Commit 60b08093 authored by Alessia Marcolini's avatar Alessia Marcolini
Browse files

Merge branch 'master' of gitlab.fbk.eu:MPBA/INF

parents b5ede9a6 0e47745e
import argparse
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('--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()
RESULTSDIR = args.resultsdir # top-level results directory
DATASET = args.dataset # 'tcga_breast'
TARGET = args.target # 'ER'
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
N_LAYERS = len(LAYERS)
MODE = 'rSNF'
assert(
Path(RESULTSDIR, DATASET).expanduser().exists()
), f"{RESULTSDIR}/{DATASET} not found"
assert(
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)
bordas = []
for datatype in [DATASET, f'{DATASET}_SNFdap']:
bordaf = f'{RESULTSDIR}/{datatype}/{TARGET}/{MODEL}/Borda_splits_50-60_{MODE}_{layers_concat}.txt'
bordas.append(pd.read_csv(bordaf, sep='\t', index_col=None))
# 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(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
print()
for nf in NF_RSNF:
cs = canberra_stability(ranks, nf)
print(f'{MODE} - {layers_concat} - stability({nf}) = {cs:.3f}')
print()
print()
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