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# -*- coding: utf-8 -*-
"""
Author: Philipp Seidl
ELLIS Unit Linz, LIT AI Lab, Institute for Machine Learning
Johannes Kepler University Linz
Contact: [email protected]
General utility functions
"""
import argparse
from collections import defaultdict
import numpy as np
import pandas as pd
import math
import torch
# used and fastest version
def top_k_accuracy(y_true, y_pred, k=5, ret_arocc=False, ret_mrocc=False, verbose=False, count_equal_as_correct=False, eps_noise=0):
""" partly from http://stephantul.github.io/python/pytorch/2020/09/18/fast_topk/
count_equal counts equal values as beein a correct choice e.g. all preds = 0 --> T1acc = 1
ret_mrocc ... also return median rank of correct choice
eps_noise ... if >0 ads noise*eps to y_pred .. recommended e.g. 1e-10
"""
if eps_noise>0:
if torch.is_tensor(y_pred):
y_pred = y_pred + torch.rand(y_pred.shape)*eps_noise
else:
y_pred = y_pred + np.random.rand(*y_pred.shape)*eps_noise
if count_equal_as_correct:
greater = (y_pred > y_pred[range(len(y_pred)), y_true][:,None]).sum(1) # how many are bigger
else:
greater = (y_pred >= y_pred[range(len(y_pred)), y_true][:,None]).sum(1) # how many are bigger or equal
if torch.is_tensor(y_pred):
greater = greater.long()
if isinstance(k, int): k = [k] # pack it into a list
tkaccs = []
for ki in k:
if count_equal_as_correct:
tkacc = (greater<=(ki-1))
else:
tkacc = (greater<=(ki))
if torch.is_tensor(y_pred):
tkacc = tkacc.float().mean().detach().cpu().numpy()
else:
tkacc = tkacc.mean()
tkaccs.append(tkacc)
if verbose: print('Top', ki, 'acc:\t', str(tkacc)[:6])
if ret_arocc:
arocc = greater.float().mean()+1
if torch.is_tensor(arocc):
arocc = arocc.detach().cpu().numpy()
return (tkaccs[0], arocc) if len(tkaccs) == 1 else (tkaccs, arocc)
if ret_mrocc:
mrocc = greater.median()+1
if torch.is_tensor(mrocc):
mrocc = mrocc.float().detach().cpu().numpy()
return (tkaccs[0], mrocc) if len(tkaccs) == 1 else (tkaccs, mrocc)
return tkaccs[0] if len(tkaccs) == 1 else tkaccs
def seed_everything(seed=70135):
""" does what it says ;) - from https://gist.github.com/KirillVladimirov/005ec7f762293d2321385580d3dbe335"""
import numpy as np
import random
import os
import torch
random.seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
torch.backends.cudnn.deterministic = True
def get_best_gpu():
'''Get the gpu with most RAM on the machine. From P. Neves'''
import torch
if torch.cuda.is_available():
gpus_ram = []
for ind in range(torch.cuda.device_count()):
gpus_ram.append(torch.cuda.get_device_properties(ind).total_memory/1e9)
return f"cuda:{gpus_ram.index(max(gpus_ram))}"
else:
raise ValueError("No gpus were detected in this machine.")
def sort_by_template_and_flatten(template_scores, prod_idx_reactants, agglo_fun=sum):
flat_results = []
for ii in range(len(template_scores)):
idx_prod_reactants = defaultdict(list)
for k,v in prod_idx_reactants[ii].items():
for iv in v:
idx_prod_reactants[iv].append(template_scores[ii,k])
d2 = {k: agglo_fun(v) for k, v in idx_prod_reactants.items()}
if len(d2)==0:
flat_results.append([])
else:
flat_results.append(pd.DataFrame.from_dict(d2, orient='index').sort_values(0, ascending=False).index.values.tolist())
return flat_results
def str2bool(v):
"""adapted from https://stackoverflow.com/questions/15008758/parsing-boolean-values-with-argparse"""
if isinstance(v, bool):
return v
if v.lower() in ('yes', 'true', 't', 'y', '1', '',' '):
return True
elif v.lower() in ('no', 'false', 'f', 'n', '0'):
return False
else:
raise argparse.ArgumentTypeError('Boolean value expected.')
@np.vectorize
def lgamma(x):
return math.lgamma(x)
def multinom_gk(array, axis=0):
"""Multinomial lgamma pooling over a given axis"""
res = lgamma(np.sum(array,axis=axis)+2) - np.sum(lgamma(array+1),axis=axis)
return res |