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description = "Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" files = [ - {file = "tqdm-4.65.0-py3-none-any.whl", hash = "sha256:c4f53a17fe37e132815abceec022631be8ffe1b9381c2e6e30aa70edc99e9671"}, - {file = "tqdm-4.65.0.tar.gz", hash = "sha256:1871fb68a86b8fb3b59ca4cdd3dcccbc7e6d613eeed31f4c332531977b89beb5"}, + {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"}, + {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"}, ] [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} [package.extras] -dev = ["py-make (>=0.1.0)", "twine", "wheel"] +dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"] notebook = ["ipywidgets (>=6)"] slack = ["slack-sdk"] telegram = ["requests"] diff --git a/pyproject.toml b/pyproject.toml index 2f07619..9805ca9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,9 +13,8 @@ jinja2 = "^3.1.2" [tool.poetry.scripts] main = "quacc.main:main" -multi = "quacc.main:estimate_multiclass" -bin = "quacc.main:estimate_binary" comp = "quacc.main:estimate_comparison" +tohost = "scp_sync:scp_sync_to_host" [tool.poetry.group.dev.dependencies] diff --git a/quacc/data.py b/quacc/data.py index df03086..1a0ae3f 100644 --- a/quacc/data.py +++ b/quacc/data.py @@ -1,4 +1,4 @@ -from typing import List, Optional, Self +from typing import List, Optional import numpy as np import math @@ -43,7 +43,7 @@ class ExtendedCollection(LabelledCollection): ): super().__init__(instances, labels, classes=classes) - def split_by_pred(self) -> List[Self]: + def split_by_pred(self): _ncl = int(math.sqrt(self.n_classes)) _indexes = ExtendedCollection._split_index_by_pred(_ncl, self.instances) if isinstance(self.instances, np.ndarray): @@ -129,7 +129,7 @@ class ExtendedCollection(LabelledCollection): @classmethod def extend_collection( cls, base: LabelledCollection, pred_proba: np.ndarray - ) -> Self: + ): n_classes = base.n_classes # n_X = [ X | predicted probs. ] diff --git a/quacc/dataset.py b/quacc/dataset.py index a844b82..a4e1735 100644 --- a/quacc/dataset.py +++ b/quacc/dataset.py @@ -7,18 +7,23 @@ from sklearn.conftest import fetch_rcv1 TRAIN_VAL_PROP = 0.5 -def get_imdb() -> Tuple[LabelledCollection]: +def get_imdb(**kwargs) -> Tuple[LabelledCollection]: train, test = qp.datasets.fetch_reviews("imdb", tfidf=True).train_test - train, validation = train.split_stratified(train_prop=TRAIN_VAL_PROP) + train, validation = train.split_stratified( + train_prop=TRAIN_VAL_PROP, random_state=0 + ) return train, validation, test -def get_spambase() -> Tuple[LabelledCollection]: +def get_spambase(**kwargs) -> Tuple[LabelledCollection]: train, test = qp.datasets.fetch_UCIDataset("spambase", verbose=False).train_test - train, validation = train.split_stratified(train_prop=TRAIN_VAL_PROP) + train, validation = train.split_stratified( + train_prop=TRAIN_VAL_PROP, random_state=0 + ) return train, validation, test -# >>> fetch_rcv1().target_names + +# >>> fetch_rcv1().target_names # array(['C11', 'C12', 'C13', 'C14', 'C15', 'C151', 'C1511', 'C152', 'C16', # 'C17', 'C171', 'C172', 'C173', 'C174', 'C18', 'C181', 'C182', # 'C183', 'C21', 'C22', 'C23', 'C24', 'C31', 'C311', 'C312', 'C313', @@ -33,11 +38,15 @@ def get_spambase() -> Tuple[LabelledCollection]: # 'GWELF', 'M11', 'M12', 'M13', 'M131', 'M132', 'M14', 'M141', # 'M142', 'M143', 'MCAT'], dtype=object) -def get_rcv1(target:str): + +def get_rcv1(target = "default", **kwargs): sample_size = qp.environ["SAMPLE_SIZE"] n_train = 23149 dataset = fetch_rcv1() + if target == "default": + target = "C12" + if target not in dataset.target_names: raise ValueError("Invalid target") @@ -46,7 +55,9 @@ def get_rcv1(target:str): all_train_l, test_l = labels[:n_train], labels[n_train:] all_train = LabelledCollection(all_train_d, all_train_l, classes=classes) test = LabelledCollection(test_d, test_l, classes=classes) - train, validation = all_train.split_stratified(train_prop=TRAIN_VAL_PROP) + train, validation = all_train.split_stratified( + train_prop=TRAIN_VAL_PROP, random_state=0 + ) return train, validation, test target_index = np.where(dataset.target_names == target)[0] @@ -58,4 +69,3 @@ def get_rcv1(target:str): d = dataset_split(dataset.data, target_labels, classes=[0, 1]) return d - diff --git a/quacc/error.py b/quacc/error.py index dfd19bd..116cc42 100644 --- a/quacc/error.py +++ b/quacc/error.py @@ -24,12 +24,12 @@ def from_name(err_name): def f1(prev): den = (2*prev[3]) + prev[1] + prev[2] if den == 0: - return 1.0 + return 0.0 else: return (2*prev[3])/den def f1e(prev): return 1 - f1(prev) -def mae(prev): +def acc(prev): return (prev[1] + prev[2]) / sum(prev) \ No newline at end of file diff --git a/quacc/evaluation.py b/quacc/evaluation.py deleted file mode 100644 index deae980..0000000 --- a/quacc/evaluation.py +++ /dev/null @@ -1,149 +0,0 @@ -import itertools -from quapy.protocol import ( - OnLabelledCollectionProtocol, - AbstractStochasticSeededProtocol, -) -from typing import Iterable, Callable, Union - -from .estimator import AccuracyEstimator -import pandas as pd -import numpy as np -import quacc.error as error -import statistics as stats - - -def estimate( - estimator: AccuracyEstimator, - protocol: AbstractStochasticSeededProtocol, -): - # ensure that the protocol returns a LabelledCollection for each iteration - protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - - base_prevs, true_prevs, estim_prevs = [], [], [] - for sample in protocol(): - e_sample = estimator.extend(sample) - estim_prev = estimator.estimate(e_sample.X, ext=True) - base_prevs.append(sample.prevalence()) - true_prevs.append(e_sample.prevalence()) - estim_prevs.append(estim_prev) - - return base_prevs, true_prevs, estim_prevs - - -def avg_groupby_distribution(lst, error_names): - def _bprev(s): - return (s[("base", "F")], s[("base", "T")]) - - def _normalize_prev(r): - for prev_name in ["true", "estim"]: - raw_prev = [v for ((k0, k1), v) in r.items() if k0 == prev_name] - norm_prev = [v / sum(raw_prev) for v in raw_prev] - for n, v in zip( - itertools.product([prev_name], ["TN", "FP", "FN", "TP"]), norm_prev - ): - r[n] = v - return r - - current_bprev = _bprev(lst[0]) - bprev_cnt = 0 - g_lst = [[]] - for s in lst: - if _bprev(s) == current_bprev: - g_lst[bprev_cnt].append(s) - else: - g_lst.append([]) - bprev_cnt += 1 - current_bprev = _bprev(s) - g_lst[bprev_cnt].append(s) - - r_lst = [] - for gs in g_lst: - assert len(gs) > 0 - r = {} - r[("base", "F")], r[("base", "T")] = _bprev(gs[0]) - - for pn in [(n1, n2) for ((n1, n2), _) in gs[0].items() if n1 != "base"]: - r[pn] = stats.mean(map(lambda s: s[pn], gs)) - - r = _normalize_prev(r) - - for en in itertools.product(["errors"], error_names): - r[en] = stats.mean(map(lambda s: s[en], gs)) - - r_lst.append(r) - - return r_lst - - -def evaluation_report( - estimator: AccuracyEstimator, - protocol: AbstractStochasticSeededProtocol, - error_metrics: Iterable[Union[str, Callable]] = "all", - aggregate: bool = True, - prevalence: bool = True, -): - def _report_columns(err_names): - base_cols = list(itertools.product(["base"], ["F", "T"])) - prev_cols = list(itertools.product(["true", "estim"], ["TN", "FP", "FN", "TP"])) - err_cols = list(itertools.product(["errors"], err_names)) - return base_cols, prev_cols, err_cols - - base_prevs, true_prevs, estim_prevs = estimate(estimator, protocol) - - if error_metrics == "all": - error_metrics = ["mae", "f1"] - - error_funcs = [ - error.from_name(e) if isinstance(e, str) else e for e in error_metrics - ] - assert all(hasattr(e, "__call__") for e in error_funcs), "invalid error function" - error_names = [e.__name__ for e in error_funcs] - error_cols = [] - for err in error_names: - if err == "mae": - error_cols.extend(["mae estim", "mae true"]) - elif err == "f1": - error_cols.extend(["f1 estim", "f1 true"]) - elif err == "f1e": - error_cols.extend(["f1e estim", "f1e true"]) - else: - error_cols.append(err) - - # df_cols = ["base_prev", "true_prev", "estim_prev"] + error_names - base_cols, prev_cols, err_cols = _report_columns(error_cols) - - lst = [] - for base_prev, true_prev, estim_prev in zip(base_prevs, true_prevs, estim_prevs): - if prevalence: - series = { - k: v - for (k, v) in zip( - base_cols + prev_cols, - np.concatenate((base_prev, true_prev, estim_prev), axis=0), - ) - } - df_cols = base_cols + prev_cols + err_cols - else: - series = {k: v for (k, v) in zip(base_cols, base_prev)} - df_cols = base_cols + err_cols - - for err in error_cols: - error_funcs = { - "mae true": lambda: error.mae(true_prev), - "mae estim": lambda: error.mae(estim_prev), - "f1 true": lambda: error.f1(true_prev), - "f1 estim": lambda: error.f1(estim_prev), - "f1e true": lambda: error.f1e(true_prev), - "f1e estim": lambda: error.f1e(estim_prev), - } - series[("errors", err)] = error_funcs[err]() - - lst.append(series) - - lst = avg_groupby_distribution(lst, error_cols) if aggregate else lst - - df = pd.DataFrame( - lst, - columns=pd.MultiIndex.from_tuples(df_cols), - ) - return df diff --git a/quacc/evaluation/__init__.py b/quacc/evaluation/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/quacc/baseline.py b/quacc/evaluation/baseline.py similarity index 58% rename from quacc/baseline.py rename to quacc/evaluation/baseline.py index 7393d01..ce36045 100644 --- a/quacc/baseline.py +++ b/quacc/evaluation/baseline.py @@ -2,52 +2,73 @@ from statistics import mean from typing import Dict import numpy as np -import quapy as qp from quapy.data import LabelledCollection from sklearn.base import BaseEstimator from sklearn.model_selection import cross_validate +import sklearn.metrics as metrics from quapy.protocol import ( AbstractStochasticSeededProtocol, OnLabelledCollectionProtocol, ) +from .report import EvaluationReport + import elsahar19_rca.rca as rca import garg22_ATC.ATC_helper as atc import guillory21_doc.doc as doc import jiang18_trustscore.trustscore as trustscore -import lipton_bbse.labelshift as bbse -import pandas as pd -import statistics as stats -def kfcv(c_model: BaseEstimator, validation: LabelledCollection) -> Dict: - scoring = ["f1_macro"] +def kfcv( + c_model: BaseEstimator, + validation: LabelledCollection, + protocol: AbstractStochasticSeededProtocol, + predict_method="predict" +): + c_model_predict = getattr(c_model, predict_method) + + scoring = ["accuracy", "f1_macro"] scores = cross_validate(c_model, validation.X, validation.y, scoring=scoring) - return {"f1_score": mean(scores["test_f1_macro"])} + acc_score = mean(scores["test_accuracy"]) + f1_score = mean(scores["test_f1_macro"]) + + # ensure that the protocol returns a LabelledCollection for each iteration + protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") + + report = EvaluationReport(prefix="kfcv") + for test in protocol(): + test_preds = c_model_predict(test.X) + meta_acc = abs(acc_score - metrics.accuracy_score(test.y, test_preds)) + meta_f1 = abs(f1_score - metrics.f1_score(test.y, test_preds)) + report.append_row( + test.prevalence(), + acc_score=(1. - acc_score), + f1_score=f1_score, + acc=meta_acc, + f1=meta_f1, + ) + + return report -def avg_groupby_distribution(results): - def base_prev(s): - return (s[("base", "F")], s[("base", "T")]) +def reference( + c_model: BaseEstimator, + validation: LabelledCollection, + protocol: AbstractStochasticSeededProtocol, +): + protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") + c_model_predict = getattr(c_model, "predict_proba") + report = EvaluationReport(prefix="ref") + for test in protocol(): + test_probs = c_model_predict(test.X) + test_preds = np.argmax(test_probs, axis=-1) + report.append_row( + test.prevalence(), + acc_score=(1 - metrics.accuracy_score(test.y, test_preds)), + f1_score=metrics.f1_score(test.y, test_preds), + ) - grouped_list = {} - for r in results: - bp = base_prev(r) - if bp in grouped_list.keys(): - grouped_list[bp].append(r) - else: - grouped_list[bp] = [r] - - series = [] - for (fp, tp), r_list in grouped_list.items(): - assert len(r_list) > 0 - r_avg = {} - r_avg[("base", "F")], r_avg[("base", "T")] = fp, tp - for pn in [(n1, n2) for ((n1, n2), _) in r_list[0].items() if n1 != "base"]: - r_avg[pn] = stats.mean(map(lambda r: r[pn], r_list)) - series.append(r_avg) - - return series + return report def atc_mc( @@ -69,25 +90,25 @@ def atc_mc( # ensure that the protocol returns a LabelledCollection for each iteration protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - cols = [ - ("base", "F"), - ("base", "T"), - ("atc mc", "accuracy"), - ] - results = [] + report = EvaluationReport(prefix="atc_mc") for test in protocol(): ## Load OOD test data probs test_probs = c_model_predict(test.X) + test_preds = np.argmax(test_probs, axis=-1) test_scores = atc.get_max_conf(test_probs) - atc_accuracy = 1.0 - (atc.get_ATC_acc(atc_thres, test_scores) / 100.0) - [f_prev, t_prev] = test.prevalence() - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, atc_accuracy])}) + atc_accuracy = atc.get_ATC_acc(atc_thres, test_scores) + meta_acc = abs(atc_accuracy - metrics.accuracy_score(test.y, test_preds)) + f1_score = atc.get_ATC_f1(atc_thres, test_scores, test_probs) + meta_f1 = abs(f1_score - metrics.f1_score(test.y, test_preds)) + report.append_row( + test.prevalence(), + acc=meta_acc, + acc_score=1.0 - atc_accuracy, + f1_score=f1_score, + f1=meta_f1, + ) - series = avg_groupby_distribution(results) - return pd.DataFrame( - series, - columns=pd.MultiIndex.from_tuples(cols), - ) + return report def atc_ne( @@ -109,25 +130,25 @@ def atc_ne( # ensure that the protocol returns a LabelledCollection for each iteration protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - cols = [ - ("base", "F"), - ("base", "T"), - ("atc ne", "accuracy"), - ] - results = [] + report = EvaluationReport(prefix="atc_ne") for test in protocol(): ## Load OOD test data probs test_probs = c_model_predict(test.X) + test_preds = np.argmax(test_probs, axis=-1) test_scores = atc.get_entropy(test_probs) - atc_accuracy = 1.0 - (atc.get_ATC_acc(atc_thres, test_scores) / 100.0) - [f_prev, t_prev] = test.prevalence() - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, atc_accuracy])}) + atc_accuracy = atc.get_ATC_acc(atc_thres, test_scores) + meta_acc = abs(atc_accuracy - metrics.accuracy_score(test.y, test_preds)) + f1_score = atc.get_ATC_f1(atc_thres, test_scores, test_probs) + meta_f1 = abs(f1_score - metrics.f1_score(test.y, test_preds)) + report.append_row( + test.prevalence(), + acc=meta_acc, + acc_score=(1.0 - atc_accuracy), + f1_score=f1_score, + f1=meta_f1, + ) - series = avg_groupby_distribution(results) - return pd.DataFrame( - series, - columns=pd.MultiIndex.from_tuples(cols), - ) + return report def trust_score( @@ -162,24 +183,16 @@ def doc_feat( # ensure that the protocol returns a LabelledCollection for each iteration protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - cols = [ - ("base", "F"), - ("base", "T"), - ("doc feat", "score"), - ] - results = [] + report = EvaluationReport(prefix="doc_feat") for test in protocol(): test_probs = c_model_predict(test.X) + test_preds = np.argmax(test_probs, axis=-1) test_scores = np.max(test_probs, axis=-1) - score = 1.0 - ((v1acc + doc.get_doc(val_scores, test_scores)) / 100.0) - [f_prev, t_prev] = test.prevalence() - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, score])}) + score = (v1acc + doc.get_doc(val_scores, test_scores)) / 100.0 + meta_acc = abs(score - metrics.accuracy_score(test.y, test_preds)) + report.append_row(test.prevalence(), acc=meta_acc, acc_score=(1.0 - score)) - series = avg_groupby_distribution(results) - return pd.DataFrame( - series, - columns=pd.MultiIndex.from_tuples(cols), - ) + return report def rca_score( @@ -194,29 +207,24 @@ def rca_score( # ensure that the protocol returns a LabelledCollection for each iteration protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - cols = [ - ("base", "F"), - ("base", "T"), - ("rca", "score"), - ] - results = [] + report = EvaluationReport(prefix="rca") for test in protocol(): - try: - [f_prev, t_prev] = test.prevalence() + try: test_pred = c_model_predict(test.X) c_model2 = rca.clone_fit(c_model, test.X, test_pred) c_model2_predict = getattr(c_model2, predict_method) val_pred2 = c_model2_predict(validation.X) rca_score = rca.get_score(val_pred1, val_pred2, validation.y) - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, rca_score])}) + meta_score = abs( + rca_score - (1 - metrics.accuracy_score(test.y, test_pred)) + ) + report.append_row(test.prevalence(), acc=meta_score, acc_score=rca_score) except ValueError: - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, float("nan")])}) + report.append_row( + test.prevalence(), acc=float("nan"), acc_score=float("nan") + ) - series = avg_groupby_distribution(results) - return pd.DataFrame( - series, - columns=pd.MultiIndex.from_tuples(cols), - ) + return report def rca_star_score( @@ -226,7 +234,9 @@ def rca_star_score( predict_method="predict", ): c_model_predict = getattr(c_model, predict_method) - validation1, validation2 = validation.split_stratified(train_prop=0.5) + validation1, validation2 = validation.split_stratified( + train_prop=0.5, random_state=0 + ) val1_pred = c_model_predict(validation1.X) c_model1 = rca.clone_fit(c_model, validation1.X, val1_pred) c_model1_predict = getattr(c_model1, predict_method) @@ -235,62 +245,23 @@ def rca_star_score( # ensure that the protocol returns a LabelledCollection for each iteration protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - cols = [ - ("base", "F"), - ("base", "T"), - ("rca*", "score"), - ] - results = [] + report = EvaluationReport(prefix="rca_star") for test in protocol(): - [f_prev, t_prev] = test.prevalence() try: test_pred = c_model_predict(test.X) c_model2 = rca.clone_fit(c_model, test.X, test_pred) c_model2_predict = getattr(c_model2, predict_method) val2_pred2 = c_model2_predict(validation2.X) rca_star_score = rca.get_score(val2_pred1, val2_pred2, validation2.y) - results.append( - {k: v for k, v in zip(cols, [f_prev, t_prev, rca_star_score])} + meta_score = abs( + rca_star_score - (1 - metrics.accuracy_score(test.y, test_pred)) + ) + report.append_row( + test.prevalence(), acc=meta_score, acc_score=rca_star_score ) except ValueError: - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, float("nan")])}) + report.append_row( + test.prevalence(), acc=float("nan"), acc_score=float("nan") + ) - series = avg_groupby_distribution(results) - return pd.DataFrame( - series, - columns=pd.MultiIndex.from_tuples(cols), - ) - - -def bbse_score( - c_model: BaseEstimator, - validation: LabelledCollection, - protocol: AbstractStochasticSeededProtocol, - predict_method="predict_proba", -): - c_model_predict = getattr(c_model, predict_method) - val_probs, val_labels = c_model_predict(validation.X), validation.y - - # ensure that the protocol returns a LabelledCollection for each iteration - protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") - - cols = [ - ("base", "F"), - ("base", "T"), - ("bbse", "score"), - ] - results = [] - for test in protocol(): - test_probs = c_model_predict(test.X) - wt = bbse.estimate_labelshift_ratio(val_labels, val_probs, test_probs, 2) - estim_prev = bbse.estimate_target_dist(wt, val_labels, 2)[1] - true_prev = test.prevalence() - [f_prev, t_prev] = true_prev - acc = qp.error.ae(true_prev, estim_prev) - results.append({k: v for k, v in zip(cols, [f_prev, t_prev, acc])}) - - series = avg_groupby_distribution(results) - return pd.DataFrame( - series, - columns=pd.MultiIndex.from_tuples(cols), - ) + return report diff --git a/quacc/evaluation/method.py b/quacc/evaluation/method.py new file mode 100644 index 0000000..0c69ba1 --- /dev/null +++ b/quacc/evaluation/method.py @@ -0,0 +1,149 @@ +import multiprocessing +import time + +import pandas as pd +import quapy as qp +from quapy.data import LabelledCollection +from quapy.protocol import ( + APP, + AbstractStochasticSeededProtocol, + OnLabelledCollectionProtocol, +) +from sklearn.base import BaseEstimator +from sklearn.linear_model import LogisticRegression + +import quacc.error as error +import quacc.evaluation.baseline as baseline +from quacc.dataset import get_imdb, get_rcv1, get_spambase +from quacc.evaluation.report import EvaluationReport + +from ..estimator import ( + AccuracyEstimator, + BinaryQuantifierAccuracyEstimator, + MulticlassAccuracyEstimator, +) + +qp.environ["SAMPLE_SIZE"] = 100 + +pd.set_option("display.float_format", "{:.4f}".format) + +n_prevalences = 21 +repreats = 100 + + +def estimate( + estimator: AccuracyEstimator, + protocol: AbstractStochasticSeededProtocol, +): + # ensure that the protocol returns a LabelledCollection for each iteration + protocol.collator = OnLabelledCollectionProtocol.get_collator("labelled_collection") + + base_prevs, true_prevs, estim_prevs = [], [], [] + for sample in protocol(): + e_sample = estimator.extend(sample) + estim_prev = estimator.estimate(e_sample.X, ext=True) + base_prevs.append(sample.prevalence()) + true_prevs.append(e_sample.prevalence()) + estim_prevs.append(estim_prev) + + return base_prevs, true_prevs, estim_prevs + + +def evaluation_report( + estimator: AccuracyEstimator, + protocol: AbstractStochasticSeededProtocol, + method: str, +) -> EvaluationReport: + base_prevs, true_prevs, estim_prevs = estimate(estimator, protocol) + report = EvaluationReport(prefix=method) + + for base_prev, true_prev, estim_prev in zip(base_prevs, true_prevs, estim_prevs): + acc_score = error.acc(estim_prev) + f1_score = error.f1(estim_prev) + report.append_row( + base_prev, + acc_score=1. - acc_score, + acc = abs(error.acc(true_prev) - acc_score), + f1_score=f1_score, + f1=abs(error.f1(true_prev) - f1_score) + ) + + return report + + +def evaluate( + c_model: BaseEstimator, + validation: LabelledCollection, + protocol: AbstractStochasticSeededProtocol, + method: str, +): + estimator : AccuracyEstimator = { + "bin": BinaryQuantifierAccuracyEstimator, + "mul": MulticlassAccuracyEstimator, + }[method](c_model) + estimator.fit(validation) + return evaluation_report(estimator, protocol, method) + + +def evaluate_binary(model, validation, protocol): + return evaluate(model, validation, protocol, "bin") + + +def evaluate_multiclass(model, validation, protocol): + return evaluate(model, validation, protocol, "mul") + + +def fit_and_estimate(_estimate, train, validation, test): + model = LogisticRegression() + + model.fit(*train.Xy) + protocol = APP(test, n_prevalences=n_prevalences, repeats=repreats) + start = time.time() + result = _estimate(model, validation, protocol) + end = time.time() + + return { + "name": _estimate.__name__, + "result": result, + "time": end - start, + } + + +def evaluate_comparison(dataset: str, **kwargs) -> EvaluationReport: + train, validation, test = { + "spambase": get_spambase, + "imdb": get_imdb, + "rcv1": get_rcv1, + }[dataset](**kwargs) + + for k,v in kwargs.items(): + print(k, ":", v) + + prevs = { + "train": train.prevalence(), + "validation": validation.prevalence(), + } + + start = time.time() + with multiprocessing.Pool(8) as pool: + estimators = [ + evaluate_binary, + evaluate_multiclass, + baseline.kfcv, + baseline.atc_mc, + baseline.atc_ne, + baseline.doc_feat, + baseline.rca_score, + baseline.rca_star_score, + ] + tasks = [(estim, train, validation, test) for estim in estimators] + results = [pool.apply_async(fit_and_estimate, t) for t in tasks] + results = list(map(lambda r: r.get(), results)) + er = EvaluationReport.combine_reports(*list(map(lambda r: r["result"], results))) + times = {r["name"]:r["time"] for r in results} + end = time.time() + times["tot"] = end - start + er.times = times + er.prevs = prevs + + return er diff --git a/quacc/evaluation/report.py b/quacc/evaluation/report.py new file mode 100644 index 0000000..97c514e --- /dev/null +++ b/quacc/evaluation/report.py @@ -0,0 +1,162 @@ +from email import header +from typing import Tuple +import statistics as stats +import numpy as np +import pandas as pd + +def _in_div(s): + return "
" + s + "
\n" + +def _header_footer(s): + return ( + """ + + + + + + """ + + s + + "" + ) + +class EvaluationReport: + def __init__(self, prefix=None): + self.base = [] + self.dict = {} + self._grouped = False + self._grouped_base = [] + self._grouped_dict = {} + self._dataframe = None + self.prefix = prefix if prefix is not None else "default" + self._times = {} + self._prevs = {} + self._target = "default" + + def append_row(self, base: np.ndarray | Tuple, **row): + if isinstance(base, np.ndarray): + base = tuple(base.tolist()) + self.base.append(base) + for k, v in row.items(): + if (k, self.prefix) in self.dict: + self.dict[(k, self.prefix)].append(v) + else: + self.dict[(k, self.prefix)] = [v] + self._grouped = False + self._dataframe = None + + @property + def columns(self): + return self.dict.keys() + + @property + def grouped(self): + if self._grouped: + return self._grouped_dict + + self._grouped_base = [] + self._grouped_dict = {k: [] for k in self.dict.keys()} + + last_end = 0 + for ind, bp in enumerate(self.base): + if ind < (len(self.base) - 1) and bp == self.base[ind + 1]: + continue + + self._grouped_base.append(bp) + for col in self.dict.keys(): + self._grouped_dict[col].append( + stats.mean(self.dict[col][last_end : ind + 1]) + ) + + last_end = ind + 1 + + self._grouped = True + return self._grouped_dict + + @property + def gbase(self): + self.grouped + return self._grouped_base + + def get_dataframe(self, metrics=None): + if self._dataframe is None: + self_columns = sorted(self.columns, key=lambda c: c[0]) + self._dataframe = pd.DataFrame( + self.grouped, + index=self.gbase, + columns=pd.MultiIndex.from_tuples(self_columns), + ) + + df = pd.DataFrame(self._dataframe) + if metrics is not None: + df = df.drop( + [(c0, c1) for (c0, c1) in df.columns if c0 not in metrics], axis=1 + ) + + if len(set(k0 for k0, k1 in df.columns)) == 1: + df = df.droplevel(0, axis=1) + + return df + + def merge(self, other): + if not all(v1 == v2 for v1, v2 in zip(self.base, other.base)): + raise ValueError("other has not same base prevalences of self") + + if len(set(self.dict.keys()).intersection(set(other.dict.keys()))) > 0: + raise ValueError("self and other have matching keys") + + report = EvaluationReport() + report.base = self.base + report.dict = self.dict | other.dict + return report + + @property + def times(self): + return self._times + + @times.setter + def times(self, val): + self._times = val + + @property + def prevs(self): + return self._prevs + + @prevs.setter + def prevs(self, val): + self._prevs = val + + @property + def target(self): + return self._target + + @target.setter + def target(self, val): + self._target = val + + def to_html(self, *metrics): + res = _in_div("target: " + self.target) + for k,v in self.prevs.items(): + res += _in_div(f"{k}: {str(v)}") + for k,v in self.times.items(): + res += _in_div(f"{k}: {v:.3f}s") + res += "\n" + for m in metrics: + res += self.get_dataframe(metrics=m).to_html() + "\n\n" + + return _header_footer(res) + + + @staticmethod + def combine_reports(*args): + er = args[0] + for r in args[1:]: + er = er.merge(r) + + return er diff --git a/quacc/main.py b/quacc/main.py index d58a65e..96a056b 100644 --- a/quacc/main.py +++ b/quacc/main.py @@ -1,133 +1,41 @@ -import pandas as pd -import quapy as qp -from quapy.protocol import APP -from sklearn.linear_model import LogisticRegression -from quacc import utils +import traceback +import quacc.evaluation.method as method -import quacc.evaluation as eval -import quacc.baseline as baseline -from quacc.estimator import ( - BinaryQuantifierAccuracyEstimator, - MulticlassAccuracyEstimator, -) - -from quacc.dataset import get_imdb, get_rcv1, get_spambase - -qp.environ["SAMPLE_SIZE"] = 100 - -pd.set_option("display.float_format", "{:.4f}".format) - -dataset_name = "imdb" - - -def estimate_multiclass(): - print(dataset_name) - train, validation, test = get_imdb() - - model = LogisticRegression() - - print(f"fitting model {model.__class__.__name__}...", end=" ", flush=True) - model.fit(*train.Xy) - print("fit") - - estimator = MulticlassAccuracyEstimator(model) - - print( - f"fitting qmodel {estimator.q_model.__class__.__name__}...", end=" ", flush=True - ) - estimator.fit(train) - print("fit") - - n_prevalences = 21 - repreats = 1000 - protocol = APP(test, n_prevalences=n_prevalences, repeats=repreats) - print( - f"Tests:\n\ - protocol={protocol.__class__.__name__}\n\ - n_prevalences={n_prevalences}\n\ - repreats={repreats}\n\ - executing...\n" - ) - df = eval.evaluation_report( - estimator, - protocol, - aggregate=True, - ) - # print(df.to_latex()) - print(df.to_string()) - # print(df.to_html()) - print() - - -def estimate_binary(): - print(dataset_name) - train, validation, test = get_imdb() - - model = LogisticRegression() - - print(f"fitting model {model.__class__.__name__}...", end=" ", flush=True) - model.fit(*train.Xy) - print("fit") - - estimator = BinaryQuantifierAccuracyEstimator(model) - - print( - f"fitting qmodel {estimator.q_model_0.__class__.__name__}...", - end=" ", - flush=True, - ) - estimator.fit(train) - print("fit") - - n_prevalences = 21 - repreats = 1000 - protocol = APP(test, n_prevalences=n_prevalences, repeats=repreats) - print( - f"Tests:\n\ - protocol={protocol.__class__.__name__}\n\ - n_prevalences={n_prevalences}\n\ - repreats={repreats}\n\ - executing...\n" - ) - df = eval.evaluation_report( - estimator, - protocol, - aggregate=True, - ) - # print(df.to_latex(float_format="{:.4f}".format)) - print(df.to_string()) - # print(df.to_html()) - print() +DATASET = "imdb" +OUTPUT_FILE = "out_" + DATASET + ".html" +TARGETS = { + "rcv1" : [ + 'C12', + 'C13', 'C15', 'C151', 'C1511', 'C152', 'C17', 'C172', + 'C18', 'C181', 'C21', 'C24', 'C31', 'C42', 'CCAT' + 'E11', 'E12', 'E21', 'E211', 'E212', 'E41', 'E51', 'ECAT', + 'G15', 'GCAT', 'GCRIM', 'GDIP', 'GPOL', 'GVIO', 'GVOTE', 'GWEA', + 'GWELF', 'M11', 'M12', 'M13', 'M131', 'M132', 'M14', 'M141', + 'M142', 'M143', 'MCAT' + ], + "spambase": ["default"], + "imdb": ["default"], +} def estimate_comparison(): - train, validation, test = get_spambase() - model = LogisticRegression() - model.fit(*train.Xy) + open(OUTPUT_FILE, "w").close() + targets = TARGETS[DATASET] + for target in targets: + try: + er = method.evaluate_comparison(DATASET, target=target) + er.target = target + with open(OUTPUT_FILE, "a") as f: + f.write(er.to_html(["acc"], ["f1"])) + except Exception: + traceback.print_exc() - n_prevalences = 21 - repreats = 1000 - protocol = APP(test, n_prevalences=n_prevalences, repeats=repreats) + # print(df.to_latex(float_format="{:.4f}".format)) + # print(utils.avg_group_report(df).to_latex(float_format="{:.4f}".format)) - estimator = BinaryQuantifierAccuracyEstimator(model) - estimator.fit(validation) - df = eval.evaluation_report(estimator, protocol, prevalence=False) - - df = utils.combine_dataframes( - baseline.atc_mc(model, validation, protocol), - baseline.atc_ne(model, validation, protocol), - baseline.doc_feat(model, validation, protocol), - baseline.rca_score(model, validation, protocol), - baseline.rca_star_score(model, validation, protocol), - baseline.bbse_score(model, validation, protocol), - df, - df_index=[("base", "F"), ("base", "T")] - ) - - print(df.to_latex(float_format="{:.4f}".format)) - print(utils.avg_group_report(df).to_latex(float_format="{:.4f}".format)) def main(): estimate_comparison() + if __name__ == "__main__": main() diff --git a/quacc/utils.py b/quacc/utils.py index 6da5b39..d38b9f6 100644 --- a/quacc/utils.py +++ b/quacc/utils.py @@ -2,7 +2,7 @@ import functools import pandas as pd -def combine_dataframes(*dfs, df_index=[]) -> pd.DataFrame: +def combine_dataframes(dfs, df_index=[]) -> pd.DataFrame: if len(dfs) < 1: raise ValueError if len(dfs) == 1: