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Description
Biological organisms are made up of cells containing numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted, manifesting as disease symptoms. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for activities including diagnosing diseases and drug development. Scientists studying these interconnected processes have identified various pathways involved in drug metabolism, diseases, and signal transduction, etc. High-throughput technologies, new algorithms and speed improvements over the last decade have resulted in deeper knowledge about biological systems, leading to more refined pathways. Such pathways tend to be large and complex, making it difficult for an individual to remember all aspects. Thus, computer models are needed to represent and analyze them. The refinement activity itself requires reasoning with a pathway model by posing queries against it and comparing the results against the real biological system. Many existing models focus on structural and/or factoid questions, relying on surface-level information. These are generally not the kind of questions that a biologist may ask someone to test their understanding of biological processes. Examples of questions requiring understanding of biological processes are available in introductory college level biology text books. Such questions serve as a model for the question answering system developed in this thesis. Thus, the main goal of this thesis is to develop a system that allows the encoding of knowledge about biological pathways to answer questions demonstrating understanding of the pathways. To that end, a language is developed to specify a pathway and pose questions against it. Some existing tools are modified and used to accomplish this goal. The utility of the framework developed in this thesis is illustrated with applications in the biological domain. Finally, the question answering system is used in real world applications by extracting pathway knowledge from text and answering questions related to drug development.
ContributorsAnwar, Saadat (Author) / Baral, Chitta (Thesis advisor) / Inoue, Katsumi (Committee member) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Lee, Joohyung (Committee member) / Arizona State University (Publisher)
Created2014
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 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
Description
This thesis concerns the adoption of health information technology in the medical sector, specifically electronic health records (EHRs). EHRs have been seen as a great benefit to the healthcare system and will improve the quality of patient care. The federal government, has seen the benefit EHRs can offer, has been advocating the use and adoption of EHR for nearly a decade now. They have created policies that guide medical providers on how to implement EHRs. However, this thesis concerns the attitudes medical providers in Phoenix have towards government implementation. By interviewing these individuals and cross-referencing their answers with the literature this thesis wants to discover the pitfalls of federal government policy toward EHR implementation and EHR implementation in general. What this thesis found was that there are pitfalls that the federal government has failed to address including loss of provider productivity, lack of interoperability, and workflow improvement. However, the providers do say there is still a place for government to be involved in the implementation of EHR.
ContributorsKaldawi, Nicholas Emad (Author) / Lewis, Paul (Thesis director) / Cortese, Denis (Committee member) / Jones, Ruth (Committee member) / Barrett, The Honors College (Contributor) / School of Politics and Global Studies (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2013-05
Description
Instructional prompts are a novel technique that can significantly improve the performance of natural language processing tasks by specifying the task instruction to the language model. This is the first paper that uses instructional prompts to improve performance of the question answering task in biomedical domain. This work makes two significant contributions. Firstly, a question answer dataset of 600K question answer pairs has been developed by using the medical textbook ‘Differential Diagnosis Primary Care’, which contains information on how to diagnose a patient by observing their disease symptoms. Secondly, a question answering language model augmented with instructional prompts has been developed by training on the medical information extracted from the book ‘Differential Diagnosis Primary Care’. Experiments have been conducted to demonstrate that it performs better than a normal question answering model that does not use instructional prompts. Instructional prompts are based on prompt tuning and prefix tuning, which are novel techniques which can help train language model to do specific downstream tasks by keeping majority of model parameters frozen, and only optimizing a small number of continuous task-specific vectors (called the prefixes).
ContributorsSaxena, Sharad (Author) / Baral, Chitta (Thesis advisor) / Blanco, Eduardo (Committee member) / Anwar, Saadat (Committee member) / Arizona State University (Publisher)
Created2021
Description
In this thesis, I present two new datasets and a modification to the existing models in the form of a novel attention mechanism for Natural Language Inference (NLI). The new datasets have been carefully synthesized from various existing corpora released for different tasks.
The task of NLI is to determine the possibility of a sentence referred to as “Hypothesis” being true given that another sentence referred to as “Premise” is true. In other words, the task is to identify whether the “Premise” entails, contradicts or remains neutral with regards to the “Hypothesis”. NLI is a precursor to solving many Natural Language Processing (NLP) tasks such as Question Answering and Semantic Search. For example, in Question Answering systems, the question is paraphrased to form a declarative statement which is treated as the hypothesis. The options are treated as the premise. The option with the maximum entailment score is considered as the answer. Considering the applications of NLI, the importance of having a strong NLI system can't be stressed enough.
Many large-scale datasets and models have been released in order to advance the field of NLI. While all of these models do get good accuracy on the test sets of the datasets they were trained on, they fail to capture the basic understanding of “Entities” and “Roles”. They often make the mistake of inferring that “John went to the market.” from “Peter went to the market.” failing to capture the notion of “Entities”. In other cases, these models don't understand the difference in the “Roles” played by the same entities in “Premise” and “Hypothesis” sentences and end up wrongly inferring that “Peter drove John to the stadium.” from “John drove Peter to the stadium.”
The lack of understanding of “Roles” can be attributed to the lack of such examples in the various existing datasets. The reason for the existing model’s failure in capturing the notion of “Entities” is not just due to the lack of such examples in the existing NLI datasets. It can also be attributed to the strict use of vector similarity in the “word-to-word” attention mechanism being used in the existing architectures.
To overcome these issues, I present two new datasets to help make the NLI systems capture the notion of “Entities” and “Roles”. The “NER Changed” (NC) dataset and the “Role-Switched” (RS) dataset contains examples of Premise-Hypothesis pairs that require the understanding of “Entities” and “Roles” respectively in order to be able to make correct inferences. This work shows how the existing architectures perform poorly on the “NER Changed” (NC) dataset even after being trained on the new datasets. In order to help the existing architectures, understand the notion of “Entities”, this work proposes a modification to the “word-to-word” attention mechanism. Instead of relying on vector similarity alone, the modified architectures learn to incorporate the “Symbolic Similarity” as well by using the Named-Entity features of the Premise and Hypothesis sentences. The new modified architectures not only perform significantly better than the unmodified architectures on the “NER Changed” (NC) dataset but also performs as well on the existing datasets.
The task of NLI is to determine the possibility of a sentence referred to as “Hypothesis” being true given that another sentence referred to as “Premise” is true. In other words, the task is to identify whether the “Premise” entails, contradicts or remains neutral with regards to the “Hypothesis”. NLI is a precursor to solving many Natural Language Processing (NLP) tasks such as Question Answering and Semantic Search. For example, in Question Answering systems, the question is paraphrased to form a declarative statement which is treated as the hypothesis. The options are treated as the premise. The option with the maximum entailment score is considered as the answer. Considering the applications of NLI, the importance of having a strong NLI system can't be stressed enough.
Many large-scale datasets and models have been released in order to advance the field of NLI. While all of these models do get good accuracy on the test sets of the datasets they were trained on, they fail to capture the basic understanding of “Entities” and “Roles”. They often make the mistake of inferring that “John went to the market.” from “Peter went to the market.” failing to capture the notion of “Entities”. In other cases, these models don't understand the difference in the “Roles” played by the same entities in “Premise” and “Hypothesis” sentences and end up wrongly inferring that “Peter drove John to the stadium.” from “John drove Peter to the stadium.”
The lack of understanding of “Roles” can be attributed to the lack of such examples in the various existing datasets. The reason for the existing model’s failure in capturing the notion of “Entities” is not just due to the lack of such examples in the existing NLI datasets. It can also be attributed to the strict use of vector similarity in the “word-to-word” attention mechanism being used in the existing architectures.
To overcome these issues, I present two new datasets to help make the NLI systems capture the notion of “Entities” and “Roles”. The “NER Changed” (NC) dataset and the “Role-Switched” (RS) dataset contains examples of Premise-Hypothesis pairs that require the understanding of “Entities” and “Roles” respectively in order to be able to make correct inferences. This work shows how the existing architectures perform poorly on the “NER Changed” (NC) dataset even after being trained on the new datasets. In order to help the existing architectures, understand the notion of “Entities”, this work proposes a modification to the “word-to-word” attention mechanism. Instead of relying on vector similarity alone, the modified architectures learn to incorporate the “Symbolic Similarity” as well by using the Named-Entity features of the Premise and Hypothesis sentences. The new modified architectures not only perform significantly better than the unmodified architectures on the “NER Changed” (NC) dataset but also performs as well on the existing datasets.
ContributorsShrivastava, Ishan (Author) / Baral, Chitta (Thesis advisor) / Anwar, Saadat (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2019
Description
Social networking sites like Twitter have provided people a platform to connect
with each other, to discuss and share information and news or to entertain themselves. As the number of users continues to grow there has been explosive growth in the data generated by these users. Such a vast data source has provided researchers a way to study and monitor public health.
Accurately analyzing tweets is a difficult task mainly because of their short length, the inventive spellings and creative language expressions. Instead of focusing at the topic level, identifying tweets that have personal health experience mentions would be more helpful to researchers, governments and other organizations. Another important limitation in the current systems for social media health applications is the use of a disease-specific model and dataset to study a particular disease. Identifying adverse drug reactions is an important part of the drug development process. Detecting and extracting adverse drug mentions in tweets can supplement the list of adverse drug reactions that result from the drug trials and can help in the improvement of the drugs.
This thesis aims to address these two challenges and proposes three systems. A generalizable system to identify personal health experience mentions across different disease domains, a system for automatic classifications of adverse effects mentions in tweets and a system to extract adverse drug mentions from tweets. The proposed systems use the transfer learning from language models to achieve notable scores on Social Media Mining for Health Applications(SMM4H) 2019 (Weissenbacher et al. 2019) shared tasks.
with each other, to discuss and share information and news or to entertain themselves. As the number of users continues to grow there has been explosive growth in the data generated by these users. Such a vast data source has provided researchers a way to study and monitor public health.
Accurately analyzing tweets is a difficult task mainly because of their short length, the inventive spellings and creative language expressions. Instead of focusing at the topic level, identifying tweets that have personal health experience mentions would be more helpful to researchers, governments and other organizations. Another important limitation in the current systems for social media health applications is the use of a disease-specific model and dataset to study a particular disease. Identifying adverse drug reactions is an important part of the drug development process. Detecting and extracting adverse drug mentions in tweets can supplement the list of adverse drug reactions that result from the drug trials and can help in the improvement of the drugs.
This thesis aims to address these two challenges and proposes three systems. A generalizable system to identify personal health experience mentions across different disease domains, a system for automatic classifications of adverse effects mentions in tweets and a system to extract adverse drug mentions from tweets. The proposed systems use the transfer learning from language models to achieve notable scores on Social Media Mining for Health Applications(SMM4H) 2019 (Weissenbacher et al. 2019) shared tasks.
ContributorsGondane, Shubham Bhagwan (Author) / Baral, Chitta (Thesis advisor) / Anwar, Saadat (Committee member) / Devarakonda, Murthy (Committee member) / Arizona State University (Publisher)
Created2019
Description
Significance of real-world knowledge for Natural Language Understanding(NLU) is well-known for decades. With advancements in technology, challenging tasks like question-answering, text-summarizing, and machine translation are made possible with continuous efforts in the field of Natural Language Processing(NLP). Yet, knowledge integration to answer common sense questions is still a daunting task. Logical reasoning has been a resort for many of the problems in NLP and has achieved considerable results in the field, but it is difficult to resolve the ambiguities in a natural language. Co-reference resolution is one of the problems where ambiguity arises due to the semantics of the sentence. Another such problem is the cause and result statements which require causal commonsense reasoning to resolve the ambiguity. Modeling these type of problems is not a simple task with rules or logic. State-of-the-art systems addressing these problems use a trained neural network model, which claims to have overall knowledge from a huge trained corpus. These systems answer the questions by using the knowledge embedded in their trained language model. Although the language models embed the knowledge from the data, they use occurrences of words and frequency of co-existing words to solve the prevailing ambiguity. This limits the performance of language models to solve the problems in common-sense reasoning task as it generalizes the concept rather than trying to answer the problem specific to its context. For example, "The painting in Mark's living room shows an oak tree. It is to the right of a house", is a co-reference resolution problem which requires knowledge. Language models can resolve whether "it" refers to "painting" or "tree", since "house" and "tree" are two common co-occurring words so the models can resolve "tree" to be the co-reference. On the other hand, "The large ball crashed right through the table. Because it was made of Styrofoam ." to resolve for "it" which can be either "table" or "ball", is difficult for a language model as it requires more information about the problem.
In this work, I have built an end-to-end framework, which uses the automatically extracted knowledge based on the problem. This knowledge is augmented with the language models using an explicit reasoning module to resolve the ambiguity. This system is built to improve the accuracy of the language models based approaches for commonsense reasoning. This system has proved to achieve the state of the art accuracy on the Winograd Schema Challenge.
In this work, I have built an end-to-end framework, which uses the automatically extracted knowledge based on the problem. This knowledge is augmented with the language models using an explicit reasoning module to resolve the ambiguity. This system is built to improve the accuracy of the language models based approaches for commonsense reasoning. This system has proved to achieve the state of the art accuracy on the Winograd Schema Challenge.
ContributorsPrakash, Ashok (Author) / Baral, Chitta (Thesis advisor) / Devarakonda, Murthy (Committee member) / Anwar, Saadat (Committee member) / Arizona State University (Publisher)
Created2019
Description
Question answering is a challenging problem and a long term goal of Artificial Intelligence. There are many approaches proposed to solve this problem, including end to end machine learning systems, Information Retrieval based approaches and Textual Entailment. Despite being popular, these methods find difficulty in solving problems that require multi level reasoning and combining independent pieces of knowledge, for example, a question like "What adaptation is necessary in intertidal ecosystems but not in reef ecosystems?'', requires the system to consider qualities, behaviour or features of an organism living in an intertidal ecosystem and compare with that of an organism in a reef ecosystem to find the answer. The proposed solution is to solve a genre of questions, which is questions based on "Adaptation, Variation and Behavior in Organisms", where there are various different independent sets of knowledge required for answering questions along with reasoning. This method is implemented using Answer Set Programming and Natural Language Inference (which is based on machine learning ) for finding which of the given options is more probable to be the answer by matching it with the knowledge base. To evaluate this approach, a dataset of questions and a knowledge base in the domain of "Adaptation, Variation and Behavior in Organisms" is created.
ContributorsBatni, Vaishnavi (Author) / Baral, Chitta (Thesis advisor) / Anwar, Saadat (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2019
Description
Artificial general intelligence consists of many components, one of which is Natural Language Understanding (NLU). One of the applications of NLU is Reading Comprehension where it is expected that a system understand all aspects of a text. Further, understanding natural procedure-describing text that deals with existence of entities and effects of actions on these entities while doing reasoning and inference at the same time is a particularly difficult task. A recent natural language dataset by the Allen Institute of Artificial Intelligence, ProPara, attempted to address the challenges to determine entity existence and entity tracking in natural text.
As part of this work, an attempt is made to address the ProPara challenge. The Knowledge Representation and Reasoning (KRR) community has developed effective techniques for modeling and reasoning about actions and similar techniques are used in this work. A system consisting of Inductive Logic Programming (ILP) and Answer Set Programming (ASP) is used to address the challenge and achieves close to state-of-the-art results and provides an explainable model. An existing semantic role label parser is modified and used to parse the dataset.
On analysis of the learnt model, it was found that some of the rules were not generic enough. To overcome the issue, the Proposition Bank dataset is then used to add knowledge in an attempt to generalize the ILP learnt rules to possibly improve the results.
As part of this work, an attempt is made to address the ProPara challenge. The Knowledge Representation and Reasoning (KRR) community has developed effective techniques for modeling and reasoning about actions and similar techniques are used in this work. A system consisting of Inductive Logic Programming (ILP) and Answer Set Programming (ASP) is used to address the challenge and achieves close to state-of-the-art results and provides an explainable model. An existing semantic role label parser is modified and used to parse the dataset.
On analysis of the learnt model, it was found that some of the rules were not generic enough. To overcome the issue, the Proposition Bank dataset is then used to add knowledge in an attempt to generalize the ILP learnt rules to possibly improve the results.
ContributorsBhattacharjee, Aurgho (Author) / Baral, Chitta (Thesis advisor) / Yang, Yezhou (Committee member) / Anwar, Saadat (Committee member) / Arizona State University (Publisher)
Created2019
Description
Information Retrieval (IR) is the task of obtaining pieces of data (such as documents or snippets of text) that are relevant to a particular query or need from a large repository of information. IR is a valuable component of several downstream Natural Language Processing (NLP) tasks, such as Question Answering. Practically, IR is at the heart of many widely-used technologies like search engines.
While probabilistic ranking functions, such as the Okapi BM25 function, have been utilized in IR systems since the 1970's, modern neural approaches pose certain advantages compared to their classical counterparts. In particular, the release of BERT (Bidirectional Encoder Representations from Transformers) has had a significant impact in the NLP community by demonstrating how the use of a Masked Language Model (MLM) trained on a considerable corpus of data can improve a variety of downstream NLP tasks, including sentence classification and passage re-ranking.
IR Systems are also important in the biomedical and clinical domains. Given the continuously-increasing amount of scientific literature across biomedical domain, the ability find answers to specific clinical queries from a repository of millions of articles is a matter of practical value to medics, doctors, and other medical professionals. Moreover, there are domain-specific challenges present in the biomedical domain, including handling clinical jargon and evaluating the similarity or relatedness of various medical symptoms when determining the relevance between a query and a sentence.
This work presents contributions to several aspects of the Biomedical Semantic Information Retrieval domain. First, it introduces Multi-Perspective Sentence Relevance, a novel methodology of utilizing BERT-based models for contextual IR. The system is evaluated using the BioASQ Biomedical IR Challenge. Finally, practical contributions in the form of a live IR system for medics and a proposed challenge on the Living Systematic Review clinical task are provided.
While probabilistic ranking functions, such as the Okapi BM25 function, have been utilized in IR systems since the 1970's, modern neural approaches pose certain advantages compared to their classical counterparts. In particular, the release of BERT (Bidirectional Encoder Representations from Transformers) has had a significant impact in the NLP community by demonstrating how the use of a Masked Language Model (MLM) trained on a considerable corpus of data can improve a variety of downstream NLP tasks, including sentence classification and passage re-ranking.
IR Systems are also important in the biomedical and clinical domains. Given the continuously-increasing amount of scientific literature across biomedical domain, the ability find answers to specific clinical queries from a repository of millions of articles is a matter of practical value to medics, doctors, and other medical professionals. Moreover, there are domain-specific challenges present in the biomedical domain, including handling clinical jargon and evaluating the similarity or relatedness of various medical symptoms when determining the relevance between a query and a sentence.
This work presents contributions to several aspects of the Biomedical Semantic Information Retrieval domain. First, it introduces Multi-Perspective Sentence Relevance, a novel methodology of utilizing BERT-based models for contextual IR. The system is evaluated using the BioASQ Biomedical IR Challenge. Finally, practical contributions in the form of a live IR system for medics and a proposed challenge on the Living Systematic Review clinical task are provided.
ContributorsRawal, Samarth (Author) / Baral, Chitta (Thesis advisor) / Devarakonda, Murthy (Committee member) / Anwar, Saadat (Committee member) / Arizona State University (Publisher)
Created2020