Optimized Realization of Bayesian Networks in Reduced Normal Form using Latent Variable Model

Bayesian networks in their Factor Graph Reduced Normal Form (FGrn) are a powerful paradigm for implementing inference graphs. Unfortunately, the computational and memory costs of these networks may be considerable, even for relatively small networks, and this is one of the main reasons why these structures have often been underused in practice. In this work, through a detailed algorithmic and structural analysis, various solutions for cost reduction are proposed. An online version of the classic batch learning algorithm is also analyzed, showing very similar results (in an unsupervised context); which is essential even if multilevel structures are to be built. The solutions proposed, together with the possible online learning algorithm, are included in a C++ library that is quite efficient, especially if compared to the direct use of the well-known sum-product and Maximum Likelihood (ML) algorithms. The results are discussed with particular reference to a Latent Variable Model (LVM) structure.Comment: 20 pages, 8 figure

Domain Adaptation and Domain Generalization with Representation Learning

Machine learning has achieved great successes in the area of computer vision, especially in object recognition or classification. One of the core factors of the successes is the availability of massive labeled image or video data for training, collected manually by human. Labeling source training data, however, can be expensive and time consuming. Furthermore, a large amount of labeled source data may not always guarantee traditional machine learning techniques to generalize well; there is a potential bias or mismatch in the data, i.e., the training data do not represent the target environment. To mitigate the above dataset bias/mismatch, one can consider domain adaptation: utilizing labeled training data and unlabeled target data to develop a well-performing classifier on the target environment. In some cases, however, the unlabeled target data are nonexistent, but multiple labeled sources of data exist. Such situations can be addressed by domain generalization: using multiple source training sets to produce a classifier that generalizes on the unseen target domain. Although several domain adaptation and generalization approaches have been proposed, the domain mismatch in object recognition remains a challenging, open problem – the model performance has yet reached to a satisfactory level in real world applications. The overall goal of this thesis is to progress towards solving dataset bias in visual object recognition through representation learning in the context of domain adaptation and domain generalization. Representation learning is concerned with finding proper data representations or features via learning rather than via engineering by human experts. This thesis proposes several representation learning solutions based on deep learning and kernel methods. This thesis introduces a robust-to-noise deep neural network for handwritten digit classification trained on “clean” images only, which we name Deep Hybrid Network (DHN). DHNs are based on a particular combination of sparse autoencoders and restricted Boltzmann machines. The results show that DHN performs better than the standard deep neural network in recognizing digits with Gaussian and impulse noise, block and border occlusions. This thesis proposes the Domain Adaptive Neural Network (DaNN), a neural network based domain adaptation algorithm that minimizes the classification error and the domain discrepancy between the source and target data representations. The experiments show the competitiveness of DaNN against several state-of-the-art methods on a benchmark object dataset. This thesis develops the Multi-task Autoencoder (MTAE), a domain generalization algorithm based on autoencoders trained via multi-task learning. MTAE learns to transform the original image into its analogs in multiple related domains simultaneously. The results show that the MTAE’s representations provide better classification performance than some alternative autoencoder-based models as well as the current state-of-the-art domain generalization algorithms. This thesis proposes a fast kernel-based representation learning algorithm for both domain adaptation and domain generalization, Scatter Component Analysis (SCA). SCA finds a data representation that trades between maximizing the separability of classes, minimizing the mismatch between domains, and maximizing the separability of the whole data points. The results show that SCA performs much faster than some competitive algorithms, while providing state-of-the-art accuracy in both domain adaptation and domain generalization. Finally, this thesis presents the Deep Reconstruction-Classification Network (DRCN), a deep convolutional network for domain adaptation. DRCN learns to classify labeled source data and also to reconstruct unlabeled target data via a shared encoding representation. The results show that DRCN provides competitive or better performance than the prior state-of-the-art model on several cross-domain object datasets

Unsupervised learning for vascular heterogeneity assessment of glioblastoma based on magnetic resonance imaging: The Hemodynamic Tissue Signature

[ES] El futuro de la imagen médica está ligado a la inteligencia artificial. El análisis manual de imágenes médicas es hoy en día una tarea ardua, propensa a errores y a menudo inasequible para los humanos, que ha llamado la atención de la comunidad de Aprendizaje Automático (AA). La Imagen por Resonancia Magnética (IRM) nos proporciona una rica variedad de representaciones de la morfología y el comportamiento de lesiones inaccesibles sin una intervención invasiva arriesgada. Sin embargo, explotar la potente pero a menudo latente información contenida en la IRM es una tarea muy complicada, que requiere técnicas de análisis computacional inteligente. Los tumores del sistema nervioso central son una de las enfermedades más críticas estudiadas a través de IRM. Específicamente, el glioblastoma representa un gran desafío, ya que, hasta la fecha, continua siendo un cáncer letal que carece de una terapia satisfactoria. Del conjunto de características que hacen del glioblastoma un tumor tan agresivo, un aspecto particular que ha sido ampliamente estudiado es su heterogeneidad vascular. La fuerte proliferación vascular del glioblastoma, así como su robusta angiogénesis han sido consideradas responsables de la alta letalidad de esta neoplasia. Esta tesis se centra en la investigación y desarrollo del método Hemodynamic Tissue Signature (HTS): un método de AA no supervisado para describir la heterogeneidad vascular de los glioblastomas mediante el análisis de perfusión por IRM. El método HTS se basa en el concepto de hábitat, que se define como una subregión de la lesión con un perfil de IRM que describe un comportamiento fisiológico concreto. El método HTS delinea cuatro hábitats en el glioblastoma: el hábitat HAT, como la región más perfundida del tumor con captación de contraste; el hábitat LAT, como la región del tumor con un perfil angiogénico más bajo; el hábitat IPE, como la región adyacente al tumor con índices de perfusión elevados; y el hábitat VPE, como el edema restante de la lesión con el perfil de perfusión más bajo. La investigación y desarrollo de este método ha originado una serie de contribuciones enmarcadas en esta tesis. Primero, para verificar la fiabilidad de los métodos de AA no supervisados en la extracción de patrones de IRM, se realizó una comparativa para la tarea de segmentación de gliomas de grado alto. Segundo, se propuso un algoritmo de AA no supervisado dentro de la familia de los Spatially Varying Finite Mixture Models. El algoritmo propone una densidad a priori basada en un Markov Random Field combinado con la función probabilística Non-Local Means, para codificar la idea de que píxeles vecinos tienden a pertenecer al mismo objeto. Tercero, se presenta el método HTS para describir la heterogeneidad vascular del glioblastoma. El método se ha aplicado a casos reales en una cohorte local de un solo centro y en una cohorte internacional de más de 180 pacientes de 7 centros europeos. Se llevó a cabo una evaluación exhaustiva del método para medir el potencial pronóstico de los hábitats HTS. Finalmente, la tecnología desarrollada en la tesis se ha integrado en la plataforma online ONCOhabitats (https://www.oncohabitats.upv.es). La plataforma ofrece dos servicios: 1) segmentación de tejidos de glioblastoma, y 2) evaluación de la heterogeneidad vascular del tumor mediante el método HTS. Los resultados de esta tesis han sido publicados en diez contribuciones científicas, incluyendo revistas y conferencias de alto impacto en las áreas de Informática Médica, Estadística y Probabilidad, Radiología y Medicina Nuclear y Aprendizaje Automático. También se emitió una patente industrial registrada en España, Europa y EEUU. Finalmente, las ideas originales concebidas en esta tesis dieron lugar a la creación de ONCOANALYTICS CDX, una empresa enmarcada en el modelo de negocio de los companion diagnostics de compuestos farmacéuticos.[EN] The future of medical imaging is linked to Artificial Intelligence (AI). The manual analysis of medical images is nowadays an arduous, error-prone and often unaffordable task for humans, which has caught the attention of the Machine Learning (ML) community. Magnetic Resonance Imaging (MRI) provides us with a wide variety of rich representations of the morphology and behavior of lesions completely inaccessible without a risky invasive intervention. Nevertheless, harnessing the powerful but often latent information contained in MRI acquisitions is a very complicated task, which requires computational intelligent analysis techniques. Central nervous system tumors are one of the most critical diseases studied through MRI. Specifically, glioblastoma represents a major challenge, as it remains a lethal cancer that, to date, lacks a satisfactory therapy. Of the entire set of characteristics that make glioblastoma so aggressive, a particular aspect that has been widely studied is its vascular heterogeneity. The strong vascular proliferation of glioblastomas, as well as their robust angiogenesis and extensive microvasculature heterogeneity have been claimed responsible for the high lethality of the neoplasm. This thesis focuses on the research and development of the Hemodynamic Tissue Signature (HTS) method: an unsupervised ML approach to describe the vascular heterogeneity of glioblastomas by means of perfusion MRI analysis. The HTS builds on the concept of habitats. A habitat is defined as a sub-region of the lesion with a particular MRI profile describing a specific physiological behavior. The HTS method delineates four habitats within the glioblastoma: the HAT habitat, as the most perfused region of the enhancing tumor; the LAT habitat, as the region of the enhancing tumor with a lower angiogenic profile; the potentially IPE habitat, as the non-enhancing region adjacent to the tumor with elevated perfusion indexes; and the VPE habitat, as the remaining edema of the lesion with the lowest perfusion profile. The research and development of the HTS method has generated a number of contributions to this thesis. First, in order to verify that unsupervised learning methods are reliable to extract MRI patterns to describe the heterogeneity of a lesion, a comparison among several unsupervised learning methods was conducted for the task of high grade glioma segmentation. Second, a Bayesian unsupervised learning algorithm from the family of Spatially Varying Finite Mixture Models is proposed. The algorithm integrates a Markov Random Field prior density weighted by the probabilistic Non-Local Means function, to codify the idea that neighboring pixels tend to belong to the same semantic object. Third, the HTS method to describe the vascular heterogeneity of glioblastomas is presented. The HTS method has been applied to real cases, both in a local single-center cohort of patients, and in an international retrospective cohort of more than 180 patients from 7 European centers. A comprehensive evaluation of the method was conducted to measure the prognostic potential of the HTS habitats. Finally, the technology developed in this thesis has been integrated into an online open-access platform for its academic use. The ONCOhabitats platform is hosted at https://www.oncohabitats.upv.es, and provides two main services: 1) glioblastoma tissue segmentation, and 2) vascular heterogeneity assessment of glioblastomas by means of the HTS method. The results of this thesis have been published in ten scientific contributions, including top-ranked journals and conferences in the areas of Medical Informatics, Statistics and Probability, Radiology & Nuclear Medicine and Machine Learning. An industrial patent registered in Spain, Europe and EEUU was also issued. Finally, the original ideas conceived in this thesis led to the foundation of ONCOANALYTICS CDX, a company framed into the business model of companion diagnostics for pharmaceutical compounds.[CA] El futur de la imatge mèdica està lligat a la intel·ligència artificial. L'anàlisi manual d'imatges mèdiques és hui dia una tasca àrdua, propensa a errors i sovint inassequible per als humans, que ha cridat l'atenció de la comunitat d'Aprenentatge Automàtic (AA). La Imatge per Ressonància Magnètica (IRM) ens proporciona una àmplia varietat de representacions de la morfologia i el comportament de lesions inaccessibles sense una intervenció invasiva arriscada. Tanmateix, explotar la potent però sovint latent informació continguda a les adquisicions de IRM esdevé una tasca molt complicada, que requereix tècniques d'anàlisi computacional intel·ligent. Els tumors del sistema nerviós central són una de les malalties més crítiques estudiades a través de IRM. Específicament, el glioblastoma representa un gran repte, ja que, fins hui, continua siguent un càncer letal que manca d'una teràpia satisfactòria. Del conjunt de característiques que fan del glioblastoma un tumor tan agressiu, un aspecte particular que ha sigut àmpliament estudiat és la seua heterogeneïtat vascular. La forta proliferació vascular dels glioblastomes, així com la seua robusta angiogènesi han sigut considerades responsables de l'alta letalitat d'aquesta neoplàsia. Aquesta tesi es centra en la recerca i desenvolupament del mètode Hemodynamic Tissue Signature (HTS): un mètode d'AA no supervisat per descriure l'heterogeneïtat vascular dels glioblastomas mitjançant l'anàlisi de perfusió per IRM. El mètode HTS es basa en el concepte d'hàbitat, que es defineix com una subregió de la lesió amb un perfil particular d'IRM, que descriu un comportament fisiològic concret. El mètode HTS delinea quatre hàbitats dins del glioblastoma: l'hàbitat HAT, com la regió més perfosa del tumor amb captació de contrast; l'hàbitat LAT, com la regió del tumor amb un perfil angiogènic més baix; l'hàbitat IPE, com la regió adjacent al tumor amb índexs de perfusió elevats, i l'hàbitat VPE, com l'edema restant de la lesió amb el perfil de perfusió més baix. La recerca i desenvolupament del mètode HTS ha originat una sèrie de contribucions emmarcades a aquesta tesi. Primer, per verificar la fiabilitat dels mètodes d'AA no supervisats en l'extracció de patrons d'IRM, es va realitzar una comparativa en la tasca de segmentació de gliomes de grau alt. Segon, s'ha proposat un algorisme d'AA no supervisat dintre de la família dels Spatially Varying Finite Mixture Models. L'algorisme proposa un densitat a priori basada en un Markov Random Field combinat amb la funció probabilística Non-Local Means, per a codificar la idea que els píxels veïns tendeixen a pertànyer al mateix objecte semàntic. Tercer, es presenta el mètode HTS per descriure l'heterogeneïtat vascular dels glioblastomas. El mètode HTS s'ha aplicat a casos reals en una cohort local d'un sol centre i en una cohort internacional de més de 180 pacients de 7 centres europeus. Es va dur a terme una avaluació exhaustiva del mètode per mesurar el potencial pronòstic dels hàbitats HTS. Finalment, la tecnologia desenvolupada en aquesta tesi s'ha integrat en una plataforma online ONCOhabitats (https://www.oncohabitats.upv.es). La plataforma ofereix dos serveis: 1) segmentació dels teixits del glioblastoma, i 2) avaluació de l'heterogeneïtat vascular dels glioblastomes mitjançant el mètode HTS. Els resultats d'aquesta tesi han sigut publicats en deu contribucions científiques, incloent revistes i conferències de primer nivell a les àrees d'Informàtica Mèdica, Estadística i Probabilitat, Radiologia i Medicina Nuclear i Aprenentatge Automàtic. També es va emetre una patent industrial registrada a Espanya, Europa i els EEUU. Finalment, les idees originals concebudes en aquesta tesi van donar lloc a la creació d'ONCOANALYTICS CDX, una empresa emmarcada en el model de negoci dels companion diagnostics de compostos farmacèutics.En este sentido quiero agradecer a las diferentes instituciones y estructuras de financiación de investigación que han contribuido al desarrollo de esta tesis. En especial quiero agradecer a la Universitat Politècnica de València, donde he desarrollado toda mi carrera acadèmica y científica, así como al Ministerio de Ciencia e Innovación, al Ministerio de Economía y Competitividad, a la Comisión Europea, al EIT Health Programme y a la fundación Caixa ImpulseJuan Albarracín, J. (2020). Unsupervised learning for vascular heterogeneity assessment of glioblastoma based on magnetic resonance imaging: The Hemodynamic Tissue Signature [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/149560TESI

A probabilistic reasoning and learning system based on Bayesian belief networks

SIGLEAvailable from British Library Document Supply Centre- DSC:DX173015 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

From Points to Probability Measures: Statistical Learning on Distributions with Kernel Mean Embedding

The dissertation presents a novel learning framework on probability measures which has abundant real-world applications. In classical setup, it is assumed that the data are points that have been drawn independent and identically (i.i.d.) from some unknown distribution. In many scenarios, however, representing data as distributions may be more preferable. For instance, when the measurement is noisy, we may tackle the uncertainty by treating the data themselves as distributions, which is often the case for microarray data and astronomical data where the measurement process is imprecise and replication is often required. Distributions not only embody individual data points, but also constitute information about their interactions which can be beneficial for structural learning in high-energy physics, cosmology, causality, and so on. Moreover, classical problems in statistics such as statistical estimation, hypothesis testing, and causal inference, may be interpreted in a decision-theoretic sense as machine learning problems on empirical distributions. Rephrasing these problems as such leads to novel approach for statistical inference and estimation. Hence, allowing learning algorithms to operate directly on distributions prompts a wide range of future applications. To work with distributions, the key methodology adopted in this thesis is the kernel mean embedding of distributions which represents each distribution as a mean function in a reproducing kernel Hilbert space (RKHS). In particular, the kernel mean embedding has been applied successfully in two-sample testing, graphical model, and probabilistic inference. On the other hand, this thesis will focus mainly on the predictive learning on distributions, i.e., when the observations are distributions and the goal is to make prediction about the previously unseen distributions. More importantly, the thesis investigates kernel mean estimation which is one of the most fundamental problems of kernel methods. Probability distributions, as opposed to data points, constitute information at a higher level such as aggregate behavior of data points, how the underlying process evolves over time and domains, and a complex concept that cannot be described merely by individual points. Intelligent organisms have the ability to recognize and exploit such information naturally. Thus, this work may shed light on future development of intelligent machines, and most importantly, may provide clues on the true meaning of intelligence

Recent Advances in Transfer Learning for Cross-Dataset Visual Recognition: A Problem-Oriented Perspective

This paper takes a problem-oriented perspective and presents a comprehensive review of transfer learning methods, both shallow and deep, for cross-dataset visual recognition. Specifically, it categorises the cross-dataset recognition into seventeen problems based on a set of carefully chosen data and label attributes. Such a problem-oriented taxonomy has allowed us to examine how different transfer learning approaches tackle each problem and how well each problem has been researched to date. The comprehensive problem-oriented review of the advances in transfer learning with respect to the problem has not only revealed the challenges in transfer learning for visual recognition, but also the problems (e.g. eight of the seventeen problems) that have been scarcely studied. This survey not only presents an up-to-date technical review for researchers, but also a systematic approach and a reference for a machine learning practitioner to categorise a real problem and to look up for a possible solution accordingly

Automatic Speech Recognition for Low-resource Languages and Accents Using Multilingual and Crosslingual Information

This thesis explores methods to rapidly bootstrap automatic speech recognition systems for languages, which lack resources for speech and language processing. We focus on finding approaches which allow using data from multiple languages to improve the performance for those languages on different levels, such as feature extraction, acoustic modeling and language modeling. Under application aspects, this thesis also includes research work on non-native and Code-Switching speech

Deception and Disclosure: A Socio-Legal Analysis of HIV Transmission Offences and Mobile Dating Applications

In England and Wales, the criminalisation of disease transmission has principally arisen in cases involving HIV transmission. This includes Rowe [2018] where intentional transmission was established for the first time, in part through digital evidence. Criminal law scholarship on transmission offences has acknowledged that issues of HIV (non-)disclosure can be contentious, presenting particular challenges stemming from various disclosure expectations and understandings of HIV transmission risk which exist in different contexts/communities. Such issues have been compounded by the proliferation of HIV disclosure features on mobile “dating” applications targeted at men who have sex with men in recent years. How these new technologies influence and supplant existing expectations, knowledge of risk, and distributions of responsibility is an issue which has yet to be considered in empirical socio-legal literature. Utilising a visual, scenario-driven, methodology, this project analyses the responses of 102 application users who use these apps to connect with men and demonstrates that these features are understood in several complex and often contradictory ways. Firstly, this thesis illustrates how participants’ conceptualisations of risk and safety might challenge existing approaches to “sexual responsibility” and the uneven distribution of responsibility for HIV prevention. Secondly, it highlights how contextual disclosure expectations and the perceived “right to know” have the potential to influence legal debates on “conditional consent”. Thirdly, it demonstrates how discourses on responsibility and agency, as well as participants’ often erroneous understanding of the law, are shaped by these disclosure features. This thesis, therefore, makes a significant and original contribution to criminal law scholarship. It emphasises the importance of proper appraisal of contextual norms and knowledge in transmission cases and concludes by summarising that whilst applications offer new ways to understand culpability, responsibility and obligation in transmission cases, this can only be achieved justly through a detailed examination of social context in which these are used, which is not achieved if applications are presented as straightforward and unnuanced at trial

Space Communications: Theory and Applications. Volume 3: Information Processing and Advanced Techniques. A Bibliography, 1958 - 1963

Annotated bibliography on information processing and advanced communication techniques - theory and applications of space communication