AIMC Topic: Machine Learning

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Gynecological Surgery and Machine Learning: Complications and Length of Stay Prediction.

Studies in health technology and informatics
In this study we are developing predictive models for a length of stay after a gynecological surgery, complications and the length of the surgery using machine learning methods. The study was performed with the data of patients with the diseases of t...

CATH functional families predict functional sites in proteins.

Bioinformatics (Oxford, England)
MOTIVATION: Identification of functional sites in proteins is essential for functional characterization, variant interpretation and drug design. Several methods are available for predicting either a generic functional site, or specific types of funct...

LightBBB: computational prediction model of blood-brain-barrier penetration based on LightGBM.

Bioinformatics (Oxford, England)
MOTIVATION: Identification of blood-brain barrier (BBB) permeability of a compound is a major challenge in neurotherapeutic drug discovery. Conventional approaches for BBB permeability measurement are expensive, time-consuming and labor-intensive. BB...

A representation model for biological entities by fusing structured axioms with unstructured texts.

Bioinformatics (Oxford, England)
MOTIVATION: Structured semantic resources, for example, biological knowledge bases and ontologies, formally define biological concepts, entities and their semantic relationships, manifested as structured axioms and unstructured texts (e.g. textual de...

High-throughput image segmentation and machine learning approaches in the plant sciences across multiple scales.

Emerging topics in life sciences
Agriculture has benefited greatly from the rise of big data and high-performance computing. The acquisition and analysis of data across biological scales have resulted in strategies modeling inter- actions between plant genotype and environment, mode...

Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning.

Briefings in bioinformatics
MOTIVATION: The genome-wide discovery of microRNAs (miRNAs) involves identifying sequences having the highest chance of being a novel miRNA precursor (pre-miRNA), within all the possible sequences in a complete genome. The known pre-miRNAs are usuall...

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches.

Briefings in bioinformatics
The multi-omics molecular characterization of cancer opened a new horizon for our understanding of cancer biology and therapeutic strategies. However, a tumor biopsy comprises diverse types of cells limited not only to cancerous cells but also to tum...

DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges.

Briefings in bioinformatics
Atomic charges play a very important role in drug-target recognition. However, computation of atomic charges with high-level quantum mechanics (QM) calculations is very time-consuming. A number of machine learning (ML)-based atomic charge prediction ...

State-of-the-art web services for de novo protein structure prediction.

Briefings in bioinformatics
Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent...

scCancer: a package for automated processing of single-cell RNA-seq data in cancer.

Briefings in bioinformatics
Molecular heterogeneities and complex microenvironments bring great challenges for cancer diagnosis and treatment. Recent advances in single-cell RNA-sequencing (scRNA-seq) technology make it possible to study cancer cell heterogeneities and microenv...