KnowLife: A Versatile Approach for Constructing a Large Knowledge Graph for Biomedical Sciences

BACKGROUND: Biomedical knowledge bases (KB’s) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. RESULTS: We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB’s based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. CONCLUSION: KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0549-5) contains supplementary material, which is available to authorized users

A survey of statistical network models

Networks are ubiquitous in science and have become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active network community and a substantial literature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning network literature in statistical physics and computer science. The growth of the World Wide Web and the emergence of online networking communities such as Facebook, MySpace, and LinkedIn, and a host of more specialized professional network communities has intensified interest in the study of networks and network data. Our goal in this review is to provide the reader with an entry point to this burgeoning literature. We begin with an overview of the historical development of statistical network modeling and then we introduce a number of examples that have been studied in the network literature. Our subsequent discussion focuses on a number of prominent static and dynamic network models and their interconnections. We emphasize formal model descriptions, and pay special attention to the interpretation of parameters and their estimation. We end with a description of some open problems and challenges for machine learning and statistics.Comment: 96 pages, 14 figures, 333 reference

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

Automating the Annotation of Data through Machine Learning and Semantic Technologies

The ever-increasing scale and complexity of scientific research is surpassing our means to assimilate newly produced knowledge. Computer tools are necessary for the organisation, retrieval, and interpretation of new scientific knowledge and data. The efficacy of such tools requires that research outputs are described by rich machine-readable metadata. Ontologies provide the framework to unambiguously describe the meaning of knowledge and data, so that it may be re-used or combined to synthesise new knowledge. However, manually annotating research with ontology terms, a process called semantic annotation, is also infeasible due to the aforementioned scale. This thesis describes research to develop deep learning-based tools for semantic annotation. The approaches described explore different methods for exploiting the domain knowledge encoded into ontologies to avoid the need to manually curate training corpora. They also take advantage of the inherent integrative capabilities of ontologies, to leverage combinations of heterogeneous knowledge to improve annotation performance and model interpretability. Several models exceeded previous benchmarks for semantic annotation in the bio-medical domain. This thesis concludes with a discussion of the strengths and limitations of the methods, and the implications for multi-domain ontology semantic annotation and for explainable artificial intelligence

Network Analysis on Incomplete Structures.

Over the past decade, networks have become an increasingly popular abstraction for problems in the physical, life, social and information sciences. Network analysis can be used to extract insights into an underlying system from the structure of its network representation. One of the challenges of applying network analysis is the fact that networks do not always have an observed and complete structure. This dissertation focuses on the problem of imputation and/or inference in the presence of incomplete network structures. I propose four novel systems, each of which, contain a module that involves the inference or imputation of an incomplete network that is necessary to complete the end task. I first propose EdgeBoost, a meta-algorithm and framework that repeatedly applies a non-deterministic link predictor to improve the efficacy of community detection algorithms on networks with missing edges. On average EdgeBoost improves performance of existing algorithms by 7% on artificial data and 17% on ego networks collected from Facebook. The second system, Butterworth, identifies a social network user's topic(s) of interests and automatically generates a set of social feed ``rankers'' that enable the user to see topic specific sub-feeds. Butterworth uses link prediction to infer the missing semantics between members of a user's social network in order to detect topical clusters embedded in the network structure. For automatically generated topic lists, Butterworth achieves an average top-10 precision of 78%, as compared to a time-ordered baseline of 45%. Next, I propose Dobby, a system for constructing a knowledge graph of user-defined keyword tags. Leveraging a sparse set of labeled edges, Dobby trains a supervised learning algorithm to infer the hypernym relationships between keyword tags. Dobby was evaluated by constructing a knowledge graph of LinkedIn's skills dataset, achieving an average precision of 85% on a set of human labeled hypernym edges between skills. Lastly, I propose Lobbyback, a system that automatically identifies clusters of documents that exhibit text reuse and generates ``prototypes'' that represent a canonical version of text shared between the documents. Lobbyback infers a network structure in a corpus of documents and uses community detection in order to extract the document clusters.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133443/1/mattburg_1.pd

Entity-centric knowledge discovery for idiosyncratic domains

Technical and scientific knowledge is produced at an ever-accelerating pace, leading to increasing issues when trying to automatically organize or process it, e.g., when searching for relevant prior work. Knowledge can today be produced both in unstructured (plain text) and structured (metadata or linked data) forms. However, unstructured content is still themost dominant formused to represent scientific knowledge. In order to facilitate the extraction and discovery of relevant content, new automated and scalable methods for processing, structuring and organizing scientific knowledge are called for. In this context, a number of applications are emerging, ranging fromNamed Entity Recognition (NER) and Entity Linking tools for scientific papers to specific platforms leveraging information extraction techniques to organize scientific knowledge. In this thesis, we tackle the tasks of Entity Recognition, Disambiguation and Linking in idiosyncratic domains with an emphasis on scientific literature. Furthermore, we study the related task of co-reference resolution with a specific focus on named entities. We start by exploring Named Entity Recognition, a task that aims to identify the boundaries of named entities in textual contents. We propose a newmethod to generate candidate named entities based on n-gram collocation statistics and design several entity recognition features to further classify them. In addition, we show how the use of external knowledge bases (either domain-specific like DBLP or generic like DBPedia) can be leveraged to improve the effectiveness of NER for idiosyncratic domains. Subsequently, we move to Entity Disambiguation, which is typically performed after entity recognition in order to link an entity to a knowledge base. We propose novel semi-supervised methods for word disambiguation leveraging the structure of a community-based ontology of scientific concepts. Our approach exploits the graph structure that connects different terms and their definitions to automatically identify the correct sense that was originally picked by the authors of a scientific publication. We then turn to co-reference resolution, a task aiming at identifying entities that appear using various forms throughout the text. We propose an approach to type entities leveraging an inverted index built on top of a knowledge base, and to subsequently re-assign entities based on the semantic relatedness of the introduced types. Finally, we describe an application which goal is to help researchers discover and manage scientific publications. We focus on the problem of selecting relevant tags to organize collections of research papers in that context. We experimentally demonstrate that the use of a community-authored ontology together with information about the position of the concepts in the documents allows to significantly increase the precision of tag selection over standard methods

Robust Entity Linking in Heterogeneous Domains

Entity Linking is the task of mapping terms in arbitrary documents to entities in a knowledge base by identifying the correct semantic meaning. It is applied in the extraction of structured data in RDF (Resource Description Framework) from textual documents, but equally so in facilitating artificial intelligence applications, such as Semantic Search, Reasoning and Question and Answering. Most existing Entity Linking systems were optimized for specific domains (e.g., general domain, biomedical domain), knowledge base types (e.g., DBpedia, Wikipedia), or document structures (e.g., tables) and types (e.g., news articles, tweets). This led to very specialized systems that lack robustness and are only applicable for very specific tasks. In this regard, this work focuses on the research and development of a robust Entity Linking system in terms of domains, knowledge base types, and document structures and types. To create a robust Entity Linking system, we first analyze the following three crucial components of an Entity Linking algorithm in terms of robustness criteria: (i) the underlying knowledge base, (ii) the entity relatedness measure, and (iii) the textual context matching technique. Based on the analyzed components, our scientific contributions are three-fold. First, we show that a federated approach leveraging knowledge from various knowledge base types can significantly improve robustness in Entity Linking systems. Second, we propose a new state-of-the-art, robust entity relatedness measure for topical coherence computation based on semantic entity embeddings. Third, we present the neural-network-based approach Doc2Vec as a textual context matching technique for robust Entity Linking. Based on our previous findings and outcomes, our main contribution in this work is DoSeR (Disambiguation of Semantic Resources). DoSeR is a robust, knowledge-base-agnostic Entity Linking framework that extracts relevant entity information from multiple knowledge bases in a fully automatic way. The integrated algorithm represents a collective, graph-based approach that utilizes semantic entity and document embeddings for entity relatedness and textual context matching computation. Our evaluation shows, that DoSeR achieves state-of-the-art results over a wide range of different document structures (e.g., tables), document types (e.g., news documents) and domains (e.g., general domain, biomedical domain). In this context, DoSeR outperforms all other (publicly available) Entity Linking algorithms on most data sets

A Survey of Statistical Network Models

Networks are ubiquitous in science and have become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active “network community” and a substantial liter- ature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning net- work literature in statistical physics and computer science. The growthof the World Wide Web and the emergence of online “networking com- munities” such as Facebook, MySpace, and LinkedIn, and a host of more specialized professional network communities has intensified interest in the study of networks and network data. Our goal in this review is to provide the reader with an entry point to this burgeoning literature. We begin with an overview of the historical development of statistical network modeling and then we introduce a number of examples that have been studied in the network literature. Our subsequent discussion focuses on a number of prominent static and dynamic network models and their interconnections. We emphasize for- mal model descriptions, and pay special attention to the interpretation of parameters and their estimation. We end with a description of some open problems and challenges for machine learning and statistics.Statistic

On cross-domain social semantic learning

Approximately 2.4 billion people are now connected to the Internet, generating massive amounts of data through laptops, mobile phones, sensors and other electronic devices or gadgets. Not surprisingly then, ninety percent of the world's digital data was created in the last two years. This massive explosion of data provides tremendous opportunity to study, model and improve conceptual and physical systems from which the data is produced. It also permits scientists to test pre-existing hypotheses in various fields with large scale experimental evidence. Thus, developing computational algorithms that automatically explores this data is the holy grail of the current generation of computer scientists. Making sense of this data algorithmically can be a complex process, specifically due to two reasons. Firstly, the data is generated by different devices, capturing different aspects of information and resides in different web resources/ platforms on the Internet. Therefore, even if two pieces of data bear singular conceptual similarity, their generation, format and domain of existence on the web can make them seem considerably dissimilar. Secondly, since humans are social creatures, the data often possesses inherent but murky correlations, primarily caused by the causal nature of direct or indirect social interactions. This drastically alters what algorithms must now achieve, necessitating intelligent comprehension of the underlying social nature and semantic contexts within the disparate domain data and a quantifiable way of transferring knowledge gained from one domain to another. Finally, the data is often encountered as a stream and not as static pages on the Internet. Therefore, we must learn, and re-learn as the stream propagates. The main objective of this dissertation is to develop learning algorithms that can identify specific patterns in one domain of data which can consequently augment predictive performance in another domain. The research explores existence of specific data domains which can function in synergy with another and more importantly, proposes models to quantify the synergetic information transfer among such domains. We include large-scale data from various domains in our study: social media data from Twitter, multimedia video data from YouTube, video search query data from Bing Videos, Natural Language search queries from the web, Internet resources in form of web logs (blogs) and spatio-temporal social trends from Twitter. Our work presents a series of solutions to address the key challenges in cross-domain learning, particularly in the field of social and semantic data. We propose the concept of bridging media from disparate sources by building a common latent topic space, which represents one of the first attempts toward answering sociological problems using cross-domain (social) media. This allows information transfer between social and non-social domains, fostering real-time socially relevant applications. We also engineer a concept network from the semantic web, called semNet, that can assist in identifying concept relations and modeling information granularity for robust natural language search. Further, by studying spatio-temporal patterns in this data, we can discover categorical concepts that stimulate collective attention within user groups.Includes bibliographical references (pages 210-214)