Related papers: Single-cell RNA-seq data imputation using Feature …

Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the intrinsic, nonlinear dependencies. No existing simulator jointly models gene-gene and cell-cell…

RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…

Predicting spatial gene expression from routine H\&E enables large-scale molecular profiling, yet current models treat this as isolated pointwise tasks, thereby overlooking essential biological structures like gene coordination and spatial…

Single-cell RNA sequencing (scRNA-seq) enables single-cell transcriptomic profiling, revealing cellular heterogeneity and rare populations. Recent deep learning models like Geneformer and Mouse-Geneformer perform well on tasks such as…

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which…

Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer…

Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…

Closed Form is a propagation based matting algorithm, functioning well on images with good propagation . The deficiency of the Closed Form method is that for complex areas with poor image propagation , such as hole areas or areas of long…

The clear transparency of Deep Neural Networks (DNNs) is hampered by complex internal structures and nonlinear transformations along deep hierarchies. In this paper, we propose a new attribution method, Relative Sectional Propagation (RSP),…

We aim to tackle the problem of point-based interactive segmentation, in which the key challenge is to propagate the user-provided annotations to unlabeled regions efficiently. Existing methods tackle this challenge by utilizing…

Recent advancements in single-cell genomics necessitate precision in gene panel selection to interpret complex biological data effectively. Those methods aim to streamline the analysis of scRNA-seq data by focusing on the most informative…

Federated clustering addresses the critical challenge of extracting patterns from decentralized, unlabeled data. However, it is hampered by the flaw that current approaches are forced to accept a compromise between performance and privacy:…

Single-cell-resolution spatial transcriptomics profiles gene expression at cellular locations in native tissues, yet accurate cell-type annotation remains challenging: imaging-based platforms are constrained by targeted gene panels, whereas…

A Bayesian feature allocation model (FAM) is presented for identifying cell subpopulations based on multiple samples of cell surface or intracellular marker expression level data obtained by cytometry by time of flight (CyTOF). Cell…

To characterize circumstellar systems in high contrast imaging, the fundamental step is to construct a best point spread function (PSF) template for the non-circumstellar signals (i.e., star light and speckles) and separate it from the…

The advent of single-cell multi-omics technologies has enabled the simultaneous profiling of diverse omics layers within individual cells. Integrating such multimodal data provides unprecedented insights into cellular identity, regulatory…

Sheaf Neural Networks (SNNs) naturally extend Graph Neural Networks (GNNs) by endowing a cellular sheaf over the graph, equipping nodes and edges with vector spaces and defining linear mappings between them. While the attached geometric…

Background: Single-cell foundation models such as Geneformer and scGPT encode rich biological information, but whether this includes causal regulatory logic rather than statistical co-expression remains unclear. Sparse autoencoders (SAEs)…

While Graph Neural Networks (GNNs) have recently become the de facto standard for modeling relational data, they impose a strong assumption on the availability of the node or edge features of the graph. In many real-world applications,…

We introduce the two-point propagation field (TPPF), a real-valued, phase-sensitive quantity defined as the functional derivative of the single-photon detection probability with respect to an infinitesimal opaque perturbation placed between…