCo environments show that USFs can greatly accelerate training when learning multiple tasks and can effectively transfer knowledge to new tasks.
Unsupervised one-to-many image translation
Samuel Lavoie-Marchildon
R Devon Hjelm
W2GAN: RECOVERING AN OPTIMAL TRANSPORT MAP WITH A GAN
Leygonie Jacob*
Jennifer She*
Amjad Almahairi
Sai Rajeswar
Where Off-Policy Deep Reinforcement Learning Fails
This work examines batch reinforcement learning–the task of maximally exploiting a given batch of off-policy data, without further data co… (voir plus)llection. We demonstrate that due to errors introduced by extrapolation, standard off-policy deep reinforcement learning algorithms, such as DQN and DDPG, are only capable of learning with data correlated to their current policy, making them ineffective for most off-policy applications. We introduce a novel class of off-policy algorithms, batch-constrained reinforcement learning, which restricts the action space to force the agent towards behaving on-policy with respect to a subset of the given data. We extend this notion to deep reinforcement learning, and to the best of our knowledge, present the first continuous control deep reinforcement learning algorithm which can learn effectively from uncorrelated off-policy data.
Width of Minima Reached by Stochastic Gradient Descent is Influenced by Learning Rate to Batch Size Ratio
Stanisław Jastrzębski
Amos Storkey
Exploring Uncertainty Measures in Deep Networks for Multiple Sclerosis Lesion Detection and Segmentation
Tanya Nair
Douglas L. Arnold
Deep learning (DL) networks have recently been shown to outperform other segmentation methods on various public, medical-image challenge dat… (voir plus)asets [3,11,16], especially for large pathologies. However, in the context of diseases such as Multiple Sclerosis (MS), monitoring all the focal lesions visible on MRI sequences, even very small ones, is essential for disease staging, prognosis, and evaluating treatment efficacy. Moreover, producing deterministic outputs hinders DL adoption into clinical routines. Uncertainty estimates for the predictions would permit subsequent revision by clinicians. We present the first exploration of multiple uncertainty estimates based on Monte Carlo (MC) dropout [4] in the context of deep networks for lesion detection and segmentation in medical images. Specifically, we develop a 3D MS lesion segmentation CNN, augmented to provide four different voxel-based uncertainty measures based on MC dropout. We train the network on a proprietary, large-scale, multi-site, multi-scanner, clinical MS dataset, and compute lesion-wise uncertainties by accumulating evidence from voxel-wise uncertainties within detected lesions. We analyze the performance of voxel-based segmentation and lesion-level detection by choosing operating points based on the uncertainty. Empirical evidence suggests that uncertainty measures consistently allow us to choose superior operating points compared only using the network's sigmoid output as a probability.
How can deep learning advance computational modeling of sensory information processing?
Jessica A.F. Thompson
Elia Formisano
Marc Schönwiesner
Deep learning, computational neuroscience, and cognitive science have overlapping goals related to understanding intelligence such that perc… (voir plus)eption and behaviour can be simulated in computational systems. In neuroimaging, machine learning methods have been used to test computational models of sensory information processing. Recently, these model comparison techniques have been used to evaluate deep neural networks (DNNs) as models of sensory information processing. However, the interpretation of such model evaluations is muddied by imprecise statistical conclusions. Here, we make explicit the types of conclusions that can be drawn from these existing model comparison techniques and how these conclusions change when the model in question is a DNN. We discuss how DNNs are amenable to new model comparison techniques that allow for stronger conclusions to be made about the computational mechanisms underlying sensory information processing.
On the Learning Dynamics of Deep Neural Networks
Remi Tachet des Combes
Samira Shabanian
While a lot of progress has been made in recent years, the dynamics of learning in deep nonlinear neural networks remain to this day largely… (voir plus) misunderstood. In this work, we study the case of binary classification and prove various properties of learning in such networks under strong assumptions such as linear separability of the data. Extending existing results from the linear case, we confirm empirical observations by proving that the classification error also follows a sigmoidal shape in nonlinear architectures. We show that given proper initialization, learning expounds parallel independent modes and that certain regions of parameter space might lead to failed training. We also demonstrate that input norm and features' frequency in the dataset lead to distinct convergence speeds which might shed some light on the generalization capabilities of deep neural networks. We provide a comparison between the dynamics of learning with cross-entropy and hinge losses, which could prove useful to understand recent progress in the training of generative adversarial networks. Finally, we identify a phenomenon that we baptize \textit{gradient starvation} where the most frequent features in a dataset prevent the learning of other less frequent but equally informative features.
CNN Prediction of Future Disease Activity for Multiple Sclerosis Patients from Baseline MRI and Lesion Labels
Tal Hassner
Douglas Arnold
3D U-Net for Brain Tumour Segmentation
Raghav Mehta
How to Exploit Weaknesses in Biomedical Challenge Design and Organization
Annika Reinke
Matthias Eisenmann
Sinan Onogur
Marko Stankovic
Patrick Scholz
Peter M. Full
Hrvoje Bogunovic
Bennett Landman
Oskar Maier
Bjoern Menze
Gregory C. Sharp
Korsuk Sirinukunwattana
Stefanie Speidel
F. V. D. Sommen
Guoyan Zheng
Henning Müller
Michal Kozubek
Andrew P. Bradley
Pierre Jannin … (voir 2 de plus)
Annette Kopp-Schneider
Lena Maier-Hein