AIMC Topic: Software

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PyNoetic: A modular python framework for no-code development of EEG brain-computer interfaces.

PloS one Aug 6, 2025
Electroencephalography (EEG)-based Brain-Computer Interfaces (BCIs) have emerged as a transformative technology with applications spanning robotics, virtual reality, medicine, and rehabilitation. However, existing BCI frameworks face several limitati...
Algorithms Brain Electroencephalography Humans Software Signal Processing, Computer-Assisted Brain-Computer Interfaces
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varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction.

Genome medicine Aug 4, 2025
BACKGROUND: Machine learning and artificial intelligence are increasingly being applied to identify phenotypically causal genetic variation. These data-driven methods require comprehensive training sets to deliver reliable results. However, large unb...
Humans Genomics Computational Biology Databases, Genetic Machine Learning Software Genome-Wide Association Study Genetic Variation Genome, Human
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Semi-supervised contrastive learning variational autoencoder Integrating single-cell multimodal mosaic datasets.

BMC bioinformatics Aug 4, 2025
As single-cell sequencing technology became widely used, scientists found that single-modality data alone could not fully meet the research needs of complex biological systems. To address this issue, researchers began simultaneously collect multi-mod...
Single-Cell Analysis Computational Biology Cluster Analysis Supervised Machine Learning Autoencoder Humans Software Algorithms
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Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials.

Journal of chemical information and modeling Jul 29, 2025
We introduce Atomistic learned potentials in JAX (apax), a flexible and efficient open source software package for training and inference of machine-learned interatomic potentials. Built on the JAX framework, apax supports GPU acceleration and implem...
Machine Learning Software Ionic Liquids Neural Networks, Computer
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PuMA: PubMed gene/cell type-relation Atlas.

BMC bioinformatics Jul 29, 2025
BACKGROUND: Rapid extraction and visualization of cell-specific gene expression is important for automatic cell type annotation, e.g. in single cell analysis. There is an emerging field in which tools such as curated databases or machine learning met...
Databases, Genetic PubMed Animals Mice Humans Machine Learning Software
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Prediction of hub genes in pulpal inflammation and regeneration using autoencoders and a generative AI approach.

Scientific reports Jul 19, 2025
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...
Software Gene Expression Profiling Transcriptome Protein Interaction Maps Gene Regulatory Networks Humans Artificial Intelligence Pulpitis Autoencoder Dental Pulp Regeneration Gene Ontology Computational Biology Inflammation
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Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using Human Proteome.

Journal of proteome research Jul 18, 2025
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...
Tandem Mass Spectrometry Gene Library Proteome Mass Spectrometry Chromatography, Liquid Recombinant Proteins Proteomics Humans Software Peptides Deep Learning
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Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.

NAR genomics and bioinformatics Jul 17, 2025
The metagenome analysis of complex environments with thousands of datasets, such as those in the Sequence Read Archive, requires substantial computational resources for it to be completed within a reasonable time frame. Efficient use of infrastructur...
Cloud Computing Metagenome Workflow Metagenomics Machine Learning Software
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Statistical toolkit for analysis of radiotherapy DICOM data.

Biomedical physics & engineering express Jul 17, 2025
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...
Radiotherapy Dosage Organs at Risk Humans Radiotherapy Planning, Computer-Assisted Retrospective Studies Software Neoplasms Algorithms Principal Component Analysis Databases, Factual
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Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution.

BMC bioinformatics Jul 16, 2025
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 ...
Computational Biology Software Graph Neural Networks Humans Databases, Genetic Algorithms Neural Networks, Computer Gene Regulatory Networks
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