Chong Peng

Xinxing Wu, Chong Peng, Peter T. Nelson et al.

Alzheimer's disease (AD), as a progressive brain disease, affects cognition, memory, and behavior. Similarly, limbic-predominant age-related TDP-43 encephalopathy (LATE) is a recently defined common neurodegenerative disease that mimics the clinical symptoms of AD. At present, the risk factors implicated in LATE and those distinguishing LATE from AD are largely unknown. We leveraged an integrated feature selection-based algorithmic approach, to identify important factors differentiating subjects with LATE and/or AD from Control on significantly imbalanced data. We analyzed two datasets ROSMAP and NACC and discovered that alcohol consumption was a top lifestyle and environmental factor linked with LATE and AD and their associations were differential. In particular, we identified a specific subpopulation consisting of APOE e4 carriers. We found that, for this subpopulation, light-to-moderate alcohol intake was a protective factor against both AD and LATE, but its protective role against AD appeared stronger than LATE. The codes for our algorithms are available at https://github.com/xinxingwu-uk/PFV.

Chenglizhao Chen, Hengsen Wang, Yuming Fang et al.

The existing state-of-the-art (SOTA) video salient object detection (VSOD) models have widely followed short-term methodology, which dynamically determines the balance between spatial and temporal saliency fusion by solely considering the current consecutive limited frames. However, the short-term methodology has one critical limitation, which conflicts with the real mechanism of our visual system -- a typical long-term methodology. As a result, failure cases keep showing up in the results of the current SOTA models, and the short-term methodology becomes the major technical bottleneck. To solve this problem, this paper proposes a novel VSOD approach, which performs VSOD in a complete long-term way. Our approach converts the sequential VSOD, a sequential task, to a data mining problem, i.e., decomposing the input video sequence to object proposals in advance and then mining salient object proposals as much as possible in an easy-to-hard way. Since all object proposals are simultaneously available, the proposed approach is a complete long-term approach, which can alleviate some difficulties rooted in conventional short-term approaches. In addition, we devised an online updating scheme that can grasp the most representative and trustworthy pattern profile of the salient objects, outputting framewise saliency maps with rich details and smoothing both spatially and temporally. The proposed approach outperforms almost all SOTA models on five widely used benchmark datasets.

Xinxing 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.

Chong 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.

Xinxing Wu, Chong Peng, Richard Charnigo et al.

Interpreting critical variables involved in complex biological processes related to survival time can help understand prediction from survival models, evaluate treatment efficacy, and develop new therapies for patients. Currently, the predictive results of deep learning (DL)-based models are better than or as good as standard survival methods, they are often disregarded because of their lack of transparency and little interpretability, which is crucial to their adoption in clinical applications. In this paper, we introduce a novel, easily deployable approach, called EXplainable CEnsored Learning (EXCEL), to iteratively exploit critical variables and simultaneously implement (DL) model training based on these variables. First, on a toy dataset, we illustrate the principle of EXCEL; then, we mathematically analyze our proposed method, and we derive and prove tight generalization error bounds; next, on two semi-synthetic datasets, we show that EXCEL has good anti-noise ability and stability; finally, we apply EXCEL to a variety of real-world survival datasets including clinical data and genetic data, demonstrating that EXCEL can effectively identify critical features and achieve performance on par with or better than the original models. It is worth pointing out that EXCEL is flexibly deployed in existing or emerging models for explainable survival data in the presence of right censoring.