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- Creators: Ye, Jieping
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
A story is defined as "an actor(s) taking action(s) that culminates in a resolution(s)''. I present novel sets of features to facilitate story detection among text via supervised classification and further reveal different forms within stories via unsupervised clustering. First, I investigate the utility of a new set of semantic features compared to standard keyword features combined with statistical features, such as density of part-of-speech (POS) tags and named entities, to develop a story classifier. The proposed semantic features are based on triplets that can be extracted using a shallow parser. Experimental results show that a model of memory-based semantic linguistic features alongside statistical features achieves better accuracy. Next, I further improve the performance of story detection with a novel algorithm which aggregates the triplets producing generalized concepts and relations. A major challenge in automated text analysis is that different words are used for related concepts. Analyzing text at the surface level would treat related concepts (i.e. actors, actions, targets, and victims) as different objects, potentially missing common narrative patterns. The algorithm clusters triplets into generalized concepts by utilizing syntactic criteria based on common contexts and semantic corpus-based statistical criteria based on "contextual synonyms''. Generalized concepts representation of text (1) overcomes surface level differences (which arise when different keywords are used for related concepts) without drift, (2) leads to a higher-level semantic network representation of related stories, and (3) when used as features, they yield a significant (36%) boost in performance for the story detection task. Finally, I implement co-clustering based on generalized concepts/relations to automatically detect story forms. Overlapping generalized concepts and relationships correspond to archetypes/targets and actions that characterize story forms. I perform co-clustering of stories using standard unigrams/bigrams and generalized concepts. I show that the residual error of factorization with concept-based features is significantly lower than the error with standard keyword-based features. I also present qualitative evaluations by a subject matter expert, which suggest that concept-based features yield more coherent, distinctive and interesting story forms compared to those produced by using standard keyword-based features.
ContributorsCeran, Saadet Betul (Author) / Davulcu, Hasan (Thesis advisor) / Corman, Steven R. (Committee member) / Shakarian, Paulo (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2016