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- All Subjects: Machine Learning
- All Subjects: Question Answering
- Resource Type: Text
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
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
One of the measures to determine the intelligence of a system is through Question Answering, as it requires a system to comprehend a question and reason using its knowledge base to accurately answer it. Qualitative word problems are an important subset of such problems, as they require a system to recognize and reason with qualitative knowledge expressed in natural language. Traditional approaches in this domain include multiple modules to parse a given problem and to perform the required reasoning. Recent approaches involve using large pre-trained Language models like the Bidirection Encoder Representations from Transformers for downstream question answering tasks through supervision. These approaches however either suffer from errors between multiple modules, or are not interpretable with respect to the reasoning process employed. The proposed solution in this work aims to overcome these drawbacks through a single end-to-end trainable model that performs both the required parsing and reasoning. The parsing is achieved through an attention mechanism, whereas the reasoning is performed in vector space using soft logic operations. The model also enforces constraints in the form of auxiliary loss terms to increase the interpretability of the underlying reasoning process. The work achieves state of the art accuracy on the QuaRel dataset and matches that of the QuaRTz dataset with additional interpretability.
ContributorsNarayana, Sanjay (Author) / Baral, Chitta (Thesis advisor) / Mitra, Arindam (Committee member) / Anwar, Saadat (Committee member) / Arizona State University (Publisher)
Created2020