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  1. Abstract Spatially resolved transcriptomics technologies enable the measurement of transcriptome information while retaining the spatial context at the regional, cellular or sub-cellular level. While previous computational methods have relied on gene expression information alone for clustering single-cell populations, more recent methods have begun to leverage spatial location and histology information to improve cell clustering and cell-type identification. In this study, using seven semi-synthetic datasets with real spatial locations, simulated gene expression and histology images as well as ground truth cell-type labels, we evaluate 15 clustering methods based on clustering accuracy, robustness to data variation and input parameters, computational efficiency, and software usability. Our analysis demonstrates that even though incorporating the additional spatial and histology information leads to increased accuracy in some datasets, it does not consistently improve clustering compared with using only gene expression data. Our results indicate that for the clustering of spatial transcriptomics data, there are still opportunities to enhance the overall accuracy and robustness by improving information extraction and feature selection from spatial and histology data.
    Free, publicly-accessible full text available January 1, 2024
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  5. Recent advances in precision manufacturing technology and a thorough understanding of the properties of piezoelectric materials have made it possible for researchers to develop innovative microrobotic systems, which draw more attention to the challenges of utilizing microrobots in areas that are inaccessible to ordinary robots. This review paper provides an overview of the recent advances in the application of piezoelectric materials in microrobots. The challenges of microrobots in the direction of autonomy are categorized into four sections: mechanisms, power, sensing, and control. In each section, innovative research ideas are presented to inspire researchers in their prospective microrobot designs according to specific applications. Novel mechanisms for the mobility of piezoelectric microrobots are reviewed and described. Additionally, as the piezoelectric micro-actuators require high-voltage electronics and onboard power supplies, we review ways of energy harvesting technology and lightweight micro-sensing mechanisms that contain piezoelectric devices to provide feedback, facilitating the use of control strategies to achieve the autonomous untethered movement of microrobots.
    Free, publicly-accessible full text available September 1, 2023
  6. Multi-label image recognition has been an indispensable fundamental component for many real computer vision applications. However, a severe threat of privacy leakage in multi-label image recognition has been overlooked by existing studies. To fill this gap, two privacy-preserving models, Privacy-Preserving Multi-label Graph Convolutional Networks (P2-ML-GCN) and Robust P2-ML-GCN (RP2-ML-GCN), are developed in this article, where differential privacy mechanism is implemented on the model’s outputs so as to defend black-box attack and avoid large aggregated noise simultaneously. In particular, a regularization term is exploited in the loss function of RP2-ML-GCN to increase the model prediction accuracy and robustness. After that, a proper differential privacy mechanism is designed with the intention of decreasing the bias of loss function in P2-ML-GCN and increasing prediction accuracy. Besides, we analyze that a bounded global sensitivity can mitigate excessive noise’s side effect and obtain a performance improvement for multi-label image recognition in our models. Theoretical proof shows that our two models can guarantee differential privacy for model’s outputs, weights and input features while preserving model robustness. Finally, comprehensive experiments are conducted to validate the advantages of our proposed models, including the implementation of differential privacy on model’s outputs, the incorporation of regularization term into loss function,more »and the adoption of bounded global sensitivity for multi-label image recognition.« less
    Free, publicly-accessible full text available August 31, 2023
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  10. Abstract Background

    Estimating and accounting for hidden variables is widely practiced as an important step in molecular quantitative trait locus (molecular QTL, henceforth “QTL”) analysis for improving the power of QTL identification. However, few benchmark studies have been performed to evaluate the efficacy of the various methods developed for this purpose.


    Here we benchmark popular hidden variable inference methods including surrogate variable analysis (SVA), probabilistic estimation of expression residuals (PEER), and hidden covariates with prior (HCP) against principal component analysis (PCA)—a well-established dimension reduction and factor discovery method—via 362 synthetic and 110 real data sets. We show that PCA not only underlies the statistical methodology behind the popular methods but is also orders of magnitude faster, better-performing, and much easier to interpret and use.


    To help researchers use PCA in their QTL analysis, we provide an R package along with a detailed guide, both of which are freely available at We believe that using PCA rather than SVA, PEER, or HCP will substantially improve and simplify hidden variable inference in QTL mapping as well as increase the transparency and reproducibility of QTL research.