Investigations into the value of labeled and unlabeled data in biomedical entity recognition and word sense disambiguation

Human annotations, especially in highly technical domains, are expensive and time consuming togather, and can also be erroneous. As a result, we never have sufficiently accurate data to train andevaluate supervised methods. In this thesis, we address this problem by taking a semi-supervised approach to biomedical namedentity recognition (NER), and by proposing an inventory-independent evaluation framework for supervised and unsupervised word sense disambiguation. Our contributions are as follows: We introduce a novel graph-based semi-supervised approach to named entity recognition(NER) and exploit pre-trained contextualized word embeddings in several biomedical NER tasks. We propose a new evaluation framework for word sense disambiguation that permits a fair comparison between supervised methods trained on different sense inventories as well as unsupervised methods without a fixed sense inventory

Coreference resolution with and for Wikipedia

Wikipédia est une ressource embarquée dans de nombreuses applications du traite- ment des langues naturelles. Pourtant, aucune étude à notre connaissance n’a tenté de mesurer la qualité de résolution de coréférence dans les textes de Wikipédia, une étape préliminaire à la compréhension de textes. La première partie de ce mémoire consiste à construire un corpus de coréférence en anglais, construit uniquement à partir des articles de Wikipédia. Les mentions sont étiquetées par des informations syntaxiques et séman- tiques, avec lorsque cela est possible un lien vers les entités FreeBase équivalentes. Le but est de créer un corpus équilibré regroupant des articles de divers sujets et tailles. Notre schéma d’annotation est similaire à celui suivi dans le projet OntoNotes. Dans la deuxième partie, nous allons mesurer la qualité des systèmes de détection de coréférence à l’état de l’art sur une tâche simple consistant à mesurer les mentions du concept décrit dans une page Wikipédia (p. ex : les mentions du président Obama dans la page Wiki- pédia dédiée à cette personne). Nous tenterons d’améliorer ces performances en faisant usage le plus possible des informations disponibles dans Wikipédia (catégories, redi- rects, infoboxes, etc.) et Freebase (information du genre, du nombre, type de relations avec autres entités, etc.).Wikipedia is a resource of choice exploited in many NLP applications, yet we are not aware of recent attempts to adapt coreference resolution to this resource, a prelim- inary step to understand Wikipedia texts. The first part of this master thesis is to build an English coreference corpus, where all documents are from the English version of Wikipedia. We annotated each markable with coreference type, mention type and the equivalent Freebase topic. Our corpus has no restriction on the topics of the documents being annotated, and documents of various sizes have been considered for annotation. Our annotation scheme follows the one of OntoNotes with a few disparities. In part two, we propose a testbed for evaluating coreference systems in a simple task of measuring the particulars of the concept described in a Wikipedia page (eg. The statements of Pres- ident Obama the Wikipedia page dedicated to that person). We show that by exploiting the Wikipedia markup (categories, redirects, infoboxes, etc.) of a document, as well as links to external knowledge bases such as Freebase (information of the type, num- ber, type of relationship with other entities, etc.), we can acquire useful information on entities that helps to classify mentions as coreferent or not

Establishing a Framework for the development of Multimodal Virtual Reality Interfaces with Applicability in Education and Clinical Practice

The development of Virtual Reality (VR) and Augmented Reality (AR) content with multiple sources of both input and output has led to countless contributions in a great many number of fields, among which medicine and education. Nevertheless, the actual process of integrating the existing VR/AR media and subsequently setting it to purpose is yet a highly scattered and esoteric undertaking. Moreover, seldom do the architectures that derive from such ventures comprise haptic feedback in their implementation, which in turn deprives users from relying on one of the paramount aspects of human interaction, their sense of touch. Determined to circumvent these issues, the present dissertation proposes a centralized albeit modularized framework that thus enables the conception of multimodal VR/AR applications in a novel and straightforward manner. In order to accomplish this, the aforesaid framework makes use of a stereoscopic VR Head Mounted Display (HMD) from Oculus Rift©, a hand tracking controller from Leap Motion©, a custom-made VR mount that allows for the assemblage of the two preceding peripherals and a wearable device of our own design. The latter is a glove that encompasses two core modules in its innings, one that is able to convey haptic feedback to its wearer and another that deals with the non-intrusive acquisition, processing and registering of his/her Electrocardiogram (ECG), Electromyogram (EMG) and Electrodermal Activity (EDA). The software elements of the aforementioned features were all interfaced through Unity3D©, a powerful game engine whose popularity in academic and scientific endeavors is evermore increasing. Upon completion of our system, it was time to substantiate our initial claim with thoroughly developed experiences that would attest to its worth. With this premise in mind, we devised a comprehensive repository of interfaces, amid which three merit special consideration: Brain Connectivity Leap (BCL), Ode to Passive Haptic Learning (PHL) and a Surgical Simulator

Self-supervised Face Representation Learning

This thesis investigates fine-tuning deep face features in a self-supervised manner for discriminative face representation learning, wherein we develop methods to automatically generate pseudo-labels for training a neural network. Most importantly solving this problem helps us to advance the state-of-the-art in representation learning and can be beneficial to a variety of practical downstream tasks. Fortunately, there is a vast amount of videos on the internet that can be used by machines to learn an effective representation. We present methods that can learn a strong face representation from large-scale data be the form of images or video. However, while learning a good representation using a deep learning algorithm requires a large-scale dataset with manually curated labels, we propose self-supervised approaches to generate pseudo-labels utilizing the temporal structure of the video data and similarity constraints to get supervision from the data itself. We aim to learn a representation that exhibits small distances between samples from the same person, and large inter-person distances in feature space. Using metric learning one could achieve that as it is comprised of a pull-term, pulling data points from the same class closer, and a push-term, pushing data points from a different class further away. Metric learning for improving feature quality is useful but requires some form of external supervision to provide labels for the same or different pairs. In the case of face clustering in TV series, we may obtain this supervision from tracks and other cues. The tracking acts as a form of high precision clustering (grouping detections within a shot) and is used to automatically generate positive and negative pairs of face images. Inspired from that we propose two variants of discriminative approaches: Track-supervised Siamese network (TSiam) and Self-supervised Siamese network (SSiam). In TSiam, we utilize the tracking supervision to obtain the pair, additional we include negative training pairs for singleton tracks -- tracks that are not temporally co-occurring. As supervision from tracking may not always be available, to enable the use of metric learning without any supervision we propose an effective approach SSiam that can generate the required pairs automatically during training. In SSiam, we leverage dynamic generation of positive and negative pairs based on sorting distances (i.e. ranking) on a subset of frames and do not have to only rely on video/track based supervision. Next, we present a method namely Clustering-based Contrastive Learning (CCL), a new clustering-based representation learning approach that utilizes automatically discovered partitions obtained from a clustering algorithm (FINCH) as weak supervision along with inherent video constraints to learn discriminative face features. As annotating datasets is costly and difficult, using label-free and weak supervision obtained from a clustering algorithm as a proxy learning task is promising. Through our analysis, we show that creating positive and negative training pairs using clustering predictions help to improve the performance for video face clustering. We then propose a method face grouping on graphs (FGG), a method for unsupervised fine-tuning of deep face feature representations. We utilize a graph structure with positive and negative edges over a set of face-tracks based on their temporal structure of the video data and similarity-based constraints. Using graph neural networks, the features communicate over the edges allowing each track\u27s feature to exchange information with its neighbors, and thus push each representation in a direction in feature space that groups all representations of the same person together and separates representations of a different person. Having developed these methods to generate weak-labels for face representation learning, next we propose to learn compact yet effective representation for describing face tracks in videos into compact descriptors, that can complement previous methods towards learning a more powerful face representation. Specifically, we propose Temporal Compact Bilinear Pooling (TCBP) to encode the temporal segments in videos into a compact descriptor. TCBP possesses the ability to capture interactions between each element of the feature representation with one-another over a long-range temporal context. We integrated our previous methods TSiam, SSiam and CCL with TCBP and demonstrated that TCBP has excellent capabilities in learning a strong face representation. We further show TCBP has exceptional transfer abilities to applications such as multimodal video clip representation that jointly encodes images, audio, video and text, and video classification. All of these contributions are demonstrated on benchmark video clustering datasets: The Big Bang Theory, Buffy the Vampire Slayer and Harry Potter 1. We provide extensive evaluations on these datasets achieving a significant boost in performance over the base features, and in comparison to the state-of-the-art results

Diamond-based models for scientific visualization

Hierarchical spatial decompositions are a basic modeling tool in a variety of application domains including scientific visualization, finite element analysis and shape modeling and analysis. A popular class of such approaches is based on the regular simplex bisection operator, which bisects simplices (e.g. line segments, triangles, tetrahedra) along the midpoint of a predetermined edge. Regular simplex bisection produces adaptive simplicial meshes of high geometric quality, while simplifying the extraction of crack-free, or conforming, approximations to the original dataset. Efficient multiresolution representations for such models have been achieved in 2D and 3D by clustering sets of simplices sharing the same bisection edge into structures called diamonds. In this thesis, we introduce several diamond-based approaches for scientific visualization. We first formalize the notion of diamonds in arbitrary dimensions in terms of two related simplicial decompositions of hypercubes. This enables us to enumerate the vertices, simplices, parents and children of a diamond. In particular, we identify the number of simplices involved in conforming updates to be factorial in the dimension and group these into a linear number of subclusters of simplices that are generated simultaneously. The latter form the basis for a compact pointerless representation for conforming meshes generated by regular simplex bisection and for efficiently navigating the topological connectivity of these meshes. Secondly, we introduce the supercube as a high-level primitive on such nested meshes based on the atomic units within the underlying triangulation grid. We propose the use of supercubes to associate information with coherent subsets of the full hierarchy and demonstrate the effectiveness of such a representation for modeling multiresolution terrain and volumetric datasets. Next, we introduce Isodiamond Hierarchies, a general framework for spatial access structures on a hierarchy of diamonds that exploits the implicit hierarchical and geometric relationships of the diamond model. We use an isodiamond hierarchy to encode irregular updates to a multiresolution isosurface or interval volume in terms of regular updates to diamonds. Finally, we consider nested hypercubic meshes, such as quadtrees, octrees and their higher dimensional analogues, through the lens of diamond hierarchies. This allows us to determine the relationships involved in generating balanced hypercubic meshes and to propose a compact pointerless representation of such meshes. We also provide a local diamond-based triangulation algorithm to generate high-quality conforming simplicial meshes

The effects of climate change on the global migration of birds

Migration is one of the most spectacular wonders of the natural world but is increasingly threatened by large-scale environmental change. Migrants are key components of biological systems at higher latitudes, where the magnitude and velocity of climate change is most pronounced. In this thesis, I consider how the distribution of migratory species may change in the future, across the globe, in response to environmental change. Using global data on avian species distributions, the environmental and biological factors that affect migratory species richness were investigated. The cost of migration distance between breeding and non-breeding areas, and resident species richness were two important determinants of migrant species richness in a given location. Species distribution models (SDMs) were used to relate migratory species occurrence in breeding and non-breeding seasons to contemporary climatic variables. The importance of climatic variables for predicting migrant species’ occupancy depended on season (breeding or non-breeding). Whilst most SDMs focus on individual species breeding ranges, and model within the occupied realm, this can be problematic for migratory species that frequently use multiple realms, especially if trying to project newly suitable areas in future. Here, I developed a novel method to assess climatic suitability for migratory species globally, within species migration flyways. Selecting absence data to condition SDMs for species occurring across multiple realms can be problematic, as regions distant from the range may be suitable but unoccupied. To minimise this issue, I developed a modelling approach that selected absences preferentially from closer to a species distribution, using a distance weighting function; compared to other methods, this improved model performance on withheld test data. Using this approach, I projected the potential future breeding and non-breeding ranges of all global terrestrial long-distance migrants under climate change. Migrant breeding ranges were projected to shift poleward, but non-breeding range shift projections are less consistent in direction. To date, predictions of migratory changes under future climate scenarios have usually estimated a single distance between breeding and non-breeding range centroids. However, this approach ignores the variation in migratory movements within species. I developed a method to estimate the range of potential migration distances for individual populations, both now and in the future, which agreed well with recovery data for a well-recorded European trans-Saharan migrant. This approach projected longer median migratory distances in the future for many species. This thesis highlights the importance of climate for migratory species, and suggests that the observed general decline in many long-distance migratory species may be exacerbated by ongoing climate change

Parameterization using Generative Adversarial Networks for Control Space Reduction in Data Assimilation.

This thesis examines the use of generative adversarial networks (GANs) as a parameterization tool for inverse problems solved with ensemble-based data assimilation methods. Ensemble methods often rely on the assumption of Gaussian distributed parameters in cases where this assumption is not valid, the parameter estimation can be invalid. Parameterization methods allow the transformation of these non-Gaussian parameters into a better suited distribution, and optimally reduce their dimension. Another limitation of ensemble methods is the injection of prior information of the physical relation as a constraint between parameters such as spatial coherence or physical balances. Optimal parameterization should encompass these different properties to facilitate the estimation. The novel approach presented in this work relies on GANs to achieve these objectives. Two application domains are tackled through the present work. In a first application, subsurface reservoir characterization, the objective is to determine geological properties of a numerical reservoir model from the observation of the reservoir dynamical response by the way of data assimilation. Rock facies, that describe the type of rock present in each cell of the numerical model, have to be determined due to their strong influence on the dynamical response. The rock facies spatial distribution is ruled by geological phenomena such as sedimentation and forms well known patterns, like channels, called heterogeneities. The noncontinuous property and their spatial coherence make their characterization by ensemble-based data assimilation algorithms difficult, and requires parameterization. Parameterization is a challenge for numerous heterogeneities, notably channels, due to the numerical cost or the statistical representation of their spatial distribution. A Second application domain is the atmospheric balance in the context of numerical weather prediction. When new observations are available, correction of the atmospheric state is done using ensemblebased data assimilation methods. This correction step can introduce imbalance in the physical state and cause numerical instability during the integration in time of the atmosphere, deteriorating the information brought by the previous observations. The importance of generating or correcting balanced climate, also called initialized atmospheric state, during data assimilation is then a key step in numerical weather prediction. This work aims at presenting the performance of GAN parameterization and its multi-disciplinary applicability to researchers who are not familiar with the domain of deep learning. GAN is an unsupervised deep learning method belonging to the deep generative network family, able to learn a dataset distribution and generate new samples from the learned distribution in an unsupervised way. These synthetic samples are encoded in a low-dimensional latent space that can be sampled from a Gaussian distribution that is suited to perform ensemble data assimilation. Their recent ability to generate complex images led us to consider them as a good candidate for parameterization method. The unsupervised property of this type of parameterization makes it applicable to several diverse domains such as learning the pattern of geological heterogeneities or learning the physical constraints that makes an atmospheric state balanced. This study shows how to train GANs for two different applications : subsurface reservoir and climate data. The use of the parameterization in an ensemble based data assimilation such as ensemble smoother with multiple data assimilation (ES-MDA) is demonstrated for subsurface reservoir. Finally, a posteriori conditioning of the GAN function is examined using derivative free optimization

Towards Multilingual Coreference Resolution

The current work investigates the problems that occur when coreference resolution is considered as a multilingual task. We assess the issues that arise when a framework using the mention-pair coreference resolution model and memory-based learning for the resolution process are used. Along the way, we revise three essential subtasks of coreference resolution: mention detection, mention head detection and feature selection. For each of these aspects we propose various multilingual solutions including both heuristic, rule-based and machine learning methods. We carry out a detailed analysis that includes eight different languages (Arabic, Catalan, Chinese, Dutch, English, German, Italian and Spanish) for which datasets were provided by the only two multilingual shared tasks on coreference resolution held so far: SemEval-2 and CoNLL-2012. Our investigation shows that, although complex, the coreference resolution task can be targeted in a multilingual and even language independent way. We proposed machine learning methods for each of the subtasks that are affected by the transition, evaluated and compared them to the performance of rule-based and heuristic approaches. Our results confirmed that machine learning provides the needed flexibility for the multilingual task and that the minimal requirement for a language independent system is a part-of-speech annotation layer provided for each of the approached languages. We also showed that the performance of the system can be improved by introducing other layers of linguistic annotations, such as syntactic parses (in the form of either constituency or dependency parses), named entity information, predicate argument structure, etc. Additionally, we discuss the problems occurring in the proposed approaches and suggest possibilities for their improvement