AIMC Topic: Phenotype

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Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).

GigaScience Jan 2, 2024
BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenoty...
Mutation Opsins Animals Genotype Genetic Association Studies Databases, Genetic Machine Learning Phenotype Humans
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Deep learning links localized digital pathology phenotypes with transcriptional subtype and patient outcome in glioblastoma.

GigaScience Jan 2, 2024
BACKGROUND: Deep learning has revolutionized medical image analysis in cancer pathology, where it had a substantial clinical impact by supporting the diagnosis and prognostic rating of cancer. Among the first available digital resources in the field ...
Humans Neural Networks, Computer Brain Neoplasms Deep Learning Phenotype Prognosis Glioblastoma
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A Large Language Model Outperforms Other Computational Approaches to the High-Throughput Phenotyping of Physician Notes.

AMIA ... Annual Symposium proceedings. AMIA Symposium Jan 1, 2024
High-throughput phenotyping, the automated mapping of patient signs and symptoms to standardized ontology concepts, is essential for realizing value from electronic health records (EHR) in support of precision medicine. Despite technological advances...
Machine Learning Phenotype Humans Artificial Intelligence Deep Learning Natural Language Processing Large Language Models Electronic Health Records Language
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Machine Learning Strategies for Improved Phenotype Prediction in Underrepresented Populations.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2024
Precision medicine models often perform better for populations of European ancestry due to the over-representation of this group in the genomic datasets and large-scale biobanks from which the models are constructed. As a result, prediction models ma...
Computational Biology White People Minority Groups UK Biobank Machine Learning Humans Phenotype
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SSLpheno: a self-supervised learning approach for gene-phenotype association prediction using protein-protein interactions and gene ontology data.

Bioinformatics (Oxford, England) Nov 1, 2023
MOTIVATION: Medical genomics faces significant challenges in interpreting disease phenotype and genetic heterogeneity. Despite the establishment of standardized disease phenotype databases, computational methods for predicting gene-phenotype associat...
Gene Ontology Neural Networks, Computer Genomics Supervised Machine Learning Phenotype
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Automated and reproducible cell identification in mass cytometry using neural networks.

Briefings in bioinformatics Sep 22, 2023
The principal use of mass cytometry is to identify distinct cell types and changes in their composition, phenotype and function in different samples and conditions. Combining data from different studies has the potential to increase the power of thes...
COVID-19 Humans Phenotype Neural Networks, Computer Flow Cytometry
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SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding.

Briefings in bioinformatics Sep 22, 2023
Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. A...
Genome, Plant Humans Plant Breeding Phenotype Deep Learning Genomics Glycine max
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Spatially aware deep learning reveals tumor heterogeneity patterns that encode distinct kidney cancer states.

Cell reports. Medicine Sep 19, 2023
Clear cell renal cell carcinoma (ccRCC) is molecularly heterogeneous, immune infiltrated, and selectively sensitive to immune checkpoint inhibition (ICI). However, the joint tumor-immune states that mediate ICI response remain elusive. We develop spa...
Kidney Neoplasms Carcinoma, Renal Cell Deep Learning Humans Carcinoma Phenotype
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Deep learning-based activity recognition and fine motor identification using 2D skeletons of cynomolgus monkeys.

Zoological research Sep 18, 2023
Video-based action recognition is becoming a vital tool in clinical research and neuroscientific study for disorder detection and prediction. However, action recognition currently used in non-human primate (NHP) research relies heavily on intense man...
Deep Learning Mutation Macaca fascicularis Skeleton Phenotype Animals
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ActivePPI: quantifying protein-protein interaction network activity with Markov random fields.

Bioinformatics (Oxford, England) Sep 2, 2023
MOTIVATION: Protein-protein interactions (PPI) are crucial components of the biomolecular networks that enable cells to function. Biological experiments have identified a large number of PPI, and these interactions are stored in knowledge bases. Howe...
Probability Mass Spectrometry Knowledge Bases Phenotype Protein Interaction Maps
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