AIMC Topic: Software

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PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease.

Bioinformatics (Oxford, England)
MOTIVATION: Whole-exome sequencing (WES) is now being used in clinical practice for the diagnosis of the causal genes of Mendelian diseases. In order to make the diagnosis, however, the clinical phenotypes [e.g. Human Phenotype Ontology (HPO) terms] ...

[Study on the Clinical Evaluation of Image-based Artificial Intelligence Aided Diagnosis Software Approved in the United States].

Zhongguo yi liao qi xie za zhi = Chinese journal of medical instrumentation
Artificial intelligence, as the breakthrough of current information technology, is gaining importance and being applied in more and more industries. Research on the application of artificial intelligence to the medical field has gradually matured and...

HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.

Nucleic acids research
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragm...

DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy and interpretability.

refineD: improved protein structure refinement using machine learning based restrained relaxation.

Bioinformatics (Oxford, England)
MOTIVATION: Protein structure refinement aims to bring moderately accurate template-based protein models closer to the native state through conformational sampling. However, guiding the sampling towards the native state by effectively using restraint...

Biological sequence modeling with convolutional kernel networks.

Bioinformatics (Oxford, England)
MOTIVATION: The growing number of annotated biological sequences available makes it possible to learn genotype-phenotype relationships from data with increasingly high accuracy. When large quantities of labeled samples are available for training a mo...

Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Current protocols in human genetics
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnost...

Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging.

Bioinformatics (Oxford, England)
MOTIVATION: Functional imaging at single-neuron resolution offers a highly efficient tool for studying the functional connectomics in the brain. However, mainstream neuron-detection methods focus on either the morphologies or activities of neurons, w...

Introduction of a Pathophysiology-Based Diagnostic Decision Support System and Its Potential Impact on the Use of AI in Healthcare.

Studies in health technology and informatics
Many currently available Diagnostic Decision Support Systems (DDSS) are based on causal condition-symptom relations that exhibit certain shortcomings. Ada's new approach explores the capabilities of DDSS based on pathophysiology, describing a disease...