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exp_lit.py
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181 lines (152 loc) · 5.6 KB
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from genericpath import exists
import numpy as np
import models.train_and_evaluate
import json
import copy
import os
import figure_auc_roc_curve
import figure_cm
import figure_cv_bacc
def load_spec(path):
with open(path, 'r') as f:
return json.load(f)
def main():
""" Model Comparisons on the SMF task """
mn_spec = load_spec("cfgs/smf_mn_model.json")
mn_spec['target_col'] = 'is_viable'
run_smf_cv_on_spec(mn_spec, 's-mn')
campos_spec = load_spec("cfgs/smf_campos_model.json")
run_smf_cv_on_spec(campos_spec, 'smf_campos')
lou_spec = load_spec("cfgs/smf_lou_model.json")
run_smf_cv_on_spec(lou_spec, "smf_lou")
mistry_spec = load_spec("cfgs/smf_mistry_model.json")
run_smf_cv_on_spec(mistry_spec, "smf_mistry")
generate_smf_figures()
""" Model Comparisons on the Negative vs All GI task """
mn_spec = load_spec("cfgs/gi_mn_model.json")
mn_spec['target_col'] = 'is_not_negative'
run_gi_cv_on_spec(mn_spec, "d-mn")
slant_spec = load_spec("cfgs/gi_slant_model.json")
run_gi_cv_on_spec(slant_spec, "gi_slant")
yu_spec = load_spec("cfgs/gi_yu_model.json")
run_gi_cv_on_spec(yu_spec, "gi_yu", n_workers=10)
alanis_spec = load_spec("cfgs/gi_alanis-lobato_model.json")
run_gi_cv_on_spec(alanis_spec, "gi_alanis-lobato")
generate_gi_figures()
def run_smf_cv_on_spec(model_spec, name):
postfix = '_lit'
if name == 's-mn':
postfix = ''
models.train_and_evaluate.cv(model_spec,
"../generated-data/dataset_yeast_smf%s.feather" % postfix,
"../generated-data/splits/dataset_yeast_smf.npz",
"cv",
"../results/exp_lit/%s" % name,
n_workers=16,
no_train=False)
def run_gi_cv_on_spec(model_spec, name, n_workers=16):
postfix = '_lit'
sg_path = "../generated-data/dataset_yeast_allppc.feather"
if name == 'd-mn':
postfix = '_mn'
if name == 'gi_yu':
sg_path = "../generated-data/dataset_yeast_smf_yu.feather"
models.train_and_evaluate.cv(model_spec,
"../generated-data/dataset_yeast_gi_hybrid%s.feather" % postfix,
"../generated-data/splits/dataset_yeast_gi_hybrid.npz",
"cv",
"../results/exp_lit/%s" % name,
n_workers=n_workers,
no_train=False,
sg_path=sg_path)
def generate_smf_figures():
output_dir = "../results/exp_lit/figures/smf"
os.makedirs(output_dir, exist_ok=True)
spec = {
"models": [
{
"title": "S-MN",
"color": "#3A90FF",
"name" : "s-mn"
},
{
"title": "Campos 2019",
"color": "#b300ff",
"name" : "smf_campos",
"fsize" : 50
},
{
"title": "Mistry 2017",
"color": "orange",
"name" : "smf_mistry"
},
{
"title": "Lou 2015",
"color": "#FF0000",
"name" : "smf_lou"
}
],
"classes": [
"Lethal",
"Viable"
],
"short_classes": [
"L",
"V"
],
"ylim" : [0,1],
"aspect" : 1
}
figure_cv_bacc.generate_figures(spec, "../results/exp_lit", os.path.join(output_dir, 'overall_bacc.png'))
for model in spec['models']:
model['results_path'] = "../results/exp_lit/%s/results.json" % (model['name'])
figure_cm.plot_cm(model['results_path'], model['color'], spec['short_classes'], os.path.join(output_dir, "cm_%s.png" % model['name']))
for i in range(len(spec['classes'])):
figure_auc_roc_curve.plot_auc_roc_curves(spec, i, os.path.join(output_dir, "auc_roc%s.png" % spec["short_classes"][i]))
def generate_gi_figures():
output_dir = "../results/exp_lit/figures/gi"
os.makedirs(output_dir, exist_ok=True)
spec = {
"models": [
{
"title": "D-MN",
"color": "#3A90FF",
"name" : "d-mn"
},
{
"title": "Benstead-Hume 2019",
"color": "#b300ff",
"name" : "gi_slant",
"fsize" : 40
},
{
"title": "Yu 2015",
"color": "orange",
"name" : "gi_yu"
},
{
"title": "Alanis-Lobato 2013",
"color": "#FF0000",
"name" : "gi_alanis-lobato",
"fsize" : 40
}
],
"classes": [
"Negative GI",
"All"
],
"short_classes": [
"-",
"All"
],
"ylim" : [0,1],
"aspect" : 1
}
figure_cv_bacc.generate_figures(spec, "../results/exp_lit", os.path.join(output_dir, 'overall_bacc.png'))
for model in spec['models']:
model['results_path'] = "../results/exp_lit/%s/results.json" % (model['name'])
figure_cm.plot_cm(model['results_path'], model['color'], spec['short_classes'], os.path.join(output_dir, "cm_%s.png" % model['name']))
for i in range(len(spec['classes'])):
figure_auc_roc_curve.plot_auc_roc_curves(spec, i, os.path.join(output_dir, "auc_roc%s.png" % spec["short_classes"][i]))
if __name__ == "__main__":
main()