Multi-Source Multi-View Clustering via Discrepancy Penalty

With the advance of technology, entities can be observed in multiple views. Multiple views containing different types of features can be used for clustering. Although multi-view clustering has been successfully applied in many applications, the previous methods usually assume the complete instance mapping between different views. In many real-world applications, information can be gathered from multiple sources, while each source can contain multiple views, which are more cohesive for learning. The views under the same source are usually fully mapped, but they can be very heterogeneous. Moreover, the mappings between different sources are usually incomplete and partially observed, which makes it more difficult to integrate all the views across different sources. In this paper, we propose MMC (Multi-source Multi-view Clustering), which is a framework based on collective spectral clustering with a discrepancy penalty across sources, to tackle these challenges. MMC has several advantages compared with other existing methods. First, MMC can deal with incomplete mapping between sources. Second, it considers the disagreements between sources while treating views in the same source as a cohesive set. Third, MMC also tries to infer the instance similarities across sources to enhance the clustering performance. Extensive experiments conducted on real-world data demonstrate the effectiveness of the proposed approach

Directionally Dependent Multi-View Clustering Using Copula Model

In recent biomedical scientific problems, it is a fundamental issue to integratively cluster a set of objects from multiple sources of datasets. Such problems are mostly encountered in genomics, where data is collected from various sources, and typically represent distinct yet complementary information. Integrating these data sources for multi-source clustering is challenging due to their complex dependence structure including directional dependency. Particularly in genomics studies, it is known that there is certain directional dependence between DNA expression, DNA methylation, and RNA expression, widely called The Central Dogma. Most of the existing multi-view clustering methods either assume an independent structure or pair-wise (non-directional) dependency, thereby ignoring the directional relationship. Motivated by this, we propose a copula-based multi-view clustering model where a copula enables the model to accommodate the directional dependence existing in the datasets. We conduct a simulation experiment where the simulated datasets exhibiting inherent directional dependence: it turns out that ignoring the directional dependence negatively affects the clustering performance. As a real application, we applied our model to the breast cancer tumor samples collected from The Cancer Genome Altas (TCGA)

LATTE: Application Oriented Social Network Embedding

In recent years, many research works propose to embed the network structured data into a low-dimensional feature space, where each node is represented as a feature vector. However, due to the detachment of embedding process with external tasks, the learned embedding results by most existing embedding models can be ineffective for application tasks with specific objectives, e.g., community detection or information diffusion. In this paper, we propose study the application oriented heterogeneous social network embedding problem. Significantly different from the existing works, besides the network structure preservation, the problem should also incorporate the objectives of external applications in the objective function. To resolve the problem, in this paper, we propose a novel network embedding framework, namely the "appLicAtion orienTed neTwork Embedding" (Latte) model. In Latte, the heterogeneous network structure can be applied to compute the node "diffusive proximity" scores, which capture both local and global network structures. Based on these computed scores, Latte learns the network representation feature vectors by extending the autoencoder model model to the heterogeneous network scenario, which can also effectively unite the objectives of network embedding and external application tasks. Extensive experiments have been done on real-world heterogeneous social network datasets, and the experimental results have demonstrated the outstanding performance of Latte in learning the representation vectors for specific application tasks.Comment: 11 Pages, 12 Figures, 1 Tabl

Statistical Methods for Integrative Analysis, Subgroup Identification, and Variable Selection Using Cancer Genomic Data

In recent years, comprehensive cancer genomics platform, such as The Cancer Genome Atlas (TCGA), provides access to an enormous amount of high throughput genomic datasets for each patient, including gene expression, DNA copy number alteration, DNA methylation, and somatic mutation. Currently most existing analysis approaches focused only on gene-level analysis and suffered from limited interpretability and low reproducibility of findings. Additionally, with increasing availability of the modern compositional data including immune cellular fraction data and high-dimensional zero-inflated microbiome data, variable selection techniques for compositional data became of great interest because they allow inference of key immune cell types (immunology data) and key microbial species (microbiome data) associated with development and progression of various diseases. In the first dissertation aim, we address these challenges by developing a Bayesian sparse latent factor model for pathway-guided integrative genomic data analysis. Specifically, we constructed a unified framework to simultaneously identify cancer patient subgroups (clustering) and key molecular markers (variable selection) based on the joint analysis of continuous, binary and count data. In addition, we applied Polya-Gamma mixtures of normal for binary and count data to promote an exact and fully automatic posterior sampling. Moreover, pathway information was used to improve accuracy and robustness in identification of cancer patient subgroups and key molecular features. In the second dissertation aim, we developed the R package InGRiD , a comprehensive software for pathway-guided integrative genomic data analysis. We further implemented the statistical model developed in Aim 1 and provide it as a part of this software. The third dissertation aim exploits variable selection in compositional data analysis with application to immunology data and microbiome data. Specifically, we identified key immune cell types by applying a stepwise pairwise log-ratio procedure to the immune cellular fractions data, while selecting key species in the microbiome data by using zero-inflated Wilcoxon rank sum test. These approaches consider key components specific to these data types, such as compositionality (i.e., sum-to-one), zero inflation, and high dimensionality, among others. The proposed methods were developed and evaluated on: 1) large scale, high dimensional, and multi-modal datasets from the TCGA database, including gene expression, DNA copy number alteration, and somatic mutation data (Aim 1); 2) cellular fraction data induced from Colorectal Adenocarcinoma TCGA Pan-Cancer study (Aim 3); 3) high dimensional zero-inflated microbiome data from studies of colorectal cancer (Aim 3)