Grounding Gene Mentions with Respect to Gene Database Identifiers

We describe our submission for task 1B of the BioCreAtIvE competition which is concerned with grounding gene mentions with respect to databases of organism gene identifiers. Several approaches to gene identification, lookup, and disambiguation are presented. Results are presented with two possible baseline systems and a discussion of the source of precision and recall errors as well as an estimate of precision and recall for an organism-specific tagger bootstrapped from gene synonym lists and the task 1B training data. 1

Probabilistic Bag-Of-Hyperlinks Model for Entity Linking

Many fundamental problems in natural language processing rely on determining what entities appear in a given text. Commonly referenced as entity linking, this step is a fundamental component of many NLP tasks such as text understanding, automatic summarization, semantic search or machine translation. Name ambiguity, word polysemy, context dependencies and a heavy-tailed distribution of entities contribute to the complexity of this problem. We here propose a probabilistic approach that makes use of an effective graphical model to perform collective entity disambiguation. Input mentions (i.e.,~linkable token spans) are disambiguated jointly across an entire document by combining a document-level prior of entity co-occurrences with local information captured from mentions and their surrounding context. The model is based on simple sufficient statistics extracted from data, thus relying on few parameters to be learned. Our method does not require extensive feature engineering, nor an expensive training procedure. We use loopy belief propagation to perform approximate inference. The low complexity of our model makes this step sufficiently fast for real-time usage. We demonstrate the accuracy of our approach on a wide range of benchmark datasets, showing that it matches, and in many cases outperforms, existing state-of-the-art methods

Entity-Oriented Search

This open access book covers all facets of entity-oriented search—where “search” can be interpreted in the broadest sense of information access—from a unified point of view, and provides a coherent and comprehensive overview of the state of the art. It represents the first synthesis of research in this broad and rapidly developing area. Selected topics are discussed in-depth, the goal being to establish fundamental techniques and methods as a basis for future research and development. Additional topics are treated at a survey level only, containing numerous pointers to the relevant literature. A roadmap for future research, based on open issues and challenges identified along the way, rounds out the book. The book is divided into three main parts, sandwiched between introductory and concluding chapters. The first two chapters introduce readers to the basic concepts, provide an overview of entity-oriented search tasks, and present the various types and sources of data that will be used throughout the book. Part I deals with the core task of entity ranking: given a textual query, possibly enriched with additional elements or structural hints, return a ranked list of entities. This core task is examined in a number of different variants, using both structured and unstructured data collections, and numerous query formulations. In turn, Part II is devoted to the role of entities in bridging unstructured and structured data. Part III explores how entities can enable search engines to understand the concepts, meaning, and intent behind the query that the user enters into the search box, and how they can provide rich and focused responses (as opposed to merely a list of documents)—a process known as semantic search. The final chapter concludes the book by discussing the limitations of current approaches, and suggesting directions for future research. Researchers and graduate students are the primary target audience of this book. A general background in information retrieval is sufficient to follow the material, including an understanding of basic probability and statistics concepts as well as a basic knowledge of machine learning concepts and supervised learning algorithms

Natural language processing

Beginning with the basic issues of NLP, this chapter aims to chart the major research activities in this area since the last ARIST Chapter in 1996 (Haas, 1996), including: (i) natural language text processing systems - text summarization, information extraction, information retrieval, etc., including domain-specific applications; (ii) natural language interfaces; (iii) NLP in the context of www and digital libraries ; and (iv) evaluation of NLP systems