AIMC Topic: Software

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VNC-Dist: A machine learning-based semi-automated pipeline for quantification of neuronal position in the C. elegans ventral nerve cord.

PloS one
The C. elegans ventral nerve cord (VNC) provides a genetically tractable model for investigating the developmental mechanisms involved in neuronal positioning and organization. The VNC of newly hatched larvae contains a set of 22 motoneurons organize...

Developing a hybrid machine learning model to predict treatment time duration as a workflow regulation tool in public and private dental clinics.

Scientific reports
This study aimed to design a desktop application that implements machine learning algorithms to predict dental treatment time durations, assess the accuracy of the model, and assess its clinical efficiency. The Python programming language was used to...

GNODEVAE: a graph-based ODE-VAE enhances clustering for single-cell data.

BMC genomics
BACKGROUND: Single-cell RNA sequencing analysis faces critical challenges including high dimensionality, sparsity, and complex topological relationships between cells. Current methods struggle to simultaneously preserve global structure, model cellul...

NetStart 2.0: prediction of eukaryotic translation initiation sites using a protein language model.

BMC bioinformatics
BACKGROUND: Accurate identification of translation initiation sites is essential for the proper translation of mRNA into functional proteins. In eukaryotes, the choice of the translation initiation site is influenced by multiple factors, including it...

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

PloS one
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...

Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX.

Journal of proteomics
The rapid pace of shotgun proteomics data generation presents challenges for timely data analysis. In parallel, the scientific community is creating novel data interpretation tools, such as artificial intelligence, that have not yet been integrated i...

varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction.

Genome medicine
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...

Semi-supervised contrastive learning variational autoencoder Integrating single-cell multimodal mosaic datasets.

BMC bioinformatics
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...

Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials.

Journal of chemical information and modeling
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...

PuMA: PubMed gene/cell type-relation Atlas.

BMC bioinformatics
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...