Advanced Methods for Entity Linking in the Life Sciences

The amount of knowledge increases rapidly due to the increasing number of available data sources. However, the autonomy of data sources and the resulting heterogeneity prevent comprehensive data analysis and applications. Data integration aims to overcome heterogeneity by unifying different data sources and enriching unstructured data. The enrichment of data consists of different subtasks, amongst other the annotation process. The annotation process links document phrases to terms of a standardized vocabulary. Annotated documents enable effective retrieval methods, comparability of different documents, and comprehensive data analysis, such as finding adversarial drug effects based on patient data. A vocabulary allows the comparability using standardized terms. An ontology can also represent a vocabulary, whereas concepts, relationships, and logical constraints additionally define an ontology. The annotation process is applicable in different domains. Nevertheless, there is a difference between generic and specialized domains according to the annotation process. This thesis emphasizes the differences between the domains and addresses the identified challenges. The majority of annotation approaches focuses on the evaluation of general domains, such as Wikipedia. This thesis evaluates the developed annotation approaches with case report forms that are medical documents for examining clinical trials. The natural language provides different challenges, such as similar meanings using different phrases. The proposed annotation method, AnnoMap, considers the fuzziness of natural language. A further challenge is the reuse of verified annotations. Existing annotations represent knowledge that can be reused for further annotation processes. AnnoMap consists of a reuse strategy that utilizes verified annotations to link new documents to appropriate concepts. Due to the broad spectrum of areas in the biomedical domain, different tools exist. The tools perform differently regarding a particular domain. This thesis proposes a combination approach to unify results from different tools. The method utilizes existing tool results to build a classification model that can classify new annotations as correct or incorrect. The results show that the reuse and the machine learning-based combination improve the annotation quality compared to existing approaches focussing on the biomedical domain. A further part of data integration is entity resolution to build unified knowledge bases from different data sources. A data source consists of a set of records characterized by attributes. The goal of entity resolution is to identify records representing the same real-world entity. Many methods focus on linking data sources consisting of records being characterized by attributes. Nevertheless, only a few methods can handle graph-structured knowledge bases or consider temporal aspects. The temporal aspects are essential to identify the same entities over different time intervals since these aspects underlie certain conditions. Moreover, records can be related to other records so that a small graph structure exists for each record. These small graphs can be linked to each other if they represent the same. This thesis proposes an entity resolution approach for census data consisting of person records for different time intervals. The approach also considers the graph structure of persons given by family relationships. For achieving qualitative results, current methods apply machine-learning techniques to classify record pairs as the same entity. The classification task used a model that is generated by training data. In this case, the training data is a set of record pairs that are labeled as a duplicate or not. Nevertheless, the generation of training data is a time-consuming task so that active learning techniques are relevant for reducing the number of training examples. The entity resolution method for temporal graph-structured data shows an improvement compared to previous collective entity resolution approaches. The developed active learning approach achieves comparable results to supervised learning methods and outperforms other limited budget active learning methods. Besides the entity resolution approach, the thesis introduces the concept of evolution operators for communities. These operators can express the dynamics of communities and individuals. For instance, we can formulate that two communities merged or split over time. Moreover, the operators allow observing the history of individuals. Overall, the presented annotation approaches generate qualitative annotations for medical forms. The annotations enable comprehensive analysis across different data sources as well as accurate queries. The proposed entity resolution approaches improve existing ones so that they contribute to the generation of qualitative knowledge graphs and data analysis tasks

Automatically building research reading lists

All new researchers face the daunting task of familiarizing themselves with the existing body of research literature in their respective fields. Recommender algorithms could aid in preparing these lists, but most current algorithms do not understand how to rate the importance of a paper within the literature, which might limit their effectiveness in this domain. We explore several methods for augmenting exist-ing collaborative and content-based filtering algorithms with measures of the influence of a paper within the web of cita-tions. We measure influence using well-known algorithms, such as HITS and PageRank, for measuring a node’s im-portance in a graph. Among these augmentation methods is a novel method for using importance scores to influence collaborative filtering. We present a task-centered evalua-tion, including both an offline analysis and a user study, of the performance of the algorithms. Results from these stud-ies indicate that collaborative filtering outperforms content-based approaches for generating introductory reading lists

Information fusion for automated question answering

Until recently, research efforts in automated Question Answering (QA) have mainly focused on getting a good understanding of questions to retrieve correct answers. This includes deep parsing, lookups in ontologies, question typing and machine learning of answer patterns appropriate to question forms. In contrast, I have focused on the analysis of the relationships between answer candidates as provided in open domain QA on multiple documents. I argue that such candidates have intrinsic properties, partly regardless of the question, and those properties can be exploited to provide better quality and more user-oriented answers in QA.Information fusion refers to the technique of merging pieces of information from different sources. In QA over free text, it is motivated by the frequency with which different answer candidates are found in different locations, leading to a multiplicity of answers. The reason for such multiplicity is, in part, the massive amount of data used for answering, and also its unstructured and heterogeneous content: Besides am¬ biguities in user questions leading to heterogeneity in extractions, systems have to deal with redundancy, granularity and possible contradictory information. Hence the need for answer candidate comparison. While frequency has proved to be a significant char¬ acteristic of a correct answer, I evaluate the value of other relationships characterizing answer variability and redundancy.Partially inspired by recent developments in multi-document summarization, I re¬ define the concept of "answer" within an engineering approach to QA based on the Model-View-Controller (MVC) pattern of user interface design. An "answer model" is a directed graph in which nodes correspond to entities projected from extractions and edges convey relationships between such nodes. The graph represents the fusion of information contained in the set of extractions. Different views of the answer model can be produced, capturing the fact that the same answer can be expressed and pre¬ sented in various ways: picture, video, sound, written or spoken language, or a formal data structure. Within this framework, an answer is a structured object contained in the model and retrieved by a strategy to build a particular view depending on the end user (or taskj's requirements.I describe shallow techniques to compare entities and enrich the model by discovering four broad categories of relationships between entities in the model: equivalence, inclusion, aggregation and alternative. Quantitatively, answer candidate modeling im¬ proves answer extraction accuracy. It also proves to be more robust to incorrect answer candidates than traditional techniques. Qualitatively, models provide meta-information encoded by relationships that allow shallow reasoning to help organize and generate the final output