Related papers: NTRFINDER: A Software Tool to Find Nested Tandem R…

Semantic matching, which aims to determine the matching degree between two texts, is a fundamental problem for many NLP applications. Recently, deep learning approach has been applied to this problem and significant improvements have been…

OpenTensor is a reproduction of AlphaTensor, which discovered a new algorithm that outperforms the state-of-the-art methods for matrix multiplication by Deep Reinforcement Learning (DRL). While AlphaTensor provides a promising framework for…

In many applications, a large number of features are collected with the goal to identify a few important ones. Sometimes, these features lie in a metric space with a known distance matrix, which partially reflects their co-importance…

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…

DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…

Tensor ring (TR) decomposition is a powerful tool for exploiting the low-rank nature of multiway data and has demonstrated great potential in a variety of important applications. In this paper, nonnegative tensor ring (NTR) decomposition…

There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…

In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…

Spectral clustering and co-clustering are well-known techniques in data analysis, and recent work has extended spectral clustering to square, symmetric tensors and hypermatrices derived from a network. We develop a new tensor spectral…

Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…

Named entity recognition (NER) is a well-studied task in natural language processing. However, the widely-used sequence labeling framework is difficult to detect entities with nested structures. In this work, we view nested NER as…

Recently, the transform-based tensor representation has attracted increasing attention in multimedia data (e.g., images and videos) recovery problems, which consists of two indispensable components, i.e., transform and characterization.…

After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…

Graph neural networks (GNNs) have been successfully applied in many structured data domains, with applications ranging from molecular property prediction to the analysis of social networks. Motivated by the broad applicability of GNNs, we…

Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…

We present a new table structure recognition (TSR) approach, called TSRFormer, to robustly recognizing the structures of complex tables with geometrical distortions from various table images. Unlike previous methods, we formulate table…

Sequential pattern mining (SPM) is an important branch of knowledge discovery that aims to mine frequent sub-sequences (patterns) in a sequential database. Various SPM methods have been investigated, and most of them are classical SPM…

Recurrent Neural Networks (RNNs) are among the most successful machine learning models for sequence modelling, but tend to suffer from an exponential increase in the number of parameters when dealing with large multidimensional data. To…

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…