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Browsing by Author "He, Yicheng"
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Item Drug Selection via Joint Push and Learning to Rank(IEEE, 2018-06) He, Yicheng; Liu, Junfeng; Ning, Xia; Medical and Molecular Genetics, School of MedicineSelecting the right drugs for the right patients is a primary goal of precision medicine. In this manuscript, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1). the ranking positions of sensitive drugs and 2). the ranking orders among sensitive drugs in cancer cell lines based on their responses to cancer drugs. We have developed a new learning-to-rank method, denoted as pLETORg, that predicts drug ranking structures in each cell line via using drug latent vectors and cell line latent vectors. The pLETORg method learns such latent vectors through explicitly enforcing that, in the drug ranking list of each cell line, the sensitive drugs are pushed above insensitive drugs, and meanwhile the ranking orders among sensitive drugs are correct. Genomics information on cell lines is leveraged in learning the latent vectors. Our experimental results on a benchmark cell line-drug response dataset demonstrate that the new pLETORg significantly outperforms the state-of-the-art method in prioritizing new sensitive drugs.Item Simplicity of Kmeans versus Deepness of Deep Learning: A Case of Unsupervised Feature Learning with Limited Data(IEEE, 2015-12) Dundar, Murat; Kou, Qiang; Zhang, Baichuan; He, Yicheng; Rajwa, Bartek; Department of Computer and Information Sciences, School of ScienceWe study a bio-detection application as a case study to demonstrate that Kmeans -- based unsupervised feature learning can be a simple yet effective alternative to deep learning techniques for small data sets with limited intra-as well as inter-class diversity. We investigate the effect on the classifier performance of data augmentation as well as feature extraction with multiple patch sizes and at different image scales. Our data set includes 1833 images from four different classes of bacteria, each bacterial culture captured at three different wavelengths and overall data collected during a three-day period. The limited number and diversity of images present, potential random effects across multiple days, and the multi-mode nature of class distributions pose a challenging setting for representation learning. Using images collected on the first day for training, on the second day for validation, and on the third day for testing Kmeans -- based representation learning achieves 97% classification accuracy on the test data. This compares very favorably to 56% accuracy achieved by deep learning and 74% accuracy achieved by handcrafted features. Our results suggest that data augmentation or dropping connections between units offers little help for deep-learning algorithms, whereas significant boost can be achieved by Kmeans -- based representation learning by augmenting data and by concatenating features obtained at multiple patch sizes or image scales.