Related papers: Anchor points for genome alignment based on Filter…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
In this work, we propose an enhancement to the Boyer-Moore-Horspool algorithm tailored for natural language text. The approach involves preprocessing the search pattern to identify its statistically least frequent character, referred to as…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Despite significant progress of deep learning in recent years, state-of-the-art semantic matching methods still rely on legacy features such as SIFT or HoG. We argue that the strong invariance properties that are key to the success of…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
In the time series analysis field, there is not a unique recipe for studying signal similarities. On the other hand, averaging signals of the same nature is an essential tool in the analysis of different kinds of data. Here we propose a…
Motivation: Despite significant advances in Third-Generation Sequencing (TGS) technologies, Next-Generation Sequencing (NGS) technologies remain dominant in the current sequencing market. This is due to the lower error rates and richer…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
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…
Discriminative features are critical for machine learning applications. Most existing deep learning approaches, however, rely on convolutional neural networks (CNNs) for learning features, whose discriminant power is not explicitly…
Sound correspondence patterns form the basis of cognate detection and phonological reconstruction in historical language comparison. Methods for the automatic inference of correspondence patterns from phonetically aligned cognate sets have…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
Word embedding models offer continuous vector representations that can capture rich contextual semantics based on their word co-occurrence patterns. While these word vectors can provide very effective features used in many NLP tasks such as…
It has been known in potential theory that, for some kernels matrices corresponding to well-separated point sets, fast analytical low-rank approximation can be achieved via the use of proxy points. This proxy point method gives a…
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…
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…
Data coding as a building block of several image processing algorithms has been received great attention recently. Indeed, the importance of the locality assumption in coding approaches is studied in numerous works and several methods are…
Existing works often focus on reducing the architecture redundancy for accelerating image classification but ignore the spatial redundancy of the input image. This paper proposes an efficient image classification pipeline to solve this…
We propose a modified MSA algorithm on quantum annealers with applications in areas of bioinformatics and genetic sequencing. To understand the human genome, researchers compare extensive sets of these genetic sequences -- or their protein…