相关论文: Deciphering hierarchical organization of topologic…

Chromosome conformation capture experiments such as Hi-C are used to map the three-dimensional spatial organization of genomes. One specific feature of the 3D organization is known as topologically associating domains (TADs), which are…

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…

Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is…

To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…

Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (1) it is capable of…

Researchers developed chromosome capture methods such as Hi-C to better understand DNA's 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is…

Motivation: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution,…

To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These…

Molecular and genetic definitions of human-specific changes to genomic regulatory networks (GRNs) contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of…

Genome-wide proximity placement analysis of 10,598 HSGRL within the context of the principal regulatory structures of the interphase chromatin, namely topologically-associating domains (TADs) and specific sub-TAD structures termed…

Accurate detection of cancer tissue regions (CTR) enables deeper analysis of the tumor microenvironment and offers crucial insights into treatment response. Traditional CTR detection methods, which typically rely on the rich cellular…

Graph Anomaly Detection (GAD) has demonstrated great effectiveness in identifying unusual patterns within graph-structured data. However, while labeled anomalies are often scarce in emerging applications, existing supervised GAD approaches…

A significant number of anomalous nodes in the real world, such as fake news, noncompliant users, malicious transactions, and malicious posts, severely compromises the health of the graph data ecosystem and urgently requires effective…

This paper introduces a novel heterogenous domain adaptation (HDA) method for hyperspectral image classification with a limited amount of labeled samples in both domains. The method is achieved in the way of cross-domain collaborative…

Test-time adaptation allows pretrained models to adjust to incoming data streams, addressing distribution shifts between source and target domains. However, standard methods rely on single-dimensional linear classification layers, which…

Camouflaged object detection (COD) aims to localize targets that exhibit minimal perceptual differences from backgrounds through physical attributes. Existing methods, constrained by the static train-then-freeze paradigm, suffer from domain…

Hybrid Question-Answering (HQA), which targets reasoning over tables and passages linked from table cells, has witnessed significant research in recent years. A common challenge in HQA and other passage-table QA datasets is that it is…

We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC…

This paper focuses on a significant yet challenging task: out-of-distribution detection (OOD detection), which aims to distinguish and reject test samples with semantic shifts, so as to prevent models trained on in-distribution (ID) data…

Numerous diseases, particularly autoimmune disorders, are associated with the human leukocyte antigen (HLA), a small genomic region located on human chromosome 6. Adequate characterization of linkage disequilibrium (LD) in the HLA across…