One-Class Classification: Taxonomy of Study and Review of Techniques

One-class classification (OCC) algorithms aim to build classification models when the negative class is either absent, poorly sampled or not well defined. This unique situation constrains the learning of efficient classifiers by defining class boundary just with the knowledge of positive class. The OCC problem has been considered and applied under many research themes, such as outlier/novelty detection and concept learning. In this paper we present a unified view of the general problem of OCC by presenting a taxonomy of study for OCC problems, which is based on the availability of training data, algorithms used and the application domains applied. We further delve into each of the categories of the proposed taxonomy and present a comprehensive literature review of the OCC algorithms, techniques and methodologies with a focus on their significance, limitations and applications. We conclude our paper by discussing some open research problems in the field of OCC and present our vision for future research.Comment: 24 pages + 11 pages of references, 8 figure

Network-Based Biomarker Discovery : Development of Prognostic Biomarkers for Personalized Medicine by Integrating Data and Prior Knowledge

Advances in genome science and technology offer a deeper understanding of biology while at the same time improving the practice of medicine. The expression profiling of some diseases, such as cancer, allows for identifying marker genes, which could be able to diagnose a disease or predict future disease outcomes. Marker genes (biomarkers) are selected by scoring how well their expression levels can discriminate between different classes of disease or between groups of patients with different clinical outcome (e.g. therapy response, survival time, etc.). A current challenge is to identify new markers that are directly related to the underlying disease mechanism

A survey on computational intelligence approaches for predictive modeling in prostate cancer

Predictive modeling in medicine involves the development of computational models which are capable of analysing large amounts of data in order to predict healthcare outcomes for individual patients. Computational intelligence approaches are suitable when the data to be modelled are too complex forconventional statistical techniques to process quickly and eciently. These advanced approaches are based on mathematical models that have been especially developed for dealing with the uncertainty and imprecision which is typically found in clinical and biological datasets. This paper provides a survey of recent work on computational intelligence approaches that have been applied to prostate cancer predictive modeling, and considers the challenges which need to be addressed. In particular, the paper considers a broad definition of computational intelligence which includes evolutionary algorithms (also known asmetaheuristic optimisation, nature inspired optimisation algorithms), Artificial Neural Networks, Deep Learning, Fuzzy based approaches, and hybrids of these,as well as Bayesian based approaches, and Markov models. Metaheuristic optimisation approaches, such as the Ant Colony Optimisation, Particle Swarm Optimisation, and Artificial Immune Network have been utilised for optimising the performance of prostate cancer predictive models, and the suitability of these approaches are discussed

Machine learning methods for omics data integration

High-throughput technologies produce genome-scale transcriptomic and metabolomic (omics) datasets that allow for the system-level studies of complex biological processes. The limitation lies in the small number of samples versus the larger number of features represented in these datasets. Machine learning methods can help integrate these large-scale omics datasets and identify key features from each dataset. A novel class dependent feature selection method integrates the F statistic, maximum relevance binary particle swarm optimization (MRBPSO), and class dependent multi-category classification (CDMC) system. A set of highly differentially expressed genes are pre-selected using the F statistic as a filter for each dataset. MRBPSO and CDMC function as a wrapper to select desirable feature subsets for each class and classify the samples using those chosen class-dependent feature subsets. The results indicate that the class-dependent approaches can effectively identify unique biomarkers for each cancer type and improve classification accuracy compared to class independent feature selection methods. The integration of transcriptomics and metabolomics data is based on a classification framework. Compared to principal component analysis and non-negative matrix factorization based integration approaches, our proposed method achieves 20-30% higher prediction accuracies on Arabidopsis tissue development data. Metabolite-predictive genes and gene-predictive metabolites are selected from transcriptomic and metabolomic data respectively. The constructed gene-metabolite correlation network can infer the functions of unknown genes and metabolites. Tissue-specific genes and metabolites are identified by the class-dependent feature selection method. Evidence from subcellular locations, gene ontology, and biochemical pathways support the involvement of these entities in different developmental stages and tissues in Arabidopsis

Recuperação multimodal e interativa de informação orientada por diversidade

Orientador: Ricardo da Silva TorresTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Os métodos de Recuperação da Informação, especialmente considerando-se dados multimídia, evoluíram para a integração de múltiplas fontes de evidência na análise de relevância de itens em uma tarefa de busca. Neste contexto, para atenuar a distância semântica entre as propriedades de baixo nível extraídas do conteúdo dos objetos digitais e os conceitos semânticos de alto nível (objetos, categorias, etc.) e tornar estes sistemas adaptativos às diferentes necessidades dos usuários, modelos interativos que consideram o usuário mais próximo do processo de recuperação têm sido propostos, permitindo a sua interação com o sistema, principalmente por meio da realimentação de relevância implícita ou explícita. Analogamente, a promoção de diversidade surgiu como uma alternativa para lidar com consultas ambíguas ou incompletas. Adicionalmente, muitos trabalhos têm tratado a ideia de minimização do esforço requerido do usuário em fornecer julgamentos de relevância, à medida que mantém níveis aceitáveis de eficácia. Esta tese aborda, propõe e analisa experimentalmente métodos de recuperação da informação interativos e multimodais orientados por diversidade. Este trabalho aborda de forma abrangente a literatura acerca da recuperação interativa da informação e discute sobre os avanços recentes, os grandes desafios de pesquisa e oportunidades promissoras de trabalho. Nós propusemos e avaliamos dois métodos de aprimoramento do balanço entre relevância e diversidade, os quais integram múltiplas informações de imagens, tais como: propriedades visuais, metadados textuais, informação geográfica e descritores de credibilidade dos usuários. Por sua vez, como integração de técnicas de recuperação interativa e de promoção de diversidade, visando maximizar a cobertura de múltiplas interpretações/aspectos de busca e acelerar a transferência de informação entre o usuário e o sistema, nós propusemos e avaliamos um método multimodal de aprendizado para ranqueamento utilizando realimentação de relevância sobre resultados diversificados. Nossa análise experimental mostra que o uso conjunto de múltiplas fontes de informação teve impacto positivo nos algoritmos de balanceamento entre relevância e diversidade. Estes resultados sugerem que a integração de filtragem e re-ranqueamento multimodais é eficaz para o aumento da relevância dos resultados e também como mecanismo de potencialização dos métodos de diversificação. Além disso, com uma análise experimental minuciosa, nós investigamos várias questões de pesquisa relacionadas à possibilidade de aumento da diversidade dos resultados e a manutenção ou até mesmo melhoria da sua relevância em sessões interativas. Adicionalmente, nós analisamos como o esforço em diversificar afeta os resultados gerais de uma sessão de busca e como diferentes abordagens de diversificação se comportam para diferentes modalidades de dados. Analisando a eficácia geral e também em cada iteração de realimentação de relevância, nós mostramos que introduzir diversidade nos resultados pode prejudicar resultados iniciais, enquanto que aumenta significativamente a eficácia geral em uma sessão de busca, considerando-se não apenas a relevância e diversidade geral, mas também o quão cedo o usuário é exposto ao mesmo montante de itens relevantes e nível de diversidadeAbstract: Information retrieval methods, especially considering multimedia data, have evolved towards the integration of multiple sources of evidence in the analysis of the relevance of items considering a given user search task. In this context, for attenuating the semantic gap between low-level features extracted from the content of the digital objects and high-level semantic concepts (objects, categories, etc.) and making the systems adaptive to different user needs, interactive models have brought the user closer to the retrieval loop allowing user-system interaction mainly through implicit or explicit relevance feedback. Analogously, diversity promotion has emerged as an alternative for tackling ambiguous or underspecified queries. Additionally, several works have addressed the issue of minimizing the required user effort on providing relevance assessments while keeping an acceptable overall effectiveness. This thesis discusses, proposes, and experimentally analyzes multimodal and interactive diversity-oriented information retrieval methods. This work, comprehensively covers the interactive information retrieval literature and also discusses about recent advances, the great research challenges, and promising research opportunities. We have proposed and evaluated two relevance-diversity trade-off enhancement work-flows, which integrate multiple information from images, such as: visual features, textual metadata, geographic information, and user credibility descriptors. In turn, as an integration of interactive retrieval and diversity promotion techniques, for maximizing the coverage of multiple query interpretations/aspects and speeding up the information transfer between the user and the system, we have proposed and evaluated a multimodal learning-to-rank method trained with relevance feedback over diversified results. Our experimental analysis shows that the joint usage of multiple information sources positively impacted the relevance-diversity balancing algorithms. Our results also suggest that the integration of multimodal-relevance-based filtering and reranking was effective on improving result relevance and also boosted diversity promotion methods. Beyond it, with a thorough experimental analysis we have investigated several research questions related to the possibility of improving result diversity and keeping or even improving relevance in interactive search sessions. Moreover, we analyze how much the diversification effort affects overall search session results and how different diversification approaches behave for the different data modalities. By analyzing the overall and per feedback iteration effectiveness, we show that introducing diversity may harm initial results whereas it significantly enhances the overall session effectiveness not only considering the relevance and diversity, but also how early the user is exposed to the same amount of relevant items and diversityDoutoradoCiência da ComputaçãoDoutor em Ciência da ComputaçãoP-4388/2010140977/2012-0CAPESCNP

Learning for Optimization with Virtual Savant

Optimization problems arising in multiple fields of study demand efficient algorithms that can exploit modern parallel computing platforms. The remarkable development of machine learning offers an opportunity to incorporate learning into optimization algorithms to efficiently solve large and complex problems. This thesis explores Virtual Savant, a paradigm that combines machine learning and parallel computing to solve optimization problems. Virtual Savant is inspired in the Savant Syndrome, a mental condition where patients excel at a specific ability far above the average. In analogy to the Savant Syndrome, Virtual Savant extracts patterns from previously-solved instances to learn how to solve a given optimization problem in a massively-parallel fashion. In this thesis, Virtual Savant is applied to three optimization problems related to software engineering, task scheduling, and public transportation. The efficacy of Virtual Savant is evaluated in different computing platforms and the experimental results are compared against exact and approximate solutions for both synthetic and realistic instances of the studied problems. Results show that Virtual Savant can find accurate solutions, effectively scale in the problem dimension, and take advantage of the availability of multiple computing resources.Los problemas de optimización que surgen en múltiples campos de estudio demandan algoritmos eficientes que puedan explotar las plataformas modernas de computación paralela. El notable desarrollo del aprendizaje automático ofrece la oportunidad de incorporar el aprendizaje en algoritmos de optimización para resolver problemas complejos y de grandes dimensiones de manera eficiente. Esta tesis explora Savant Virtual, un paradigma que combina aprendizaje automático y computación paralela para resolver problemas de optimización. Savant Virtual está inspirado en el Sı́ndrome de Savant, una condición mental en la que los pacientes se destacan en una habilidad especı́fica muy por encima del promedio. En analogı́a con el sı́ndrome de Savant, Savant Virtual extrae patrones de instancias previamente resueltas para aprender a resolver un determinado problema de optimización de forma masivamente paralela. En esta tesis, Savant Virtual se aplica a tres problemas de optimización relacionados con la ingenierı́a de software, la planificación de tareas y el transporte público. La eficacia de Savant Virtual se evalúa en diferentes plataformas informáticas y los resultados se comparan con soluciones exactas y aproximadas para instancias tanto sintéticas como realistas de los problemas estudiados. Los resultados muestran que Savant Virtual puede encontrar soluciones precisas, escalar eficazmente en la dimensión del problema y aprovechar la disponibilidad de múltiples recursos de cómputo.Fundación Carolina Agencia Nacional de Investigación e Innovación (ANII, Uruguay) Universidad de Cádiz Universidad de la Repúblic

Finding the online cry for help : automatic text classification for suicide prevention

Successful prevention of suicide, a serious public health concern worldwide, hinges on the adequate detection of suicide risk. While online platforms are increasingly used for expressing suicidal thoughts, manually monitoring for such signals of distress is practically infeasible, given the information overload suicide prevention workers are confronted with. In this thesis, the automatic detection of suicide-related messages is studied. It presents the first classification-based approach to online suicidality detection, and focuses on Dutch user-generated content. In order to evaluate the viability of such a machine learning approach, we developed a gold standard corpus, consisting of message board and blog posts. These were manually labeled according to a newly developed annotation scheme, grounded in suicide prevention practice. The scheme provides for the annotation of a post's relevance to suicide, and the subject and severity of a suicide threat, if any. This allowed us to derive two tasks: the detection of suicide-related posts, and of severe, high-risk content. In a series of experiments, we sought to determine how well these tasks can be carried out automatically, and which information sources and techniques contribute to classification performance. The experimental results show that both types of messages can be detected with high precision. Therefore, the amount of noise generated by the system is minimal, even on very large datasets, making it usable in a real-world prevention setting. Recall is high for the relevance task, but at around 60%, it is considerably lower for severity. This is mainly attributable to implicit references to suicide, which often go undetected. We found a variety of information sources to be informative for both tasks, including token and character ngram bags-of-words, features based on LSA topic models, polarity lexicons and named entity recognition, and suicide-related terms extracted from a background corpus. To improve classification performance, the models were optimized using feature selection, hyperparameter, or a combination of both. A distributed genetic algorithm approach proved successful in finding good solutions for this complex search problem, and resulted in more robust models. Experiments with cascaded classification of the severity task did not reveal performance benefits over direct classification (in terms of F1-score), but its structure allows the use of slower, memory-based learning algorithms that considerably improved recall. At the end of this thesis, we address a problem typical of user-generated content: noise in the form of misspellings, phonetic transcriptions and other deviations from the linguistic norm. We developed an automatic text normalization system, using a cascaded statistical machine translation approach, and applied it to normalize the data for the suicidality detection tasks. Subsequent experiments revealed that, compared to the original data, normalized data resulted in fewer and more informative features, and improved classification performance. This extrinsic evaluation demonstrates the utility of automatic normalization for suicidality detection, and more generally, text classification on user-generated content