Matching Items (6)
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- All Subjects: Evaluation
- Creators: Baral, Chitta
- Creators: Armfield, Jessica Ann
- Status: Published
Description
Biological systems are complex in many dimensions as endless transportation and communication networks all function simultaneously. Our ability to intervene within both healthy and diseased systems is tied directly to our ability to understand and model core functionality. The progress in increasingly accurate and thorough high-throughput measurement technologies has provided a deluge of data from which we may attempt to infer a representation of the true genetic regulatory system. A gene regulatory network model, if accurate enough, may allow us to perform hypothesis testing in the form of computational experiments. Of great importance to modeling accuracy is the acknowledgment of biological contexts within the models -- i.e. recognizing the heterogeneous nature of the true biological system and the data it generates. This marriage of engineering, mathematics and computer science with systems biology creates a cycle of progress between computer simulation and lab experimentation, rapidly translating interventions and treatments for patients from the bench to the bedside. This dissertation will first discuss the landscape for modeling the biological system, explore the identification of targets for intervention in Boolean network models of biological interactions, and explore context specificity both in new graphical depictions of models embodying context-specific genomic regulation and in novel analysis approaches designed to reveal embedded contextual information. Overall, the dissertation will explore a spectrum of biological modeling with a goal towards therapeutic intervention, with both formal and informal notions of biological context, in such a way that will enable future work to have an even greater impact in terms of direct patient benefit on an individualized level.
ContributorsVerdicchio, Michael (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Stolovitzky, Gustavo (Committee member) / Collofello, James (Committee member) / Arizona State University (Publisher)
Created2013
Description
Reverse engineering gene regulatory networks (GRNs) is an important problem in the domain of Systems Biology. Learning GRNs is challenging due to the inherent complexity of the real regulatory networks and the heterogeneity of samples in available biomedical data. Real world biological data are commonly collected from broad surveys (profiling studies) and aggregate highly heterogeneous biological samples. Popular methods to learn GRNs simplistically assume a single universal regulatory network corresponding to available data. They neglect regulatory network adaptation due to change in underlying conditions and cellular phenotype or both. This dissertation presents a novel computational framework to learn common regulatory interactions and networks underlying the different sets of relatively homogeneous samples from real world biological data. The characteristic set of samples/conditions and corresponding regulatory interactions defines the cellular context (context). Context, in this dissertation, represents the deterministic transcriptional activity within the specific cellular regulatory mechanism. The major contributions of this framework include - modeling and learning context specific GRNs; associating enriched samples with contexts to interpret contextual interactions using biological knowledge; pruning extraneous edges from the context-specific GRN to improve the precision of the final GRNs; integrating multisource data to learn inter and intra domain interactions and increase confidence in obtained GRNs; and finally, learning combinatorial conditioning factors from the data to identify regulatory cofactors. The framework, Expattern, was applied to both real world and synthetic data. Interesting insights were obtained into mechanism of action of drugs on analysis of NCI60 drug activity and gene expression data. Application to refractory cancer data and Glioblastoma multiforme yield GRNs that were readily annotated with context-specific phenotypic information. Refractory cancer GRNs also displayed associations between distinct cancers, not observed through only clustering. Performance comparisons on multi-context synthetic data show the framework Expattern performs better than other comparable methods.
ContributorsSen, Ina (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Bittner, Michael (Committee member) / Konjevod, Goran (Committee member) / Arizona State University (Publisher)
Created2011
Description
There is a serious need for early childhood intervention practices for children who are living at or below the poverty line. Since 1965 Head Start has provided a federally funded, free preschool program for children in this population. The City of Phoenix Head Start program consists of nine delegate agencies, seven of which reside in school districts. These agencies are currently not conducting local longitudinal evaluations of their preschool graduates. The purpose of this study was to recommend initial steps the City of Phoenix grantee and the delegate agencies can take to begin a longitudinal evaluation process of their Head Start programs. Seven City of Phoenix Head Start agency directors were interviewed. These interviews provided information about the attitudes of the directors when considering longitudinal evaluations and how Head Start already evaluates their programs through internal assessments. The researcher also took notes on the Third Grade Follow-Up to the Head Start Executive Summary in order to make recommendations to the City of Phoenix Head Start programs about the best practices for longitudinal student evaluations.
ContributorsArmfield, Jessica Ann (Author) / Duggan, Mary Anne (Thesis director) / Dumka, Larry (Committee member) / Barrett, The Honors College (Contributor) / T. Denny Sanford School of Social and Family Dynamics (Contributor) / School of International Letters and Cultures (Contributor)
Created2014-05
Description
Science instructors need questions for use in exams, homework assignments, class discussions, reviews, and other instructional activities. Textbooks never have enough questions, so instructors must find them from other sources or generate their own questions. In order to supply instructors with biology questions, a semantic network approach was developed for generating open response biology questions. The generated questions were compared to professional authorized questions.
To boost students’ learning experience, adaptive selection was built on the generated questions. Bayesian Knowledge Tracing was used as embedded assessment of the student’s current competence so that a suitable question could be selected based on the student’s previous performance. A between-subjects experiment with 42 participants was performed, where half of the participants studied with adaptive selected questions and the rest studied with mal-adaptive order of questions. Both groups significantly improved their test scores, and the participants in adaptive group registered larger learning gains than participants in the control group.
To explore the possibility of generating rich instructional feedback for machine-generated questions, a question-paragraph mapping task was identified. Given a set of questions and a list of paragraphs for a textbook, the goal of the task was to map the related paragraphs to each question. An algorithm was developed whose performance was comparable to human annotators.
A multiple-choice question with high quality distractors (incorrect answers) can be pedagogically valuable as well as being much easier to grade than open-response questions. Thus, an algorithm was developed to generate good distractors for multiple-choice questions. The machine-generated multiple-choice questions were compared to human-generated questions in terms of three measures: question difficulty, question discrimination and distractor usefulness. By recruiting 200 participants from Amazon Mechanical Turk, it turned out that the two types of questions performed very closely on all the three measures.
To boost students’ learning experience, adaptive selection was built on the generated questions. Bayesian Knowledge Tracing was used as embedded assessment of the student’s current competence so that a suitable question could be selected based on the student’s previous performance. A between-subjects experiment with 42 participants was performed, where half of the participants studied with adaptive selected questions and the rest studied with mal-adaptive order of questions. Both groups significantly improved their test scores, and the participants in adaptive group registered larger learning gains than participants in the control group.
To explore the possibility of generating rich instructional feedback for machine-generated questions, a question-paragraph mapping task was identified. Given a set of questions and a list of paragraphs for a textbook, the goal of the task was to map the related paragraphs to each question. An algorithm was developed whose performance was comparable to human annotators.
A multiple-choice question with high quality distractors (incorrect answers) can be pedagogically valuable as well as being much easier to grade than open-response questions. Thus, an algorithm was developed to generate good distractors for multiple-choice questions. The machine-generated multiple-choice questions were compared to human-generated questions in terms of three measures: question difficulty, question discrimination and distractor usefulness. By recruiting 200 participants from Amazon Mechanical Turk, it turned out that the two types of questions performed very closely on all the three measures.
ContributorsZhang, Lishang (Author) / VanLehn, Kurt (Thesis advisor) / Baral, Chitta (Committee member) / Hsiao, Ihan (Committee member) / Wright, Christian (Committee member) / Arizona State University (Publisher)
Created2015
Description
In natural language processing, language models have achieved remarkable success over the last few years. The Transformers are at the core of most of these models. Their success can be mainly attributed to an enormous amount of curated data they are trained on. Even though such language models are trained on massive curated data, they often need specific extracted knowledge to understand better and reason. This is because often relevant knowledge may be implicit or missing, which hampers machine reasoning. Apart from that, manual knowledge curation is time-consuming and erroneous. Hence, finding fast and effective methods to extract such knowledge from data is important for improving language models. This leads to finding ideal ways to utilize such knowledge by incorporating them into language models. Successful knowledge extraction and integration lead to an important question of knowledge evaluation of such models by developing tools or introducing challenging test suites to learn about their limitations and improve them further. So to improve the transformer-based models, understanding the role of knowledge becomes important. In the pursuit to improve language models with knowledge, in this dissertation I study three broad research directions spanning across the natural language, biomedical and cybersecurity domains: (1) Knowledge Extraction (KX) - How can transformer-based language models be leveraged to extract knowledge from data? (2) Knowledge Integration (KI) - How can such specific knowledge be used to improve such models? (3) Knowledge Evaluation (KE) - How can language models be evaluated for specific skills and understand their limitations?
I propose methods to extract explicit textual, implicit structural, missing textual, and missing structural knowledge from natural language and binary programs using transformer-based language models. I develop ways to improve the language model’s multi-step and commonsense reasoning abilities using external knowledge. Finally, I develop challenging datasets which assess their numerical reasoning skills in both in-domain and out-of-domain settings.
ContributorsPal, Kuntal Kumar (Author) / Baral, Chitta (Thesis advisor) / Wang, Ruoyu (Committee member) / Blanco, Eduardo (Committee member) / Yang, Yezhou (Committee member) / Arizona State University (Publisher)
Created2023
Description
As we migrate into an era of personalized medicine, understanding how bio-molecules interact with one another to form cellular systems is one of the key focus areas of systems biology. Several challenges such as the dynamic nature of cellular systems, uncertainty due to environmental influences, and the heterogeneity between individual patients render this a difficult task. In the last decade, several algorithms have been proposed to elucidate cellular systems from data, resulting in numerous data-driven hypotheses. However, due to the large number of variables involved in the process, many of which are unknown or not measurable, such computational approaches often lead to a high proportion of false positives. This renders interpretation of the data-driven hypotheses extremely difficult. Consequently, a dismal proportion of these hypotheses are subject to further experimental validation, eventually limiting their potential to augment existing biological knowledge. This dissertation develops a framework of computational methods for the analysis of such data-driven hypotheses leveraging existing biological knowledge. Specifically, I show how biological knowledge can be mapped onto these hypotheses and subsequently augmented through novel hypotheses. Biological hypotheses are learnt in three levels of abstraction -- individual interactions, functional modules and relationships between pathways, corresponding to three complementary aspects of biological systems. The computational methods developed in this dissertation are applied to high throughput cancer data, resulting in novel hypotheses with potentially significant biological impact.
ContributorsRamesh, Archana (Author) / Kim, Seungchan (Thesis advisor) / Langley, Patrick W (Committee member) / Baral, Chitta (Committee member) / Kiefer, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2012