Related papers: Efficient seeding techniques for protein similarit…
Neural architecture search (NAS) is gaining more and more attention in recent years due to its flexibility and remarkable capability to reduce the burden of neural network design. To achieve better performance, however, the searching…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Cross-lingual embeddings aim to represent words in multiple languages in a shared vector space by capturing semantic similarities across languages. They are a crucial component for scaling tasks to multiple languages by transferring…
Purpose: This study aimed to enhance protein sequence classification using natural language processing (NLP) techniques while addressing the impact of sequence similarity on model performance. We compared various machine learning and deep…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
Medical systematic review query formulation is a highly complex task done by trained information specialists. Complexity comes from the reliance on lengthy Boolean queries, which express a detailed research question. To aid query…
The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting…
Generative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about proteins deeply hidden in rapidly growing sequence…
A new Chase-type soft-decision decoding algorithm for Reed-Solomon codes is proposed, referred to as tree-based Chase-type algorithm}. The proposed tree-based Chase-type algorithm takes the set of all vectors as the set of testing patterns,…
GNAS (Graph Neural Architecture Search) has demonstrated great effectiveness in automatically designing the optimal graph neural architectures for multiple downstream tasks, such as node classification and link prediction. However, most…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
Clustering genotypes based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of…
Multiple kernel learning algorithms are proposed to combine kernels in order to obtain a better similarity measure or to integrate feature representations coming from different data sources. Most of the previous research on such methods is…
Seed phenotyping is the idea of analyzing the morphometric characteristics of a seed to predict the behavior of the seed in terms of development, tolerance and yield in various environmental conditions. The focus of the work is the…
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…
We propose Hercules, a parallel tree-based technique for exact similarity search on massive disk-based data series collections. We present novel index construction and query answering algorithms that leverage different summarization…
We are concerned with the problem of designing large families of subsets over a common labeled ground set that have small pairwise intersections and the property that the maximum discrepancy of the label values within each of the sets is…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Graph matching aims to find the latent vertex correspondence between two edge-correlated graphs and has found numerous applications across different fields. In this paper, we study a seeded graph matching problem, which assumes that a set…
Highly accurate biomolecular structure prediction is a key component of developing biomolecular foundation models, and one of the most critical aspects of building foundation models is identifying the recipes for scaling the model. In this…