Xiaohui Yao

Shan Cong, Zhiling Sang, Hongwei Liu et al.

The distinct characteristics of multiomics data, including complex interactions within and across biological layers and disease heterogeneity (e.g., heterogeneity in etiology and clinical symptoms), drive us to develop novel designs to address unique challenges in multiomics prediction. In this paper, we propose the multi-view knowledge transfer learning (MVKTrans) framework, which transfers intra- and inter-omics knowledge in an adaptive manner by reviewing data heterogeneity and suppressing bias transfer, thereby enhancing classification performance. Specifically, we design a graph contrastive module that is trained on unlabeled data to effectively learn and transfer the underlying intra-omics patterns to the supervised task. This unsupervised pretraining promotes learning general and unbiased representations for each modality, regardless of the downstream tasks. In light of the varying discriminative capacities of modalities across different diseases and/or samples, we introduce an adaptive and bi-directional cross-omics distillation module. This module automatically identifies richer modalities and facilitates dynamic knowledge transfer from more informative to less informative omics, thereby enabling a more robust and generalized integration. Extensive experiments on four real biomedical datasets demonstrate the superior performance and robustness of MVKTrans compared to the state-of-the-art. Code and data are available at https://github.com/Yaolab-fantastic/MVKTrans.

Shan Cong, Zhoujie Fan, Hongwei Liu et al.

Brain transcriptomics provides insights into the molecular mechanisms by which the brain coordinates its functions and processes. However, existing multimodal methods for predicting Alzheimer's disease (AD) primarily rely on imaging and sometimes genetic data, often neglecting the transcriptomic basis of brain. Furthermore, while striving to integrate complementary information between modalities, most studies overlook the informativeness disparities between modalities. Here, we propose TMM, a trusted multiview multimodal graph attention framework for AD diagnosis, using extensive brain-wide transcriptomics and imaging data. First, we construct view-specific brain regional co-function networks (RRIs) from transcriptomics and multimodal radiomics data to incorporate interaction information from both biomolecular and imaging perspectives. Next, we apply graph attention (GAT) processing to each RRI network to produce graph embeddings and employ cross-modal attention to fuse transcriptomics-derived embedding with each imagingderived embedding. Finally, a novel true-false-harmonized class probability (TFCP) strategy is designed to assess and adaptively adjust the prediction confidence of each modality for AD diagnosis. We evaluate TMM using the AHBA database with brain-wide transcriptomics data and the ADNI database with three imaging modalities (AV45-PET, FDG-PET, and VBM-MRI). The results demonstrate the superiority of our method in identifying AD, EMCI, and LMCI compared to state-of-the-arts. Code and data are available at https://github.com/Yaolab-fantastic/TMM.

Bo Peng, Xiaohui Yao, Shannon L. Risacher et al.

Background:Cognitive assessments represent the most common clinical routine for the diagnosis of Alzheimer's Disease (AD). Given a large number of cognitive assessment tools and time-limited office visits, it is important to determine a proper set of cognitive tests for different subjects. Most current studies create guidelines of cognitive test selection for a targeted population, but they are not customized for each individual subject. In this manuscript, we develop a machine learning paradigm enabling personalized cognitive assessments prioritization. Method: We adapt a newly developed learning-to-rank approach PLTR to implement our paradigm. This method learns the latent scoring function that pushes the most effective cognitive assessments onto the top of the prioritization list. We also extend PLTR to better separate the most effective cognitive assessments and the less effective ones. Results: Our empirical study on the ADNI data shows that the proposed paradigm outperforms the state-of-the-art baselines on identifying and prioritizing individual-specific cognitive biomarkers. We conduct experiments in cross validation and level-out validation settings. In the two settings, our paradigm significantly outperforms the best baselines with improvement as much as 22.1% and 19.7%, respectively, on prioritizing cognitive features. Conclusions: The proposed paradigm achieves superior performance on prioritizing cognitive biomarkers. The cognitive biomarkers prioritized on top have great potentials to facilitate personalized diagnosis, disease subtyping, and ultimately precision medicine in AD.