AIMC Topic: Computational Biology

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Artificial intelligence and computational pathology.

Laboratory investigation; a journal of technical methods and pathology
Data processing and learning has become a spearhead for the advancement of medicine, with pathology and laboratory medicine has no exception. The incorporation of scientific research through clinical informatics, including genomics, proteomics, bioin...

Choroid Segmentation of Retinal OCT Images Based on CNN Classifier and - Fitter.

Computational and mathematical methods in medicine
Optical coherence tomography (OCT) is a noninvasive cross-sectional imaging technology used to examine the retinal structure and pathology of the eye. Evaluating the thickness of the choroid using OCT images is of great interests for clinicians and r...

On transformative adaptive activation functions in neural networks for gene expression inference.

PloS one
Gene expression profiling was made more cost-effective by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D-GEX method employs neural networks to infer the entire profile. H...

ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations.

Journal of molecular biology
The ELASPIC web server allows users to evaluate the effect of mutations on protein folding and protein-protein interaction on a proteome-wide scale. It uses homology models of proteins and protein-protein interactions, which have been precalculated f...

GVES: machine learning model for identification of prognostic genes with a small dataset.

Scientific reports
Machine learning may be a powerful approach to more accurate identification of genes that may serve as prognosticators of cancer outcomes using various types of omics data. However, to date, machine learning approaches have shown limited prediction a...

A 9 mRNAs-based diagnostic signature for rheumatoid arthritis by integrating bioinformatic analysis and machine-learning.

Journal of orthopaedic surgery and research
BACKGROUND: Rheumatoid arthritis (RA) is an autoimmune rheumatic disease that carries a substantial burden for both patients and society. Early diagnosis of RA is essential to prevent disease progression and select an optimal therapeutic strategy. Ho...

Analyzing Surgical Treatment of Intestinal Obstruction in Children with Artificial Intelligence.

Computational and mathematical methods in medicine
Intestinal obstruction is a common surgical emergency in children. However, it is challenging to seek appropriate treatment for childhood ileus since many diagnostic measures suitable for adults are not applicable to children. The rapid development o...

Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform.

BMC bioinformatics
BACKGROUND: Querying drug-induced gene expression profiles with machine learning method is an effective way for revealing drug mechanism of actions (MOAs), which is strongly supported by the growth of large scale and high-throughput gene expression d...

MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism.

BMC bioinformatics
BACKGROUND: Accurate prediction of binding between class I human leukocyte antigen (HLA) and neoepitope is critical for target identification within personalized T-cell based immunotherapy. Many recent prediction tools developed upon the deep learnin...