AIMC Topic: Phenotype

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Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.

Genetics in medicine : official journal of the American College of Medical Genetics
PURPOSE: Despite the successful progress next-generation sequencing technologies has achieved in diagnosing the genetic cause of rare Mendelian diseases, the current diagnostic rate is still far from satisfactory because of heterogeneity, imprecision...

Multi-task learning improves ancestral state reconstruction.

Theoretical population biology
We consider the ancestral state reconstruction problem where we need to infer phenotypes of ancestors using observations from present-day species. For this problem, we propose a multi-task learning method that uses regularized maximum likelihood to e...

Identifying facial phenotypes of genetic disorders using deep learning.

Nature medicine
Syndromic genetic conditions, in aggregate, affect 8% of the population. Many syndromes have recognizable facial features that are highly informative to clinical geneticists. Recent studies show that facial analysis technologies measured up to the ca...

Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide.

Molecular psychiatry
Suicide accounts for nearly 800,000 deaths per year worldwide with rates of both deaths and attempts rising. Family studies have estimated substantial heritability of suicidal behavior; however, collecting the sample sizes necessary for successful ge...

Computer vision-based phenotyping for improvement of plant productivity: a machine learning perspective.

GigaScience
Employing computer vision to extract useful information from images and videos is becoming a key technique for identifying phenotypic changes in plants. Here, we review the emerging aspects of computer vision for automated plant phenotyping. Recent a...

MITK Phenotyping: An open-source toolchain for image-based personalized medicine with radiomics.

Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology
Radiomics - The extraction of quantitative features from radiologic images - shows increasing potential in contributing to modern personalized medicine approaches. MITK Phenotyping is an openly distributed radiomics framework implementing an exhausti...

A Machine Learning Approach to Reveal the NeuroPhenotypes of Autisms.

International journal of neural systems
Although much research has been undertaken, the spatial patterns, developmental course, and sexual dimorphism of brain structure associated with autism remains enigmatic. One of the difficulties in investigating differences between the sexes in autis...

Identifying mouse developmental essential genes using machine learning.

Disease models & mechanisms
The genes that are required for organismal survival are annotated as 'essential genes'. Identifying all the essential genes of an animal species can reveal critical functions that are needed during the development of the organism. To inform studies o...

EHR phenotyping via jointly embedding medical concepts and words into a unified vector space.

BMC medical informatics and decision making
BACKGROUND: There has been an increasing interest in learning low-dimensional vector representations of medical concepts from Electronic Health Records (EHRs). Vector representations of medical concepts facilitate exploratory analysis and predictive ...

Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology.

PloS one
Identifying disease genes from a vast amount of genetic data is one of the most challenging tasks in the post-genomic era. Also, complex diseases present highly heterogeneous genotype, which difficult biological marker identification. Machine learnin...