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Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…

Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling…

Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…

In the treatment of complex diseases, treatment regimens using a single drug often yield limited efficacy and can lead to drug resistance. In contrast, combination drug therapies can significantly improve therapeutic outcomes through…

A major impediment to successful drug development is the complexity, cost, and scale of clinical trials. The detailed internal structure of clinical trial data can make conventional optimization difficult to achieve. Recent advances in…

Cancer survival prediction is important for developing personalized treatments and inducing disease-causing mechanisms. Multi-omics data integration is attracting widespread interest in cancer research for providing information for…

The emergence of pathology foundation models has revolutionized computational histopathology, enabling highly accurate, generalized whole-slide image analysis for improved cancer diagnosis, and prognosis assessment. While these models show…

Multidisciplinary team (MDT) consultations are the gold standard for cancer care decision-making, yet current practice lacks structured mechanisms for quantifying consensus and ensuring decision traceability. We introduce a Multi-Agent…

Background: Accurate week-ahead forecasts of continuous glucose monitoring (CGM) derived metrics could enable proactive diabetes management, but relative performance of modern tabular learning approaches is incompletely defined. Methods: We…

Foundation models have become a promising paradigm for advancing medical image analysis, particularly for segmentation tasks where downstream applications often emerge sequentially. Existing fine-tuning strategies, however, remain limited:…

Applications of single-cell RNA sequencing in various biomedical research areas have been blooming. This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique…

Foundation models have revolutionized computer vision by achieving vastly superior performance across diverse tasks through large-scale pretraining on extensive datasets. However, their application in surgical computer vision has been…

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility…

Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…

Drug-target binding affinity prediction is a fundamental task for drug discovery. It has been extensively explored in literature and promising results are reported. However, in this paper, we demonstrate that the results may be misleading…

Progress in computer-aided synthesis planning (CASP) is obscured by the lack of standardized evaluation infrastructure and the reliance on metrics that prioritize topological completion over chemical validity. We introduce RetroCast, a…

Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…

Drug repurposing is an effective strategy to identify new uses for existing drugs, providing the quickest possible transition from bench to bedside. Existing methods for drug repurposing that mainly focus on pre-clinical information may…

Foundation models have substantially advanced computational pathology by learning transferable visual representations from large histological datasets, yet their performance varies widely across tasks due to differences in training data…

Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to…