Related papers: Anchor points for genome alignment based on Filter…
Cosine similarity is a widely used measure of the relatedness of pre-trained word embeddings, trained on a language modeling goal. Datasets such as WordSim-353 and SimLex-999 rate how similar words are according to human annotators, and as…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Background: Identifying all possible mapping locations of next-generation sequencing (NGS) reads is highly essential in several applications such as prediction of genomic variants or protein binding motifs located in repeat regions, isoform…
Generative models, widely utilized in various applications, can often struggle with prompts corresponding to partial tokens. This struggle stems from tokenization, where partial tokens fall out of distribution during inference, leading to…
Learning by imitation is one of the most significant abilities of human beings and plays a vital role in human's computational neural system. In medical image analysis, given several exemplars (anchors), experienced radiologist has the…
In this work, we introduce a methodology for alignment designed to enhance the ability of large language models (LLMs) to articulate their reasoning (self-explanation) even in the absence of annotated rationale explanations. Our alignment…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Accurate grasping point prediction is a key challenge for autonomous tissue manipulation in minimally invasive surgery, particularly in complex and variable procedures such as colorectal interventions. Due to their complexity and prolonged…
Sequence alignments are used to capture patterns composed of elements representing multiple conceptual levels through the alignment of sequences that contain overlapping and variable length annotations. The alignments also determine the…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Semantic similarity measures (SSMs) refer to a set of algorithms used to quantify the similarity of two or more terms belonging to the same ontology. Ontology terms may be associated to concepts, for instance in computational biology gene…
Large-scale statistical analysis of data sets associated with genome sequences plays an important role in modern biology. A key component of such statistical analyses is the computation of $p$-values and confidence bounds for statistics…
Anchor-based techniques reduce the computational complexity of spectral clustering algorithms. Although empirical tests have shown promising results, there is currently a lack of theoretical support for the anchoring approach. We define a…
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…