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Predicting the impact of genomic and drug perturbations in cellular function is crucial for understanding gene functions and drug effects, ultimately leading to improved therapies. To this end, Causal Representation Learning (CRL)…

Continual learning (CL) is widely regarded as crucial challenge for lifelong AI. However, existing CL benchmarks, e.g. Permuted-MNIST and Split-CIFAR, make use of artificial temporal variation and do not align with or generalize to the…

Rare diseases, including Inborn Errors of Metabolism (IEM), pose significant diagnostic challenges. Case reports serve as key but computationally underutilized resources to inform diagnosis. Clinical dense information extraction refers to…

Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the…

Each year, the lack of efficient data standardization and interoperability in cancer care contributes to the severe lack of timely and effective diagnosis, while constantly adding to the burden of cost, with cancer costs nationally reaching…

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data…

Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…

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…

Training deep neural network (DNN) with noisy labels is practically challenging since inaccurate labels severely degrade the generalization ability of DNN. Previous efforts tend to handle part or full data in a unified denoising flow via…

Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…

Denoising of periodic signals and accurate waveform estimation are core tasks across many signal processing domains, including speech, music, medical diagnostics, radio, and sonar. Although deep learning methods have recently shown…

Accurate prediction of recurrence in clear cell renal cell carcinoma (ccRCC) remains a major clinical challenge due to the disease complex molecular, pathological, and clinical heterogeneity. Traditional prognostic models, which rely on…

Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have…

Biomedical imaging and RNA sequencing with single-cell resolution improves our understanding of white blood cell diseases like leukemia. By combining morphological and transcriptomic data, we can gain insights into cellular functions and…

Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…

Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can…

Numerous tools have been recently developed to predict disease phenotypes using single-cell RNA sequencing (RNA-seq) data. CloudPred is an end-to-end differentiable learning algorithm coupled with a biologically informed mixture model,…

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…

Deep learning models have achieved remarkable accuracy in chest X-ray diagnosis, yet their widespread clinical adoption remains limited by the black-box nature of their predictions. Clinicians require transparent, verifiable explanations to…

Rare diseases affect hundreds of millions worldwide, yet diagnosis often spans years. Convectional pipelines decouple noisy evidence extraction from downstream inferential diagnosis, and general/medical large language models (LLMs) face…