Deep Learning for Enhancing Precision Medicine

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dc.contributor.authorOh, Minen
dc.contributor.committeechairZhang, Liqingen
dc.contributor.committeememberYoon, Young Meeen
dc.contributor.committeememberPrakash, B. Adityaen
dc.contributor.committeememberHuang, Berten
dc.contributor.committeememberSheng, Zhien
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2021-06-08T08:00:21Zen
dc.date.available2021-06-08T08:00:21Zen
dc.date.issued2021-06-07en
dc.description.abstractMost medical treatments have been developed aiming at the best-on-average efficacy for large populations, resulting in treatments successful for some patients but not for others. It necessitates the need for precision medicine that tailors medical treatment to individual patients. Omics data holds comprehensive genetic information on individual variability at the molecular level and hence the potential to be translated into personalized therapy. However, the attempts to transform omics data-driven insights into clinically actionable models for individual patients have been limited. Meanwhile, advances in deep learning, one of the most promising branches of artificial intelligence, have produced unprecedented performance in various fields. Although several deep learning-based methods have been proposed to predict individual phenotypes, they have not established the state of the practice, due to instability of selected or learned features derived from extremely high dimensional data with low sample sizes, which often results in overfitted models with high variance. To overcome the limitation of omics data, recent advances in deep learning models, including representation learning models, generative models, and interpretable models, can be considered. The goal of the proposed work is to develop deep learning models that can overcome the limitation of omics data to enhance the prediction of personalized medical decisions. To achieve this, three key challenges should be addressed: 1) effectively reducing dimensions of omics data, 2) systematically augmenting omics data, and 3) improving the interpretability of omics data.en
dc.description.abstractgeneralMost medical treatments have been developed aiming at the best-on-average efficacy for large populations, resulting in treatments successful for some patients but not for others. It necessitates the need for precision medicine that tailors medical treatment to individual patients. Biological data such as DNA sequences and snapshots of genetic activities hold comprehensive information on individual variability and hence the potential to accelerate personalized therapy. However, the attempts to transform data-driven insights into clinical models for individual patients have been limited. Meanwhile, advances in deep learning, one of the most promising branches of artificial intelligence, have produced unprecedented performance in various fields. Although several deep learning-based methods have been proposed to predict individual treatment or outcome, they have not established the state of the practice, due to the complexity of biological data and limited availability, which often result in overfitted models that may work on training data but not on test data or unseen data. To overcome the limitation of biological data, recent advances in deep learning models, including representation learning models, generative models, and interpretable models, can be considered. The goal of the proposed work is to develop deep learning models that can overcome the limitation of omics data to enhance the prediction of personalized medical decisions. To achieve this, three key challenges should be addressed: 1) effectively reducing the complexity of biological data, 2) generating realistic biological data, and 3) improving the interpretability of biological data.en
dc.description.degreeDoctor of Philosophyen
dc.format.mediumETDen
dc.identifier.othervt_gsexam:31167en
dc.identifier.urihttp://hdl.handle.net/10919/103688en
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectDeep learning (Machine learning)en
dc.subjectPrecision Medicineen
dc.subjectOmics dataen
dc.titleDeep Learning for Enhancing Precision Medicineen
dc.typeDissertationen
thesis.degree.disciplineComputer Science and Applicationsen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.nameDoctor of Philosophyen

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