import itertools from collections import defaultdict import numpy as np def artificial_prevalence_sampling(dimensions, n_prevalences=21, repeat=1, return_constrained_dim=False): s = np.linspace(0., 1., n_prevalences, endpoint=True) s = [s] * (dimensions - 1) prevs = [p for p in itertools.product(*s, repeat=1) if sum(p)<=1] if return_constrained_dim: prevs = [p+(1-sum(p),) for p in prevs] prevs = np.asarray(prevs).reshape(len(prevs), -1) if repeat>1: prevs = np.repeat(prevs, repeat, axis=0) return prevs def prevalence_linspace(n_prevalences=21, repeat=1, smooth_limits_epsilon=0.01): """ Produces a uniformly separated values of prevalence. By default, produces an array 21 prevalences, with step 0.05 and with the limits smoothed, i.e.: [0.01, 0.05, 0.10, 0.15, ..., 0.90, 0.95, 0.99] :param n_prevalences: the number of prevalence values to sample from the [0,1] interval (default 21) :param repeat: number of times each prevalence is to be repeated (defaults to 1) :param smooth_limits_epsilon: the quantity to add and subtract to the limits 0 and 1 :return: an array of uniformly separated prevalence values """ p = np.linspace(0., 1., num=n_prevalences, endpoint=True) p[0] += smooth_limits_epsilon p[-1] -= smooth_limits_epsilon if p[0] > p[1]: raise ValueError(f'the smoothing in the limits is greater than the prevalence step') if repeat > 1: p = np.repeat(p, repeat) return p def prevalence_from_labels(labels, n_classes): if labels.ndim != 1: raise ValueError(f'param labels does not seem to be a ndarray of label predictions') unique, counts = np.unique(labels, return_counts=True) by_class = defaultdict(lambda:0, dict(zip(unique, counts))) prevalences = np.asarray([by_class[ci] for ci in range(n_classes)], dtype=np.float) prevalences /= prevalences.sum() return prevalences def prevalence_from_probabilities(posteriors, binarize: bool = False): if posteriors.ndim != 2: raise ValueError(f'param posteriors does not seem to be a ndarray of posteior probabilities') if binarize: predictions = np.argmax(posteriors, axis=-1) return prevalence_from_labels(predictions, n_classes=posteriors.shape[1]) else: prevalences = posteriors.mean(axis=0) prevalences /= prevalences.sum() return prevalences def HellingerDistance(P, Q): return np.sqrt(np.sum((np.sqrt(P) - np.sqrt(Q))**2)) def uniform_prevalence_sampling(n_classes, size=1): if n_classes == 2: u = np.random.rand(size) u = np.vstack([1-u, u]).T else: # from https://cs.stackexchange.com/questions/3227/uniform-sampling-from-a-simplex u = np.random.rand(size, n_classes-1) u.sort(axis=-1) _0s = np.zeros(shape=(size, 1)) _1s = np.ones(shape=(size, 1)) a = np.hstack([_0s, u]) b = np.hstack([u, _1s]) u = b-a if size == 1: u = u.flatten() return u #return np.asarray([uniform_simplex_sampling(n_classes) for _ in range(size)]) uniform_simplex_sampling = uniform_prevalence_sampling def strprev(prevalences, prec=3): return '['+ ', '.join([f'{p:.{prec}f}' for p in prevalences]) + ']' def adjusted_quantification(prevalence_estim, tpr, fpr, clip=True): den = tpr - fpr if den == 0: den += 1e-8 adjusted = (prevalence_estim - fpr) / den if clip: adjusted = np.clip(adjusted, 0., 1.) return adjusted def normalize_prevalence(prevalences): prevalences = np.asarray(prevalences) n_classes = prevalences.shape[-1] accum = prevalences.sum(axis=-1, keepdims=True) prevalences = np.true_divide(prevalences, accum, where=accum>0) allzeros = accum.flatten()==0 if any(allzeros): if prevalences.ndim == 1: prevalences = np.full(shape=n_classes, fill_value=1./n_classes) else: prevalences[accum.flatten()==0] = np.full(shape=n_classes, fill_value=1./n_classes) return prevalences def num_prevalence_combinations(n_prevpoints:int, n_classes:int, n_repeats:int=1): """ Computes the number of prevalence combinations in the n_classes-dimensional simplex if nprevpoints equally distant prevalences are generated and n_repeats repetitions are requested :param n_classes: number of classes :param n_prevpoints: number of prevalence points. :param n_repeats: number of repetitions for each prevalence combination :return: The number of possible combinations. For example, if n_classes=2, n_prevpoints=5, n_repeats=1, then the number of possible combinations are 5, i.e.: [0,1], [0.25,0.75], [0.50,0.50], [0.75,0.25], and [1.0,0.0] """ __cache={} def __f(nc,np): if (nc,np) in __cache: # cached result return __cache[(nc,np)] if nc==1: # stop condition return 1 else: # recursive call x = sum([__f(nc-1, np-i) for i in range(np)]) __cache[(nc,np)] = x return x return __f(n_classes, n_prevpoints) * n_repeats def get_nprevpoints_approximation(combinations_budget:int, n_classes:int, n_repeats:int=1): """ Searches for the largest number of (equidistant) prevalence points to define for each of the n_classes classes so that the number of valid prevalences generated as combinations of prevalence points (points in a n_classes-dimensional simplex) do not exceed combinations_budget. :param n_classes: number of classes :param n_repeats: number of repetitions for each prevalence combination :param combinations_budget: maximum number of combinatios allowed :return: the largest number of prevalence points that generate less than combinations_budget valid prevalences """ assert n_classes > 0 and n_repeats > 0 and combinations_budget > 0, 'parameters must be positive integers' n_prevpoints = 1 while True: combinations = num_prevalence_combinations(n_prevpoints, n_classes, n_repeats) if combinations > combinations_budget: return n_prevpoints-1 else: n_prevpoints += 1