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Leonard McMillan

Publications and source records attributed to Leonard McMillan.

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A Novel Deep Learning Architecture for Testis Histology Image Classification

Unlike other histology analysis, classification of tubule status in testis histology is very challenging due to their high similarity of texture and shape. Traditional deep learning networks have difficulties to capture nuance details among different tubule categories. In this paper, we propose a novel deep learning architecture for feature learning, image classification, and image reconstruction. It is based on stacked auto-encoders with an additional layer, called a hyperlayer, which is created to capture features of an image at different layers in the network. This addition effectively combines features at different scales and thus provides a more complete profile for further classification. Evaluation is performed on a set of 10,542 tubule image patches. We demonstrate our approach with two experiments on two different subsets of the dataset. The results show that the features learned from our architecture achieve more than 98% accuracy and represent an improvement over traditional deep network architectures.

cs.CV

IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity

We have developed a statistical method named IsoDOT to assess differential isoform expression (DIE) and differential isoform usage (DIU) using RNA-seq data. Here isoform usage refers to relative isoform expression given the total expression of the corresponding gene. IsoDOT performs two tasks that cannot be accomplished by existing methods: to test DIE/DIU with respect to a continuous covariate, and to test DIE/DIU for one case versus one control. The latter task is not an uncommon situation in practice, e.g., comparing paternal and maternal allele of one individual or comparing tumor and normal sample of one cancer patient. Simulation studies demonstrate the high sensitivity and specificity of IsoDOT. We apply IsoDOT to study the effects of haloperidol treatment on mouse transcriptome and identify a group of genes whose isoform usages respond to haloperidol treatment.

stat.AP