Commit 0e47745e authored by Marco Chierici's avatar Marco Chierici
Browse files

General improvements

parent 3827b663
......@@ -3,12 +3,17 @@ import pandas as pd
import numpy as np
from mlpy import canberra_stability
from itertools import combinations
from pathlib import Path
parser = argparse.ArgumentParser()
parser.add_argument('--resultsdir', type=str, help='Results folder')
parser.add_argument('--dataset', type=str, help='Dataset name')
parser.add_argument('--model', type=str, default='randomForest', help='Model (default: %default)')
parser.add_argument('--target', type=str, help='Clinical endpoint')
parser.add_argument('--model', type=str, default='randomForest', help='Model (default: %(default)s)')
parser.add_argument('--nf_min', type=int, default=10, help='Min #feat (default: %(default)s)')
parser.add_argument('--nf_max', type=int, default=50, help='Max #feat (default: %(default)s)')
parser.add_argument('--nf_step', type=int, default=10, help='Increase by these many feat (default: %(default)s)')
parser.add_argument('--nf_rsnf', type=int, nargs='+', help='One or more #feat for rSNF')
parser.add_argument('--layers', type=str, nargs='+', help='')
args = parser.parse_args()
......@@ -16,10 +21,22 @@ RESULTSDIR = args.resultsdir # top-level results directory
DATASET = args.dataset # 'tcga_breast'
MODEL = args.model
NF_MIN = args.nf_min
NF_MAX = args.nf_max
NF_STEP = args.nf_step
NF_RSNF = args.nf_rsnf
LAYERS = args.layers
Path(RESULTSDIR, DATASET).expanduser().exists()
), f"{RESULTSDIR}/{DATASET} not found"
Path(RESULTSDIR, f"{DATASET}_SNFdap").expanduser().exists()
), f"{RESULTSDIR}/{DATASET}_SNFdap not found"
for k in range(2, N_LAYERS+1):
for comb in combinations(LAYERS, k):
layers_concat = '_'.join(comb)
......@@ -30,7 +47,13 @@ for k in range(2, N_LAYERS+1):
# prepare ranks for canberra_stability
ranks = pd.concat([np.argsort(bordas[0]['FEATURE_ID']),
np.argsort(bordas[1]['FEATURE_ID'])], axis=1).transpose().values
for nf in np.arange(10, 60, 10):
for nf in np.arange(NF_MIN, NF_MAX + NF_STEP, NF_STEP):
cs = canberra_stability(ranks, nf)
print(f'{MODE} - {layers_concat} - stability({nf}) = {cs:.3f}')
# additional steps for NF_RSNF
for nf in NF_RSNF:
cs = canberra_stability(ranks, nf)
print(f'{MODE} - {layers_concat} - stability({nf}) = {cs:.3f}')
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