Related papers: Multiple Sequence Alignment System for Pyrosequenc…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
There are two major approaches for sequence labeling. One is the probabilistic gradient-based methods such as conditional random fields (CRF) and neural networks (e.g., RNN), which have high accuracy but drawbacks: slow training, and no…
Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the…
Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions…
Training code-switched language models is difficult due to lack of data and complexity in the grammatical structure. Linguistic constraint theories have been used for decades to generate artificial code-switching sentences to cope with this…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples…
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…
Online alignment in machine translation refers to the task of aligning a target word to a source word when the target sequence has only been partially decoded. Good online alignments facilitate important applications such as lexically…
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the…
This work proposes a multi-image matching method to estimate semantic correspondences across multiple images. In contrast to the previous methods that optimize all pairwise correspondences, the proposed method identifies and matches only a…
Copy mechanisms are employed in sequence to sequence models (seq2seq) to generate reproductions of words from the input to the output. These frameworks, operating at the lexical type level, fail to provide an explicit alignment that records…
We propose a method of aligning a source image to a target image, where the transform is specified by a dense vector field. The two images are encoded as feature hierarchies by siamese convolutional nets. Then a hierarchy of aligner modules…
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the…
We define a mapping from transition-based parsing algorithms that read sentences from left to right to sequence labeling encodings of syntactic trees. This not only establishes a theoretical relation between transition-based parsing and…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis. Unfortunately, long reads have high sequencing error rates…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
To solve time inefficiency issue, only potential pairs are compared in string-matching-based source code plagiarism detection; wherein potentiality is defined through a fast-yet-order-insensitive similarity measurement (adapted from…
Many robotics applications require alignment and fusion of observations obtained at multiple views to form a global model of the environment. Multi-way data association methods provide a mechanism to improve alignment accuracy of pairwise…