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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
ContributorsDaval, Charles (Performer) / ASU Library. Music Library (Publisher)
Created2018-03-26
DescriptionThe purpose of this project is to explore the influence of folk music in guitar compositions by Manuel Ponce from 1923 to 1932. It focuses on his Tres canciones populares mexicanas and Tropico and Rumba.
ContributorsGarcia Santos, Arnoldo (Author) / Koonce, Frank (Thesis advisor) / Rogers, Rodney (Committee member) / Rotaru, Catalin (Committee member) / Arizona State University (Publisher)
Created2014
Description
Analysis of political texts, which contains a huge amount of personal political opinions, sentiments, and emotions towards powerful individuals, leaders, organizations, and a large number of people, is an interesting task, which can lead to discover interesting interactions between the political parties and people. Recently, political blogosphere plays an increasingly important role in politics, as a forum for debating political issues. Most of the political weblogs are biased towards their political parties, and they generally express their sentiments towards their issues (i.e. leaders, topics etc.,) and also towards issues of the opposing parties. In this thesis, I have modeled the above interactions/debate as a sentimental bi-partite graph, a bi-partite graph with Blogs forming vertices of a disjoint set, and the issues (i.e. leaders, topics etc.,) forming the other disjoint set,and the edges between the two sets representing the sentiment of the blogs towards the issues. I have used American Political blog data to model the sentimental bi- partite graph, in particular, a set of popular political liberal and conservative blogs that have clearly declared positions. These blogs contain discussion about social, political, economic issues and related key individuals in their conservative/liberal view. To be more focused and more polarized, 22 most popular liberal/conservative blogs of a particular time period, May 2008 - October 2008(because of high intensity of debate and discussions), just before the presidential elections, was considered, involving around 23,800 articles. This thesis involves solving the questions: a) which is the most liberal/conservative blogs on the web? b) Who is on which side of debate and what are the issues? c) Who are the important leaders? d) How do you model the relationship between the participants of the debate and the underlying issues?
ContributorsThirumalai, Dananjayan (Author) / Davulcu, Hasan (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
ContributorsKotronakis, Dimitris (Performer) / ASU Library. Music Library (Publisher)
Created2018-03-01
ContributorsDavin, Colin (Performer) / ASU Library. Music Library (Publisher)
Created2018-10-05
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
Description
Social media is becoming increasingly popular as a platform for sharing personal health-related information. This information can be utilized for public health monitoring tasks such as pharmacovigilance via the use of Natural Language Processing (NLP) techniques. One of the critical steps in information extraction pipelines is Named Entity Recognition (NER), where the mentions of entities such as diseases are located in text and their entity type are identified. However, the language in social media is highly informal, and user-expressed health-related concepts are often non-technical, descriptive, and challenging to extract. There has been limited progress in addressing these challenges, and advanced machine learning-based NLP techniques have been underutilized. This work explores the effectiveness of different machine learning techniques, and particularly deep learning, to address the challenges associated with extraction of health-related concepts from social media. Deep learning has recently attracted a lot of attention in machine learning research and has shown remarkable success in several applications particularly imaging and speech recognition. However, thus far, deep learning techniques are relatively unexplored for biomedical text mining and, in particular, this is the first attempt in applying deep learning for health information extraction from social media.
This work presents ADRMine that uses a Conditional Random Field (CRF) sequence tagger for extraction of complex health-related concepts. It utilizes a large volume of unlabeled user posts for automatic learning of embedding cluster features, a novel application of deep learning in modeling the similarity between the tokens. ADRMine significantly improved the medical NER performance compared to the baseline systems.
This work also presents DeepHealthMiner, a deep learning pipeline for health-related concept extraction. Most of the machine learning methods require sophisticated task-specific manual feature design which is a challenging step in processing the informal and noisy content of social media. DeepHealthMiner automatically learns classification features using neural networks and utilizing a large volume of unlabeled user posts. Using a relatively small labeled training set, DeepHealthMiner could accurately identify most of the concepts, including the consumer expressions that were not observed in the training data or in the standard medical lexicons outperforming the state-of-the-art baseline techniques.
This work presents ADRMine that uses a Conditional Random Field (CRF) sequence tagger for extraction of complex health-related concepts. It utilizes a large volume of unlabeled user posts for automatic learning of embedding cluster features, a novel application of deep learning in modeling the similarity between the tokens. ADRMine significantly improved the medical NER performance compared to the baseline systems.
This work also presents DeepHealthMiner, a deep learning pipeline for health-related concept extraction. Most of the machine learning methods require sophisticated task-specific manual feature design which is a challenging step in processing the informal and noisy content of social media. DeepHealthMiner automatically learns classification features using neural networks and utilizing a large volume of unlabeled user posts. Using a relatively small labeled training set, DeepHealthMiner could accurately identify most of the concepts, including the consumer expressions that were not observed in the training data or in the standard medical lexicons outperforming the state-of-the-art baseline techniques.
ContributorsNikfarjam, Azadeh (Author) / Gonzalez, Graciela (Thesis advisor) / Greenes, Robert (Committee member) / Scotch, Matthew (Committee member) / Arizona State University (Publisher)
Created2016
Description
In the current millennium, extensive use of computers and the internet caused an exponential increase in information. Few research areas are as important as information extraction, which primarily involves extracting concepts and the relations between them from free text. Limitations in the size of training data, lack of lexicons and lack of relationship patterns are major factors for poor performance in information extraction. This is because the training data cannot possibly contain all concepts and their synonyms; and it contains only limited examples of relationship patterns between concepts. Creating training data, lexicons and relationship patterns is expensive, especially in the biomedical domain (including clinical notes) because of the depth of domain knowledge required of the curators. Dictionary-based approaches for concept extraction in this domain are not sufficient to effectively overcome the complexities that arise because of the descriptive nature of human languages. For example, there is a relatively higher amount of abbreviations (not all of them present in lexicons) compared to everyday English text. Sometimes abbreviations are modifiers of an adjective (e.g. CD4-negative) rather than nouns (and hence, not usually considered named entities). There are many chemical names with numbers, commas, hyphens and parentheses (e.g. t(3;3)(q21;q26)), which will be separated by most tokenizers. In addition, partial words are used in place of full words (e.g. up- and downregulate); and some of the words used are highly specialized for the domain. Clinical notes contain peculiar drug names, anatomical nomenclature, other specialized names and phrases that are not standard in everyday English or in published articles (e.g. "l shoulder inj"). State of the art concept extraction systems use machine learning algorithms to overcome some of these challenges. However, they need a large annotated corpus for every concept class that needs to be extracted. A novel natural language processing approach to minimize this limitation in concept extraction is proposed here using distributional semantics. Distributional semantics is an emerging field arising from the notion that the meaning or semantics of a piece of text (discourse) depends on the distribution of the elements of that discourse in relation to its surroundings. Distributional information from large unlabeled data is used to automatically create lexicons for the concepts to be tagged, clusters of contextually similar words, and thesauri of distributionally similar words. These automatically generated lexical resources are shown here to be more useful than manually created lexicons for extracting concepts from both literature and narratives. Further, machine learning features based on distributional semantics are shown to improve the accuracy of BANNER, and could be used in other machine learning systems such as cTakes to improve their performance. In addition, in order to simplify the sentence patterns and facilitate association extraction, a new algorithm using a "shotgun" approach is proposed. The goal of sentence simplification has traditionally been to reduce the grammatical complexity of sentences while retaining the relevant information content and meaning to enable better readability for humans and enhanced processing by parsers. Sentence simplification is shown here to improve the performance of association extraction systems for both biomedical literature and clinical notes. It helps improve the accuracy of protein-protein interaction extraction from the literature and also improves relationship extraction from clinical notes (such as between medical problems, tests and treatments). Overall, the two main contributions of this work include the application of sentence simplification to association extraction as described above, and the use of distributional semantics for concept extraction. The proposed work on concept extraction amalgamates for the first time two diverse research areas -distributional semantics and information extraction. This approach renders all the advantages offered in other semi-supervised machine learning systems, and, unlike other proposed semi-supervised approaches, it can be used on top of different basic frameworks and algorithms.
ContributorsJonnalagadda, Siddhartha Reddy (Author) / Gonzalez, Graciela H (Thesis advisor) / Cohen, Trevor A (Committee member) / Greenes, Robert A (Committee member) / Fridsma, Douglas B (Committee member) / Arizona State University (Publisher)
Created2011
ContributorsSanchez, Armand (Performer) / Nordstrom, Nathan (Performer) / Roubison, Ryan (Performer) / ASU Library. Music Library (Publisher)
Created2018-04-13