Related papers: scSiameseClu: A Siamese Clustering Framework for I…

Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph…

This paper introduces a novel approach to the task of data association within the context of pedestrian tracking, by introducing a two-stage learning scheme to match pairs of detections. First, a Siamese convolutional neural network (CNN)…

The identification of disease-gene associations is instrumental in understanding the mechanisms of diseases and developing novel treatments. Besides identifying genes from RNA-Seq datasets, it is often necessary to identify gene clusters…

Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. The analysis of scRNA-seq data poses…

Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…

Single-cell RNA sequencing enables high-resolution analysis of cellular heterogeneity, yet disentangling biological signal from batch effects remains a major challenge. Existing batch-correction algorithms suppress or discard batch-related…

Modeling cellular dynamics from single-cell RNA sequencing (scRNA-seq) data is critical for understanding cell development and underlying gene regulatory relationships. Many current methods rely on single-cell velocity to obtain pseudotime,…

Cell segmentation and tracking in microscopy images are of great significance to new discoveries in biology and medicine. In this study, we propose a novel approach to combine cell segmentation and cell tracking into a unified end-to-end…

Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However,…

Capturing semantic consistency among nodes is crucial for effective graph representation learning. Existing approaches typically rely on $k$-nearest neighbors ($k$NN) or other node-level full search algorithms (FSA) to mine semantic…

In the last decade, the discovery of noncoding RNA(ncRNA) has exploded. Classifying these ncRNA is critical todetermining their function. This thesis proposes a new methodemploying deep convolutional neural networks (CNNs) to classifyncRNA…

Siamese network has been a de facto benchmark framework for 3D LiDAR object tracking with a shared-parametric encoder extracting features from template and search region, respectively. This paradigm relies heavily on an additional matching…

Although Mamba models greatly improve Hyperspectral Image (HSI) classification, they have critical challenges in terms defining efficient and adaptive token sequences for improve performance. This paper therefore presents CSSMamba…

The advent of single-cell multi-omics technologies has enabled the simultaneous profiling of diverse omics layers within individual cells. Integrating such multimodal data provides unprecedented insights into cellular identity, regulatory…

We consider the problem of clustering nested or hierarchical data, where observations are grouped and there are both group-level and observation-level variables. In our motivating OneK1K dataset, observations consist of single-cell…

Identifying genes associated with diseases is crucial to understanding disease mechanisms and developing therapies. However, identification of individual genes associated with a disease often needs to be supplemented with clustering…

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST ``digital northern'', are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these…

In this paper, we introduce a neural network framework for semi-supervised clustering (SSC) with pairwise (must-link or cannot-link) constraints. In contrast to existing approaches, we decompose SSC into two simpler classification…

Single-cell transcriptomics techniques, such as scRNA-seq, attempt to characterize gene expression profiles in each cell of a heterogeneous sample individually. Due to growing amounts of data generated and the increasing complexity of the…