AIMC Topic: Software

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2023 Survey on User Experience of Artificial Intelligence Software in Radiology by the Korean Society of Radiology.

Korean journal of radiology
OBJECTIVE: In Korea, radiology has been positioned towards the early adoption of artificial intelligence-based software as medical devices (AI-SaMDs); however, little is known about the current usage, implementation, and future needs of AI-SaMDs. We ...

ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries.

Bioinformatics (Oxford, England)
MOTIVATION: The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded the chemical diversity of small molecules for drug discovery. Selecting compound...

FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology.

Bioinformatics (Oxford, England)
MOTIVATION: Human Phenotype Ontology (HPO)-based phenotype concept recognition (CR) underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing...

CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations.

Bioinformatics (Oxford, England)
MOTIVATION: High-throughput screens (HTS) provide a powerful tool to decipher the causal effects of chemical and genetic perturbations on cancer cell lines. Their ability to evaluate a wide spectrum of interventions, from single drugs to intricate dr...

A machine-learning-based alternative to phylogenetic bootstrap.

Bioinformatics (Oxford, England)
MOTIVATION: Currently used methods for estimating branch support in phylogenetic analyses often rely on the classic Felsenstein's bootstrap, parametric tests, or their approximations. As these branch support scores are widely used in phylogenetic ana...

Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model.

Bioinformatics (Oxford, England)
MOTIVATION: High-resolution Hi-C contact matrices reveal the detailed three-dimensional architecture of the genome, but high-coverage experimental Hi-C data are expensive to generate. Simultaneously, chromatin structure analyses struggle with extreme...

Quantification of follicles in human ovarian tissue using image processing software and trained artificial intelligence†.

Biology of reproduction
Cancer survival rates in prepubertal girls and young women have risen in recent decades due to increasingly efficient treatments. However, many such treatments are gonadotoxic, causing premature ovarian insufficiency, loss of fertility, and ovarian e...

DEAttentionDTA: protein-ligand binding affinity prediction based on dynamic embedding and self-attention.

Bioinformatics (Oxford, England)
MOTIVATION: Predicting protein-ligand binding affinity is crucial in new drug discovery and development. However, most existing models rely on acquiring 3D structures of elusive proteins. Combining amino acid sequences with ligand sequences and bette...

SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.

Bioinformatics (Oxford, England)
SUMMARY: The increasing development of sequence-based machine learning models has raised the demand for manipulating sequences for this application. However, existing approaches to edit and evaluate genome sequences using models have limitations, suc...