AIMC Topic: Software

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Partial least squares methods in open-source software for identification of adulterated creatine using infrared spectroscopy.

Food chemistry
Creatine is one of the most consumed food supplements by people who practice physical activity. We developed a new methodology by associating Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) with multivariate analyses for screening a...

CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network.

International journal of biological macromolecules
Cas proteins (CRISPR-associated protein) are the core components of the CRISPR-Cas system, playing critical roles in defending against foreign DNA and RNA invasions. Identifying Cas proteins can provide deeper insights into the immune mechanisms of t...

PCANN Program for Structure-Based Prediction of Protein-Protein Binding Affinity: Comparison With Other Neural-Network Predictors.

Proteins
In this communication, we introduce a new structure-based affinity predictor for protein-protein complexes. This predictor, dubbed PCANN (Protein Complex Affinity by Neural Network), uses the ESM-2 language model to encode the information about prote...

scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis.

Genome biology
Discovering a lower-dimensional embedding of single-cell data can improve downstream analysis. The embedding should encapsulate both the high-level features and low-level variations. While existing generative models attempt to learn such low-dimensio...

Can Artificial Intelligence Software be Utilised for Thyroid Multi-Disciplinary Team Outcomes?

Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery
OBJECTIVES: ChatGPT is one of the most publicly available artificial intelligence (AI) softwares. Ear, nose and throat (ENT) services are often stretched due to the increasing incidence of thyroid malignancies. This study aims to investigate whether ...

TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.

Nature communications
Tools available for inferring enzyme function from general sequence, fold, or evolutionary information are generally successful. However, they can lead to misclassification if a deviation in local structural features influences the function. Here, we...

Volume-based complete automation for ultrasound fetal biometry: A pilot approach to assess feasibility, reliability, and perspectives.

International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics
BACKGROUND: Detection algorithms targeting anatomic landmarks in three-dimensional (3D) ultrasound (US) volume (three-dimensional US) appear to be a relevant and easy-to-implement option to address junior and occasional operators' difficulties in pro...

CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.

BMC genomics
BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent yea...

PlantPathoPPI: An Ensemble-based Machine Learning Architecture for Prediction of Protein-Protein Interactions between Plants and Pathogens.

Journal of molecular biology
This study aimed to develop a machine learning-based tool for predicting protein-protein interactions (PPIs) between plant-pathogen systems, addressing the challenges of experimental PPI identification. Identifying PPIs in plant-pathogen interactions...

Real time artificial intelligence assisted carotid artery stenting: a preliminary experience.

Journal of neurointerventional surgery
BACKGROUND: Neurointerventionalists must pay close attention to multiple devices on multiple screens simultaneously, which can lead to oversights and complications. Artificial intelligence (AI) has potential application in recognizing and monitoring ...