Related papers: Multiple Sequence Alignment System for Pyrosequenc…
In sequence-to-sequence learning, e.g., natural language generation, the decoder relies on the attention mechanism to efficiently extract information from the encoder. While it is common practice to draw information from only the last…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Conformance checking encompasses a body of process mining techniques which aim to find and describe the differences between a process model capturing the expected process behavior and a corresponding event log recording the observed…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
Efficiently merging several models fine-tuned for different tasks, but stemming from the same pretrained base model, is of great practical interest. Despite extensive prior work, most evaluations of model merging in computer vision are…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…
Merging Large Language Models (LLMs) is a cost-effective technique for combining multiple expert LLMs into a single versatile model, retaining the expertise of the original ones. However, current approaches often overlook the importance of…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
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…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
A novel approach to protein multiple sequence alignment is discussed: substantially this method counterparts with substitution matrix based methods (like Blosum or PAM based methods), and implies a more deterministic approach to…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Aligning parallel sentences in multilingual corpora is essential to curating data for downstream applications such as Machine Translation. In this work, we present OneAligner, an alignment model specially designed for sentence retrieval…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
This paper addresses the problem of fault diagnosis in multistation assembly systems. Fault diagnosis is to identify process faults that cause the excessive dimensional variation of the product using dimensional measurements. For such…
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…
Learning to read words aloud is a major step towards becoming a reader. Many children struggle with the task because of the inconsistencies of English spelling-sound correspondences. Curricula vary enormously in how these patterns are…
Oxford Nanopore MinION sequencer is currently the smallest sequencing device available. While being able to produce very long reads (reads of up to 100~kbp were reported), it is prone to high sequencing error rates of up to 30%. Since most…