AIMC Topic: Machine Learning

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Relational graph convolutional networks for predicting blood-brain barrier penetration of drug molecules.

Bioinformatics (Oxford, England)
MOTIVATION: Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico predict...

A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values).

Bioinformatics (Oxford, England)
MOTIVATION: Predicting drug response is critical for precision medicine. Diverse methods have predicted drug responsiveness, as measured by the half-maximal drug inhibitory concentration (IC50), in cultured cells. Although IC50s are continuous, tradi...

Improving confidence in lipidomic annotations by incorporating empirical ion mobility regression analysis and chemical class prediction.

Bioinformatics (Oxford, England)
MOTIVATION: Mass spectrometry-based untargeted lipidomics aims to globally characterize the lipids and lipid-like molecules in biological systems. Ion mobility increases coverage and confidence by offering an additional dimension of separation and a ...

deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions.

Briefings in bioinformatics
Host-pathogen protein interactions (HPPIs) play vital roles in many biological processes and are directly involved in infectious diseases. With the outbreak of more frequent pandemics in the last couple of decades, such as the recent outburst of Covi...

Transfer learning of clinical outcomes from preclinical molecular data, principles and perspectives.

Briefings in bioinformatics
Accurate transfer learning of clinical outcomes from one cellular context to another, between cell types, developmental stages, omics modalities or species, is considered tremendously useful. When transferring a prediction task from a source domain t...

Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides.

Briefings in bioinformatics
Therapeutic peptides act on the skeletal system, digestive system and blood system, have antibacterial properties and help relieve inflammation. In order to reduce the resource consumption of wet experiments for the identification of therapeutic pept...

Knowledge-based BERT: a method to extract molecular features like computational chemists.

Briefings in bioinformatics
Molecular property prediction models based on machine learning algorithms have become important tools to triage unpromising lead molecules in the early stages of drug discovery. Compared with the mainstream descriptor- and graph-based methods for mol...

A tool for feature extraction from biological sequences.

Briefings in bioinformatics
With the advances in sequencing technologies, a huge amount of biological data is extracted nowadays. Analyzing this amount of data is beyond the ability of human beings, creating a splendid opportunity for machine learning methods to grow. The metho...

Do deep learning models make a difference in the identification of antimicrobial peptides?

Briefings in bioinformatics
In the last few decades, antimicrobial peptides (AMPs) have been explored as an alternative to classical antibiotics, which in turn motivated the development of machine learning models to predict antimicrobial activities in peptides. The first genera...

RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA-RNA interaction.

Briefings in bioinformatics
Different ribonucleic acids (RNAs) can interact to form regulatory networks that play important role in many life activities. Molecular biology experiments can confirm RNA-RNA interactions to facilitate the exploration of their biological functions, ...