Related papers: Single-Cell RNA-seq Synthesis with Latent Diffusio…

Clustering of single-cell RNA sequencing (scRNA-seq) datasets can give key insights into the biological functions of cells. Therefore, it is not surprising that network-based community detection methods (one of the better clustering…

Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this…

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, enabling detailed molecular profiling at the individual cell level. However, integrating high-dimensional single-cell data into causal mediation…

Spectral clustering is one of the fundamental unsupervised learning methods widely used in data analysis. Sparse spectral clustering (SSC) imposes sparsity to the spectral clustering and it improves the interpretability of the model. This…

Large language models (LLMs) have demonstrated remarkable advancements, primarily due to their capabilities in modeling the hidden relationships within text sequences. This innovation presents a unique opportunity in the field of life…

Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…

Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…

Single-cell RNA sequencing (scRNA-seq) enables the study of cellular heterogeneity. Yet, clustering accuracy, and with it downstream analyses based on cell labels, remain challenging due to measurement noise and biological variability. In…

Diffusion models have shown promise in text generation, but often struggle with generating long, coherent, and contextually accurate text. Token-level diffusion doesn't model word-order dependencies explicitly and operates on short, fixed…

Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular processes by enabling gene expression analysis at the individual cell level. Clustering allows for the identification of cell types and the further…

Perturbation screens hold the potential to systematically map regulatory processes at single-cell resolution, yet modeling and predicting transcriptome-wide responses to perturbations remains a major computational challenge. Existing…

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state,…

Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…

Single-cell RNA sequencing (scRNA-seq) has revolutionized biological discovery, providing an unbiased picture of cellular heterogeneity in tissues. While scRNA-seq has been used extensively to provide insight into both healthy systems and…

Single-cell RNA sequencing (scRNA-seq) determines RNA expression at single-cell resolution. It provides a powerful tool for studying immunity, regulation, and other life activities of cells. However, due to the limitations of the sequencing…

Recent advances in technology have enabled the measurement of RNA levels for individual cells. Compared to traditional tissue-level bulk RNA-seq data, single cell sequencing yields valuable insights about gene expression profiles for…

The rapid development of spatial transcriptomics (ST) technologies is revolutionizing our understanding of the spatial organization of biological tissues. Current ST methods, categorized into next-generation sequencing-based (seq-based) and…