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Out-of-distribution (OOD) detection poses a significant challenge for Graph Neural Networks (GNNs), particularly in open-world scenarios with varying distribution shifts. Most existing OOD detection methods on graphs primarily focus on…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
We propose a novel method, scTree, for single-cell Tree Variational Autoencoders, extending a hierarchical clustering approach to single-cell RNA sequencing data. scTree corrects for batch effects while simultaneously learning a…
Automated single-cell annotation is difficult when the most abundant genes are not the most discriminative ones, or when a target state is poorly covered by a fixed reference atlas. GPTCelltype-style one-shot prompting allows large language…
Object oriented data analysis (OODA) aims at statistically analyzing populations of complicated objects. This paper is motivated by a study of cell images in cell culture biology, which highlights a common critical issue: choice of data…
A crucial requirement for machine learning algorithms is not only to perform well, but also to show robustness and adaptability when encountering novel scenarios. One way to achieve these characteristics is to endow the deep learning models…
Tabular anomaly detection (TAD) aims to identify samples that deviate from the majority in tabular data and is critical in many real-world applications. However, existing methods follow a ``one model for one dataset (OFO)'' paradigm, which…
scRNA-seq clustering is a critical task for analyzing single-cell RNA sequencing (scRNA-seq) data, as it groups cells with similar gene expression profiles. Transformers, as powerful foundational models, have been applied to scRNA-seq…
Single-cell RNA-seq data are challenging because of the sparseness of the read counts, the tiny expression of many relevant genes, and the variability in the efficiency of RNA extraction for different cells. We consider a simple…
Automatic cell segmentation in microscopy images works well with the support of deep neural networks trained with full supervision. Collecting and annotating images, though, is not a sustainable solution for every new microscopy database…
Recently, data-centric AI methodology has been a dominant paradigm in single-cell transcriptomics analysis, which treats data representation rather than model complexity as the fundamental bottleneck. In the review of current studies,…
Understanding cellular mechanisms requires integrating information across DNA, RNA, and protein - the three molecular systems linked by the Central Dogma of molecular biology. While domain-specific foundation models have achieved success…
Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the regulation of each cell was measured from different modalities, i.e.…
Open Set Domain Adaptation (OSDA) aims to adapt a model trained on a source domain to a target domain that undergoes distribution shift and contains samples from novel classes outside the source domain. Source-free OSDA (SF-OSDA) techniques…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Elastic Weight Consolidation (EWC) is a technique used in overcoming catastrophic forgetting between successive tasks trained on a neural network. We use this phenomenon of information sharing between tasks for domain adaptation. Training…
Detecting Out-of-Domain (OOD) or unknown intents from user queries is essential in a task-oriented dialog system. A key challenge of OOD detection is to learn discriminative semantic features. Traditional cross-entropy loss only focuses on…
Open-set Domain Adaptation (OSDA) aims to adapt a model from a labeled source domain to an unlabeled target domain, where novel classes - also referred to as target-private unknown classes - are present. Source-free Open-set Domain…
Neurodegenerative diseases (NDDs) are complex and lack effective treatment due to their poorly understood mechanism. The increasingly used data analysis from Single nucleus RNA Sequencing (snRNA-seq) allows to explore transcriptomic events…
Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied…