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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
The objective of this research is to determine an approach for automating the learning of the initial lexicon used in translating natural language sentences to their formal knowledge representations based on lambda-calculus expressions. Using a universal knowledge representation and its associated parser, this research attempts to use word alignment techniques

The objective of this research is to determine an approach for automating the learning of the initial lexicon used in translating natural language sentences to their formal knowledge representations based on lambda-calculus expressions. Using a universal knowledge representation and its associated parser, this research attempts to use word alignment techniques to align natural language sentences to the linearized parses of their associated knowledge representations in order to learn the meanings of individual words. The work includes proposing and analyzing an approach that can be used to learn some of the initial lexicon.
ContributorsBaldwin, Amy Lynn (Author) / Baral, Chitta (Thesis director) / Vo, Nguyen (Committee member) / Industrial, Systems (Contributor) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
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Description
This research lays down foundational work in the semantic reconstruction of linguistic politeness in English-to-Japanese machine translation and thereby advances semantic-based automated translation of English into other natural languages. I developed a Java project called the PoliteParser that is intended as a plug-in to existing semantic parsers to determine whether

This research lays down foundational work in the semantic reconstruction of linguistic politeness in English-to-Japanese machine translation and thereby advances semantic-based automated translation of English into other natural languages. I developed a Java project called the PoliteParser that is intended as a plug-in to existing semantic parsers to determine whether verbs in dialogue in an English corpus should be conjugated into the plain or the polite honorific form when translated into Japanese. The PoliteParser bases this decision off of semantic information about the social relationships between the speaker and the listener, the speaker's personality, and the circumstances of the utterance. Testing undergone during the course of this research demonstrates that the PoliteParser can achieve levels of accuracy 31 percentage points higher than that of statistical translation systems when integrated with a semantic parser and 54 percentage points higher when used with pre-parsed data.
ContributorsGuiou, Jared Tyler (Author) / Baral, Chitta (Thesis director) / Tanno, Koji (Committee member) / School of International Letters and Cultures (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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Description
Medical records are increasingly being recorded in the form of electronic health records (EHRs), with a significant amount of patient data recorded as unstructured natural language text. Consequently, being able to extract and utilize clinical data present within these records is an important step in furthering clinical care. One important

Medical records are increasingly being recorded in the form of electronic health records (EHRs), with a significant amount of patient data recorded as unstructured natural language text. Consequently, being able to extract and utilize clinical data present within these records is an important step in furthering clinical care. One important aspect within these records is the presence of prescription information. Existing techniques for extracting prescription information — which includes medication names, dosages, frequencies, reasons for taking, and mode of administration — from unstructured text have focused on the application of rule- and classifier-based methods. While state-of-the-art systems can be effective in extracting many types of information, they require significant effort to develop hand-crafted rules and conduct effective feature engineering. This paper presents the use of a bidirectional LSTM with CRF tagging model initialized with precomputed word embeddings for extracting prescription information from sentences without requiring significant feature engineering. The experimental results, run on the i2b2 2009 dataset, achieve an F1 macro measure of 0.8562, and scores above 0.9449 on four of the six categories, indicating significant potential for this model.
ContributorsRawal, Samarth Chetan (Author) / Baral, Chitta (Thesis director) / Anwar, Saadat (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Description
Recent advances in techniques allow the extraction of Cyber Threat Information (CTI) from online content, such as social media, blog articles, and posts in discussion forums. Most research work focuses on social media and blog posts since their content is often contributed by cybersecurity experts and is usually of cleaner

Recent advances in techniques allow the extraction of Cyber Threat Information (CTI) from online content, such as social media, blog articles, and posts in discussion forums. Most research work focuses on social media and blog posts since their content is often contributed by cybersecurity experts and is usually of cleaner formats. While posts in online forums are noisier and less structured, online forums attract more users than other sources and contain much valuable information that may help predict cyber threats. Therefore, effectively extracting CTI from online forum posts is an important task in today's data-driven cybersecurity defenses. Many Natural Language Processing (NLP) techniques are applied to the cybersecurity domains to extract the useful information, however, there is still space to improve. In this dissertation, a new Named Entity Recognition framework for cybersecurity domains and thread structure construction methods for unstructured forums are proposed to support the extraction of CTI. Then, extend them to filter the posts in the forums to eliminate non cybersecurity related topics with Cyber Attack Relevance Scale (CARS), extract the cybersecurity knowledgeable users to enhance more information for enhancing cybersecurity, and extract trending topic phrases related to cyber attacks in the hackers forums to find the clues for potential future attacks to predict them.
ContributorsKashihara, Kazuaki (Author) / Baral, Chitta (Thesis advisor) / Doupe, Adam (Committee member) / Blanco, Eduardo (Committee member) / Wang, Ruoyu (Committee member) / Arizona State University (Publisher)
Created2022
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Description
How to teach a machine to understand natural language? This question is a long-standing challenge in Artificial Intelligence. Several tasks are designed to measure the progress of this challenge. Question Answering is one such task that evaluates a machine's ability to understand natural language, where it reads a passage of

How to teach a machine to understand natural language? This question is a long-standing challenge in Artificial Intelligence. Several tasks are designed to measure the progress of this challenge. Question Answering is one such task that evaluates a machine's ability to understand natural language, where it reads a passage of text or an image and answers comprehension questions. In recent years, the development of transformer-based language models and large-scale human-annotated datasets has led to remarkable progress in the field of question answering. However, several disadvantages of fully supervised question answering systems have been observed. Such as generalizing to unseen out-of-distribution domains, linguistic style differences in questions, and adversarial samples. This thesis proposes implicitly supervised question answering systems trained using knowledge acquisition from external knowledge sources and new learning methods that provide inductive biases to learn question answering. In particular, the following research projects are discussed: (1) Knowledge Acquisition methods: these include semantic and abductive information retrieval for seeking missing knowledge, a method to represent unstructured text corpora as a knowledge graph, and constructing a knowledge base for implicit commonsense reasoning. (2) Learning methods: these include Knowledge Triplet Learning, a method over knowledge graphs; Test-Time Learning, a method to generalize to an unseen out-of-distribution context; WeaQA, a method to learn visual question answering using image captions without strong supervision; WeaSel, weakly supervised method for relative spatial reasoning; and a new paradigm for unsupervised natural language inference. These methods potentially provide a new research direction to overcome the pitfalls of direct supervision.
ContributorsBanerjee, Pratyay (Author) / Baral, Chitta (Thesis advisor) / Yang, Yezhou (Committee member) / Blanco, Eduardo (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2022
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Description
Enabling robots to physically engage with their environment in a safe and efficient manner is an essential step towards human-robot interaction. To date, robots usually operate as pre-programmed workers that blindly execute tasks in highly structured environments crafted by skilled engineers. Changing the robots’ behavior to cover new duties or

Enabling robots to physically engage with their environment in a safe and efficient manner is an essential step towards human-robot interaction. To date, robots usually operate as pre-programmed workers that blindly execute tasks in highly structured environments crafted by skilled engineers. Changing the robots’ behavior to cover new duties or handle variability is an expensive, complex, and time-consuming process. However, with the advent of more complex sensors and algorithms, overcoming these limitations becomes within reach. This work proposes innovations in artificial intelligence, language understanding, and multimodal integration to enable next-generation grasping and manipulation capabilities in autonomous robots. The underlying thesis is that multimodal observations and instructions can drastically expand the responsiveness and dexterity of robot manipulators. Natural language, in particular, can be used to enable intuitive, bidirectional communication between a human user and the machine. To this end, this work presents a system that learns context-aware robot control policies from multimodal human demonstrations. Among the main contributions presented are techniques for (a) collecting demonstrations in an efficient and intuitive fashion, (b) methods for leveraging physical contact with the environment and objects, (c) the incorporation of natural language to understand context, and (d) the generation of robust robot control policies. The presented approach and systems are evaluated in multiple grasping and manipulation settings ranging from dexterous manipulation to pick-and-place, as well as contact-rich bimanual insertion tasks. Moreover, the usability of these innovations, especially when utilizing human task demonstrations and communication interfaces, is evaluated in several human-subject studies.
ContributorsStepputtis, Simon (Author) / Ben Amor, Heni (Thesis advisor) / Baral, Chitta (Committee member) / Yang, Yezhou (Committee member) / Lee, Stefan (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Increasing misinformation in social media channels has become more prevalent since the beginning of the COVID-19 pandemic as countless myths and rumors have circulated over the internet. This misinformation has potentially lethal consequences as many people make important health decisions based on what they read online, thus creating an urgent

Increasing misinformation in social media channels has become more prevalent since the beginning of the COVID-19 pandemic as countless myths and rumors have circulated over the internet. This misinformation has potentially lethal consequences as many people make important health decisions based on what they read online, thus creating an urgent need to combat it. Although many Natural Language Processing (NLP) techniques have been used to identify misinformation in text, prompt-based methods are under-studied for this task. This work explores prompt learning to classify COVID-19 related misinformation. To this extent, I analyze the effectiveness of this proposed approach on four datasets. Experimental results show that prompt-based classification achieves on average ~13% and ~6% improvement compared to a single-task and multi-task model, respectively. Moreover, analysis shows that prompt-based models can achieve competitive results compared to baselines in a few-shot learning scenario.
ContributorsBrown, Clinton (Author) / Baral, Chitta (Thesis director) / Walker, Shawn (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-05
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Description
Models that learn from data are widely and rapidly being deployed today for real-world use, and have become an integral and embedded part of human lives. While these technological advances are exciting and impactful, such data-driven computer vision systems often fail in inscrutable ways. This dissertation seeks to study and

Models that learn from data are widely and rapidly being deployed today for real-world use, and have become an integral and embedded part of human lives. While these technological advances are exciting and impactful, such data-driven computer vision systems often fail in inscrutable ways. This dissertation seeks to study and improve the reliability of machine learning models from several perspectives including the development of robust training algorithms to mitigate the risks of such failures, construction of new datasets that provide a new perspective on capabilities of vision models, and the design of evaluation metrics for re-calibrating the perception of performance improvements. I will first address distribution shift in image classification with the following contributions: (1) two methods for improving the robustness of image classifiers to distribution shift by leveraging the classifier's failures into an adversarial data transformation pipeline guided by domain knowledge, (2) an interpolation-based technique for flagging out-of-distribution samples, and (3) an intriguing trade-off between distributional and adversarial robustness resulting from data modification strategies. I will then explore reliability considerations for \textit{semantic vision} models that learn from both visual and natural language data; I will discuss how logical and semantic sentence transformations affect the performance of vision--language models and my contributions towards developing knowledge-guided learning algorithms to mitigate these failures. Finally, I will describe the effort towards building and evaluating complex reasoning capabilities of vision--language models towards the long-term goal of robust and reliable computer vision models that can communicate, collaborate, and reason with humans.
ContributorsGokhale, Tejas (Author) / Yang, Yezhou (Thesis advisor) / Baral, Chitta (Thesis advisor) / Ben Amor, Heni (Committee member) / Anirudh, Rushil (Committee member) / Arizona State University (Publisher)
Created2023