AIMC Topic: Software

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Prediction of hub genes in pulpal inflammation and regeneration using autoencoders and a generative AI approach.

Scientific reports
Pulpal inflammation and regeneration are crucial for enhancing endodontic treatment outcomes. Transcriptomic studies highlight the involvement of proinflammatory cytokines, NF-κB signaling, and stem cell activity. This study employs a generative AI a...

Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using Human Proteome.

Journal of proteome research
Recently, deep-learning-based spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as a library-free search, thereby making DIA analysis more accessible. H...

Statistical toolkit for analysis of radiotherapy DICOM data.

Biomedical physics & engineering express
Radiotherapy (RT) has become increasingly sophisticated, necessitating advanced tools for analyzing extensive treatment data in hospital databases. Such analyses can enhance future treatments, particularly through Knowledge-Based Planning, and aid in...

Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution.

BMC bioinformatics
BACKGROUND: Inferring Gene Regulatory Networks (GRNs) from gene expression data is a pivotal challenge in systems biology. Most existing methods fail to consider the skewed degree distribution of genes, complicating the application of directed graph ...

EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2.

PLoS computational biology
Ubiquitination is critical in biomedical research. Predicting ubiquitination sites based on deep learning model have advanced the study of ubiquitination. However, traditional supervised model limits in the scenarios where labels are scarcity across ...

Rapid Screening of Methicillin-Resistant Using MALDI-TOF MS and Machine Learning: A Randomized, Multicenter Study.

Analytical chemistry
Methicillin-resistant (MRSA) is a major cause of healthcare-associated infections including bacteremia. The rapid detection of MRSA is essential for prompt treatment and improved outcomes. However, traditional MRSA screening and confirmatory tests b...

DeepEthoProfile-Rapid Behavior Recognition in Long-Term Recorded Home-Cage Mice.

eNeuro
Animal behavior is crucial for understanding both normal brain function and dysfunction. To facilitate behavior analysis of mice within their home environments, we developed DeepEthoProfile, an open-source software powered by a deep convolutional neu...

NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks.

Journal of chemical information and modeling
Unsupervised machine learning has recently gained much attention in the field of molecular dynamics (MD). Particularly, dimensionality reduction techniques have been regularly employed to analyze large volumes of high-dimensional MD data to gain insi...

CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.

Journal of computer-aided molecular design
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...

Rprot-Vec: a deep learning approach for fast protein structure similarity calculation.

BMC bioinformatics
BACKGROUND: Predicting protein structural similarity and detecting homologous sequences remain fundamental and challenging tasks in computational biology. Accurate identification of structural homologs enables function inference for newly discovered ...