Related papers: NTRFINDER: A Software Tool to Find Nested Tandem R…
Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…
Repetitive DNA sequences underpin genome architecture and evolutionary processes, yet they remain challenging to classify accurately. Terrier is a deep learning model designed to overcome these challenges by classifying repetitive DNA…
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
We cast nested named entity recognition (NNER) as a sequence labeling task by leveraging prior work that linearizes constituency structures, effectively reducing the complexity of this structured prediction problem to straightforward token…
The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…
Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…
Extracting tables from documents is a critical task across various industries, especially on business documents like invoices and reports. Existing systems based on DEtection TRansformer (DETR) such as TAble TRansformer (TATR), offer…
This work studies the problem of high-dimensional data (referred to as tensors) completion from partially observed samplings. We consider that a tensor is a superposition of multiple low-rank components. In particular, each component can be…
With the widespread application of efficient pattern mining algorithms, sequential patterns that allow gap constraints have become a valuable tool to discover knowledge from biological data such as DNA and protein sequences. Among all kinds…
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for…
Nonnegative Tucker decomposition (NTD) is a powerful tool for the extraction of nonnegative parts-based and physically meaningful latent components from high-dimensional tensor data while preserving the natural multilinear structure of…
Sequential pattern mining (SPM) with gap constraints (or repetitive SPM or tandem repeat discovery in bioinformatics) can find frequent repetitive subsequences satisfying gap constraints, which are called positive sequential patterns with…
Tensor network (TN) representation is a powerful technique for computer vision and machine learning. TN structure search (TN-SS) aims to search for a customized structure to achieve a compact representation, which is a challenging NP-hard…
Named entity recognition (NER) is the task to detect and classify the entity spans in the text. When entity spans overlap between each other, this problem is named as nested NER. Span-based methods have been widely used to tackle the nested…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Recurrent neural networks (RNNs) are powerful tools for sequential modeling, but typically require significant overparameterization and regularization to achieve optimal performance. This leads to difficulties in the deployment of large…
Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…