Merge pull request #14 from SCAI-BIO/cleanup-build-and-functions

Cleanup build and functions

README.md

@@ -25,11 +25,18 @@ import syndat
 real = pd.read_csv("real.csv")
 synthetic = pd.read_csv("synthetic.csv")
 
-jsd = syndat.quality.jsd(real, synthetic)
-auc = syndat.quality.auc(real, synthetic)
-norm = syndat.quality.correlation(real, synthetic)
+# How similar are the statistical distributions of real and synthetic features 
+distribution_similarity_score = syndat.scores.distribution(real, synthetic)
+
+# How hard is it for a classifier to discriminate real and synthetic data
+discrimination_score = syndat.scores.discrimination(real, synthetic)
+
+# How well are pairwise feature correlations preserved
+correlation_score = syndat.scores.correlation(real, synthetic)
 ```
 
+Scores are defined in a range of 0-100, with a higher score corresponding to better data fidelity.
+
 ## Visualization
 
 Visualize real vs. synthetic data distributions and summary statistics for each feature:

setup.py

@@ -23,4 +23,31 @@
     author_email='[email protected]',
     description=DESCRIPTION,
     long_description=DESCRIPTION,
+    long_description_content_type='text/markdown',
+    install_requires=[
+        'pandas~=2.1.4',
+        'numpy~=1.26.2',
+        'scipy~=1.11.4',
+        'scikit-learn~=1.5.1',
+        'matplotlib~=3.8.2',
+        'seaborn~=0.13.0',
+        'setuptools==70.0.0'
+    ],
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Developers',
+        'License :: OSI Approved :: Apache Software License',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+    ],
+    include_package_data=True,  # Ensure non-Python files are included
+    python_requires='>=3.9',  # Specify minimum Python version
+    keywords='synthetic-data, data-quality, data-visualization',
+    project_urls={
+        'Documentation': 'https://github.com/SCAI-BIO/syndat#readme',
+        'Source': 'https://github.com/SCAI-BIO/syndat',
+        'Tracker': 'https://github.com/SCAI-BIO/syndat/issues',
+    },
 )

syndat/__init__.py

@@ -1,3 +1,3 @@
 from syndat import domain
-from syndat import quality
-from syndat import visualization
+from syndat import scores
+from syndat import visualization

syndat/quality.py → syndat/scores.py

@@ -13,11 +13,13 @@
 
 from syndat.domain import AggregationMethod
 
+logger = logging.getLogger(__name__)
+
 
 def auc(real: pandas.DataFrame, synthetic: pandas.DataFrame, n_folds=5,
         drop_na_threshold=0.9, score: bool = True) -> float:
     """
-    Computes the Differentiation Complexity Score / ROC AUC score of a classifier trained to differentiate between real
+    Computes the Discrimination Complexity Score / ROC AUC score of a classifier trained to differentiate between real
     and synthetic data.
 
     :param real: The real data.
@@ -27,18 +29,43 @@ def auc(real: pandas.DataFrame, synthetic: pandas.DataFrame, n_folds=5,
     :param score: Return result in a normalized score in [0,100]. Default is True.
     :return: Differentiation Complexity Score / AUC ROC Score
     """
+
     warnings.warn(
-        "old_function is deprecated and will be removed in a future version. Please use discrimination_score instead.",
+        "auc is deprecated and will be removed in a future version. Please use discrimination instead.",
         DeprecationWarning,
         stacklevel=2
     )
-    return discrimination_score(real, synthetic, n_folds=n_folds, drop_na_threshold=drop_na_threshold, score=score)
+    return discrimination(real, synthetic, n_folds=n_folds, drop_na_threshold=drop_na_threshold, score=score)
 
 
-def discrimination_score(real: pandas.DataFrame, synthetic: pandas.DataFrame, n_folds=5,
-                         drop_na_threshold=0.9, score: bool = True) -> float:
+def jsd(real: pd.DataFrame, synthetic: pd.DataFrame, aggregate_results: bool = True,
+        aggregation_method: AggregationMethod = AggregationMethod.AVERAGE, score: bool = True,
+        n_unique_threshold=10) -> Union[List[float], float]:
     """
-    Computes the Differentiation Complexity Score / ROC AUC score of a classifier trained to differentiate between real
+    Computes the feature distribution similarity using the Jensen-Shannon distance of real and synthetic data.
+
+    :param real: The real data.
+    :param synthetic: The synthetic data.
+    :param aggregate_results: Compute a single aggregated score for all features. Default is True.
+    :param aggregation_method: How the scores are aggregated. Default is using the median of all feature scores.
+    :param score: Return result in a normalized score in [0,100]. Default is True.
+    :param n_unique_threshold: Threshold to determine at which number of unique values bins will span over several
+    values.
+    :return: Distribution Similarity / JSD
+    """
+
+    warnings.warn(
+        "auc is deprecated and will be removed in a future version. Please use discrimination instead.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return distribution(real, synthetic, aggregate_results, aggregation_method, score, n_unique_threshold)
+
+
+def discrimination(real: pandas.DataFrame, synthetic: pandas.DataFrame, n_folds=5,
+                   drop_na_threshold=0.9, score: bool = True) -> float:
+    """
+    Computes the Discrimination Complexity Score / ROC AUC score of a classifier trained to differentiate between real
     and synthetic data.
 
     :param real: The real data.
@@ -52,10 +79,10 @@ def discrimination_score(real: pandas.DataFrame, synthetic: pandas.DataFrame, n_
     real_filtered, synthetic_filtered = __filter_rows_with_common_categories(real, synthetic)
     # check for missing values in real data
     real_clean = real_filtered.dropna(thresh=int(drop_na_threshold * len(real_filtered)), axis=1)
-    logging.info(f'Dropped {real_clean.shape[1] - real_clean.shape[1]} '
+    logger.info(f'Dropped {real_clean.shape[1] - real_clean.shape[1]} '
                  f'due to high missingness (threshold is {drop_na_threshold}).')
     real_clean = real_clean.dropna()
-    logging.info(f'Removed {len(real) - len(real_clean)} entries due to missing values.')
+    logger.info(f'Removed {len(real) - len(real_clean)} entries due to missing values.')
     # assert that both real and synthetic have same columns
     synthetic_clean = synthetic_filtered[real_clean.columns]
     # one-hot-encode categorical columns
@@ -74,9 +101,9 @@ def discrimination_score(real: pandas.DataFrame, synthetic: pandas.DataFrame, n_
         return auc_score
 
 
-def jsd(real: pd.DataFrame, synthetic: pd.DataFrame, aggregate_results: bool = True,
-        aggregation_method: AggregationMethod = AggregationMethod.AVERAGE, score: bool = True,
-        n_unique_threshold=10) -> Union[List[float], float]:
+def distribution(real: pd.DataFrame, synthetic: pd.DataFrame, aggregate_results: bool = True,
+                 aggregation_method: AggregationMethod = AggregationMethod.AVERAGE, score: bool = True,
+                 n_unique_threshold=10) -> Union[List[float], float]:
     """
     Computes the feature distribution similarity using the Jensen-Shannon distance of real and synthetic data.
 
@@ -100,7 +127,7 @@ def jsd(real: pd.DataFrame, synthetic: pd.DataFrame, aggregate_results: bool = T
         col_dtype_real = real[col].dtype
         col_dtype_synthetic = synthetic[col].dtype
         if col_dtype_real != col_dtype_synthetic:
-            logging.warning(f'Real data at col {col} is dtype {col_dtype_real} but synthetic is {col_dtype_synthetic}. '
+            logger.warning(f'Real data at col {col} is dtype {col_dtype_real} but synthetic is {col_dtype_synthetic}. '
                             f'Evaluation will be done based on the assumed data type of the real data.')
             synthetic[col] = synthetic[col].astype(col_dtype_real)
         # categorical column
@@ -216,21 +243,15 @@ def __filter_rows_with_common_categories(real: pd.DataFrame, synthetic: pd.DataF
     synthetic_categorical_cols = synthetic.select_dtypes(include=['object', 'category']).columns
     # Identify common categorical columns
     common_categorical_cols = set(real_categorical_cols) & set(synthetic_categorical_cols)
-    if not common_categorical_cols:
-        logging.warning("No common categorical columns found. Correlation will be computed on numeric data only.")
     # Filter rows with common categories in each column
     for col in common_categorical_cols:
         real_categories = set(real[col].unique())
         synthetic_categories = set(synthetic[col].unique())
         common_categories = real_categories & synthetic_categories
         if len(real_categories - common_categories) > 0:
-            logging.warning(
-                f"Categories {real_categories - common_categories} in column '{col}' "
-                f"are in real data but not in synthetic data and will be excluded.")
-        if len(synthetic_categories - common_categories) > 0:
-            logging.warning(
-                f"Categories {synthetic_categories - common_categories} in column '{col}' "
-                f"are in synthetic data but not in real data and will be excluded.")
+            logger.warning(
+                f"Categories {real_categories - common_categories} in column '{col}' are in real data but not in "
+                f"synthetic data. They will not be considered in the score computation.")
         # Filter rows to keep only common categories
         real = real[real[col].isin(common_categories)]
         synthetic = synthetic[synthetic[col].isin(common_categories)]

tests/test_auc.py

@@ -43,41 +43,41 @@ def preprocess_categorical_data(self, real_data, synthetic_data):
         return real_data_encoded, synthetic_data_encoded
 
     def test_auc_score(self):
-        auc_score = syndat.quality.auc(self.real_data, self.synthetic_data)
+        auc_score = syndat.scores.discrimination(self.real_data, self.synthetic_data)
         self.assertTrue(isinstance(auc_score, float))
         self.assertGreaterEqual(auc_score, 0.0)
         self.assertLessEqual(auc_score, 100.0)
 
     def test_auc_score_normalized(self):
-        auc_score = syndat.quality.auc(self.real_data, self.synthetic_data)
+        auc_score = syndat.scores.discrimination(self.real_data, self.synthetic_data)
         self.assertTrue(isinstance(auc_score, float))
         self.assertGreaterEqual(auc_score, 0.0)
         self.assertLessEqual(auc_score, 100.0)
 
     def test_auc_score_with_missing_values(self):
         # Introduce missing values in real data
         self.real_data.iloc[::10, 0] = np.nan  # 10% missing data
-        auc_score = syndat.quality.auc(self.real_data, self.synthetic_data)
+        auc_score = syndat.scores.discrimination(self.real_data, self.synthetic_data)
         self.assertTrue(isinstance(auc_score, float))
         self.assertGreaterEqual(auc_score, 0.0)
         self.assertLessEqual(auc_score, 100.0)
 
     def test_auc_score_with_missing_values_drop_col(self):
         # Introduce missing values in real data
         self.real_data.iloc[::2, 0] = np.nan  # 50% missing data -> col drop
-        auc_score = syndat.quality.auc(self.real_data, self.synthetic_data)
+        auc_score = syndat.scores.discrimination(self.real_data, self.synthetic_data)
         self.assertTrue(isinstance(auc_score, float))
         self.assertGreaterEqual(auc_score, 0.0)
         self.assertLessEqual(auc_score, 100.0)
 
     def test_auc_score_with_custom_folds(self):
-        auc_score = syndat.quality.auc(self.real_data, self.synthetic_data, n_folds=5)
+        auc_score = syndat.scores.discrimination(self.real_data, self.synthetic_data, n_folds=5)
         self.assertTrue(isinstance(auc_score, float))
         self.assertGreaterEqual(auc_score, 0.0)
         self.assertLessEqual(auc_score, 100.0)
 
     def test_auc_score_with_categorical_data(self):
-        auc_score = syndat.quality.auc(self.real_data_cat, self.synthetic_data_cat)
+        auc_score = syndat.scores.discrimination(self.real_data_cat, self.synthetic_data_cat)
         self.assertTrue(isinstance(auc_score, float))
         self.assertGreaterEqual(auc_score, 0.0)
         self.assertLessEqual(auc_score, 100.0)

tests/test_correlation.py

@@ -2,7 +2,7 @@
 
 import pandas as pd
 
-from syndat.quality import correlation
+from syndat.scores import correlation
 
 
 class TestCorrelation(unittest.TestCase):

tests/test_jsd.py

@@ -17,8 +17,8 @@ def test_jsd_zero_int64(self):
             'feature1': [6, 7, 8, 9, 10],
             'feature2': [15, 16, 17, 18, 19]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertEqual(0, jsd)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertEqual(0, distribution)
 
     def test_jsd_zero_int64_float64(self):
         synthetic = pd.DataFrame({
@@ -30,8 +30,8 @@ def test_jsd_zero_int64_float64(self):
             'feature1': [6, 7, 8, 9, 10],
             'feature2': [0.6, 0.7, 0.8, 0.9, 1.0]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertEqual(jsd, 0)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertEqual(distribution, 0)
 
     def test_jsd_perfect_int64(self):
         synthetic = pd.DataFrame({
@@ -43,8 +43,8 @@ def test_jsd_perfect_int64(self):
             'feature1': [1, 2, 1, 2, 3],
             'feature2': [11, 12, 13, 14, 15]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertEqual(jsd, 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertEqual(distribution, 100)
 
     def test_jsd_perfect_int64_and_float64(self):
         synthetic = pd.DataFrame({
@@ -56,8 +56,8 @@ def test_jsd_perfect_int64_and_float64(self):
             'feature1': [1, 2, 1, 2, 3],
             'feature2': [0.1, 0.2, 0.3, 0.4, 0.5]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertEqual(jsd, 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertEqual(distribution, 100)
 
     def test_jsd_different_col_types(self):
         synthetic = pd.DataFrame({
@@ -69,7 +69,7 @@ def test_jsd_different_col_types(self):
             'feature1': [1.2, 2.1, 1.1, 2.1, 3.1],
             'feature2': [1, 2, 3, 4, 5]
         })
-        jsd = syndat.quality.jsd(real, synthetic, score=False)
+        distribution = syndat.scores.distribution(real, synthetic, score=False)
 
     def test_jsd_negative_int64(self):
         synthetic = pd.DataFrame({
@@ -81,7 +81,7 @@ def test_jsd_negative_int64(self):
             'feature1': [-1, 2, 3, 4, 5],
             'feature2': [1, 2, 3, 4, 5]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
+        distribution = syndat.scores.distribution(real, synthetic)
 
     def test_jsd_single_outlier(self):
         synthetic = pd.DataFrame({
@@ -93,8 +93,8 @@ def test_jsd_single_outlier(self):
             'feature1': [1, 1, 1, 1, 1, 1, 2, 3, 4, 5, 6, 7, 8, 9, 9],
             'feature2': [1, 1, 1, 1, 1, 1, 2, 3, 4, 5, 6, 7, 8, 9, 100],
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertTrue(jsd < 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertTrue(distribution < 100)
 
     def test_jsd_categorical_equal(self):
         synthetic = pd.DataFrame({
@@ -106,8 +106,8 @@ def test_jsd_categorical_equal(self):
             'feature1': ['A', 'B', 'A', 'B', 'C'],
             'feature2': ['X', 'Y', 'Y', 'X', 'Z']
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertEqual(jsd, 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertEqual(distribution, 100)
 
     def test_jsd_categorical_different(self):
         synthetic = pd.DataFrame({
@@ -119,8 +119,8 @@ def test_jsd_categorical_different(self):
             'feature1': ['A', 'B', 'A', 'B', 'D'],
             'feature2': ['X', 'Y', 'Z', 'X', 'W']
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertTrue(jsd < 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertTrue(distribution < 100)
 
     def test_jsd_categorical_mixed(self):
         synthetic = pd.DataFrame({
@@ -132,8 +132,8 @@ def test_jsd_categorical_mixed(self):
             'feature1': ['A', 'B', 'C', 'F', 'G'],
             'feature2': [1.0, 2.0, 3.0, 6.0, 7.0]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertTrue(jsd < 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertTrue(distribution < 100)
 
     def test_jsd_categorical_with_numerical(self):
         synthetic = pd.DataFrame({
@@ -145,8 +145,8 @@ def test_jsd_categorical_with_numerical(self):
             'feature1': ['A', 'B', 'C', 'A', 'D'],
             'feature2': [1.0, 2.0, 3.0, 4.0, 6.0]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertTrue(jsd < 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertTrue(distribution < 100)
 
     def test_jsd_categorical_with_nan(self):
         synthetic = pd.DataFrame({
@@ -158,8 +158,8 @@ def test_jsd_categorical_with_nan(self):
             'feature1': ['A', 'B', 'C', 'D', None],
             'feature2': [1.0, 2.0, None, 4.0, 5.0]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertTrue(jsd < 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertTrue(distribution < 100)
 
     def test_jsd_categorical_all_nan(self):
         synthetic = pd.DataFrame({
@@ -171,5 +171,5 @@ def test_jsd_categorical_all_nan(self):
             'feature1': [None, None, None, None, None],
             'feature2': [None, None, None, None, None]
         })
-        jsd = syndat.quality.jsd(real, synthetic)
-        self.assertEqual(jsd, 100)
+        distribution = syndat.scores.distribution(real, synthetic)
+        self.assertEqual(distribution, 100)