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Fernando hpcrun #8

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Fernando hpcrun #8

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9364787
Add hyperparameter-viz plot
fguntoro Jul 21, 2021
e46c19b
add dash table for params
fguntoro Jul 22, 2021
5779a29
add eval metric plots
fguntoro Jul 22, 2021
85eda9f
Add summary plots
fguntoro Jul 23, 2021
7359543
change styling dark 30%
fguntoro Jul 24, 2021
663a766
styling dark 100%
fguntoro Jul 26, 2021
4612f7b
moved buttons and corrected data dependencies
fguntoro Jul 26, 2021
5a84ce3
Add files for meeting update
fguntoro Jul 28, 2021
c346bf0
ingotdr implementation
fguntoro Aug 7, 2021
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13 changes: 7 additions & 6 deletions config.yaml
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Original file line number Diff line number Diff line change
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#PATH_DATA: "/mnt/c/Users/Fernando/Documents/Project_2/Pipeline_dataset"
PATH_DATA: "/rds/general/user/fg520/home/Project2/pipeline_dataset" # specifiy path to folder where data is stored (only folder name, no / afterwards)

#BACTERIA: ["test_bacterium"]
BACTERIA: ["mtb"]
BACTERIA: ["e_coli"]

#OUTPUT_DIR: "/mnt/c/Users/Fernando/Documents/Project_2/output"
OUTPUT_DIR: "/rds/general/user/fg520/home/Project2/output"

REPRESENTATION: ["gene_presence_absence"] # 'snps', 'gene_presence_absence'

# LABEL_TYPE: Susceptibility # 'Susceptibility' or 'MIC'
#TODO LABEL_TYPE: Susceptibility # 'Susceptibility' or 'MIC'

DRUGS: ["amikacin", "capreomycin", "ciprofloxacin", "ethambutol", "ethionamide", "isoniazid", "kanamycin", "moxifloxacin", "ofloxacin", "pyrazinamide", "rifampicin", "streptomycin"]
DRUGS: ["AMC", "AMP", "AMX", "CET", "CIP", "CTX", "CTZ", "CXM", "GEN", "TBM", "TMP", "TZP"]
# "AMC", "AMP", "AMX", "CET", "CIP", "CTX", "CTZ", "CXM", "GEN", "TBM", "TMP", "TZP"

METHODS: ["LR_l1", "LR_l2", "LR_elasticnet", "SGD_l1", "SGD_l2", "SGD_elasticnet", "DT", "RF", "ET", "ADB", "GBT", "GNB", "CNB", "SVM_l1", "SVM_l2", "KNN"]
METHODS: ["INGOT"]
# "LR_elasticnet", "SGD_l1", "SGD_l2", "SGD_elasticnet", "DT", "RF", "ET", "ADB", "GBT", "SVM_l1", "KNN", "LR_l1", "LR_l2", "SVM_l2", "GNB", "CNB"

OPTIMIZATION: GridSearchCV # 'GridSearchCV', 'RandomizedSearchCV', 'BayesSearchCV' and "none"
OPTIMIZATION: "GridSearchCV" # 'GridSearchCV', 'RandomizedSearchCV', 'BayesSearchCV' and "none"
Empty file removed data/acinetobacter_baumannii/kmer/.gitkeep
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3 changes: 0 additions & 3 deletions data/gene_data/0_matrix.csv
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22,377 changes: 0 additions & 22,377 deletions data/gene_data/AllLabels.csv
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