Matching Items (3)
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- All Subjects: Natural language processing (Computer science)
- Creators: Gonzalez, Graciela
- Creators: Bansal, Srividya
Description
Automating aspects of biocuration through biomedical information extraction could significantly impact biomedical research by enabling greater biocuration throughput and improving the feasibility of a wider scope. An important step in biomedical information extraction systems is named entity recognition (NER), where mentions of entities such as proteins and diseases are located within natural-language text and their semantic type is determined. This step is critical for later tasks in an information extraction pipeline, including normalization and relationship extraction. BANNER is a benchmark biomedical NER system using linear-chain conditional random fields and the rich feature set approach. A case study with BANNER locating genes and proteins in biomedical literature is described. The first corpus for disease NER adequate for use as training data is introduced, and employed in a case study of disease NER. The first corpus locating adverse drug reactions (ADRs) in user posts to a health-related social website is also described, and a system to locate and identify ADRs in social media text is created and evaluated. The rich feature set approach to creating NER feature sets is argued to be subject to diminishing returns, implying that additional improvements may require more sophisticated methods for creating the feature set. This motivates the first application of multivariate feature selection with filters and false discovery rate analysis to biomedical NER, resulting in a feature set at least 3 orders of magnitude smaller than the set created by the rich feature set approach. Finally, two novel approaches to NER by modeling the semantics of token sequences are introduced. The first method focuses on the sequence content by using language models to determine whether a sequence resembles entries in a lexicon of entity names or text from an unlabeled corpus more closely. The second method models the distributional semantics of token sequences, determining the similarity between a potential mention and the token sequences from the training data by analyzing the contexts where each sequence appears in a large unlabeled corpus. The second method is shown to improve the performance of BANNER on multiple data sets.
ContributorsLeaman, James Robert (Author) / Gonzalez, Graciela (Thesis advisor) / Baral, Chitta (Thesis advisor) / Cohen, Kevin B (Committee member) / Liu, Huan (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2013
Description
Text mining of biomedical literature and clinical notes is a very active field of research in biomedical science. Semantic analysis is one of the core modules for different Natural Language Processing (NLP) solutions. Methods for calculating semantic relatedness of two concepts can be very useful in solutions solving different problems such as relationship extraction, ontology creation and question / answering [1–6]. Several techniques exist in calculating semantic relatedness of two concepts. These techniques utilize different knowledge sources and corpora. So far, researchers attempted to find the best hybrid method for each domain by combining semantic relatedness techniques and data sources manually. In this work, attempts were made to eliminate the needs for manually combining semantic relatedness methods targeting any new contexts or resources through proposing an automated method, which attempted to find the best combination of semantic relatedness techniques and resources to achieve the best semantic relatedness score in every context. This may help the research community find the best hybrid method for each context considering the available algorithms and resources.
ContributorsEmadzadeh, Ehsan (Author) / Gonzalez, Graciela (Thesis advisor) / Greenes, Robert (Committee member) / Scotch, Matthew (Committee member) / Arizona State University (Publisher)
Created2016
Description
With the inception of World Wide Web, the amount of data present on the internet is tremendous. This makes the task of navigating through this enormous amount of data quite difficult for the user. As users struggle to navigate through this wealth of information, the need for the development of an automated system that can extract the required information becomes urgent. The aim of this thesis is to develop a Question Answering system to ease the process of information retrieval.
Question Answering systems have been around for quite some time and are a sub-field of information retrieval and natural language processing. The task of any Question Answering system is to seek an answer to a free form factual question. The difficulty of pinpointing and verifying the precise answer makes question answering more challenging than simple information retrieval done by search engines. Text REtrieval Conference (TREC) is a yearly conference which provides large - scale infrastructure and resources to support research in information retrieval domain. TREC has a question answering track since 1999 where the questions dataset contains a list of factual questions (Vorhees & Tice, 1999). DBpedia (Bizer et al., 2009) is a community driven effort to extract and structure the data present in Wikipedia.
The research objective of this thesis is to develop a novel approach to Question Answering based on a composition of conventional approaches of Information Retrieval and Natural Language processing. The focus is also on exploring the use of a structured and annotated knowledge base as opposed to an unstructured knowledge base. The knowledge base used here is DBpedia and the final system is evaluated on the TREC 2004 questions dataset.
Question Answering systems have been around for quite some time and are a sub-field of information retrieval and natural language processing. The task of any Question Answering system is to seek an answer to a free form factual question. The difficulty of pinpointing and verifying the precise answer makes question answering more challenging than simple information retrieval done by search engines. Text REtrieval Conference (TREC) is a yearly conference which provides large - scale infrastructure and resources to support research in information retrieval domain. TREC has a question answering track since 1999 where the questions dataset contains a list of factual questions (Vorhees & Tice, 1999). DBpedia (Bizer et al., 2009) is a community driven effort to extract and structure the data present in Wikipedia.
The research objective of this thesis is to develop a novel approach to Question Answering based on a composition of conventional approaches of Information Retrieval and Natural Language processing. The focus is also on exploring the use of a structured and annotated knowledge base as opposed to an unstructured knowledge base. The knowledge base used here is DBpedia and the final system is evaluated on the TREC 2004 questions dataset.
ContributorsChandurkar, Avani (Author) / Bansal, Ajay (Thesis advisor) / Bansal, Srividya (Committee member) / Lindquist, Timothy (Committee member) / Arizona State University (Publisher)
Created2016