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algorithm python » algorithm within (Expand Search), algorithms within (Expand Search), algorithm both (Expand Search)
algorithm three » algorithm where (Expand Search), algorithm pre (Expand Search)
python function » protein function (Expand Search)
three function » three functional (Expand Search), tree functional (Expand Search), time function (Expand Search)
algorithm gene » algorithm where (Expand Search), algorithm etc (Expand Search), algorithm pre (Expand Search)
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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Published 2019“…BOFdat has a modular implementation that divides the BOF definition process into three independent modules defined here as steps: 1) the coefficients for major macromolecules are calculated, 2) coenzymes and inorganic ions are identified and their stoichiometric coefficients estimated, 3) the remaining species-specific metabolic biomass precursors are algorithmically extracted in an unbiased way from experimental data. …”
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Mechanomics Code - JVT
Published 2025“…The functions were tested respectively in: MATLAB 2018a or youger, Python 3.9.4, R 4.0.3.…”
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Code
Published 2025“…We divided the dataset into training and test sets, using 70% of the genes for training and 30% for testing. We implemented machine learning algorithms using the following R packages: rpart for Decision Trees, gbm for Gradient Boosting Machines (GBM), ranger for Random Forests, the glm function for Generalized Linear Models (GLM), and xgboost for Extreme Gradient Boosting (XGB). …”
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Core data
Published 2025“…We divided the dataset into training and test sets, using 70% of the genes for training and 30% for testing. We implemented machine learning algorithms using the following R packages: rpart for Decision Trees, gbm for Gradient Boosting Machines (GBM), ranger for Random Forests, the glm function for Generalized Linear Models (GLM), and xgboost for Extreme Gradient Boosting (XGB). …”
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Expression vs genomics for predicting dependencies
Published 2024“…</p><p dir="ltr"><br></p><p dir="ltr">GeneRelationships.csv: A list of genes and their related (partner) genes, with the type of relationship (self, protein-protein interaction, CORUM complex membership, paralog). …”