Python sklearn.metrics.balanced_accuracy_score() Examples

def fit(self, X_train, y_train, X_val, y_val, categoricals=None):
        results = dict()

        self.all_nan = np.all(np.isnan(X_train), axis=0)
        X_train = X_train[:, ~self.all_nan]
        X_val = X_val[:, ~self.all_nan]

        X_train = np.nan_to_num(X_train)
        X_val = np.nan_to_num(X_val)

        categoricals = [ind for ind in range(X_train.shape[1]) if isinstance(X_train[0,ind], str)]

        early_stopping = 150 if X_train.shape[0]>10000 else max(round(150*10000/X_train.shape[0]), 10)

        X_train_pooled = Pool(data=X_train, label=y_train, cat_features=categoricals)
        X_val_pooled = Pool(data=X_val, label=y_val, cat_features=categoricals)

        self.model = CatBoostClassifier(**self.config)
        self.model.fit(X_train_pooled, eval_set=X_val_pooled, use_best_model=True, early_stopping_rounds=early_stopping)

        pred_train = self.model.predict_proba(X_train)
        pred_val = self.model.predict_proba(X_val)

        results["val_preds"] = pred_val.tolist()
        results["labels"] = y_val.tolist()

        try:
            pred_train = np.argmax(pred_train, axis=1)
            pred_val = np.argmax(pred_val, axis=1)
        except:
            print("==> No probabilities provided in predictions")

        results["train_acc"] = metrics.accuracy_score(y_train, pred_train)
        results["train_balanced_acc"] = metrics.balanced_accuracy_score(y_train, pred_train)
        results["val_acc"] = metrics.accuracy_score(y_val, pred_val)
        results["val_balanced_acc"] = metrics.balanced_accuracy_score(y_val, pred_val)

        return results 

def infer(test_queue, model, criterion):
    model.eval()
    objs = utils.AverageMeter()
    test_true = []
    test_pred = []
    with torch.no_grad():
        for i, (data, label) in enumerate(test_queue):
            data, label = data.to(DEVICE), label.to(DEVICE).squeeze()
            data = data.permute(0, 2, 1).unsqueeze(3)

            out, out_aux = model(data)

            pred = out.max(dim=1)[1]
            test_true.append(label.cpu().numpy())
            test_pred.append(pred.detach().cpu().numpy())
            loss = criterion(out, label.squeeze())

            n = label.size(0)
            objs.update(loss.item(), n)

        test_true = np.concatenate(test_true)
        test_pred = np.concatenate(test_pred)
        overall_acc = metrics.accuracy_score(test_true, test_pred)
        class_acc = metrics.balanced_accuracy_score(test_true, test_pred)
    return overall_acc, class_acc, objs.avg 

def fit(self, X_train, y_train, X_val, y_val):
        results = dict()

        self.model = SVC(**self.config)

        self.all_nan = np.all(np.isnan(X_train), axis=0)
        X_train = X_train[:, ~self.all_nan]
        X_val = X_val[:, ~self.all_nan]

        self.model.fit(X_train, y_train)

        pred_val_probas = self.model.predict_proba(X_val)

        pred_train = self.model.predict(X_train)
        pred_val = self.model.predict(X_val)

        results["train_acc"] = metrics.accuracy_score(y_train, pred_train)
        results["train_balanced_acc"] = metrics.balanced_accuracy_score(y_train, pred_train)
        results["val_acc"] = metrics.accuracy_score(y_val, pred_val)
        results["val_balanced_acc"] = metrics.balanced_accuracy_score(y_val, pred_val)
        results["val_preds"] = pred_val_probas.tolist()
        results["labels"] = y_val.tolist()

        return results 

def test_sklearn_custom_scoring_and_cv(tmp_dir):
    tuner = sklearn_tuner.Sklearn(
        oracle=kt.oracles.BayesianOptimization(
            objective=kt.Objective('score', 'max'),
            max_trials=10),
        hypermodel=build_model,
        scoring=metrics.make_scorer(metrics.balanced_accuracy_score),
        cv=model_selection.StratifiedKFold(5),
        directory=tmp_dir)

    x = np.random.uniform(size=(50, 10))
    y = np.random.randint(0, 2, size=(50,))
    tuner.search(x, y)

    assert len(tuner.oracle.trials) == 10

    best_trial = tuner.oracle.get_best_trials()[0]
    assert best_trial.status == 'COMPLETED'
    assert best_trial.score is not None
    assert best_trial.best_step == 0
    assert best_trial.metrics.exists('score')

    # Make sure best model can be reloaded.
    best_model = tuner.get_best_models()[0]
    best_model.score(x, y) 

def infer(model, test_loader, criterion, opt):
    model.eval()
    test_true = []
    test_pred = []
    with torch.no_grad():
        for i, (data, label) in enumerate(test_loader):
            data, label = data.to(opt.device), label.to(opt.device).squeeze()
            data = data.permute(0, 2, 1).unsqueeze(-1)

            logits = model(data)
            loss = criterion(logits, label.squeeze())

            pred = logits.max(dim=1)[1]
            test_true.append(label.cpu().numpy())
            test_pred.append(pred.detach().cpu().numpy())

            opt.test_losses.update(loss.item())

        test_true = np.concatenate(test_true)
        test_pred = np.concatenate(test_pred)
        overall_acc = metrics.accuracy_score(test_true, test_pred)
        class_acc = metrics.balanced_accuracy_score(test_true, test_pred)
    return overall_acc, class_acc, opt 

def train_step(model, train_loader, optimizer, criterion, opt):
    model.train()

    train_pred = []
    train_true = []
    for data, label in train_loader:
        data, label = data.to(opt.device), label.to(opt.device).squeeze()
        data = data.permute(0, 2, 1).unsqueeze(-1)

        optimizer.zero_grad()
        logits = model(data)
        loss = criterion(logits, label)
        loss.backward()
        optimizer.step()

        opt.train_losses.update(loss.item())

        preds = logits.max(dim=1)[1]
        train_true.append(label.cpu().numpy())
        train_pred.append(preds.detach().cpu().numpy())

    train_true = np.concatenate(train_true)
    train_pred = np.concatenate(train_pred)
    overall_acc = metrics.accuracy_score(train_true, train_pred)
    class_acc = metrics.balanced_accuracy_score(train_true, train_pred)
    return overall_acc, class_acc, opt 

def test_balanced_accuracy():
    output = torch.rand((16, 4))
    output_np = output.numpy()
    target = torch.randint(0, 4, (16,))
    target_np = target.numpy()
    expected = 100 * balanced_accuracy_score(target_np, np.argmax(output_np, 1))
    result = BalancedAccuracy()(output, target).flatten().numpy()
    assert np.allclose(expected, result) 

def test_sklearn_additional_metrics(tmp_dir):
    tuner = sklearn_tuner.Sklearn(
        oracle=kt.oracles.BayesianOptimization(
            objective=kt.Objective('score', 'max'),
            max_trials=10),
        hypermodel=build_model,
        metrics=[metrics.balanced_accuracy_score,
                 metrics.recall_score],
        directory=tmp_dir)

    x = np.random.uniform(size=(50, 10))
    y = np.random.randint(0, 2, size=(50,))
    tuner.search(x, y)

    assert len(tuner.oracle.trials) == 10

    best_trial = tuner.oracle.get_best_trials()[0]
    assert best_trial.status == 'COMPLETED'
    assert best_trial.score is not None
    assert best_trial.best_step == 0
    assert best_trial.metrics.exists('score')
    assert best_trial.metrics.exists('balanced_accuracy_score')
    assert best_trial.metrics.exists('recall_score')

    # Make sure best model can be reloaded.
    best_model = tuner.get_best_models()[0]
    best_model.score(x, y) 

def score(self, X_test, y_test):
        results = dict()

        y_pred = self.predict(X_test)

        results["test_acc"] = metrics.accuracy_score(y_test, y_pred)
        results["test_balanced_acc"] = metrics.balanced_accuracy_score(y_test, y_pred)
        
        return results 

def test_balanced_accuracy_score_unseen():
    assert_warns_message(UserWarning, 'y_pred contains classes not in y_true',
                         balanced_accuracy_score, [0, 0, 0], [0, 0, 1]) 

def score(self, X_test, y_test):
        results = dict()

        y_pred = self.predict(X_test)

        results["test_acc"] = metrics.accuracy_score(y_test, y_pred)
        results["test_balanced_acc"] = metrics.balanced_accuracy_score(y_test, y_pred)

        return results 

def fit(self, X_train, y_train, X_val, y_val):
        results = dict()

        self.all_nan = np.all(np.isnan(X_train), axis=0)
        X_train = X_train[:, ~self.all_nan]
        X_val = X_val[:, ~self.all_nan]

        X_train = np.nan_to_num(X_train)
        X_val = np.nan_to_num(X_val)

        self.config["warm_start"] = False
        self.num_classes = len(np.unique(y_train))
        if self.num_classes>2:
            print("==> Using warmstarting for multiclass")
            final_n_estimators = self.config["n_estimators"]
            self.config["n_estimators"] = 8
            self.config["warm_start"] = True

        self.model = RandomForestClassifier(**self.config)
        
        self.model.fit(X_train, y_train)
        if self.config["warm_start"]:
            self.model.n_estimators = final_n_estimators
            self.model.fit(X_train, y_train)

        pred_val_probas = self.model.predict_proba(X_val)

        pred_train = self.model.predict(X_train)
        pred_val = self.model.predict(X_val)

        results["train_acc"] = metrics.accuracy_score(y_train, pred_train)
        results["train_balanced_acc"] = metrics.balanced_accuracy_score(y_train, pred_train)
        results["val_acc"] = metrics.accuracy_score(y_val, pred_val)
        results["val_balanced_acc"] = metrics.balanced_accuracy_score(y_val, pred_val)
        results["val_preds"] = pred_val_probas.tolist()
        results["labels"] = y_val.tolist()

        return results 

def fit(self, X_train, y_train, X_val, y_val):
        results = dict()

        self.all_nan = np.all(np.isnan(X_train), axis=0)
        X_train = X_train[:, ~self.all_nan]
        X_val = X_val[:, ~self.all_nan]

        X_train = np.nan_to_num(X_train)
        X_val = np.nan_to_num(X_val)

        self.config["warm_start"] = False
        self.num_classes = len(np.unique(y_train))
        if self.num_classes>2:
            print("==> Using warmstarting for multiclass")
            final_n_estimators = self.config["n_estimators"]
            self.config["n_estimators"] = 8
            self.config["warm_start"] = True

        self.model = ExtraTreesClassifier(**self.config)

        self.model.fit(X_train, y_train)
        if self.config["warm_start"]:
            self.model.n_estimators = final_n_estimators
            self.model.fit(X_train, y_train)


        pred_val_probas = self.model.predict_proba(X_val)

        pred_train = self.model.predict(X_train)
        pred_val = self.model.predict(X_val)

        results["train_acc"] = metrics.accuracy_score(y_train, pred_train)
        results["train_balanced_acc"] = metrics.balanced_accuracy_score(y_train, pred_train)
        results["val_acc"] = metrics.accuracy_score(y_val, pred_val)
        results["val_balanced_acc"] = metrics.balanced_accuracy_score(y_val, pred_val)
        results["val_preds"] = pred_val_probas.tolist()
        results["labels"] = y_val.tolist()

        return results 

def score(self, X_test, y_test):
        results = dict()

        y_pred = self.predict(X_test)

        results["test_acc"] = metrics.accuracy_score(y_test, y_pred)
        results["test_balanced_acc"] = metrics.balanced_accuracy_score(y_test, y_pred)

        return results 

def fit(self, X_train, y_train, X_val, y_val):
        results = dict()

        self.all_nan = np.all(np.isnan(X_train), axis=0)
        X_train = X_train[:, ~self.all_nan]
        X_val = X_val[:, ~self.all_nan]

        self.categoricals = np.array([isinstance(X_train[0,ind], str) for ind in range(X_train.shape[1])])
        X_train = X_train[:, ~self.categoricals]
        X_val = X_val[:, ~self.categoricals]

        X_train = np.nan_to_num(X_train)
        X_val = np.nan_to_num(X_val)

        self.num_classes = len(np.unique(y_train))
        
        self.model = KNeighborsClassifier(**self.config)
        self.model.fit(X_train, y_train)

        pred_val_probas = self.model.predict_proba(X_val)

        pred_train = self.model.predict(X_train)
        pred_val = self.model.predict(X_val)

        results["train_acc"] = metrics.accuracy_score(y_train, pred_train)
        results["train_balanced_acc"] = metrics.balanced_accuracy_score(y_train, pred_train)
        results["val_acc"] = metrics.accuracy_score(y_val, pred_val)
        results["val_balanced_acc"] = metrics.balanced_accuracy_score(y_val, pred_val)
        results["val_preds"] = pred_val_probas.tolist()
        results["labels"] = y_val.tolist()

        return results 

def score(self, X_test, y_test):
        results = dict()

        y_pred = self.predict(X_test)

        results["test_acc"] = metrics.accuracy_score(y_test, y_pred)
        results["test_balanced_acc"] = metrics.balanced_accuracy_score(y_test, y_pred)

        return results 

def infer(valid_queue, model, criterion, valid_losses):
    model.eval()
    test_true = []
    test_pred = []
    valid_losses.reset()

    with torch.no_grad():
        for i, data in enumerate(valid_queue):
            data = data.to(DEVICE)
            inputs = data.pos.transpose(2, 1).unsqueeze(3)
            gt = data.y
            out = model(inputs)

            pred = out.max(dim=1)[1]
            test_true.append(gt.cpu().numpy())
            test_pred.append(pred.detach().cpu().numpy())
            loss = criterion(out, gt.squeeze())

            n = gt.size(0)
            valid_losses.update(loss.item(), n)

        test_true = np.concatenate(test_true)
        test_pred = np.concatenate(test_pred)
        overall_acc = metrics.accuracy_score(test_true, test_pred)
        class_acc = metrics.balanced_accuracy_score(test_true, test_pred)
    return overall_acc, class_acc, valid_losses 

def train_step(train_queue, model, criterion, optimizer, args):
    objs = utils.AverageMeter()
    train_true = []
    train_pred = []
    for step, (data, label) in enumerate(tqdm(train_queue)):
        model.train()
        data, label = data.to(DEVICE), label.to(DEVICE).squeeze()
        data = data.permute(0, 2, 1).unsqueeze(3)
        n = data.size(0)

        optimizer.zero_grad()
        out, out_aux = model(data)
        loss = criterion(out, label)
        if args.auxiliary:
            loss_aux = criterion(out_aux, label)
            loss += args.auxiliary_weight * loss_aux

        loss.backward()
        nn.utils.clip_grad_norm_(model.parameters(), args.grad_clip)
        optimizer.step()

        pred = out.max(dim=1)[1]
        train_true.append(label.cpu().numpy())
        train_pred.append(pred.detach().cpu().numpy())
        objs.update(loss.item(), n)

    train_true = np.concatenate(train_true)
    train_pred = np.concatenate(train_pred)
    overall_acc = metrics.accuracy_score(train_true, train_pred)
    class_acc = metrics.balanced_accuracy_score(train_true, train_pred)
    return overall_acc, class_acc, objs.avg 

def test_balanced_accuracy_score(y_true, y_pred):
    macro_recall = recall_score(y_true, y_pred, average='macro',
                                labels=np.unique(y_true))
    with ignore_warnings():
        # Warnings are tested in test_balanced_accuracy_score_unseen
        balanced = balanced_accuracy_score(y_true, y_pred)
    assert balanced == pytest.approx(macro_recall)
    adjusted = balanced_accuracy_score(y_true, y_pred, adjusted=True)
    chance = balanced_accuracy_score(y_true, np.full_like(y_true, y_true[0]))
    assert adjusted == (balanced - chance) / (1 - chance) 

def fit(self, X_train, y_train, X_val, y_val, categoricals=None):
        results = dict()

        self.num_classes = len(np.unique(y_train))
        self.config["num_class"] = self.num_classes

        self.all_nan = np.all(np.isnan(X_train), axis=0)
        X_train = X_train[:, ~self.all_nan]
        X_val = X_val[:, ~self.all_nan]

        X_train = np.nan_to_num(X_train)
        X_val = np.nan_to_num(X_val)

        early_stopping = 150 if X_train.shape[0]>10000 else max(round(150*10000/X_train.shape[0]), 10)
        self.config["early_stopping_rounds"] = early_stopping

        categoricals = [ind for ind in range(X_train.shape[1]) if isinstance(X_train[0,ind], str)]
        X_train, X_val, self.encode_dicts = encode_categoricals(X_train, X_val, encode_dicts=None)

        self.model = LGBMClassifier(**self.config)
        self.model.fit(X_train, y_train, eval_set=[(X_val, y_val)])

        pred_train = self.model.predict_proba(X_train)
        pred_val = self.model.predict_proba(X_val)

        # This fixes a bug
        if self.num_classes==2:
            pred_train = pred_train.transpose()[0:len(y_train)]
            pred_val = pred_val.transpose()[0:len(y_val)]

        results["val_preds"] = pred_val.tolist()
        results["labels"] = y_val.tolist()

        pred_train = np.argmax(pred_train, axis=1)
        pred_val = np.argmax(pred_val, axis=1)

        results["train_acc"] = metrics.accuracy_score(y_train, pred_train)
        results["train_balanced_acc"] = metrics.balanced_accuracy_score(y_train, pred_train)
        results["val_acc"] = metrics.accuracy_score(y_val, pred_val)
        results["val_balanced_acc"] = metrics.balanced_accuracy_score(y_val, pred_val)
        
        return results 

def return_scoreval(scoretype, y_true, y_preds, y_proba, modeltype):
    if modeltype.endswith('Classification'):
        if scoretype == 'f1':
            try:
                scoreval = f1_score(y_true, y_preds)
            except:
                scoreval = f1_score(y_true, y_preds, average = 'micro')
        elif scoretype == 'roc_auc':
            #### ROC AUC can be computed only for Binary classifications ###
            try:
                scoreval = roc_auc_score(y_true, y_proba)
            except:
                scoreval = balanced_accuracy_score(y_true, y_preds)
                print('Multi-class problem. Instead of ROC-AUC, Balanced Accuracy computed')
        elif scoretype == 'precision':
            try:
                scoreval = precision_score(y_true, y_preds)
            except:
                scoreval = precision_score(y_true, y_preds, average='micro')
        elif scoretype == 'recall':
            try:
                scoreval = recall_score(y_true, y_preds)
            except:
                scoreval = recall_score(y_true, y_preds, average='micro')
        elif scoretype in ['balanced_accuracy','accuracy','balanced-accuracy']:
            try:
                scoreval = balanced_accuracy_score(y_true, y_preds)
            except:
                scoreval = accuracy(y_true, y_preds)
        else:
            print('Scoring Type not Recognized - selecting default as F1.')
            scoretype == 'f1'
            try:
                scoreval = f1_score(y_true, y_preds)
            except:
                scoreval = f1_score(y_true, y_preds, average='micro')
    else:
        if scoretype == 'rmse':
            try:
                scoreval = np.sqrt(mean_squared_error(y_true, y_preds))
            except:
                scoreval = 0
        elif scoretype == 'mae':
            try:
                scoreval = np.sqrt(mean_absolute_error(y_true, y_preds))
            except:
                scoreval = 0
        else:
            print('Scoring Type not Recognized.')
            scoretype == 'mae'
            scoreval = mean_absolute_error(y_true, y_preds)
    return scoreval
######### Print the % count of each class in a Target variable  #####