AIMC Topic: Software

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Architecture and usability of OntoKeeper, an ontology evaluation tool.

BMC medical informatics and decision making
BACKGROUND: The existing community-wide bodies of biomedical ontologies are known to contain quality and content problems. Past research has revealed various errors related to their semantics and logical structure. Automated tools may help to ease th...

PaleAle 5.0: prediction of protein relative solvent accessibility by deep learning.

Amino acids
Predicting the three-dimensional structure of proteins is a long-standing challenge of computational biology, as the structure (or lack of a rigid structure) is well known to determine a protein's function. Predicting relative solvent accessibility (...

Performance of machine learning software to classify breast lesions using BI-RADS radiomic features on ultrasound images.

European radiology experimental
BACKGROUND: The purpose of this work was to evaluate computable Breast Imaging Reporting and Data System (BI-RADS) radiomic features to classify breast masses on ultrasound B-mode images.

A neural network-based software to recognise blepharospasm symptoms and to measure eye closure time.

Computers in biology and medicine
Blepharospasm (BSP) is an adult-onset focal dystonia with phenomenologically heterogeneous effects, including, but not limited to, blinks, brief or prolonged spasms, and a narrowing or closure of the eyelids. In spite of the clear and well-known symp...

Sequence assignment for low-resolution modelling of protein crystal structures.

Acta crystallographica. Section D, Structural biology
The performance of automated model building in crystal structure determination usually decreases with the resolution of the experimental data, and may result in fragmented models and incorrect side-chain assignment. Presented here are new methods for...

Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.

Nature methods
Although structures determined at near-atomic resolution are now routinely reported by cryo-electron microscopy (cryo-EM), many density maps are determined at an intermediate resolution, and extracting structure information from these maps is still a...

Machine Vision Methods, Natural Language Processing, and Machine Learning Algorithms for Automated Dispersion Plot Analysis and Chemical Identification from Complex Mixtures.

Analytical chemistry
Gas-phase trace chemical detection techniques such as ion mobility spectrometry (IMS) and differential mobility spectrometry (DMS) can be used in many settings, such as evaluating the health condition of patients or detecting explosives at airports. ...

ROBOT: A Tool for Automating Ontology Workflows.

BMC bioinformatics
BACKGROUND: Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and appl...

A Guide for Using Deep Learning for Complex Trait Genomic Prediction.

Genes
Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability to predict phenotypic values from molecular data is less well studied. Here, we describe the theoreti...