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Reliability in cell type annotation is challenging in single-cell RNA-sequencing data analysis because both expert-driven and automated methods can be biased or constrained by their training data, especially for novel or rare cell types.…

Single-cell RNA-seq (scRNA-seq) enables atlas-scale profiling of complex tissues, revealing rare lineages and transient states. Yet, assigning biologically valid cell identities remains a bottleneck because markers are tissue- and…

Single-cell RNA sequencing (scRNAseq) is rapidly advancing our understanding of cellular composition within complex tissues and organisms. A major limitation in most scRNAseq analysis pipelines is the reliance on manual annotations to…

Foundation models like CLIP allow zero-shot transfer on various tasks without additional training data. Yet, the zero-shot performance is less competitive than a fully supervised one. Thus, to enhance the performance, fine-tuning and…

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…

Zero-shot single-cell cell-type annotation aims to determine a cell's type from a given set of expressed genes without any training. Existing knowledge-graph-based RAG approaches retrieve evidence by expanding from source entities and…

Accurate cell type annotation is a crucial step in analyzing single-cell RNA sequencing (scRNA-seq) data, which provides valuable insights into cellular heterogeneity. However, due to the high dimensionality and prevalence of zero elements…

Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of…

Clustering analysis is fundamental in single-cell RNA sequencing (scRNA-seq) data analysis for elucidating cellular heterogeneity and diversity. Recent graph-based scRNA-seq clustering methods, particularly graph neural networks (GNNs),…

In recent years, single cell RNA sequencing has become a widely used technique to study cellular diversity and function. However, accurately annotating cell types from single cell data has been a challenging task, as it requires extensive…

Column type annotation is the task of annotating the columns of a relational table with the semantic type of the values contained in each column. Column type annotation is an important pre-processing step for data search and data…

Contrastive Language-Image Pretraining (CLIP) has gained popularity for its remarkable zero-shot capacity. Recent research has focused on developing efficient fine-tuning methods, such as prompt learning and adapter, to enhance CLIP's…

Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate…

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…

Latent space optimization (LSO) is a powerful method for designing discrete, high-dimensional biological sequences that maximize expensive black-box functions, such as wet lab experiments. This is accomplished by learning a latent space…

Multi-modal image-text models such as CLIP and LiT have demonstrated impressive performance on image classification benchmarks and their zero-shot generalization ability is particularly exciting. While the top-5 zero-shot accuracies of…

Categorizing individual cells into one of many known cell type categories, also known as cell type annotation, is a critical step in the analysis of single-cell genomics data. The current process of annotation is time-intensive and…

Prompt-based continual learning (CL) provides a parameter-efficient approach for adapting large language models (LLMs) across task sequences. However, most existing methods rely on task-aware inference and maintain a growing set of…

Vision-language models (VLMs) like CLIP have been cherished for their ability to perform zero-shot visual recognition on open-vocabulary concepts. This is achieved by selecting the object category whose textual representation bears the…

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…