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b/test/test_maui.py |
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import os |
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import pytest |
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import tempfile |
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from unittest import mock |
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import numpy as np |
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import pandas as pd |
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from maui import Maui |
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from maui.maui_warnings import MauiWarning |
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samples = [f"Sample_{i}" for i in range(10)] |
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n_features_1 = 20 |
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df1 = pd.DataFrame( |
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np.random.randn(n_features_1, len(samples)), |
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columns=samples, |
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index=[f"data1_feature_{i}" for i in range(n_features_1)], |
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) |
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n_features_2 = 6 |
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df2 = pd.DataFrame( |
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np.random.randn(n_features_2, len(samples)), |
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columns=samples, |
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index=[f"data2_feature_{i}" for i in range(n_features_2)], |
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) |
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df_empty = pd.DataFrame( |
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np.random.randn(0, len(samples)), |
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columns=samples, |
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index=[f"data0_feature_{i}" for i in range(0)], |
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) |
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def test_validate_X_fails_if_not_dict(): |
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maui_model = Maui() |
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with pytest.raises(ValueError): |
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maui_model._validate_X([1, 2, 3]) |
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def test_validate_X_fails_if_samples_mismatch(): |
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maui_model = Maui() |
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with pytest.raises(ValueError): |
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df2_bad = df2.iloc[:, :2] |
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data_with_mismatching_samples = {"a": df1, "b": df2_bad} |
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maui_model._validate_X(data_with_mismatching_samples) |
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def test_validate_X_fails_if_some_data_empty(): |
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maui_model = Maui() |
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with pytest.raises(ValueError): |
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maui_model._validate_X({"a": df1, "e": df_empty}) |
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def test_validate_X_returns_true_on_valid_data(): |
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maui_model = Maui() |
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valid_data = {"a": df1, "b": df2} |
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assert maui_model._validate_X(valid_data) |
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def test_dict2array(): |
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maui_model = Maui() |
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arr = maui_model._dict2array({"data1": df1, "data2": df2}) |
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assert arr.shape[0] == len(df1.columns) |
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assert arr.shape[1] == len(df1.index) + len(df2.index) |
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def test_maui_saves_feature_correlations(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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z = maui_model.fit_transform({"d1": df1, "d2": df2}) |
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r = maui_model.get_feature_correlations() |
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assert r is not None |
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assert hasattr(maui_model, "feature_correlations_") |
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def test_maui_saves_w(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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z = maui_model.fit_transform({"d1": df1, "d2": df2}) |
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w = maui_model.get_linear_weights() |
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assert w is not None |
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assert hasattr(maui_model, "w_") |
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def test_maui_saves_neural_weight_product(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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z = maui_model.fit_transform({"d1": df1, "d2": df2}) |
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nwp = maui_model.get_neural_weight_product() |
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assert nwp is not None |
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assert hasattr(maui_model, "nwp_") |
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print(maui_model.encoder.summary()) |
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w1 = maui_model.encoder.layers[2].get_weights()[0] |
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w2 = maui_model.encoder.layers[3].get_weights()[0] |
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nwp_11 = np.dot(w1[0, :], w2[:, 0]) |
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assert np.allclose(nwp_11, nwp.iloc[0, 0]) |
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def test_maui_updates_neural_weight_product_when_training(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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z_before = maui_model.fit_transform({"d1": df1, "d2": df2}) |
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nwp_before_fine_tuning = maui_model.get_neural_weight_product() |
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maui_model.fine_tune({"d1": df1, "d2": df2}) |
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z_after = maui_model.transform({"d1": df1, "d2": df2}) |
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nwp_after_fine_tuning = maui_model.get_neural_weight_product() |
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assert not np.allclose(z_before, z_after) |
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assert not np.allclose(nwp_before_fine_tuning, nwp_after_fine_tuning) |
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def test_maui_clusters_with_single_k(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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np.random.randn(10, 2), |
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index=[f"sample {i}" for i in range(10)], |
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columns=["LF1", "LF2"], |
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) |
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maui_model.x_ = pd.DataFrame( |
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np.random.randn(20, 10), |
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index=[f"feature {i}" for i in range(20)], |
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columns=[f"sample {i}" for i in range(10)], |
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) |
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yhat = maui_model.cluster(5) |
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assert yhat.shape == (10,) |
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def test_maui_clusters_picks_optimal_k_by_ami(): |
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ami_mock = mock.Mock() |
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ami_mock.side_effect = [ |
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2, |
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3, |
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1, |
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] # the optimal AMI will be given at the second trial |
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with mock.patch("sklearn.metrics.adjusted_mutual_info_score", ami_mock): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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np.random.randn(10, 2), |
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index=[f"sample {i}" for i in range(10)], |
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columns=["LF1", "LF2"], |
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) |
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maui_model.x_ = pd.DataFrame( |
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np.random.randn(20, 10), |
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index=[f"feature {i}" for i in range(20)], |
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columns=[f"sample {i}" for i in range(10)], |
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) |
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the_y = pd.Series(np.arange(10), index=maui_model.z_.index) |
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maui_model.cluster( |
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ami_y=the_y, optimal_k_range=[1, 2, 3] |
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) # the second trial is k=2 |
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print(maui_model.kmeans_scores) |
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assert maui_model.optimal_k_ == 2 |
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def test_maui_clusters_picks_optimal_k_by_silhouette(): |
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silhouette_mock = mock.Mock() |
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silhouette_mock.side_effect = [ |
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2, |
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3, |
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1, |
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] # the optimal silhouette will be given at the second trial |
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with mock.patch("sklearn.metrics.silhouette_score", silhouette_mock): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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np.random.randn(10, 2), |
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index=[f"sample {i}" for i in range(10)], |
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columns=["LF1", "LF2"], |
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) |
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maui_model.x_ = pd.DataFrame( |
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np.random.randn(20, 10), |
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index=[f"feature {i}" for i in range(20)], |
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columns=[f"sample {i}" for i in range(10)], |
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) |
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maui_model.cluster( |
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optimal_k_method="silhouette", optimal_k_range=[1, 2, 3] |
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) # the second trial is k=2 |
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assert maui_model.optimal_k_ == 2 |
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def test_maui_clusters_picks_optimal_k_with_custom_scoring(): |
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scorer = mock.Mock() |
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scorer.side_effect = [2, 3, 1] # the optimal AMI will be given at the second trial |
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scorer.__name__ = "mock_scorer" |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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np.random.randn(10, 2), |
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index=[f"sample {i}" for i in range(10)], |
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columns=["LF1", "LF2"], |
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) |
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maui_model.x_ = pd.DataFrame( |
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np.random.randn(20, 10), |
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index=[f"feature {i}" for i in range(20)], |
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columns=[f"sample {i}" for i in range(10)], |
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) |
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maui_model.cluster( |
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optimal_k_method=scorer, optimal_k_range=[1, 2, 3] |
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) # the second trial is k=2 |
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assert maui_model.optimal_k_ == 2 |
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def test_maui_computes_roc_and_auc(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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[ |
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[0, 1, 1, 1, 0, 1, 1, 0, 0], |
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[1, 0, 0, 0, 0, 0, 1, 1, 0], |
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[1, 0, 1, 0, 0, 0, 1, 1, 0], |
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[1, 0, 0, 1, 0, 0, 1, 1, 0], |
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[1, 0, 0, 0, 1, 1, 1, 1, 0], |
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[1, 1, 1, 0, 0, 0, 1, 1, 1], |
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], |
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index=[f"sample {i}" for i in range(6)], |
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columns=[f"LF{i}" for i in range(9)], |
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) |
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y = pd.Series(["a", "b", "a", "c", "b", "c"], index=maui_model.z_.index) |
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rocs = maui_model.compute_roc(y, cv_folds=2) |
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assert rocs == maui_model.roc_curves_ |
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assert "a" in rocs |
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assert "b" in rocs |
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assert "c" in rocs |
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assert "mean" in rocs |
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aucs = maui_model.compute_auc(y, cv_folds=2) |
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assert aucs == maui_model.aucs_ |
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def test_maui_clusters_only_samples_in_y_index_when_optimizing(): |
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np.random.seed(0) |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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np.random.randn(10, 2), |
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index=[f"sample {i}" for i in range(10)], |
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columns=["LF1", "LF2"], |
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) |
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maui_model.x_ = pd.DataFrame( |
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np.random.randn(20, 10), |
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index=[f"feature {i}" for i in range(20)], |
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columns=[f"sample {i}" for i in range(10)], |
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) |
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y = pd.Series( |
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["a", "a", "a", "b", "b", "b"], index=[f"sample {i}" for i in range(6)] |
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) |
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yhat = maui_model.cluster(ami_y=y, optimal_k_range=[1, 2, 3]) |
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assert set(yhat.index) == set(y.index) |
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def test_select_clinical_factors(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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[ |
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[1, 1, 1, 0, 0, 0, 1, 0, 1], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 1, 0, 0, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 1, 1, 1, 1], |
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], |
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index=[f"sample {i}" for i in range(11)], |
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columns=[f"LF{i}" for i in range(9)], |
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) # here the first 3 factors separate the groups and the last 6 do not |
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durations = [ |
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1, |
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2, |
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3, |
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4, |
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5, |
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6, |
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1000, |
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2000, |
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3000, |
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4000, |
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5000, |
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] # here the first 3 have short durations, the last 3 longer ones |
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observed = [True] * 11 # all events observed |
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survival = pd.DataFrame( |
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dict(duration=durations, observed=observed), |
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index=[f"sample {i}" for i in range(11)], |
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) |
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z_clin = maui_model.select_clinical_factors(survival, cox_penalizer=1, alpha=0.1) |
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assert "LF0" in z_clin.columns |
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assert "LF5" not in z_clin.columns |
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300 |
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def test_maui_computes_harrells_c(): |
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maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
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maui_model.z_ = pd.DataFrame( |
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304 |
[ |
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[1, 1, 1, 0, 0, 0, 1, 0, 1], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 0, 1, 1, 1, 0], |
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[1, 1, 1, 1, 1, 0, 0, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 0, 1, 1, 0], |
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[0, 0, 0, 1, 0, 1, 1, 1, 1], |
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], |
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index=[f"sample {i}" for i in range(11)], |
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columns=[f"LF{i}" for i in range(9)], |
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) # here the first 3 factors separate the groups and the last 6 do not |
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durations = [ |
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1, |
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2, |
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3, |
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4, |
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5, |
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6, |
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1000, |
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2000, |
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3000, |
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4000, |
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5000, |
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] # here the first 3 have short durations, the last 3 longer ones |
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observed = [True] * 11 # all events observed |
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survival = pd.DataFrame( |
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dict(duration=durations, observed=observed), |
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index=[f"sample {i}" for i in range(11)], |
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) |
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cs = maui_model.c_index( |
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survival, |
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clinical_only=True, |
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duration_column="duration", |
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observed_column="observed", |
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cox_penalties=[0.1, 1, 10, 100, 1000, 10000], |
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cv_folds=3, |
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sel_clin_alpha=0.1, |
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347 |
sel_clin_penalty=1, |
|
|
348 |
) |
|
|
349 |
print(cs) |
|
|
350 |
assert np.allclose(cs, [0.5, 0.8, 0.5], atol=0.05) |
|
|
351 |
|
|
|
352 |
|
|
|
353 |
def test_maui_produces_same_prediction_when_run_twice(): |
|
|
354 |
"""This is to show the maui encoder model picks the mean of |
|
|
355 |
the distribution, not a sample.""" |
|
|
356 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
357 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
358 |
z1 = maui_model.transform({"d1": df1, "d2": df2}) |
|
|
359 |
z2 = maui_model.transform({"d1": df1, "d2": df2}) |
|
|
360 |
assert np.allclose(z1, z2) |
|
|
361 |
|
|
|
362 |
|
|
|
363 |
def test_maui_produces_different_prediction_when_run_twice_with_sampling(): |
|
|
364 |
"""This is to show the maui encoder model picks the mean of |
|
|
365 |
the distribution, not a sample.""" |
|
|
366 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
367 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
368 |
z1 = maui_model.transform({"d1": df1, "d2": df2}, encoder="sample") |
|
|
369 |
z2 = maui_model.transform({"d1": df1, "d2": df2}, encoder="sample") |
|
|
370 |
assert not np.allclose(z1, z2) |
|
|
371 |
|
|
|
372 |
|
|
|
373 |
def test_maui_produces_nonnegative_zs_if_relu_embedding_true(): |
|
|
374 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1, relu_embedding=True) |
|
|
375 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
376 |
z1 = maui_model.transform({"d1": df1, "d2": df2}) |
|
|
377 |
assert np.all(z1 >= 0) |
|
|
378 |
|
|
|
379 |
|
|
|
380 |
def test_maui_produces_pos_and_neg_zs_if_relu_embedding_false(): |
|
|
381 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1, relu_embedding=False) |
|
|
382 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
383 |
z1 = maui_model.transform({"d1": df1, "d2": df2}) |
|
|
384 |
assert not np.all(z1 >= 0) |
|
|
385 |
|
|
|
386 |
|
|
|
387 |
def test_maui_runs_with_deep_not_stacked_vae(): |
|
|
388 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1, architecture="deep") |
|
|
389 |
z = maui_model.fit_transform({"d1": df1, "d2": df2}) |
|
|
390 |
|
|
|
391 |
|
|
|
392 |
def test_maui_complains_if_wrong_architecture(): |
|
|
393 |
with pytest.raises(ValueError): |
|
|
394 |
maui_model = Maui( |
|
|
395 |
n_hidden=[10], n_latent=2, epochs=1, architecture="wrong value" |
|
|
396 |
) |
|
|
397 |
|
|
|
398 |
|
|
|
399 |
def test_maui_supports_single_layer_vae(): |
|
|
400 |
maui_model = Maui(n_hidden=None, n_latent=2, epochs=1) |
|
|
401 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
402 |
z1 = maui_model.transform({"d1": df1, "d2": df2}) |
|
|
403 |
|
|
|
404 |
|
|
|
405 |
def test_maui_supports_not_deep_deep_vae(): |
|
|
406 |
maui_model = Maui(n_hidden=None, n_latent=2, epochs=1, architecture="deep") |
|
|
407 |
z = maui_model.fit_transform({"d1": df1, "d2": df2}) |
|
|
408 |
|
|
|
409 |
|
|
|
410 |
def test_maui_drops_unexplanatody_factors_by_r2(): |
|
|
411 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
412 |
maui_model.z_ = pd.DataFrame( |
|
|
413 |
[ |
|
|
414 |
[1, 1, 1, 0, 0, 0, 1, 0, 0], |
|
|
415 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
416 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
417 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
418 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
419 |
[1, 1, 1, 1, 1, 0, 0, 1, 0], |
|
|
420 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
421 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
422 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
423 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
424 |
[0, 0, 0, 1, 0, 1, 1, 1, 0], |
|
|
425 |
], |
|
|
426 |
index=[f"sample {i}" for i in range(11)], |
|
|
427 |
columns=[f"LF{i}" for i in range(9)], |
|
|
428 |
dtype=float, |
|
|
429 |
) # here the first 8 latent factors have R2 above threshold, the last does not |
|
|
430 |
maui_model.x_ = pd.DataFrame( |
|
|
431 |
[[1], [1], [1], [1], [1], [1], [0], [0], [0], [0], [0]], |
|
|
432 |
index=[f"sample {i}" for i in range(11)], |
|
|
433 |
columns=["Feature 1"], |
|
|
434 |
dtype=float, |
|
|
435 |
) |
|
|
436 |
|
|
|
437 |
z_filt = maui_model.drop_unexplanatory_factors() |
|
|
438 |
|
|
|
439 |
assert z_filt.shape[1] == 8 |
|
|
440 |
|
|
|
441 |
|
|
|
442 |
def test_maui_merges_latent_factors(): |
|
|
443 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
444 |
maui_model.z_ = pd.DataFrame( |
|
|
445 |
[ |
|
|
446 |
[1, 1, 1, 0, 0, 0, 1, 0, 0], |
|
|
447 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
448 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
449 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
450 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
451 |
[1, 1, 1, 1, 1, 0, 0, 1, 0], |
|
|
452 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
453 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
454 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
455 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
456 |
[0, 0, 0, 1, 0, 1, 1, 1, 0], |
|
|
457 |
], |
|
|
458 |
index=[f"sample {i}" for i in range(11)], |
|
|
459 |
columns=[f"LF{i}" for i in range(9)], |
|
|
460 |
dtype=float, |
|
|
461 |
) # expect 0,1,2 to be merged, and 3,7 to be merged |
|
|
462 |
|
|
|
463 |
z_merged = maui_model.merge_similar_latent_factors(distance_metric="euclidean") |
|
|
464 |
assert z_merged.shape[1] == 6 |
|
|
465 |
assert "0_1_2" in z_merged.columns |
|
|
466 |
assert "3_7" in z_merged.columns |
|
|
467 |
|
|
|
468 |
|
|
|
469 |
def test_maui_merges_latent_factors_by_w(): |
|
|
470 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
471 |
maui_model.z_ = pd.DataFrame( |
|
|
472 |
[ |
|
|
473 |
[1, 1, 1, 0, 0, 0, 1, 0, 0], |
|
|
474 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
475 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
476 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
477 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
478 |
[1, 1, 1, 1, 1, 0, 0, 1, 0], |
|
|
479 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
480 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
481 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
482 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
483 |
[0, 0, 0, 1, 0, 1, 1, 1, 0], |
|
|
484 |
], |
|
|
485 |
index=[f"sample {i}" for i in range(11)], |
|
|
486 |
columns=[f"LF{i}" for i in range(9)], |
|
|
487 |
dtype=float, |
|
|
488 |
) |
|
|
489 |
maui_model.x_ = pd.DataFrame( |
|
|
490 |
[[1], [1], [1], [1], [1], [1], [0], [0], [0], [0], [0]], |
|
|
491 |
index=[f"sample {i}" for i in range(11)], |
|
|
492 |
columns=["Feature 1"], |
|
|
493 |
dtype=float, |
|
|
494 |
) |
|
|
495 |
# with these z and x, expect 0,1,2 and 4,5 and 3,6,7 |
|
|
496 |
z_merged = maui_model.merge_similar_latent_factors( |
|
|
497 |
distance_in="w", distance_metric="euclidean" |
|
|
498 |
) |
|
|
499 |
assert z_merged.shape[1] == 4 |
|
|
500 |
assert "0_1_2" in z_merged.columns |
|
|
501 |
assert "3_6_7" in z_merged.columns |
|
|
502 |
assert "4_5" in z_merged.columns |
|
|
503 |
|
|
|
504 |
|
|
|
505 |
def test_maui_merge_latent_factors_complains_if_unknown_merge_by(): |
|
|
506 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
507 |
maui_model.z_ = pd.DataFrame( |
|
|
508 |
[ |
|
|
509 |
[1, 1, 1, 0, 0, 0, 1, 0, 0], |
|
|
510 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
511 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
512 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
513 |
[1, 1, 1, 1, 0, 1, 1, 1, 0], |
|
|
514 |
[1, 1, 1, 1, 1, 0, 0, 1, 0], |
|
|
515 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
516 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
517 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
518 |
[0, 0, 0, 1, 0, 0, 1, 1, 0], |
|
|
519 |
[0, 0, 0, 1, 0, 1, 1, 1, 0], |
|
|
520 |
], |
|
|
521 |
index=[f"sample {i}" for i in range(11)], |
|
|
522 |
columns=[f"LF{i}" for i in range(9)], |
|
|
523 |
dtype=float, |
|
|
524 |
) # expect 0,1,2 to be merged, and 3,7 to be merged |
|
|
525 |
|
|
|
526 |
with pytest.raises(Exception): |
|
|
527 |
z_merged = maui_model.merge_similar_latent_factors( |
|
|
528 |
distance_in="xxx", distance_metric="euclidean" |
|
|
529 |
) |
|
|
530 |
|
|
|
531 |
|
|
|
532 |
def test_maui_can_save_to_folder(): |
|
|
533 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
534 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
535 |
with tempfile.TemporaryDirectory() as tmpdirname: |
|
|
536 |
maui_model.save(tmpdirname) |
|
|
537 |
assert os.path.isfile(os.path.join(tmpdirname, "maui_weights.h5")) |
|
|
538 |
assert os.path.isfile(os.path.join(tmpdirname, "maui_args.json")) |
|
|
539 |
|
|
|
540 |
|
|
|
541 |
def test_maui_can_load_from_folder(): |
|
|
542 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
543 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
544 |
with tempfile.TemporaryDirectory() as tmpdirname: |
|
|
545 |
maui_model.save(tmpdirname) |
|
|
546 |
maui_model_from_disk = Maui.load(tmpdirname) |
|
|
547 |
|
|
|
548 |
assert maui_model_from_disk.n_latent == maui_model.n_latent |
|
|
549 |
assert np.allclose( |
|
|
550 |
maui_model.vae.get_weights()[0], maui_model_from_disk.vae.get_weights()[0] |
|
|
551 |
) |
|
|
552 |
assert np.allclose( |
|
|
553 |
maui_model.transform({"d1": df1, "d2": df2}), |
|
|
554 |
maui_model_from_disk.transform({"d1": df1, "d2": df2}), |
|
|
555 |
) |
|
|
556 |
|
|
|
557 |
|
|
|
558 |
def test_maui_can_print_verbose_training(capsys): |
|
|
559 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
560 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
561 |
|
|
|
562 |
stdout, stderr = capsys.readouterr() |
|
|
563 |
assert stdout == "" |
|
|
564 |
|
|
|
565 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1, verbose=1) |
|
|
566 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
567 |
|
|
|
568 |
stdout, stderr = capsys.readouterr() |
|
|
569 |
assert "Epoch" in stdout |
|
|
570 |
|
|
|
571 |
|
|
|
572 |
def test_maui_model_makes_2_layer_vae(): |
|
|
573 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1, input_dim=10) |
|
|
574 |
layers_names = [l.name for l in maui_model.vae.layers] |
|
|
575 |
|
|
|
576 |
assert "hidden_dim_0_mean" in layers_names |
|
|
577 |
assert "latent_mean" in layers_names |
|
|
578 |
assert "decode_hidden_0" in layers_names |
|
|
579 |
assert "reconstruction" in layers_names |
|
|
580 |
|
|
|
581 |
assert "decode_hidden_1" not in layers_names |
|
|
582 |
|
|
|
583 |
|
|
|
584 |
def test_maui_model_makes_one_layer_vae(): |
|
|
585 |
maui_model = Maui(n_hidden=[], n_latent=2, epochs=1, input_dim=10) |
|
|
586 |
layers_names = [l.name for l in maui_model.vae.layers] |
|
|
587 |
|
|
|
588 |
print(layers_names) |
|
|
589 |
|
|
|
590 |
assert layers_names[-1] == "reconstruction" |
|
|
591 |
|
|
|
592 |
assert not any( |
|
|
593 |
"decode_hidden" in name for name in layers_names |
|
|
594 |
), "Has a decode hidden..." |
|
|
595 |
assert not any("hidden_dim" in name for name in layers_names), "Has a hidden dim..." |
|
|
596 |
|
|
|
597 |
|
|
|
598 |
def test_maui_model_validates_feature_names_on_predict_after_fit(): |
|
|
599 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
600 |
maui_model.fit({"d1": df1, "d2": df2}) |
|
|
601 |
|
|
|
602 |
z = maui_model.transform({"d1": df1, "d2": df2}) |
|
|
603 |
|
|
|
604 |
df1_wrong_features = df1.reindex(df1.index[: len(df1.index) - 1]) |
|
|
605 |
with pytest.raises(ValueError): |
|
|
606 |
z = maui_model.transform({"df1": df1_wrong_features, "df2": df2}) |
|
|
607 |
|
|
|
608 |
|
|
|
609 |
def test_maui_model_saves_feature_names_to_disk(): |
|
|
610 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
611 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
612 |
with tempfile.TemporaryDirectory() as tmpdirname: |
|
|
613 |
maui_model.save(tmpdirname) |
|
|
614 |
maui_model_from_disk = Maui.load(tmpdirname) |
|
|
615 |
assert maui_model.feature_names == maui_model_from_disk.feature_names |
|
|
616 |
|
|
|
617 |
|
|
|
618 |
def test_maui_model_loads_model_without_feature_names_from_disk_and_warns(): |
|
|
619 |
maui_model = Maui(n_hidden=[10], n_latent=2, epochs=1) |
|
|
620 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
621 |
with tempfile.TemporaryDirectory() as tmpdirname: |
|
|
622 |
maui_model.save(tmpdirname) |
|
|
623 |
os.remove(os.path.join(tmpdirname, "maui_feature_names.txt")) |
|
|
624 |
with pytest.warns(MauiWarning): |
|
|
625 |
maui_model_from_disk = Maui.load(tmpdirname) |
|
|
626 |
assert maui_model_from_disk.feature_names is None |
|
|
627 |
|
|
|
628 |
|
|
|
629 |
def test_maui_can_fine_tune(): |
|
|
630 |
maui_model = Maui(n_hidden=[], n_latent=2, epochs=1) |
|
|
631 |
maui_model = maui_model.fit({"d1": df1, "d2": df2}) |
|
|
632 |
maui_model.fine_tune({"d1": df1, "d2": df2}, epochs=1) |
|
|
633 |
|
|
|
634 |
|
|
|
635 |
def test_maui_complains_if_fine_tune_with_wrong_features(): |
|
|
636 |
maui_model = Maui(n_hidden=[], n_latent=2, epochs=1) |
|
|
637 |
maui_model.fit({"d1": df1, "d2": df2}) |
|
|
638 |
|
|
|
639 |
df1_wrong_features = df1.reindex(df1.index[: len(df1.index) - 1]) |
|
|
640 |
with pytest.raises(ValueError): |
|
|
641 |
z = maui_model.fine_tune({"df1": df1_wrong_features, "df2": df2}) |