Related papers: Hypercomplex cross-correlation of DNA sequences
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
Deep hashing has recently received attention in cross-modal retrieval for its impressive advantages. However, existing hashing methods for cross-modal retrieval cannot fully capture the heterogeneous multi-modal correlation and exploit the…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
Visualization of high-dimensional data is counter-intuitive using conventional graphs. Parallel coordinates are proposed as an alternative to explore multivariate data more effectively. However, it is difficult to extract relevant…
Image classification is a fundamental computer vision task and an important baseline for deep metric learning. In decades efforts have been made on enhancing image classification accuracy by using deep learning models while less attention…
Despite extensive research spanning several decades, class imbalance is still considered a profound difficulty for both machine learning and deep learning models. While data oversampling is the foremost technique to address this issue,…
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Multi-contrast MRI images provide complementary contrast information about the characteristics of anatomical structures and are commonly used in clinical practice. Recently, a multi-flip-angle (FA) and multi-echo GRE method (MULTIPLEX MRI)…
In real-world data, information is stored in extremely large feature vectors. These variables are typically correlated due to complex interactions involving many features simultaneously. Such correlations qualitatively correspond to…
Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
This paper considers the problems of detecting a change point and estimating the location in the correlation matrices of a sequence of high-dimensional vectors, where the dimension is large enough to be comparable to the sample size or even…
Storage systems often rely on multiple copies of the same compressed data, enabling recovery in case of binary data errors, of course, at the expense of a higher storage cost. In this paper we show that a wiser method of duplication entails…
Data-Oriented Parsing (dop) ranks among the best parsing schemes, pairing state-of-the art parsing accuracy to the psycholinguistic insight that larger chunks of syntactic structures are relevant grammatical and probabilistic units. Parsing…
We introduce a novel matching algorithm, called DeepMatching, to compute dense correspondences between images. DeepMatching relies on a hierarchical, multi-layer, correlational architecture designed for matching images and was inspired by…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
Data representation is usually a natural form with their attribute values. On this basis, data processing is an attribute-centered calculation. However, there are three limitations in the attribute-centered calculation, saying, inflexible…