Related papers: Anchor points for genome alignment based on Filter…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
This article proposes a novel approach to statistical alignment of nucleotide sequences by introducing a context dependent structure on the substitution process in the underlying evolutionary model. We propose to estimate alignments and…
Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the…
Local explanation methods highlight the input tokens that have a considerable impact on the outcome of classifying the document at hand. For example, the Anchor algorithm applies a statistical analysis of the sensitivity of the classifier…
Region anchors are the cornerstone of modern object detection techniques. State-of-the-art detectors mostly rely on a dense anchoring scheme, where anchors are sampled uniformly over the spatial domain with a predefined set of scales and…
The paper presents methods for evaluating the accuracy of alignments between transcriptions and audio recordings. The methods have been applied to the Spoken British National Corpus, which is an extensive and varied corpus of natural…
Adaptation to local environments often occurs through natural selection acting on a large number of loci, each having a weak phenotypic effect. One way to detect these loci is to identify genetic polymorphisms that exhibit high correlation…
The most common tools for word-alignment rely on a large amount of parallel sentences, which are then usually processed according to one of the IBM model algorithms. The training data is, however, the same as for machine translation (MT)…
Machine Learning methods have of late made significant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
In object detection, determining which anchors to assign as positive or negative samples, known as anchor assignment, has been revealed as a core procedure that can significantly affect a model's performance. In this paper we propose a…
An important component of any generation system is the mapping dictionary, a lexicon of elementary semantic expressions and corresponding natural language realizations. Typically, labor-intensive knowledge-based methods are used to…
The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Lyrics alignment in long music recordings can be memory exhaustive when performed in a single pass. In this study, we present a novel method that performs audio-to-lyrics alignment with a low memory consumption footprint regardless of the…
This paper proposes an algorithm for alignment-free sequence comparison using Logical Match. Here, we compute the score using fuzzy membership values which generate automatically from the number of matches and mismatches. We demonstrate the…