Related papers: Multiple Sequence Alignment System for Pyrosequenc…

Motivation: The multiple sequence alignment (MSA) problem has been extensively studied, with numerous approaches developed over recent years. With the rapid growth of sequence data, there is an increasing need for fast and accurate MSA…

This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…

Online sequence prediction is the problem of predicting the next element of a sequence given previous elements. This problem has been extensively studied in the context of individual sequence prediction, where no prior assumptions are made…

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…

Fast matching of regular expressions with bounded repetition, aka counting, such as (ab){50,100}, i.e., matching linear in the length of the text and independent of the repetition bounds, has been an open problem for at least two decades.…

Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…

Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can…

Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality. The best existing…

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…

Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…

Correspondence learning is a fundamental problem in robotics, which aims to learn a mapping between state, action pairs of agents of different dynamics or embodiments. However, current correspondence learning methods either leverage…

Purpose: The aim of this work is to develop a neural network training framework for continual training of small amounts of medical imaging data and create heuristics to assess training in the absence of a hold-out validation or test set.…

This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…

Streaming automatic speech recognition (ASR) aims to emit each hypothesized word as quickly and accurately as possible. However, emitting fast without degrading quality, as measured by word error rate (WER), is highly challenging. Existing…

Sparse coding consists in representing signals as sparse linear combinations of atoms selected from a dictionary. We consider an extension of this framework where the atoms are further assumed to be embedded in a tree. This is achieved…

Despite the remarkable advances in language modeling, current mainstream decoding methods still struggle to generate texts that align with human texts across different aspects. In particular, sampling-based methods produce less-repetitive…

Diarization is a crucial component in meeting transcription systems to ease the challenges of speech enhancement and attribute the transcriptions to the correct speaker. Particularly in the presence of overlapping or noisy speech, these…

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…

Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…

We consider the problem of detecting the overlap between a pair of short fragments sampled in random locations from an exponentially longer sequence, via their possibly noisy reads. We consider a noiseless setting, in which the reads are…