PRIME: Uncovering Circadian Oscillation Patterns and Associations with AD in Untimed Genome-wide Gene Expression across Multiple Brain RegionsXinxing Wu, Chong Peng, Gregory Jicha et al.
The disruption of circadian rhythm is a cardinal symptom for Alzheimer's disease (AD) patients. The full circadian rhythm orchestration of gene expression in the human brain and its inherent associations with AD remain largely unknown. We present a novel comprehensive approach, PRIME, to detect and analyze rhythmic oscillation patterns in untimed high-dimensional gene expression data across multiple datasets. To demonstrate the utility of PRIME, firstly, we validate it by a time course expression dataset from mouse liver as a cross-species and cross-organ validation. Then, we apply it to study oscillation patterns in untimed genome-wide gene expression from 19 human brain regions of controls and AD patients. Our findings reveal clear, synchronized oscillation patterns in 15 pairs of brain regions of control, while these oscillation patterns either disappear or dim for AD. It is worth noting that PRIME discovers the circadian rhythmic patterns without requiring the sample's timestamps. The codes for PRIME, along with codes to reproduce the figures in this paper, are available at https://github.com/xinxingwu-uk/PRIME.
5.8LGApr 22, 2022
Log-based Sparse Nonnegative Matrix Factorization for Data RepresentationChong Peng, Yiqun Zhang, Yongyong Chen et al.
Nonnegative matrix factorization (NMF) has been widely studied in recent years due to its effectiveness in representing nonnegative data with parts-based representations. For NMF, a sparser solution implies better parts-based representation.However, current NMF methods do not always generate sparse solutions.In this paper, we propose a new NMF method with log-norm imposed on the factor matrices to enhance the sparseness.Moreover, we propose a novel column-wisely sparse norm, named $\ell_{2,\log}$-(pseudo) norm to enhance the robustness of the proposed method.The $\ell_{2,\log}$-(pseudo) norm is invariant, continuous, and differentiable.For the $\ell_{2,\log}$ regularized shrinkage problem, we derive a closed-form solution, which can be used for other general problems.Efficient multiplicative updating rules are developed for the optimization, which theoretically guarantees the convergence of the objective value sequence.Extensive experimental results confirm the effectiveness of the proposed method, as well as the enhanced sparseness and robustness.