Hoseung Song

Batch effects in microbiome data arise from differential processing of specimens and can lead to spurious findings and obscure true signals. Strategies designed for genomic data to mitigate batch effects usually fail to address the zero-inflated and over-dispersed microbiome data. Most strategies tailored for microbiome data are restricted to association testing or specialized study designs, failing to allow other analytic goals or general designs. Here, we develop the Conditional Quantile Regre

Summary A nonparametric framework for changepoint detection, based on scan statistics utilizing graphs that represent similarities among observations, is gaining attention owing to its flexibility and good performance for high-dimensional and non-Euclidean data sequences. However, this graph-based framework faces challenges when there are repeated observations in the sequence, which is often the case for discrete data such as network data. In this article we extend the graph-based framework to s

Summary Kernel two-sample tests have been widely used for multivariate data to test equality of distributions. However, existing tests based on mapping distributions into a reproducing kernel Hilbert space mainly target specific alternatives and do not work well for some scenarios when the dimension of the data is moderate to high due to the curse of dimensionality. We propose a new test statistic that makes use of a common pattern under moderate and high dimensions and achieves substantial powe

BACKGROUND: Microbial communities are known to be closely related to many diseases, such as obesity and HIV, and it is of interest to identify differentially abundant microbial species between two or more environments. Since the abundances or counts of microbial species usually have different scales and suffer from zero-inflation or over-dispersion, normalization is a critical step before conducting differential abundance analysis. Several normalization approaches have been proposed, but it is d

Cluster-correlated data receives a lot of attention in biomedical and longitudinal studies and it is of interest to assess the generalized dependence between two multivariate variables under the cluster-correlated structure. The Hilbert-Schmidt independence criterion (HSIC) is a powerful kernel-based test statistic that captures various dependence between two random vectors and can be applied to an arbitrary non-Euclidean domain. However, the existing HSIC is not directly applicable to cluster-c

OBJECTIVE: In premenopausal individuals, vaginal microbiota diversity and lack of Lactobacillus dominance are associated with greater mucosal inflammation, which is linked to a higher risk of cervical dysplasia and infections. It is not known if the association between the vaginal microbiota and inflammation is present after menopause, when the vaginal microbiota is generally higher-diversity and fewer people have Lactobacillus dominance. METHODS: This is a post hoc analysis of a subset of postm

New multi-sample tests for testing whether multiple samples are from the same distribution. They work well particularly for high-dimensional data. Song, H. and Chen, H. (2022) &lt;<a href="https://doi.org/10.48550/arXiv.2205.13787" target="_top">doi:10.48550/arXiv.2205.13787</a>&gt;.

Dataset shift refers to the problem where the input data distribution may change over time (e.g., between training and test stages). Since this can be a critical bottleneck in several safety-critical applications such as healthcare, drug-discovery, etc., dataset shift detection has become an important research issue in machine learning. Though several existing efforts have focused on image/video data, applications with graph-structured data have not received sufficient attention. Therefore, in t

Change-point analysis plays a significant role in various fields to reveal discrepancies in distribution in a sequence of observations. While a number of algorithms have been proposed for high-dimensional data, kernel-based methods have not been well explored due to difficulties in controlling false discoveries and mediocre performance. In this paper, we propose a new kernel-based framework that makes use of an important pattern of data in high dimensions to boost power. Analytic approximations

Testing the equality in distributions of multiple samples is a common task in many fields. However, this problem for high-dimensional or non-Euclidean data has not been well explored. In this paper, we propose new nonparametric tests based on a similarity graph constructed on the pooled observations from multiple samples, and make use of both within-sample edges and between-sample edges, a straightforward but yet not explored idea. The new tests exhibit substantial power improvements over existi

New kernel-based test and fast tests for testing whether two samples are from the same distribution. They work well particularly for high-dimensional data. Song, H. and Chen, H. (2023) &lt;<a href="https://doi.org/10.48550/arXiv.2011.06127" target="_top">doi:10.48550/arXiv.2011.06127</a>&gt;.

Kernel two-sample tests have been widely used for multivariate data to test equality of distributions. However, existing tests based on mapping distributions into a reproducing kernel Hilbert space mainly target specific alternatives and do not work well for some scenarios when the dimension of the data is moderate to high due to the curse of dimensionality. We propose a new test statistic that makes use of a common pattern under moderate and high dimensions and achieves substantial power improv

In the regime of change-point detection, a nonparametric framework based on scan statistics utilizing graphs representing similarities among observations is gaining attention due to its flexibility and good performances for high-dimensional and non-Euclidean data sequences, which are ubiquitous in this big data era. However, this graph-based framework encounters problems when there are repeated observations in the sequence, which often happens for discrete data, such as network data. In this wor

Spatial summary statistics based on point process theory are widely used to quantify the spatial organization of cell populations in single-cell spatial proteomics data. Among these, Ripley's $K$ is a popular metric for assessing whether cells are spatially clustered or are randomly dispersed. However, the key assumption of spatial homogeneity is frequently violated in spatial proteomics data, leading to overestimates of cell clustering and colocalization. To address this, we propose a novel $K$

New kernel-based test and fast tests for detecting change-points or changed-intervals where the distributions abruptly change. They work well particularly for high-dimensional data. Song, H. and Chen, H. (2022) &lt;<a href="https://doi.org/10.48550/arXiv.2206.01853" target="_top">doi:10.48550/arXiv.2206.01853</a>&gt;.