Knowledge-driven entity recognition and disambiguation in biomedical text

Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.Die Erkennung und Disambiguierung von Entitäten für den biomedizinischen Bereich stellen, wegen der vielfältigen Arten von biomedizinischen Entitäten sowie deren oft langen und variantenreichen Namen, große Herausforderungen dar. Vorhergehende Arbeiten konzentrieren sich in zweierlei Hinsicht fast ausschließlich auf molekulare Entitäten. Erstens fokussieren sie sich auf wissenschaftliche Publikationen als Genre der Eingabetexte. Zweitens fokussieren sie sich auf einzelne, sehr spezialisierte Entitätstypen wie Chemikalien, Gene und Proteine. Allerdings bietet das Internet neben diesen Quellen eine Vielzahl an Inhalten biomedizinischen Wissens, das vernachlässigt wird. Um alle verfügbaren Informationen auszunutzen besteht der Bedarf weitere Internet-Inhalte als zusätzliche Quellen zu erschließen. Außerdem ist es auch erforderlich andere Entitätstypen wie Symptome und Risikofaktoren in Betracht zu ziehen, da diese für zahlreiche Inhalte im Internet, wie zum Beispiel Verbraucherinformationen im Gesundheitssektor, relevant sind. Das Ziel dieser Dissertation ist es, Methoden zur Erkennung und Disambiguierung von Entitäten zu erforschen, die alle Entitätstypen in Betracht ziehen und sowohl auf wissenschaftliche Publikationen als auch auf andere Internet-Inhalte anwendbar sind. Darüber hinaus setzen wir Schwerpunkte auf oft vernachlässigte Aspekte der biomedizinischen Erkennung und Disambiguierung von Entitäten, nämlich Skalierbarkeit, lange Nominalphrasen und fehlende Entitäten in einer Wissensbank. In dieser Hinsicht leistet diese Dissertation vier Hauptbeiträge, denen allen das Wissen von UMLS (Unified Medical Language System), der größten und wichtigsten Wissensbank im biomedizinischen Bereich, zu Grunde liegt. Der erste Beitrag ist eine schnelle Methode zur Erkennung von Entitäten mittels Lexikonabgleich, welche den Durchsatz maximiert und gleichzeitig den Verlust in Genauigkeit und Trefferquote (precision and recall) balanciert. Der zweite Beitrag ist eine Methode zur Klassifizierung der semantischen Typen von Nomen, die sich auf gebräuchliche Nomen von langen Nominalphrasen richtet und auf einer selbstentwickelten Sammlung von semantischen Typen beruht, die die Verwendung der Nomen erfasst. Neben biomedizinischen können diese Typen auch nicht-biomedizinische und allgemeine, informationsarme Verwendungen behandeln. Der dritte Beitrag ist eine schnelle Heuristikmethode zur Disambiguierung von Entitäten in MEDLINE Kurzfassungen, welche den Durchsatz maximiert, aber auch die Genauigkeit erhält. Der vierte Beitrag ist eine korpusgetriebene Methode zur Disambiguierung von Entitäten, die speziell fehlende Entitäten in einer Wissensbank behandelt. Die Methode wandelt erst die Entitäten, die in einem Textkorpus ausgedrückt aber nicht notwendigerweise in einer Wissensbank sind, in latente Darstellungen um und führt anschließend die Disambiguierung durch

Human-in-the-Loop Learning From Crowdsourcing and Social Media

Computational social studies using public social media data have become more and more popular because of the large amount of user-generated data available. The richness of social media data, coupled with noise and subjectivity, raise significant challenges for computationally studying social issues in a feasible and scalable manner. Machine learning problems are, as a result, often subjective or ambiguous when humans are involved. That is, humans solving the same problems might come to legitimate but completely different conclusions, based on their personal experiences and beliefs. When building supervised learning models, particularly when using crowdsourced training data, multiple annotations per data item are usually reduced to a single label representing ground truth. This inevitably hides a rich source of diversity and subjectivity of opinions about the labels. Label distribution learning associates for each data item a probability distribution over the labels for that item, thus it can preserve diversities of opinions, beliefs, etc. that conventional learning hides or ignores. We propose a humans-in-the-loop learning framework to model and study large volumes of unlabeled subjective social media data with less human effort. We study various annotation tasks given to crowdsourced annotators and methods for aggregating their contributions in a manner that preserves subjectivity and disagreement. We introduce a strategy for learning label distributions with only five-to-ten labels per item by aggregating human-annotated labels over multiple, semantically related data items. We conduct experiments using our learning framework on data related to two subjective social issues (work and employment, and suicide prevention) that touch many people worldwide. Our methods can be applied to a broad variety of problems, particularly social problems. Our experimental results suggest that specific label aggregation methods can help provide reliable representative semantics at the population level

Implicit emotion detection in text

In text, emotion can be expressed explicitly, using emotion-bearing words (e.g. happy, guilty) or implicitly without emotion-bearing words. Existing approaches focus on the detection of explicitly expressed emotion in text. However, there are various ways to express and convey emotions without the use of these emotion-bearing words. For example, given two sentences: “The outcome of my exam makes me happy” and “I passed my exam”, both sentences express happiness, with the first expressing it explicitly and the other implying it. In this thesis, we investigate implicit emotion detection in text. We propose a rule-based approach for implicit emotion detection, which can be used without labeled corpora for training. Our results show that our approach outperforms the lexicon matching method consistently and gives competitive performance in comparison to supervised classifiers. Given that emotions such as guilt and admiration which often require the identification of blameworthiness and praiseworthiness, we also propose an approach for the detection of blame and praise in text, using an adapted psychology model, Path model to blame. Lack of benchmarking dataset led us to construct a corpus containing comments of individuals’ emotional experiences annotated as blame, praise or others. Since implicit emotion detection might be useful for conflict-of-interest (CoI) detection in Wikipedia articles, we built a CoI corpus and explored various features including linguistic and stylometric, presentation, bias and emotion features. Our results show that emotion features are important when using Nave Bayes, but the best performance is obtained with SVM on linguistic and stylometric features only. Overall, we show that a rule-based approach can be used to detect implicit emotion in the absence of labelled data; it is feasible to adopt the psychology path model to blame for blame/praise detection from text, and implicit emotion detection is beneficial for CoI detection in Wikipedia articles

Text Mining and Gene Expression Analysis Towards Combined Interpretation of High Throughput Data

Microarrays can capture gene expression activity for thousands of genes simultaneously and thus make it possible to analyze cell physiology and disease processes on molecular level. The interpretation of microarray gene expression experiments profits from knowledge on the analyzed genes and proteins and the biochemical networks in which they play a role. The trend is towards the development of data analysis methods that integrate diverse data types. Currently, the most comprehensive biomedical knowledge source is a large repository of free text articles. Text mining makes it possible to automatically extract and use information from texts. This thesis addresses two key aspects, biomedical text mining and gene expression data analysis, with the focus on providing high-quality methods and data that contribute to the development of integrated analysis approaches. The work is structured in three parts. Each part begins by providing the relevant background, and each chapter describes the developed methods as well as applications and results. Part I deals with biomedical text mining: Chapter 2 summarizes the relevant background of text mining; it describes text mining fundamentals, important text mining tasks, applications and particularities of text mining in the biomedical domain, and evaluation issues. In Chapter 3, a method for generating high-quality gene and protein name dictionaries is described. The analysis of the generated dictionaries revealed important properties of individual nomenclatures and the used databases (Fundel and Zimmer, 2006). The dictionaries are publicly available via a Wiki, a web service, and several client applications (Szugat et al., 2005). In Chapter 4, methods for the dictionary-based recognition of gene and protein names in texts and their mapping onto unique database identifiers are described. These methods make it possible to extract information from texts and to integrate text-derived information with data from other sources. Three named entity identification systems have been set up, two of them building upon the previously existing tool ProMiner (Hanisch et al., 2003). All of them have shown very good performance in the BioCreAtIvE challenges (Fundel et al., 2005a; Hanisch et al., 2005; Fundel and Zimmer, 2007). In Chapter 5, a new method for relation extraction (Fundel et al., 2007) is presented. It was applied on the largest collection of biomedical literature abstracts, and thus a comprehensive network of human gene and protein relations has been generated. A classification approach (Küffner et al., 2006) can be used to specify relation types further; e. g., as activating, direct physical, or gene regulatory relation. Part II deals with gene expression data analysis: Gene expression data needs to be processed so that differentially expressed genes can be identified. Gene expression data processing consists of several sequential steps. Two important steps are normalization, which aims at removing systematic variances between measurements, and quantification of differential expression by p-value and fold change determination. Numerous methods exist for these tasks. Chapter 6 describes the relevant background of gene expression data analysis; it presents the biological and technical principles of microarrays and gives an overview of the most relevant data processing steps. Finally, it provides a short introduction to osteoarthritis, which is in the focus of the analyzed gene expression data sets. In Chapter 7, quality criteria for the selection of normalization methods are described, and a method for the identification of differentially expressed genes is proposed, which is appropriate for data with large intensity variances between spots representing the same gene (Fundel et al., 2005b). Furthermore, a system is described that selects an appropriate combination of feature selection method and classifier, and thus identifies genes which lead to good classification results and show consistent behavior in different sample subgroups (Davis et al., 2006). The analysis of several gene expression data sets dealing with osteoarthritis is described in Chapter 8. This chapter contains the biomedical analysis of relevant disease processes and distinct disease stages (Aigner et al., 2006a), and a comparison of various microarray platforms and osteoarthritis models. Part III deals with integrated approaches and thus provides the connection between parts I and II: Chapter 9 gives an overview of different types of integrated data analysis approaches, with a focus on approaches that integrate gene expression data with manually compiled data, large-scale networks, or text mining. In Chapter 10, a method for the identification of genes which are consistently regulated and have a coherent literature background (Küffner et al., 2005) is described. This method indicates how gene and protein name identification and gene expression data can be integrated to return clusters which contain genes that are relevant for the respective experiment together with literature information that supports interpretation. Finally, in Chapter 11 ideas on how the described methods can contribute to current research and possible future directions are presented

An empirical study on credit evaluation of SMEs based on detailed loan data

Small and micro-sized Enterprises (SMEs) are an important part of Chinese economic system.The establishment of credit evaluating model of SMEs can effectively help financial intermediaries to reveal credit risk of enterprises and reduce the cost of enterprises information acquisition. Besides it can also serve as a guide to investors which also helps companies with good credit. This thesis conducts an empirical study based on loan data from a Chinese bank of loans granted to SMEs. The study aims to develop a data-driven model that can accurately predict if a given loan has an acceptable risk from the bank’s perspective, or not. Furthermore, we test different methods to deal with the problem of unbalanced class and uncredible sample. Lastly, the importance of variables is analyzed. Remaining Unpaid Principal, Floating Interest Rate, Time Until Maturity Date, Real Interest Rate, Amount of Loan all have significant effects on the final result of the prediction.The main contribution of this study is to build a credit evaluation model of small and micro enterprises, which not only helps commercial banks accurately identify the credit risk of small and micro enterprises, but also helps to overcome creditdifficulties of small and micro enterprises.As pequenas e microempresas constituem uma parte importante do sistema económico chinês. A definição de um modelo de avaliação de crédito para estas empresas pode ajudar os intermediários financeiros a revelarem o risco de crédito das empresas e a reduzirem o custo de aquisição de informação das empresas. Além disso, pode igualmente servir como guia para os investidores, auxiliando também empresas com bom crédito. Na presente tese apresenta-se um estudo empírico baseado em dados de um banco chinês relativos a empréstimos concedidos a pequenas e microempresas. O estudo visa desenvolver um modelo empírico que possa prever com precisão se um determinado empréstimo tem um risco aceitável do ponto de vista do banco, ou não. Além disso, são efetuados testes com diferentes métodos que permitem lidar com os problemas de classes de dados não balanceadas e de amostras que não refletem o problema real a modelar. Finalmente, é analisada a importância relativa das variáveis. O montante da dívida por pagar, a taxa de juro variável, o prazo até a data de vencimento, a taxa de juro real, o montante do empréstimo, todas têm efeitos significativos no resultado final da previsão. O principal contributo deste estudo é, assim, a construção de um modelo de avaliação de crédito que permite apoiar os bancos comerciais a identificarem com precisão o risco de crédito das pequenas e micro empresas e ajudar também estas empresas a superarem as suas dificuldades de crédito