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Machine learning

University of Kentucky

Genetics and Genomics

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Full-Text Articles in Physical Sciences and Mathematics

Recurrent Neural Networks And Their Applications To Rna Secondary Structure Inference, Devin Willmott Jan 2018

Recurrent Neural Networks And Their Applications To Rna Secondary Structure Inference, Devin Willmott

Theses and Dissertations--Mathematics

Recurrent neural networks (RNNs) are state of the art sequential machine learning tools, but have difficulty learning sequences with long-range dependencies due to the exponential growth or decay of gradients backpropagated through the RNN. Some methods overcome this problem by modifying the standard RNN architecure to force the recurrent weight matrix W to remain orthogonal throughout training. The first half of this thesis presents a novel orthogonal RNN architecture that enforces orthogonality of W by parametrizing with a skew-symmetric matrix via the Cayley transform. We present rules for backpropagation through the Cayley transform, show how to deal with the Cayley …

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Identification Of Prognostic Genes And Gene Sets For Early-Stage Non-Small Cell Lung Cancer Using Bi-Level Selection Methods, Suyan Tian, Chi Wang, Howard H. Chang, Jianguo Sun Apr 2017

Identification Of Prognostic Genes And Gene Sets For Early-Stage Non-Small Cell Lung Cancer Using Bi-Level Selection Methods, Suyan Tian, Chi Wang, Howard H. Chang, Jianguo Sun

Biostatistics Faculty Publications

In contrast to feature selection and gene set analysis, bi-level selection is a process of selecting not only important gene sets but also important genes within those gene sets. Depending on the order of selections, a bi-level selection method can be classified into three categories – forward selection, which first selects relevant gene sets followed by the selection of relevant individual genes; backward selection which takes the reversed order; and simultaneous selection, which performs the two tasks simultaneously usually with the aids of a penalized regression model. To test the existence of subtype-specific prognostic genes for non-small cell lung cancer …

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