Publications

Glucocorticoid sensitivity in a subset of human RUNX1-mutated acute myeloid leukemia
Frédéric Leduc
Maude Wur
Geneviève Boucher
Rose-Marie Rébillard
Valérie Bordeleau
Julie Bergeron
Nadine Mayotte
Anne-Marie Côté
Véronique Lisi
Elliot D. Drobetsky
Tarik Möröy
Lambert Busque
Jean-Sébastien Delisle
Martin Sauvageau
Josée Hébert
Guy Sauvageau
Purpose: RUNX1-mutated (RUNX1mut) acute myeloid leukemia (AML) is associated with adverse outcome, highlighting the urgent need for a bett… (voir plus)er genetic characterization of this AML subgroup and for the design of efficient therapeutic strategies for this disease. Toward this goal, we further dissected the mutational spectrum and gene expression profile of RUNX1mut AML and correlated these results to drug sensitivity to identify novel compounds targeting this AML subgroup. Experimental Design: RNA-sequencing of 47 RUNX1mut primary AML specimens was performed and sequencing results were compared to those of RUNX1 wild-type samples. Chemical screens were also conducted using RUNX1mut specimens to identify compounds selectively affecting the viability of RUNX1mut AML. Results: We show that samples with no remaining RUNX1 wild-type allele are clinically and genetically distinct and display a more homogeneous gene expression profile. Chemical screening revealed that most RUNX1mut specimens are sensitive to glucocorticoids (GCs) and we confirmed that GCs inhibit AML cell proliferation through their interaction with the glucocorticoid receptor (GR). We observed that specimens harboring RUNX1 mutations expected to result in low residual RUNX1 activity are most sensitive to GCs, and that coassociating mutations as well as GR levels contribute to GC sensitivity. Accordingly, acquired glucocorticoid sensitivity was achieved by negatively regulating RUNX1 expression in human AML cells. Conclusions: Our findings show the profound impact of RUNX1 allele dosage on gene expression profile and glucocorticoid sensitivity in AML, thereby opening opportunities for preclinical testing which may lead to drug repurposing and improved disease characterization. Clin Cancer Res; 23(22); 6969–81. ©2017 AACR.
Twin Networks: Using the Future as a Regularizer
Nan Rosemary Ke
Christopher Pal
Being able to model long-term dependencies in sequential data, such as text, has been among the long-standing challenges of recurrent neural… (voir plus) networks (RNNs). This issue is strictly related to the absence of explicit planning in current RNN architectures. More explicitly, the RNNs are trained to predict only the next token given previous ones. In this paper, we introduce a simple way of encouraging the RNNs to plan for the future. In order to accomplish this, we introduce an additional neural network which is trained to generate the sequence in reverse order, and we require closeness between the states of the forward RNN and backward RNN that predict the same token. At each step, the states of the forward RNN are required to match the future information contained in the backward states. We hypothesize that the approach eases modeling of long-term dependencies thus helping in generating more globally consistent samples. The model trained with conditional generation for a speech recognition task achieved 12\% relative improvement (CER of 6.7 compared to a baseline of 7.6).
Dynamic Layer Normalization for Adaptive Neural Acoustic Modeling in Speech Recognition
Layer normalization is a recently introduced technique for normalizing the activities of neurons in deep neural networks to improve the trai… (voir plus)ning speed and stability. In this paper, we introduce a new layer normalization technique called Dynamic Layer Normalization (DLN) for adaptive neural acoustic modeling in speech recognition. By dynamically generating the scaling and shifting parameters in layer normalization, DLN adapts neural acoustic models to the acoustic variability arising from various factors such as speakers, channel noises, and environments. Unlike other adaptive acoustic models, our proposed approach does not require additional adaptation data or speaker information such as i-vectors. Moreover, the model size is fixed as it dynamically generates adaptation parameters. We apply our proposed DLN to deep bidirectional LSTM acoustic models and evaluate them on two benchmark datasets for large vocabulary ASR experiments: WSJ and TED-LIUM release 2. The experimental results show that our DLN improves neural acoustic models in terms of transcription accuracy by dynamically adapting to various speakers and environments.
Improving Speech Recognition by Revising Gated Recurrent Units
Speech recognition is largely taking advantage of deep learning, showing that substantial benefits can be obtained by modern Recurrent Neura… (voir plus)l Networks (RNNs). The most popular RNNs are Long Short-Term Memory (LSTMs), which typically reach state-of-the-art performance in many tasks thanks to their ability to learn long-term dependencies and robustness to vanishing gradients. Nevertheless, LSTMs have a rather complex design with three multiplicative gates, that might impair their efficient implementation. An attempt to simplify LSTMs has recently led to Gated Recurrent Units (GRUs), which are based on just two multiplicative gates. This paper builds on these efforts by further revising GRUs and proposing a simplified architecture potentially more suitable for speech recognition. The contribution of this work is two-fold. First, we suggest to remove the reset gate in the GRU design, resulting in a more efficient single-gate architecture. Second, we propose to replace tanh with ReLU activations in the state update equations. Results show that, in our implementation, the revised architecture reduces the per-epoch training time with more than 30% and consistently improves recognition performance across different tasks, input features, and noisy conditions when compared to a standard GRU.
End-to-end optimization of goal-driven and visually grounded dialogue systems
Jérémie Mary
Bilal Piot
Olivier Pietquin
End-to-end design of dialogue systems has recently become a popular research topic thanks to powerful tools such as encoder-decoder architec… (voir plus)tures for sequence-to-sequence learning. Yet, most current approaches cast human-machine dialogue management as a supervised learning problem, aiming at predicting the next utterance of a participant given the full history of the dialogue. This vision is too simplistic to render the intrinsic planning problem inherent to dialogue as well as its grounded nature , making the context of a dialogue larger than the sole history. This is why only chitchat and question answering tasks have been addressed so far using end-to-end architectures. In this paper, we introduce a Deep Reinforcement Learning method to optimize visually grounded task-oriented dialogues , based on the policy gradient algorithm. This approach is tested on a dataset of 120k dialogues collected through Mechanical Turk and provides encouraging results at solving both the problem of generating natural dialogues and the task of discovering a specific object in a complex picture.
A Closer Look at Memorization in Deep Networks
We examine the role of memorization in deep learning, drawing connections to capacity, generalization, and adversarial robustness. While dee… (voir plus)p networks are capable of memorizing noise data, our results suggest that they tend to prioritize learning simple patterns first. In our experiments, we expose qualitative differences in gradient-based optimization of deep neural networks (DNNs) on noise vs. real data. We also demonstrate that for appropriately tuned explicit regularization (e.g., dropout) we can degrade DNN training performance on noise datasets without compromising generalization on real data. Our analysis suggests that the notions of effective capacity which are dataset independent are unlikely to explain the generalization performance of deep networks when trained with gradient based methods because training data itself plays an important role in determining the degree of memorization.
Adversarial Generation of Natural Language
Sai Rajeswar
Christopher Pal
Generative Adversarial Networks (GANs) have gathered a lot of attention from the computer vision community, yielding impressive results for … (voir plus)image generation. Advances in the adversarial generation of natural language from noise however are not commensurate with the progress made in generating images, and still lag far behind likelihood based methods. In this paper, we take a step towards generating natural language with a GAN objective alone. We introduce a simple baseline that addresses the discrete output space problem without relying on gradient estimators and show that it is able to achieve state-of-the-art results on a Chinese poem generation dataset. We present quantitative results on generating sentences from context-free and probabilistic context-free grammars, and qualitative language modeling results. A conditional version is also described that can generate sequences conditioned on sentence characteristics.
Approximate Value Iteration with Temporally Extended Actions (Extended Abstract)
Timothy A. Mann
Shie Mannor
The options framework provides a concrete way to implement and reason about temporally extended actions. Existing literature has demonstrate… (voir plus)d the value of planning with options empirically, but there is a lack of theoretical analysis formalizing when planning with options is more efficient than planning with primitive actions. We provide a general analysis of the convergence rate of a popular Approximate Value Iteration (AVI) algorithm called Fitted Value Iteration (FVI) with options. Our analysis reveals that longer duration options and a pessimistic estimate of the value function both lead to faster convergence. Furthermore, options can improve convergence even when they are suboptimal and sparsely distributed throughout the state space. Next we consider generating useful options for planning based on a subset of landmark states. This suggests a new algorithm, Landmarkbased AVI (LAVI), that represents the value function only at landmark states. We analyze OFVI and LAVI using the proposed landmark-based options and compare the two algorithms. Our theoretical and experimental results demonstrate that options can play an important role in AVI by decreasing approximation error and inducing fast convergence.
Plan, Attend, Generate: Character-Level Neural Machine Translation with Planning
We investigate the integration of a planning mechanism into an encoder-decoder architecture with attention. We develop a model that can plan… (voir plus) ahead when it computes alignments between the source and target sequences not only for a single time-step but for the next k time-steps as well by constructing a matrix of proposed future alignments and a commitment vector that governs whether to follow or recompute the plan. This mechanism is inspired by strategic attentive reader and writer (STRAW) model, a recent neural architecture for planning with hierarchical reinforcement learning that can also learn higher level temporal abstractions. Our proposed model is end-to-end trainable with differentiable operations. We show that our model outperforms strong baselines on character-level translation task from WMT’15 with fewer parameters and computes alignments that are qualitatively intuitive.
Predicting Success in Goal-Driven Human-Human Dialogues
Michael Noseworthy
Jackie CK Cheung
In goal-driven dialogue systems, success is often defined based on a structured definition of the goal. This requires that the dialogue syst… (voir plus)em be constrained to handle a specific class of goals and that there be a mechanism to measure success with respect to that goal. However, in many human-human dialogues the diversity of goals makes it infeasible to define success in such a way. To address this scenario, we consider the task of automatically predicting success in goal-driven human-human dialogues using only the information communicated between participants in the form of text. We build a dataset from stackoverflow.com which consists of exchanges between two users in the technical domain where ground-truth success labels are available. We then propose a turn-based hierarchical neural network model that can be used to predict success without requiring a structured goal definition. We show this model outperforms rule-based heuristics and other baselines as it is able to detect patterns over the course of a dialogue and capture notions such as gratitude.
A Benchmark for Endoluminal Scene Segmentation of Colonoscopy Images
Jorge Bernal
F. Javier Sánchez
Gloria Fernández-Esparrach
Antonio M. López
Adriana Romero
Colorectal cancer (CRC) is the third cause of cancer death worldwide. Currently, the standard approach to reduce CRC-related mortality is to… (voir plus) perform regular screening in search for polyps and colonoscopy is the screening tool of choice. The main limitations of this screening procedure are polyp miss-rate and inability to perform visual assessment of polyp malignancy. These drawbacks can be reduced by designing Decision Support Systems (DSS) aiming to help clinicians in the different stages of the procedure by providing endoluminal scene segmentation. Thus, in this paper, we introduce an extended benchmark of colonoscopy image, with the hope of establishing a new strong benchmark for colonoscopy image analysis research. We provide new baselines on this dataset by training standard fully convolutional networks (FCN) for semantic segmentation and significantly outperforming, without any further post-processing, prior results in endoluminal scene segmentation.
Self-organized Hierarchical Softmax
We propose a new self-organizing hierarchical softmax formulation for neural-network-based language models over large vocabularies. Instead … (voir plus)of using a predefined hierarchical structure, our approach is capable of learning word clusters with clear syntactical and semantic meaning during the language model training process. We provide experiments on standard benchmarks for language modeling and sentence compression tasks. We find that this approach is as fast as other efficient softmax approximations, while achieving comparable or even better performance relative to similar full softmax models.