Related papers: CellMaster: Collaborative Cell Type Annotation in …
Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias…
We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set…
Accurate cell type annotation across datasets is a key challenge in single-cell analysis. snRNA-seq enables profiling of frozen or difficult-to-dissociate tissues, complementing scRNA-seq by capturing fragile or rare cell types. However,…
Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level…
Single-cell RNA-seq (scRNA-seq) technology is a powerful tool for unraveling the complexity of biological systems. One of essential and fundamental tasks in scRNA-seq data analysis is Cell Type Annotation (CTA). In spite of tremendous…
Cellular image segmentation is essential for quantitative biology yet remains difficult due to heterogeneous modalities, morphological variability, and limited annotations. We present GenCellAgent, a training-free multi-agent framework that…
With the rapid development of large language models (LLMs), their application to cell type annotation has drawn increasing attention. However, general-purpose LLMs often face limitations in this specific task due to the lack of guidance…
We introduce HiCat (Hybrid Cell Annotation using Transformative embeddings), a novel semi-supervised pipeline for annotating cell types from single-cell RNA sequencing data. HiCat fuses the strengths of supervised learning for known cell…
Generative AI foundation models offer transformative potential for processing structured biological data, particularly in single-cell RNA sequencing, where datasets are rapidly scaling toward billions of cells. We propose the use of agentic…
Cytometry enables precise single-cell phenotyping within heterogeneous populations. These cell types are traditionally annotated via manual gating, but this method suffers from a lack of reproducibility and sensitivity to batch-effect.…
Accurate and scalable cell type annotation remains a challenge in single-cell transcriptomics, especially when datasets exhibit strong batch effects or contain previously unseen cell populations. Here we introduce SpikGPT, a hybrid deep…
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) 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…
Single-cell RNA sequencing (scRNA-seq) offers detailed insights into cellular heterogeneity. Recent advancements leverage single-cell large language models (scLLMs) for effective representation learning. These models focus exclusively on…
Recent trends in cell segmentation have shifted towards universal models to handle diverse cell morphologies and imaging modalities. However, for continuously emerging cell types and imaging techniques, these models still require hundreds…
In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…
Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…
The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…
Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…
We introduce CellARC, a synthetic benchmark for abstraction and reasoning built from multicolor 1D cellular automata (CA). Each episode has five support pairs and one query serialized in 256 tokens, enabling rapid iteration with small…