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Publication# Structured Sequence Modeling with Graph Convolutional Recurrent Networks

Résumé

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed.

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In this thesis, we propose new algorithms to solve inverse problems in the context of biomedical images. Due to ill-posedness, solving these problems require some prior knowledge of the statistics of the underlying images. The traditional algorithms, in the field, assume prior knowledge related to smoothness or sparsity of these images. Recently, they have been outperformed by the second generation algorithms which harness the power of neural networks to learn required statistics from training data. Even more recently, last generation deep-learning-based methods have emerged which require neither training nor training data. This thesis devises algorithms which progress through these generations. It extends these generations to novel formulations and applications while bringing more robustness. In parallel, it also progresses in terms of complexity, from proposing algorithms for problems with 1D data and an exact known forward model to the ones with 4D data and an unknown parametric forward model. We introduce five main contributions. The last three of them propose deep-learning-based latest-generation algorithms that require no prior training. 1) We develop algorithms to solve the continuous-domain formulation of inverse problems with both classical Tikhonov and total-variation regularizations. We formalize the problems, characterize the solution set, and devise numerical approaches to find the solutions. 2) We propose an algorithm that improves upon end-to-end neural-network-based second generation algorithms. In our method, a neural network is first trained as a projector on a training set, and is then plugged in as a projector inside the projected gradient descent (PGD). Since the problem is nonconvex, we relax the PGD to ensure convergence to a local minimum under some constraints. This method outperforms all the previous generation algorithms for Computed Tomography (CT). 3) We develop a novel time-dependent deep-image-prior algorithm for modalities that involve a temporal sequence of images. We parameterize them as the output of an untrained neural network fed with a sequence of latent variables. To impose temporal directionality, the latent variables are assumed to lie on a 1D manifold. The network is then tuned to minimize the data fidelity. We obtain state-of-the-art results in dynamic magnetic resonance imaging (MRI) and even recover intra-frame images. 4) We propose a novel reconstruction paradigm for cryo-electron-microscopy (CryoEM) called CryoGAN. Motivated by generative adversarial networks (GANs), we reconstruct a biomolecule's 3D structure such that its CryoEM measurements resemble the acquired data in a distributional sense. The algorithm is pose-or-likelihood-estimation-free, needs no ab initio, and is proven to have a theoretical guarantee of recovery of the true structure. 5) We extend CryoGAN to reconstruct continuously varying conformations of a structure from heterogeneous data. We parameterize the conformations as the output of a neural network fed with latent variables on a low-dimensional manifold. The method is shown to recover continuous protein conformations and their energy landscape.

In this thesis, we investigate a hierarchical approach for estimating the phonetic class-conditional probabilities using a multilayer perceptron (MLP) neural network. The architecture consists of two MLP classifiers in cascade. The first MLP is trained in the conventional way using standard acoustic features with a temporal context of around 90 ms. The second MLP is trained on the phonetic class-conditional probabilities (or posterior features) estimated by the first classifier, but with a relatively longer temporal context of around 150-250 ms. The hierarchical architecture is motivated towards exploiting the useful contextual information in the sequence of posterior features which includes the evolution of the probability values within a phoneme (sub-phonemic) and its transition to/from neighboring phonemes (sub-lexical). As the posterior features are sparse and simple, the second classifier is able to learn the contextual information spanning a context as long as 250 ms. Extensive experiments on the recognition of phonemes on read speech as well as conversational speech show that the hierarchical approach yields significantly higher recognition accuracies. Analysis of the second MLP classifier using Volterra series reveal that it has learned the phonetic-temporal patterns in the posterior feature space which captures the confusions in phoneme classification at the output of the first classifier as well as the phonotactics of the language as observed in the training data. Furthermore, we show that the second MLP can be simple in terms of the number of model parameters and that it can be trained on lesser training data. The usefulness of the proposed hierarchical acoustic modeling in automatic speech recognition (ASR) is demonstrated using two applications (a) task adaptation where the goal is to exploit MLPs trained on large amount of data and available off-the-shelf to new tasks and (b) large vocabulary continuous ASR on broadcast news and broadcast conversations in Mandarin. Small vocabulary isolated word recognition and task adaptation studies are performed on the Phonebook database and the large vocabulary speech recognition studies are performed on the DARPA GALE Mandarin database.

In this thesis, we explore the use of machine learning techniques for information retrieval. More specifically, we focus on ad-hoc retrieval, which is concerned with searching large corpora to identify the documents relevant to user queries. This identification is performed through a ranking task. Given a user query, an ad-hoc retrieval system ranks the corpus documents, so that the documents relevant to the query ideally appear above the others. In a machine learning framework, we are interested in proposing learning algorithms that can benefit from limited training data in order to identify a ranker likely to achieve high retrieval performance over unseen documents and queries. This problem presents novel challenges compared to traditional learning tasks, such as regression or classification. First, our task is a ranking problem, which means that the loss for a given query cannot be measured as a sum of an individual loss suffered for each corpus document. Second, most retrieval queries present a highly unbalanced setup, with a set of relevant documents accounting only for a very small fraction of the corpus. Third, ad-hoc retrieval corresponds to a kind of "double" generalization problem, since the learned model should not only generalize to new documents but also to new queries. Finally, our task also presents challenging efficiency constraints, since ad-hoc retrieval is typically applied to large corpora. The main objective of this thesis is to investigate the discriminative learning of ad-hoc retrieval models. For that purpose, we propose different models based on kernel machines or neural networks adapted to different retrieval contexts. The proposed approaches rely on different online learning algorithms that allow efficient learning over large corpora. The first part of the thesis focuses on text retrieval. In this case, we adopt a classical approach to the retrieval ranking problem, and order the text documents according to their estimated similarity to the text query. The assessment of semantic similarity between text items plays a key role in that setup and we propose a learning approach to identify an effective measure of text similarity. This identification is not performed relying on a set of queries with their corresponding relevant document sets, since such data are especially expensive to label and hence rare. Instead, we propose to rely on hyperlink data, since hyperlinks convey semantic proximity information that is relevant to similarity learning. This setup is hence a transfer learning setup, where we benefit from the proximity information encoded by hyperlinks to improve the performance over the ad-hoc retrieval task. We then investigate another retrieval problem, i.e. the retrieval of images from text queries. Our approach introduces a learning procedure optimizing a criterion related to the ranking performance. This criterion adapts our previous learning objective for learning textual similarity to the image retrieval problem. This yields an image ranking model that addresses the retrieval problem directly. This approach contrasts with previous research that relies on an intermediate image annotation task. Moreover, our learning procedure builds upon recent work on the online learning of kernel-based classifiers. This yields an efficient, scalable algorithm, which can benefit from recent kernels developed for image comparison. In the last part of the thesis, we show that the objective function used in the previous retrieval problems can be applied to the task of keyword spotting, i.e. the detection of given keywords in speech utterances. For that purpose, we formalize this problem as a ranking task: given a keyword, the keyword spotter should order the utterances so that the utterances containing the keyword appear above the others. Interestingly, this formulation yields an objective directly maximizing the area under the receiver operating curve, the most common keyword spotter evaluation measure. This objective is then used to train a model adapted to this intrinsically sequential problem. This model is then learned with a procedure derived from the algorithm previously introduced for the image retrieval task. To conclude, this thesis introduces machine learning approaches for ad-hoc retrieval. We propose learning models for various multi-modal retrieval setups, i.e. the retrieval of text documents from text queries, the retrieval of images from text queries and the retrieval of speech recordings from written keywords. Our approaches rely on discriminative learning and enjoy efficient training procedures, which yields effective and scalable models. In all cases, links with prior approaches were investigated and experimental comparisons were conducted.