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Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges.…

Breast cancer has long been a prominent cause of mortality among women. Diagnosis, therapy, and prognosis are now possible, thanks to the availability of RNA sequencing tools capable of recording gene expression data. Molecular subtyping…

Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…

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…

Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain…

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and…

Molecular subtyping of breast cancer is crucial for personalized treatment and prognosis. Traditional classification approaches rely on either histopathological images or gene expression profiling, limiting their predictive power. In this…

This paper introduces a generic method which enables to use conventional deep neural networks as end-to-end one-class classifiers. The method is based on splitting given data from one class into two subsets. In one-class classification,…

Single-cell reference atlases are large-scale, cell-level maps that capture cellular heterogeneity within an organ using single cell genomics. Given their size and cellular diversity, these atlases serve as high-quality training data for…

Developing clinically useful cell-level analysis tools in digital pathology remains challenging due to limitations in dataset granularity, inconsistent annotations, high computational demands, and difficulties integrating new technologies…

Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…

Single-cell RNA-Sequencing (scRNA-Seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlassing projects. With increasing numbers of datasets being deposited in public…

Semantic segmentation of microscopic cell images using deep learning is an important technique, however, it requires a large number of images and ground truth labels for training. To address the above problem, we consider an efficient…

Single-cell RNA sequencing provides tremendous insights to understand biological systems. However, the noise from dropout can corrupt the downstream biological analysis. Hence, it is desirable to impute the dropouts accurately. In this…

Trajectory inference is a critical problem in single-cell transcriptomics, which aims to reconstruct the dynamic process underlying a population of cells from sequencing data. Of particular interest is the reconstruction of differentiation…

Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are…

The development of deep convolutional neural network architecture is critical to the improvement of image classification task performance. A lot of studies of image classification based on deep convolutional neural network focus on the…

Identifying and characterizing the patient's blood samples is indispensable in diagnostics of malignance suspicious. A painstaking and sometimes subjective task is used in laboratories to manually classify white blood cells. Neural…

Our work introduces an innovative approach to graph learning by leveraging Hyperdimensional Computing. Graphs serve as a widely embraced method for conveying information, and their utilization in learning has gained significant attention.…

With the development of automatic sleep stage classification (ASSC) techniques, many classical methods such as k-means, decision tree, and SVM have been used in automatic sleep stage classification. However, few methods explore deep…