AIMC Topic: Software

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NoAC: an automatic builder for knowledge bases and query interfaces on genomes of non-model organisms.

Journal of molecular biology
The cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no ...

DCMF-PPI: a protein-protein interaction predictor based on dynamic condition and multi-feature fusion.

BMC bioinformatics
BACKGROUND: The identification of protein-protein interaction (PPI) plays a crucial role in understanding the mechanisms of complex biological processes. Current research in predicting PPI has shown remarkable progress by integrating protein informat...

Automated software bug severity classification using ensemble machine learning scheme: A real case study.

PloS one
Software bug report classification is one of the most significant processes in software development for determining the nature and severity of faults based on their causes and effects. In many projects, software experts implement this process manuall...

A comprehensive benchmark of single-cell Hi-C embedding tools.

Nature communications
Embedding is the key step in single-cell Hi-C (scHi-C) analysis which relies on capturing biological meaningful heterogeneity at various levels of genome architecture. To understand the strength and limitations of existing tools in various applicatio...

Empathi: embedding-based phage protein annotation tool by hierarchical assignment.

Nature communications
Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of ...

Remote patient monitoring system combining hardware and artificial intelligence based software.

Biomedical physics & engineering express
This study details the development of a remote patient monitoring system with a primary focus on a novel, customized Deep Neural Network (DNN) for arrhythmia detection. The system integrates hardware for real-time data collection from biomedical sens...

iPro-MP: a BERT-based model to predict multiple prokaryotic promoters.

Genome biology
BACKGROUND: Promoters, as essential cis-regulatory elements in prokaryotes, govern gene expression by mediating RNA polymerase binding through core motifs and long-range regulatory interactions, playing a pivotal role in cell metabolism and environme...

Populational influence on cephalometric landmark identification: performance of two AI-driven software programs in Brazilian and Korean images.

BMC oral health
OBJECTIVE: To assess the performance of cephalometric landmark identification performed by two AI-driven software programs in images from different populations (Brazilian and Korean).

On the effectiveness of network metrics on key class prediction: An empirical study.

PloS one
Key classes are the most important classes in a software system, which provide an excellent foundation for developers-especially those new to the field-to understand unfamiliar software systems. In the past decade, several key class prediction (KCP) ...

ParametrizANI: Fast and Accessible Dihedral Parametrization for Small Molecules.

Journal of chemical information and modeling
In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing detailed protocols for dihedral parametrization u...