Related papers: Aligning coding sequences with frameshift extensio…

Sparse representation-based classifiers have shown outstanding accuracy and robustness in image classification tasks even with the presence of intense noise and occlusion. However, it has been discovered that the performance degrades…

A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…

Image translation with convolutional autoencoders has recently been used as an approach to multimodal change detection in bitemporal satellite images. A main challenge is the alignment of the code spaces by reducing the contribution of…

Methods for alignment of protein sequences typically measure similarity by using substitution matrix with scores for all possible exchanges of one amino acid with another. Although widely used, the matrices derived from homologous sequence…

We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…

In the remote sensing community, multimodal change detection (MCD) is particularly critical due to its ability to track changes across different imaging conditions and sensor types, making it highly applicable to a wide range of real-world…

State-of-the-art methods fail to solve visual localization in scenarios where different devices use different sparse feature extraction algorithms to obtain keypoints and their corresponding descriptors. Translating feature descriptors is…

This paper addresses the Longest Filled Common Subsequence (LFCS) problem, a challenging NP-hard problem with applications in bioinformatics, including gene mutation prediction and genomic data reconstruction. Existing approaches, including…

Cross-Domain Few-Shot Learning (CDFSL) adapts models trained with large-scale general data (source domain) to downstream target domains with only scarce training data, where the research on vision-language models (e.g., CLIP) is still in…

We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic…

Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…

Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…

Handwritten text recognition aims to convert visual input into machine-readable text, and it remains challenging due to the evolving and context-dependent nature of handwriting. Character sets change over time, and character frequency…

Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…

Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…

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…

We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…

We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…

Protein language models often take into consideration the alignment between a protein sequence and its textual description. However, they do not take structural information into consideration. Traditional methods treat sequence and…