Related papers: scE2TM improves single-cell embedding interpretabi…

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.…

In this paper, we propose an easily trained yet powerful representation learning approach with performance highly competitive to deep neural networks in a digital pathology image segmentation task. The method, called sparse coding driven…

Automated segmentation of multiple sclerosis (MS) lesions from MRI scans is important to quantify disease progression. In recent years, convolutional neural networks (CNNs) have shown top performance for this task when a large amount of…

Emotion recognition using electroencephalography (EEG) signals has attracted increasing attention in recent years. However, existing methods often lack generalization in cross-corpus settings, where a model trained on one dataset is…

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…

Single-cell foundation models such as scGPT represent a significant advancement in single-cell omics, with an ability to achieve state-of-the-art performance on various downstream biological tasks. However, these models are inherently…

Modern high-throughput sequencing technologies have enabled us to profile multiple molecular modalities from the same single cell, providing unprecedented opportunities to assay celluar heterogeneity from multiple biological layers.…

This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…

The development of separate-encoder Unified multimodal models (UMMs) comes with a rapidly growing inference cost due to dense visual token processing. In this paper, we focus on understanding-side visual token reduction for improving the…

The integration of single-cell proteomic data is often hindered by the fragmented nature of targeted antibody panels. To address this limitation, we introduce scpFormer, a transformer-based foundation model designed for single-cell…

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,…

Influenced by breakthroughs in LLMs, single-cell foundation models are emerging. While these models show successful performance in cell type clustering, phenotype classification, and gene perturbation response prediction, it remains to be…

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…

Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present…

Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…

Fully-supervised polyp segmentation has accomplished significant triumphs over the years in advancing the early diagnosis of colorectal cancer. However, label-efficient solutions from weak supervision like scribbles are rarely explored yet…

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…

Induced pluripotent stem cells (iPSCs) provide a great model to study the process of reprogramming and differentiation of stem cells. Single-cell RNA sequencing (scRNA-seq) enables us to investigate the reprogramming process at single-cell…

Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced…

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…