Related papers: eDOC: Explainable Decoding Out-of-domain Cell Type…

Natural Language Understanding (NLU) is a vital component of dialogue systems, and its ability to detect Out-of-Domain (OOD) inputs is critical in practical applications, since the acceptance of the OOD input that is unsupported by the…

Recently, Out-of-distribution (OOD) detection in dynamic graphs, which aims to identify whether incoming data deviates from the distribution of the in-distribution (ID) training set, has garnered considerable attention in security-sensitive…

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…

Test-Time Adaptation (TTA) aims to mitigate distributional shifts between training and test domains during inference time. However, existing TTA methods fall short in the realistic scenario where models face both continually changing…

Cell type annotation is a fundamental step in the analysis of single-cell RNA sequencing (scRNA-seq) data. In practice, human experts often rely on the structure revealed by principal component analysis (PCA) followed by $k$-nearest…

Previous OOD detection systems only focus on the semantic gap between ID and OOD samples. Besides the semantic gap, we are faced with two additional gaps: the domain gap between source and target domains, and the class-imbalance gap between…

In many real-world settings, machine learning models need to identify user inputs that are out-of-domain (OOD) so as to avoid performing wrong actions. This work focuses on a challenging case of OOD detection, where no labels for in-domain…

Single-cell RNA sequencing (scRNA-seq) enables the study of cellular diversity at single cell level. It provides a global view of cell-type specification during the onset of biological mechanisms such as developmental processes and human…

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…

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…

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…

RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially…

The ability to measure the transcriptomes of single cells has only been feasible for a few years, and is becoming an extremely popular assay. While many types of analysis and questions can be answered using single cell RNA-sequencing, a…

Convolutional neural networks (CNNs) can learn directly from raw data, resulting in exceptional performance across various research areas. However, factors present in non-controllable environments such as unlabeled datasets with varying…

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…

We present a novel method for automated identification of putative cell types from single-cell RNA-seq (scRNA-seq) data. By iteratively applying a machine learning approach to an initial clustering of gene expression profiles of a given set…

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the cellular level. By providing data on gene expression for each individual cell, scRNA-seq generates large datasets with thousands of…

Recent developments in single-cell omics technologies have enabled the quantification of molecular profiles in individual cells at an unparalleled resolution. Deep learning, a rapidly evolving sub-field of machine learning, has instilled a…

Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…

Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…