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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

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
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Description
While developing autonomous intelligent robots has been the goal of many research programs, a more practical application involving intelligent robots is the formation of teams consisting of both humans and robots. An example of such an application is search and rescue operations where robots commanded by humans are sent to

While developing autonomous intelligent robots has been the goal of many research programs, a more practical application involving intelligent robots is the formation of teams consisting of both humans and robots. An example of such an application is search and rescue operations where robots commanded by humans are sent to environments too dangerous for humans. For such human-robot interaction, natural language is considered a good communication medium as it allows humans with less training about the robot's internal language to be able to command and interact with the robot. However, any natural language communication from the human needs to be translated to a formal language that the robot can understand. Similarly, before the robot can communicate (in natural language) with the human, it needs to formulate its communique in some formal language which then gets translated into natural language. In this paper, I develop a high level language for communication between humans and robots and demonstrate various aspects through a robotics simulation. These language constructs borrow some ideas from action execution languages and are grounded with respect to simulated human-robot interaction transcripts.
ContributorsLumpkin, Barry Thomas (Author) / Baral, Chitta (Thesis advisor) / Lee, Joohyung (Committee member) / Fainekos, Georgios (Committee member) / Arizona State University (Publisher)
Created2012
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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

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
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Description
Proliferation of social media websites and discussion forums in the last decade has resulted in social media mining emerging as an effective mechanism to extract consumer patterns. Most research on social media and pharmacovigilance have concentrated on

Adverse Drug Reaction (ADR) identification. Such methods employ a step of drug search followed

Proliferation of social media websites and discussion forums in the last decade has resulted in social media mining emerging as an effective mechanism to extract consumer patterns. Most research on social media and pharmacovigilance have concentrated on

Adverse Drug Reaction (ADR) identification. Such methods employ a step of drug search followed by classification of the associated text as consisting an ADR or not. Although this method works efficiently for ADR classifications, if ADR evidence is present in users posts over time, drug mentions fail to capture such ADRs. It also fails to record additional user information which may provide an opportunity to perform an in-depth analysis for lifestyle habits and possible reasons for any medical problems.

Pre-market clinical trials for drugs generally do not include pregnant women, and so their effects on pregnancy outcomes are not discovered early. This thesis presents a thorough, alternative strategy for assessing the safety profiles of drugs during pregnancy by utilizing user timelines from social media. I explore the use of a variety of state-of-the-art social media mining techniques, including rule-based and machine learning techniques, to identify pregnant women, monitor their drug usage patterns, categorize their birth outcomes, and attempt to discover associations between drugs and bad birth outcomes.

The technique used models user timelines as longitudinal patient networks, which provide us with a variety of key information about pregnancy, drug usage, and post-

birth reactions. I evaluate the distinct parts of the pipeline separately, validating the usefulness of each step. The approach to use user timelines in this fashion has produced very encouraging results, and can be employed for a range of other important tasks where users/patients are required to be followed over time to derive population-based measures.
ContributorsChandrashekar, Pramod Bharadwaj (Author) / Davulcu, Hasan (Thesis advisor) / Gonzalez, Graciela (Thesis advisor) / Hsiao, Sharon (Committee member) / Arizona State University (Publisher)
Created2016
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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

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.
ContributorsNikfarjam, Azadeh (Author) / Gonzalez, Graciela (Thesis advisor) / Greenes, Robert (Committee member) / Scotch, Matthew (Committee member) / Arizona State University (Publisher)
Created2016
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Description
Question Answering has been under active research for decades, but it has recently taken the spotlight following IBM Watson's success in Jeopardy! and digital assistants such as Apple's Siri, Google Now, and Microsoft Cortana through every smart-phone and browser. However, most of the research in Question Answering aims at factual

Question Answering has been under active research for decades, but it has recently taken the spotlight following IBM Watson's success in Jeopardy! and digital assistants such as Apple's Siri, Google Now, and Microsoft Cortana through every smart-phone and browser. However, most of the research in Question Answering aims at factual questions rather than deep ones such as ``How'' and ``Why'' questions.

In this dissertation, I suggest a different approach in tackling this problem. We believe that the answers of deep questions need to be formally defined before found.

Because these answers must be defined based on something, it is better to be more structural in natural language text; I define Knowledge Description Graphs (KDGs), a graphical structure containing information about events, entities, and classes. We then propose formulations and algorithms to construct KDGs from a frame-based knowledge base, define the answers of various ``How'' and ``Why'' questions with respect to KDGs, and suggest how to obtain the answers from KDGs using Answer Set Programming. Moreover, I discuss how to derive missing information in constructing KDGs when the knowledge base is under-specified and how to answer many factual question types with respect to the knowledge base.

After having the answers of various questions with respect to a knowledge base, I extend our research to use natural language text in specifying deep questions and knowledge base, generate natural language text from those specification. Toward these goals, I developed NL2KR, a system which helps in translating natural language to formal language. I show NL2KR's use in translating ``How'' and ``Why'' questions, and generating simple natural language sentences from natural language KDG specification. Finally, I discuss applications of the components I developed in Natural Language Understanding.
ContributorsVo, Nguyen Ha (Author) / Baral, Chitta (Thesis advisor) / Lee, Joohyung (Committee member) / VanLehn, Kurt (Committee member) / Tran, Son Cao (Committee member) / Arizona State University (Publisher)
Created2015