ArticleForestry research2021
HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression.
Article in Forestry research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization.NAR genomics and bioinformatics · 2023Article
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5 authors.
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Abstract
Gene expression data features high dimensionality, multicollinearity, and non-Gaussian distribution noise, posing hurdles for identification of true regulatory genes controlling a biological process or pathway. In this study, we integrated the Huber loss function and the Berhu penalty (HB) into partial least squares (PLS) framework to deal with the high dimension and multicollinearity property of gene expression data, and developed a new method called HB-PLS regression to model the relationships between regulatory genes and pathway genes. To solve the Huber-Berhu optimization problem, an accelerated proximal gradient descent algorithm with at least 10 times faster than the general convex optimization solver (CVX), was developed. Application of HB-PLS to recognize pathway regulators of lignin biosynthesis and photosynthesis in
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