Three-dimensional anatomical atlas of the human body

A thesis submitted in partial fulfillment of the requirements for the degree of Doctor in Information Management, specialization in Geographic Information SystemsAnatomical atlases allow mapping the anatomical structures of the human body. Early versions of these systems consisted of analogic representations with informative text and labelled images of the human body. With the advent of computer systems, digital versions emerged and the third dimension was introduced. Consequently, these systems increased their efficiency, allowing more realistic visualizations with improved interactivity. The development of anatomical atlases in geographic information systems (GIS) environments allows the development of platforms with a high degree of interactivity and with tools to explore and analyze the human body. In this thesis, a prototype for the human body representation is developed. The system includes a 3D GIS topological model, a graphical user interface and functions to explore and analyze the interior and the surface of the anatomical structures of the human body. The GIS approach relies essentially on the topological characteristics of the model and on the kind of available functions, which include measurement, identification, selection and analysis. With the incorporation of these functions, the final system has the ability to replicate the kind of information provided by the conventional anatomical atlases and also provides a higher level of functionality, since some of the atlases limitations are precisely features offered by GIS, namely, interactive capabilities, multilayer management, measurement tools, edition mode, allowing the expansion of the information contained in the system, and spatial analyzes

Beyond English text: Multilingual and multimedia information retrieval.

Non

Multiple costs and their combination in cost sensitive learning

University of Technology, Sydney. Faculty of Information Technology.Cost sensitive learning is firstly defined as a procedure of minimizing the costs of classification errors. It has attracted much attention in the last few years. Being cost sensitive has the strength to handle the unbalance on the misclassification errors in some real world applications. Recently, researchers have considered how to deal with two or more costs in a model, such as involving both of the misclassification costs (the cost for misclassification errors) and attribute test costs (the cost incurs as obtaining the attribute’s value) [Tur95, GGR02, LYWZ04], Cost sensitive learning involving both attribute test costs and misclassification costs is called test cost sensitive learning that is more close to real industry focus, such as medical research and business decision. Current test cost sensitive learning aims to find an optimal diagnostic policy (simply, a policy) with minimal expected sum of the misclassification cost and test cost that specifies, for example which attribute test is performed in next step based on the outcomes of previous attribute tests, and when the algorithm stops (by choosing to classify). A diagnostic policy takes the form of a decision tree whose nodes specify tests and whose leaves specify classification actions. A challenging issue is the choice of a reasonable one from all possible policies. This dissertation argues for considering both of the test cost and misclassification cost, or even more costs together, but doubts if the current way, summing up the two costs, is the only right way. Detailed studies are needed to ensure the ways of combination make sense and be “correct”, dimensionally as well as semantically. This dissertation studies fundamental properties of costs involved and designs new models to combine the costs together. Some essential properties of attribute test cost are studied. In our learning problem definition, test cost is combined into misclassification cost by choosing and performing proper tests for a better decision. Why do you choose them and how about the ones that are not chosen? Very often, only part of all attribute values are enough for making a decision and rest attributes are left as “unknown”. The values are defined as ‘absent values' as they are left as unknown purposely for some rational reasons when the information obtained is considered as enough, or when patients have no money enough to perform further tests, and so on.. This is the first work to utilize the information hidden in those “absent values” in cost sensitive learning; and the conclusion is very positive, i.e. “Absent data” is useful for decision making. The “absent values” are usually treated as ‘missing values' when left as known for unexpected reasons. This thesis studies the difference between ‘absent’ and ‘missing’. An algorithm based on lazy decision tree is proposed to identify the absent data from missing data, and a novel strategy is proposed to help patch the “real” missing values. . Two novel test cost sensitive models are designed for different real work scenarios. The first model is a general test cost sensitive learning framework with multiple cost scales. Previous works assume that the test cost and the misclassification cost must be defined on the same cost scale, such as the dollar cost incurred in a medical diagnosis. And they aim to minimize the sum of the misclassification cost and the test cost. However, costs may be measured in very different units and we may meet difficulty in defining the multiple costs on the same cost scale. It is not only a technology issue, but also a social issue. In medical diagnosis, how much money should you assign for a misclassification cost? Sometimes, a misclassification may hurt a patient’s life. And from a social point of view, life is invaluable. To tackle this issue, a target-resource budget learning framework with multiple costs is proposed. With this framework, we present a test cost sensitive decision tree model with two kinds of cost scales. The task is to minimize one cost scale, called target cost, and keep the other one within specified budgets. To the best of our knowledge, this is the first attempt to study the cost sensitive learning with multiple costs scales. The second model is based on the assumption that some attributes of an unlabeled example are known before being classified. A test cost sensitive lazy tree model is proposed to utilize the known information to reduce the overall cost. We also modify and apply this model to the batch-test problem: multiple tests are chosen and done in one shot, rather than in a sequential manner in the test-sensitive tree. It is significant in some diagnosis applications that require a decision to be made as soon as possible, such as emergency treatment. Extensive experiments are conducted for evaluating the proposed approaches, and demonstrate that the work in this dissertation is efficient and useful for many diagnostic tasks involving target cost minimization and resource utilization for obtaining missing information

Computer vision beyond the visible : image understanding through language

In the past decade, deep neural networks have revolutionized computer vision. High performing deep neural architectures trained for visual recognition tasks have pushed the field towards methods relying on learned image representations instead of hand-crafted ones, in the seek of designing end-to-end learning methods to solve challenging tasks, ranging from long-lasting ones such as image classification to newly emerging tasks like image captioning. As this thesis is framed in the context of the rapid evolution of computer vision, we present contributions that are aligned with three major changes in paradigm that the field has recently experienced, namely 1) the power of re-utilizing deep features from pre-trained neural networks for different tasks, 2) the advantage of formulating problems with end-to-end solutions given enough training data, and 3) the growing interest of describing visual data with natural language rather than pre-defined categorical label spaces, which can in turn enable visual understanding beyond scene recognition. The first part of the thesis is dedicated to the problem of visual instance search, where we particularly focus on obtaining meaningful and discriminative image representations which allow efficient and effective retrieval of similar images given a visual query. Contributions in this part of the thesis involve the construction of sparse Bag-of-Words image representations from convolutional features from a pre-trained image classification neural network, and an analysis of the advantages of fine-tuning a pre-trained object detection network using query images as training data. The second part of the thesis presents contributions to the problem of image-to-set prediction, understood as the task of predicting a variable-sized collection of unordered elements for an input image. We conduct a thorough analysis of current methods for multi-label image classification, which are able to solve the task in an end-to-end manner by simultaneously estimating both the label distribution and the set cardinality. Further, we extend the analysis of set prediction methods to semantic instance segmentation, and present an end-to-end recurrent model that is able to predict sets of objects (binary masks and categorical labels) in a sequential manner. Finally, the third part of the dissertation takes insights learned in the previous two parts in order to present deep learning solutions to connect images with natural language in the context of cooking recipes and food images. First, we propose a retrieval-based solution in which the written recipe and the image are encoded into compact representations that allow the retrieval of one given the other. Second, as an alternative to the retrieval approach, we propose a generative model to predict recipes directly from food images, which first predicts ingredients as sets and subsequently generates the rest of the recipe one word at a time by conditioning both on the image and the predicted ingredients.En l'última dècada, les xarxes neuronals profundes han revolucionat el camp de la visió per computador. Els resultats favorables obtinguts amb arquitectures neuronals profundes entrenades per resoldre tasques de reconeixement visual han causat un canvi de paradigma cap al disseny de mètodes basats en representacions d'imatges apreses de manera automàtica, deixant enrere les tècniques tradicionals basades en l'enginyeria de representacions. Aquest canvi ha permès l'aparició de tècniques basades en l'aprenentatge d'extrem a extrem (end-to-end), capaces de resoldre de manera efectiva molts dels problemes tradicionals de la visió per computador (e.g. classificació d'imatges o detecció d'objectes), així com nous problemes emergents com la descripció textual d'imatges (image captioning). Donat el context de la ràpida evolució de la visió per computador en el qual aquesta tesi s'emmarca, presentem contribucions alineades amb tres dels canvis més importants que la visió per computador ha experimentat recentment: 1) la reutilització de representacions extretes de models neuronals pre-entrenades per a tasques auxiliars, 2) els avantatges de formular els problemes amb solucions end-to-end entrenades amb grans bases de dades, i 3) el creixent interès en utilitzar llenguatge natural en lloc de conjunts d'etiquetes categòriques pre-definits per descriure el contingut visual de les imatges, facilitant així l'extracció d'informació visual més enllà del reconeixement de l'escena i els elements que la composen La primera part de la tesi està dedicada al problema de la cerca d'imatges (image retrieval), centrada especialment en l'obtenció de representacions visuals significatives i discriminatòries que permetin la recuperació eficient i efectiva d'imatges donada una consulta formulada amb una imatge d'exemple. Les contribucions en aquesta part de la tesi inclouen la construcció de representacions Bag-of-Words a partir de descriptors locals obtinguts d'una xarxa neuronal entrenada per classificació, així com un estudi dels avantatges d'utilitzar xarxes neuronals per a detecció d'objectes entrenades utilitzant les imatges d'exemple, amb l'objectiu de millorar les capacitats discriminatòries de les representacions obtingudes. La segona part de la tesi presenta contribucions al problema de predicció de conjunts a partir d'imatges (image to set prediction), entès com la tasca de predir una col·lecció no ordenada d'elements de longitud variable donada una imatge d'entrada. En aquest context, presentem una anàlisi exhaustiva dels mètodes actuals per a la classificació multi-etiqueta d'imatges, que són capaços de resoldre la tasca de manera integral calculant simultàniament la distribució probabilística sobre etiquetes i la cardinalitat del conjunt. Seguidament, estenem l'anàlisi dels mètodes de predicció de conjunts a la segmentació d'instàncies semàntiques, presentant un model recurrent capaç de predir conjunts d'objectes (representats per màscares binàries i etiquetes categòriques) de manera seqüencial. Finalment, la tercera part de la tesi estén els coneixements apresos en les dues parts anteriors per presentar solucions d'aprenentatge profund per connectar imatges amb llenguatge natural en el context de receptes de cuina i imatges de plats cuinats. En primer lloc, proposem una solució basada en algoritmes de cerca, on la recepta escrita i la imatge es codifiquen amb representacions compactes que permeten la recuperació d'una donada l'altra. En segon lloc, com a alternativa a la solució basada en algoritmes de cerca, proposem un model generatiu capaç de predir receptes (compostes pels seus ingredients, predits com a conjunts, i instruccions) directament a partir d'imatges de menjar.Postprint (published version

Discourse analysis of arabic documents and application to automatic summarization

Dans un discours, les textes et les conversations ne sont pas seulement une juxtaposition de mots et de phrases. Ils sont plutôt organisés en une structure dans laquelle des unités de discours sont liées les unes aux autres de manière à assurer à la fois la cohérence et la cohésion du discours. La structure du discours a montré son utilité dans de nombreuses applications TALN, y compris la traduction automatique, la génération de texte et le résumé automatique. L'utilité du discours dans les applications TALN dépend principalement de la disponibilité d'un analyseur de discours performant. Pour aider à construire ces analyseurs et à améliorer leurs performances, plusieurs ressources ont été annotées manuellement par des informations de discours dans des différents cadres théoriques. La plupart des ressources disponibles sont en anglais. Récemment, plusieurs efforts ont été entrepris pour développer des ressources discursives pour d'autres langues telles que le chinois, l'allemand, le turc, l'espagnol et le hindi. Néanmoins, l'analyse de discours en arabe standard moderne (MSA) a reçu moins d'attention malgré le fait que MSA est une langue de plus de 422 millions de locuteurs dans 22 pays. Le sujet de thèse s'intègre dans le cadre du traitement automatique de la langue arabe, plus particulièrement, l'analyse de discours de textes arabes. Cette thèse a pour but d'étudier l'apport de l'analyse sémantique et discursive pour la génération de résumé automatique de documents en langue arabe. Pour atteindre cet objectif, nous proposons d'étudier la théorie de la représentation discursive segmentée (SDRT) qui propose un cadre logique pour la représentation sémantique de phrases ainsi qu'une représentation graphique de la structure du texte où les relations de discours sont de nature sémantique plutôt qu'intentionnelle. Cette théorie a été étudiée pour l'anglais, le français et l'allemand mais jamais pour la langue arabe. Notre objectif est alors d'adapter la SDRT à la spécificité de la langue arabe afin d'analyser sémantiquement un texte pour générer un résumé automatique. Nos principales contributions sont les suivantes : Une étude de la faisabilité de la construction d'une structure de discours récursive et complète de textes arabes. En particulier, nous proposons : Un schéma d'annotation qui couvre la totalité d'un texte arabe, dans lequel chaque constituant est lié à d'autres constituants. Un document est alors représenté par un graphe acyclique orienté qui capture les relations explicites et les relations implicites ainsi que des phénomènes de discours complexes, tels que l'attachement, la longue distance du discours pop-ups et les dépendances croisées. Une nouvelle hiérarchie des relations de discours. Nous étudions les relations rhétoriques d'un point de vue sémantique en se concentrant sur leurs effets sémantiques et non pas sur la façon dont elles sont déclenchées par des connecteurs de discours, qui sont souvent ambigües en arabe. o une analyse quantitative (en termes de connecteurs de discours, de fréquences de relations, de proportion de relations implicites, etc.) et une analyse qualitative (accord inter-annotateurs et analyse des erreurs) de la campagne d'annotation. Un outil d'analyse de discours où nous étudions à la fois la segmentation automatique de textes arabes en unités de discours minimales et l'identification automatique des relations explicites et implicites du discours. L'utilisation de notre outil pour résumer des textes arabes. Nous comparons la représentation de discours en graphes et en arbres pour la production de résumés.Within a discourse, texts and conversations are not just a juxtaposition of words and sentences. They are rather organized in a structure in which discourse units are related to each other so as to ensure both discourse coherence and cohesion. Discourse structure has shown to be useful in many NLP applications including machine translation, natural language generation and language technology in general. The usefulness of discourse in NLP applications mainly depends on the availability of powerful discourse parsers. To build such parsers and improve their performances, several resources have been manually annotated with discourse information within different theoretical frameworks. Most available resources are in English. Recently, several efforts have been undertaken to develop manually annotated discourse information for other languages such as Chinese, German, Turkish, Spanish and Hindi. Surprisingly, discourse processing in Modern Standard Arabic (MSA) has received less attention despite the fact that MSA is a language with more than 422 million speakers in 22 countries. Computational processing of Arabic language has received a great attention in the literature for over twenty years. Several resources and tools have been built to deal with Arabic non concatenative morphology and Arabic syntax going from shallow to deep parsing. However, the field is still very vacant at the layer of discourse. As far as we know, the sole effort towards Arabic discourse processing was done in the Leeds Arabic Discourse Treebank that extends the Penn Discourse TreeBank model to MSA. In this thesis, we propose to go beyond the annotation of explicit relations that link adjacent units, by completely specifying the semantic scope of each discourse relation, making transparent an interpretation of the text that takes into account the semantic effects of discourse relations. In particular, we propose the first effort towards a semantically driven approach of Arabic texts following the Segmented Discourse Representation Theory (SDRT). Our main contributions are: A study of the feasibility of building a recursive and complete discourse structures of Arabic texts. In particular, we propose: An annotation scheme for the full discourse coverage of Arabic texts, in which each constituent is linked to other constituents. A document is then represented by an oriented acyclic graph, which captures explicit and implicit relations as well as complex discourse phenomena, such as long-distance attachments, long-distance discourse pop-ups and crossed dependencies. A novel discourse relation hierarchy. We study the rhetorical relations from a semantic point of view by focusing on their effect on meaning and not on how they are lexically triggered by discourse connectives that are often ambiguous, especially in Arabic. A thorough quantitative analysis (in terms of discourse connectives, relation frequencies, proportion of implicit relations, etc.) and qualitative analysis (inter-annotator agreements and error analysis) of the annotation campaign. An automatic discourse parser where we investigate both automatic segmentation of Arabic texts into elementary discourse units and automatic identification of explicit and implicit Arabic discourse relations. An application of our discourse parser to Arabic text summarization. We compare tree-based vs. graph-based discourse representations for producing indicative summaries and show that the full discourse coverage of a document is definitively a plus

Automatic Sign Language Recognition from Image Data

Tato práce se zabývá problematikou automatického rozpoznávání znakového jazyka z obrazových dat. Práce představuje pět hlavních přínosů v oblasti tvorby systému pro rozpoznávání, tvorby korpusů, extrakci příznaků z rukou a obličeje s využitím metod pro sledování pozice a pohybu rukou (tracking) a modelování znaků s využitím menších fonetických jednotek (sub-units). Metody využité v rozpoznávacím systému byly využity i k tvorbě vyhledávacího nástroje "search by example", který dokáže vyhledávat ve videozáznamech podle obrázku ruky. Navržený systém pro automatické rozpoznávání znakového jazyka je založen na statistickém přístupu s využitím skrytých Markovových modelů, obsahuje moduly pro analýzu video dat, modelování znaků a dekódování. Systém je schopen rozpoznávat jak izolované, tak spojité promluvy. Veškeré experimenty a vyhodnocení byly provedeny s vlastními korpusy UWB-06-SLR-A a UWB-07-SLR-P, první z nich obsahuje 25 znaků, druhý 378. Základní extrakce příznaků z video dat byla provedena na nízkoúrovňových popisech obrazu. Lepších výsledků bylo dosaženo s příznaky získaných z popisů vyšší úrovně porozumění obsahu v obraze, které využívají sledování pozice rukou a metodu pro segmentaci rukou v době překryvu s obličejem. Navíc, využitá metoda dokáže interpolovat obrazy s obličejem v době překryvu a umožňuje tak využít metody pro extrakci příznaků z obličeje, které by během překryvu nefungovaly, jako např. metoda active appearance models (AAM). Bylo porovnáno několik různých metod pro extrakci příznaků z rukou, jako např. local binary patterns (LBP), histogram of oriented gradients (HOG), vysokoúrovnové lingvistické příznaky a nové navržená metoda hand shape radial distance function (hRDF). Bylo také zkoumáno využití menších fonetických jednotek, než jsou celé znaky, tzv. sub-units. Pro první krok tvorby těchto jednotek byl navržen iterativní algoritmus, který tyto jednotky automaticky vytváří analýzou existujících dat. Bylo ukázáno, že tento koncept je vhodný pro modelování a rozpoznávání znaků. Kromě systému pro rozpoznávání je v práci navržen a představen systém "search by example", který funguje jako vyhledávací systém pro videa se záznamy znakového jazyka a může být využit například v online slovnících znakového jazyka, kde je v současné době složité či nemožné v takovýchto datech vyhledávat. Tento nástroj využívá metody, které byly použity v rozpoznávacím systému. Výstupem tohoto vyhledávacího nástroje je seřazený seznam videí, které obsahují stejný nebo podobný tvar ruky, které zadal uživatel, např. přes webkameru.Katedra kybernetikyObhájenoThis thesis addresses several issues of automatic sign language recognition, namely the creation of vision based sign language recognition framework, sign language corpora creation, feature extraction, making use of novel hand tracking with face occlusion handling, data-driven creation of sub-units and "search by example" tool for searching in sign language corpora using hand images as a search query. The proposed sign language recognition framework, based on statistical approach incorporating hidden Markov models (HMM), consists of video analysis, sign modeling and decoding modules. The framework is able to recognize both isolated signs and continuous utterances from video data. All experiments and evaluations were performed on two own corpora, UWB-06-SLR-A and UWB-07-SLR-P, the first containing 25 signs and second 378. As a baseline feature descriptors, low level image features are used. It is shown that better performance is gained by higher level features that employ hand tracking, which resolve occlusions of hands and face. As a side effect, the occlusion handling method interpolates face area in the frames during the occlusion and allows to use face feature descriptors that fail in such a case, for instance features extracted from active appearance models (AAM) tracker. Several state-of-the-art appearance-based feature descriptors were compared for tracked hands, such as local binary patterns (LBP), histogram of oriented gradients (HOG), high-level linguistic features or newly proposed hand shape radial distance function (denoted as hRDF) that enhances the feature description of hand-shape like concave regions. The concept of sub-units, that uses HMM models based on linguistic units smaller than whole sign and covers inner structures of the signs, was investigated in the proposed iterative method that is a first required step for data-driven construction of sub-units, and shows that such a concept is suitable for sign modeling and recognition tasks. Except of experiments in the sign language recognition, additional tool \textit{search by example} was created and evaluated. This tool is a search engine for sign language videos. Such a system can be incorporated into an online sign language dictionary where it is difficult to search in the sign language data. This proposed tool employs several methods which were examined in the sign language recognition task and allows to search in the video corpora based on an user-given query that consists of one or multiple images of hands. As a result, an ordered list of videos that contain the same or similar hand configurations is returned

Large-scale Multi-Modal Pre-trained Models: A Comprehensive Survey

With the urgent demand for generalized deep models, many pre-trained big models are proposed, such as BERT, ViT, GPT, etc. Inspired by the success of these models in single domains (like computer vision and natural language processing), the multi-modal pre-trained big models have also drawn more and more attention in recent years. In this work, we give a comprehensive survey of these models and hope this paper could provide new insights and helps fresh researchers to track the most cutting-edge works. Specifically, we firstly introduce the background of multi-modal pre-training by reviewing the conventional deep learning, pre-training works in natural language process, computer vision, and speech. Then, we introduce the task definition, key challenges, and advantages of multi-modal pre-training models (MM-PTMs), and discuss the MM-PTMs with a focus on data, objectives, network architectures, and knowledge enhanced pre-training. After that, we introduce the downstream tasks used for the validation of large-scale MM-PTMs, including generative, classification, and regression tasks. We also give visualization and analysis of the model parameters and results on representative downstream tasks. Finally, we point out possible research directions for this topic that may benefit future works. In addition, we maintain a continuously updated paper list for large-scale pre-trained multi-modal big models: https://github.com/wangxiao5791509/MultiModal_BigModels_SurveyComment: Accepted by Machine Intelligence Researc

Semantics of video shots for content-based retrieval

Content-based video retrieval research combines expertise from many different areas, such as signal processing, machine learning, pattern recognition, and computer vision. As video extends into both the spatial and the temporal domain, we require techniques for the temporal decomposition of footage so that specific content can be accessed. This content may then be semantically classified - ideally in an automated process - to enable filtering, browsing, and searching. An important aspect that must be considered is that pictorial representation of information may be interpreted differently by individual users because it is less specific than its textual representation. In this thesis, we address several fundamental issues of content-based video retrieval for effective handling of digital footage. Temporal segmentation, the common first step in handling digital video, is the decomposition of video streams into smaller, semantically coherent entities. This is usually performed by detecting the transitions that separate single camera takes. While abrupt transitions - cuts - can be detected relatively well with existing techniques, effective detection of gradual transitions remains difficult. We present our approach to temporal video segmentation, proposing a novel algorithm that evaluates sets of frames using a relatively simple histogram feature. Our technique has been shown to range among the best existing shot segmentation algorithms in large-scale evaluations. The next step is semantic classification of each video segment to generate an index for content-based retrieval in video databases. Machine learning techniques can be applied effectively to classify video content. However, these techniques require manually classified examples for training before automatic classification of unseen content can be carried out. Manually classifying training examples is not trivial because of the implied ambiguity of visual content. We propose an unsupervised learning approach based on latent class modelling in which we obtain multiple judgements per video shot and model the users' response behaviour over a large collection of shots. This technique yields a more generic classification of the visual content. Moreover, it enables the quality assessment of the classification, and maximises the number of training examples by resolving disagreement. We apply this approach to data from a large-scale, collaborative annotation effort and present ways to improve the effectiveness for manual annotation of visual content by better design and specification of the process. Automatic speech recognition techniques along with semantic classification of video content can be used to implement video search using textual queries. This requires the application of text search techniques to video and the combination of different information sources. We explore several text-based query expansion techniques for speech-based video retrieval, and propose a fusion method to improve overall effectiveness. To combine both text and visual search approaches, we explore a fusion technique that combines spoken information and visual information using semantic keywords automatically assigned to the footage based on the visual content. The techniques that we propose help to facilitate effective content-based video retrieval and highlight the importance of considering different user interpretations of visual content. This allows better understanding of video content and a more holistic approach to multimedia retrieval in the future