arXiv subjects

Wan He

Publications and source records attributed to Wan He.

4 recordsLinked to original sources

arXiv2025

Hypergraph Representations of scRNA-seq Data for Improved Clustering with Random Walks

Analysis of single-cell RNA sequencing data is often conducted through network projections such as coexpression networks, primarily due to the abundant availability of network analysis tools for downstream tasks. However, this approach has several limitations: loss of higher-order information, inefficient data representation caused by converting a sparse dataset to a fully connected network, and overestimation of coexpression due to zero-inflation. To address these limitations, we propose conceptualizing scRNA-seq expression data as hypergraphs, which are generalized graphs in which the hyperedges can connect more than two vertices. In the context of scRNA-seq data, the hypergraph nodes represent cells and the edges represent genes. Each hyperedge connects all cells where its corresponding gene is actively expressed and records the expression of the gene across different cells. This hypergraph conceptualization enables us to explore multi-way relationships beyond the pairwise interactions in coexpression networks without loss of information. We propose two novel clustering methods: (1) the Dual-Importance Preference Hypergraph Walk (DIPHW) and (2) the Coexpression and Memory-Integrated Dual-Importance Preference Hypergraph Walk (CoMem-DIPHW). They outperform established methods on both simulated and real scRNA-seq datasets. The improvement brought by our proposed methods is especially significant when data modularity is weak. Furthermore, CoMem-DIPHW incorporates the gene coexpression network, cell coexpression network, and the cell-gene expression hypergraph from the single-cell abundance counts data altogether for embedding computation. This approach accounts for both the local level information from single-cell level gene expression and the global level information from the pairwise similarity in the two coexpression networks.

q-bio.QM↗

arXiv2024

A Misclassification Network-Based Method for Comparative Genomic Analysis

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

q-bio.GN↗

arXiv2024

Assigning Entities to Teams as a Hypergraph Discovery Problem

We propose a team assignment algorithm based on a hypergraph approach focusing on resilience and diffusion optimization. Specifically, our method is based on optimizing the algebraic connectivity of the Laplacian matrix of an edge-dependent vertex-weighted hypergraph. We used constrained simulated annealing, where we constrained the effort agents can exert to perform a task and the minimum effort a task requires to be completed. We evaluated our methods in terms of the number of unsuccessful patches to drive our solution into the feasible region and the cost of patching. We showed that our formulation provides more robust solutions than the original data and the greedy approach. We hope that our methods motivate further research in applying hypergraphs to similar problems in different research areas and in exploring variations of our methods.

cs.SI↗

arXiv2018

Efficient Reconstructions of Common Era Climate via Integrated Nested Laplace Approximations

Paleoclimate reconstruction on the Common Era (1-2000AD) provide critical context for recent warming trends. This work leverages integrated nested Laplace approximations (INLA) to conduct inference under a Bayesian hierarchical model using data from three sources: a state-of-the-art prox database (PAGES 2k), surface temperature observations (HadCRUT4), and latest estimates of external forcings. INLA's computational efficiency allows to explore several model formulations (with or without forcings, explicitly modeling internal variability or not), as well as five data reduction techniques. Two different validation exercises find a small impact of data reduction choices, but a large impact for model choice, with best results for the two models that incorporate external forcings. These models confirm that man-made greenhouse gas emissions are the largest contributor to temperature variability over the Common Era, followed by volcanic forcing. Solar effects are indistinguishable from zero. INLA provide an efficient way to estimate the posterior mean, comparable with the much costlier Monte Carlo Markov Chain procedure, but with wider uncertainty bounds. We recommend using it for exploration of model designs, but full MCMC solutions should be used for proper uncertainty quantification.

stat.AP↗