AIMC Topic: Software

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CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions.

Nucleic acids research
Machine Learning-based scoring and classification of genetic variants aids the assessment of clinical findings and is employed to prioritize variants in diverse genetic studies and analyses. Combined Annotation-Dependent Depletion (CADD) is one of th...

Simulations of Sequence Evolution: How (Un)realistic They Are and Why.

Molecular biology and evolution
MOTIVATION: Simulating multiple sequence alignments (MSAs) using probabilistic models of sequence evolution plays an important role in the evaluation of phylogenetic inference tools and is crucial to the development of novel learning-based approaches...

CoCoPyE: feature engineering for learning and prediction of genome quality indices.

GigaScience
BACKGROUND: The exploration of the microbial world has been greatly advanced by the reconstruction of genomes from metagenomic sequence data. However, the rapidly increasing number of metagenome-assembled genomes has also resulted in a wide variation...

RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes.

GigaScience
BACKGROUND: The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health a...

CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.

GigaScience
BACKGROUND: RNA-RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico or experimental high-throug...

IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning.

GigaScience
BACKGROUND: The virome obtained through virus-like particle enrichment contains a mixture of prokaryotic and eukaryotic virus-derived fragments. Accurate identification and classification of these elements are crucial to understanding their roles and...

Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning-driven data analysis.

GigaScience
BACKGROUND: Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding consider...

[The use of artificial intelligence in modern dentistry in the Russian Federation].

Stomatologiia
OBJECTIVE: The aim of the study is to identify the prospects and possibilities of using artificial intelligence (AI) and domestic software in the provision of organization dental care in the Russian Federation.

[Modern opportunities of using computer programs and mobile devices in the frame of personality identification].

Sudebno-meditsinskaia ekspertiza
A technology of mobile devices on the basis of Android and iOS sharing, in which previously trained neural networks on the mobile device with the use of the Skull-face program place the reference points in automatic mode with subsequent analysis of t...

DNeuroMAT: A Deep-Learning-Based Neuron Morphology Analysis Toolbox.

Methods in molecular biology (Clifton, N.J.)
Digital reconstruction of neuronal structures from 3D neuron microscopy images is critical for the quantitative investigation of brain circuits and functions. Currently, neuron reconstructions are mainly obtained by manual or semiautomatic methods. H...