Related papers: Alignment-Free Sequence Analysis and Applications

The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…

In a controlled experiment of sequence-to-sequence approaches for the task of sentence correction, we find that character-based models are generally more effective than word-based models and models that encode subword information via…

A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…

The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…

Word alignment over parallel corpora has a wide variety of applications, including learning translation lexicons, cross-lingual transfer of language processing tools, and automatic evaluation or analysis of translation outputs. The great…

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…

While utilizing syntactic tools such as parts-of-speech (POS) tagging has helped us understand sentence structures and their distribution across diverse corpora, it is quite complex and poses a challenge in natural language processing…

Sequence-to-sequence translation methods based on generation with a side-conditioned language model have recently shown promising results in several tasks. In machine translation, models conditioned on source side words have been used to…

Aligning large language models to handle instructions with extremely long contexts has yet to be fully investigated. Previous studies have attempted to scale up the available data volume by synthesizing long instruction-following samples,…

After a period of decrease, interest in word alignments is increasing again for their usefulness in domains such as typological research, cross-lingual annotation projection, and machine translation. Generally, alignment algorithms only use…

Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations.…

Neural dependency parsing has achieved remarkable performance for low resource morphologically rich languages. It has also been well-studied that morphologically rich languages exhibit relatively free word order. This prompts a fundamental…

LLM alignment ensures that large language models behave safely and effectively by aligning their outputs with human values, goals, and intentions. Aligning LLMs employ huge amounts of data, computation, and time. Moreover, curating data…

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…

Parallel corpora have driven great progress in the field of Text Simplification. However, most sentence alignment algorithms either offer a limited range of alignment types supported, or simply ignore valuable clues present in comparable…

Computational approaches in historical linguistics have been increasingly applied during the past decade and many new methods that implement parts of the traditional comparative method have been proposed. Despite these increased efforts,…

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…

The Third-Generation in DNA sequencing has emerged in the last few years using new technologies that allow the production of long-read sequences. Applications of the Third-Generation sequencing enable real-time and on-site data production,…

Large Language Models (LLMs) are prone to generating content that exhibits gender biases, raising significant ethical concerns. Alignment, the process of fine-tuning LLMs to better align with desired behaviors, is recognized as an effective…

Generative Adversarial Networks (GANs) have been shown to aid in the creation of artificial data in situations where large amounts of real data are difficult to come by. This issue is especially salient in the computational linguistics…