AIMC Topic: Software

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WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.

Briefings in bioinformatics
Understanding the functional consequence of noncoding variants is of great interest. Though genome-wide association studies or quantitative trait locus analyses have identified variants associated with traits or molecular phenotypes, most of them are...

nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning.

Briefings in bioinformatics
Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identificatio...

NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning.

Briefings in bioinformatics
Neuropeptides (NPs) are the most versatile neurotransmitters in the immune systems that regulate various central anxious hormones. An efficient and effective bioinformatics tool for rapid and accurate large-scale identification of NPs is critical in ...

Knowledge bases and software support for variant interpretation in precision oncology.

Briefings in bioinformatics
Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and mole...

EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps.

Briefings in bioinformatics
Cryo-electron microscopy (cryo-EM) has become one of important experimental methods in structure determination. However, despite the rapid growth in the number of deposited cryo-EM maps motivated by advances in microscopy instruments and image proces...

SSI-DDI: substructure-substructure interactions for drug-drug interaction prediction.

Briefings in bioinformatics
A major concern with co-administration of different drugs is the high risk of interference between their mechanisms of action, known as adverse drug-drug interactions (DDIs), which can cause serious injuries to the organism. Although several computat...

A new machine learning based user-friendly software platform for automatic radiomics modeling and analysis.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Supervised machine learning methods are usually used to build a custom model for disease diagnosis and auxiliary prognosis in radiomics studies. A classical machine learning pipeline involves a series of steps and multiple algorithms, which leads to ...

Separating Hope from Hype: Artificial Intelligence Pitfalls and Challenges in Radiology.

Radiologic clinics of North America
Although recent scientific studies suggest that artificial intelligence (AI) could provide value in many radiology applications, much of the hard engineering work required to consistently realize this value in practice remains to be done. In this art...

Reproducibility standards for machine learning in the life sciences.

Nature methods
To make machine learning analyses in the life sciences more computationally reproducible, we propose standards based on data, model, and code publication, programming best practices, and workflow automation. By meeting these standards, the community ...