AIMC Topic: Software

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TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.

Communications biology Apr 5, 2025
Identifying DNA-binding proteins and their binding residues is critical for understanding diverse biological processes, but conventional experimental approaches are slow and costly. Existing machine learning methods, while faster, often lack accuracy...
Sequence Alignment Sequence Analysis, Protein Humans Software Computational Biology DNA-Binding Proteins Deep Learning
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CodonTransformer: a multispecies codon optimizer using context-aware neural networks.

Nature communications Apr 3, 2025
Degeneracy in the genetic code allows many possible DNA sequences to encode the same protein. Optimizing codon usage within a sequence to meet organism-specific preferences faces combinatorial explosion. Nevertheless, natural sequences optimized thro...
Humans Neural Networks, Computer Deep Learning Codon Genetic Code Software Algorithms Codon Usage
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Using artificial intelligence tools to automate data extraction for living evidence syntheses.

PloS one Apr 3, 2025
Living evidence synthesis (LES) involves repeatedly updating a systematic review or meta-analysis at regular intervals to incorporate new evidence into the summary results. It requires a considerable amount of human time investment in the article sea...
SARS-CoV-2 Software Meta-Analysis as Topic Systematic Reviews as Topic COVID-19 Humans Information Storage and Retrieval Artificial Intelligence
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DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration.

BMC bioinformatics Apr 1, 2025
BACKGROUND: Chromatin loops are critical for the three-dimensional organization of the genome and gene regulation. Accurate identification of chromatin loops is essential for understanding the regulatory mechanisms in disease. However, current mainst...
Computational Biology Software Humans Chromatin Deep Learning Chromatin Immunoprecipitation Sequencing
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optRF: Optimising random forest stability by determining the optimal number of trees.

BMC bioinformatics Mar 31, 2025
Machine learning is frequently used to make decisions based on big data. Among these techniques, random forest is particularly prominent. Although random forest is known to have many advantages, one aspect that is often overseen is that it is a non-d...
Algorithms Big Data Machine Learning Software Computational Biology Random Forest
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DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.

Journal of chemical information and modeling Mar 27, 2025
Machine learning potentials (MLPs) have revolutionized molecular simulation by providing efficient and accurate models for predicting atomic interactions. MLPs continue to advance and have had profound impact in applications that include drug discove...
Quantum Theory Graph Neural Networks Neural Networks, Computer Software Molecular Dynamics Simulation
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aurora: a machine learning gwas tool for analyzing microbial habitat adaptation.

Genome biology Mar 23, 2025
A primary goal of microbial genome-wide association studies is identifying genomic variants associated with a particular habitat. Existing tools fail to identify known causal variants if the analyzed trait shaped the phylogeny. Furthermore, due to in...
Machine Learning Bacteria Adaptation, Physiological Phylogeny Software Genome-Wide Association Study Ecosystem
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CasPro-ESM2: Accurate identification of Cas proteins integrating pre-trained protein language model and multi-scale convolutional neural network.

International journal of biological macromolecules Mar 22, 2025
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...
Convolutional Neural Networks Computational Biology CRISPR-Associated Proteins CRISPR-Cas Systems Neural Networks, Computer Software
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scVAEDer: integrating deep diffusion models and variational autoencoders for single-cell transcriptomics analysis.

Genome biology Mar 21, 2025
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...
Single-Cell Analysis Autoencoder Transcriptome Deep Learning Software Humans Gene Expression Profiling
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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 Mar 20, 2025
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 ...
Female Aged Software Retrospective Studies Middle Aged Thyroid Neoplasms Patient Care Team Humans Adult Male Artificial Intelligence
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