workbench 0.8.174__py3-none-any.whl → 0.8.227__py3-none-any.whl

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  1. workbench/__init__.py +1 -0
  2. workbench/algorithms/dataframe/__init__.py +1 -2
  3. workbench/algorithms/dataframe/compound_dataset_overlap.py +321 -0
  4. workbench/algorithms/dataframe/feature_space_proximity.py +168 -75
  5. workbench/algorithms/dataframe/fingerprint_proximity.py +422 -86
  6. workbench/algorithms/dataframe/projection_2d.py +44 -21
  7. workbench/algorithms/dataframe/proximity.py +259 -305
  8. workbench/algorithms/graph/light/proximity_graph.py +12 -11
  9. workbench/algorithms/models/cleanlab_model.py +382 -0
  10. workbench/algorithms/models/noise_model.py +388 -0
  11. workbench/algorithms/sql/column_stats.py +0 -1
  12. workbench/algorithms/sql/correlations.py +0 -1
  13. workbench/algorithms/sql/descriptive_stats.py +0 -1
  14. workbench/algorithms/sql/outliers.py +3 -3
  15. workbench/api/__init__.py +5 -1
  16. workbench/api/df_store.py +17 -108
  17. workbench/api/endpoint.py +14 -12
  18. workbench/api/feature_set.py +117 -11
  19. workbench/api/meta.py +0 -1
  20. workbench/api/meta_model.py +289 -0
  21. workbench/api/model.py +52 -21
  22. workbench/api/parameter_store.py +3 -52
  23. workbench/cached/cached_meta.py +0 -1
  24. workbench/cached/cached_model.py +49 -11
  25. workbench/core/artifacts/__init__.py +11 -2
  26. workbench/core/artifacts/artifact.py +7 -7
  27. workbench/core/artifacts/data_capture_core.py +8 -1
  28. workbench/core/artifacts/df_store_core.py +114 -0
  29. workbench/core/artifacts/endpoint_core.py +323 -205
  30. workbench/core/artifacts/feature_set_core.py +249 -45
  31. workbench/core/artifacts/model_core.py +133 -101
  32. workbench/core/artifacts/parameter_store_core.py +98 -0
  33. workbench/core/cloud_platform/aws/aws_account_clamp.py +48 -2
  34. workbench/core/cloud_platform/cloud_meta.py +0 -1
  35. workbench/core/pipelines/pipeline_executor.py +1 -1
  36. workbench/core/transforms/features_to_model/features_to_model.py +60 -44
  37. workbench/core/transforms/model_to_endpoint/model_to_endpoint.py +43 -10
  38. workbench/core/transforms/pandas_transforms/pandas_to_features.py +38 -2
  39. workbench/core/views/training_view.py +113 -42
  40. workbench/core/views/view.py +53 -3
  41. workbench/core/views/view_utils.py +4 -4
  42. workbench/model_script_utils/model_script_utils.py +339 -0
  43. workbench/model_script_utils/pytorch_utils.py +405 -0
  44. workbench/model_script_utils/uq_harness.py +277 -0
  45. workbench/model_scripts/chemprop/chemprop.template +774 -0
  46. workbench/model_scripts/chemprop/generated_model_script.py +774 -0
  47. workbench/model_scripts/chemprop/model_script_utils.py +339 -0
  48. workbench/model_scripts/chemprop/requirements.txt +3 -0
  49. workbench/model_scripts/custom_models/chem_info/fingerprints.py +175 -0
  50. workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +18 -7
  51. workbench/model_scripts/custom_models/chem_info/mol_standardize.py +80 -58
  52. workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +0 -1
  53. workbench/model_scripts/custom_models/chem_info/morgan_fingerprints.py +1 -2
  54. workbench/model_scripts/custom_models/proximity/feature_space_proximity.py +194 -0
  55. workbench/model_scripts/custom_models/proximity/feature_space_proximity.template +8 -10
  56. workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template +7 -8
  57. workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template +20 -21
  58. workbench/model_scripts/custom_models/uq_models/feature_space_proximity.py +194 -0
  59. workbench/model_scripts/custom_models/uq_models/gaussian_process.template +5 -11
  60. workbench/model_scripts/custom_models/uq_models/ngboost.template +15 -16
  61. workbench/model_scripts/ensemble_xgb/ensemble_xgb.template +15 -17
  62. workbench/model_scripts/meta_model/generated_model_script.py +209 -0
  63. workbench/model_scripts/meta_model/meta_model.template +209 -0
  64. workbench/model_scripts/pytorch_model/generated_model_script.py +443 -499
  65. workbench/model_scripts/pytorch_model/model_script_utils.py +339 -0
  66. workbench/model_scripts/pytorch_model/pytorch.template +440 -496
  67. workbench/model_scripts/pytorch_model/pytorch_utils.py +405 -0
  68. workbench/model_scripts/pytorch_model/requirements.txt +1 -1
  69. workbench/model_scripts/pytorch_model/uq_harness.py +277 -0
  70. workbench/model_scripts/scikit_learn/generated_model_script.py +7 -12
  71. workbench/model_scripts/scikit_learn/scikit_learn.template +4 -9
  72. workbench/model_scripts/script_generation.py +15 -12
  73. workbench/model_scripts/uq_models/generated_model_script.py +248 -0
  74. workbench/model_scripts/xgb_model/generated_model_script.py +371 -403
  75. workbench/model_scripts/xgb_model/model_script_utils.py +339 -0
  76. workbench/model_scripts/xgb_model/uq_harness.py +277 -0
  77. workbench/model_scripts/xgb_model/xgb_model.template +367 -399
  78. workbench/repl/workbench_shell.py +18 -14
  79. workbench/resources/open_source_api.key +1 -1
  80. workbench/scripts/endpoint_test.py +162 -0
  81. workbench/scripts/lambda_test.py +73 -0
  82. workbench/scripts/meta_model_sim.py +35 -0
  83. workbench/scripts/ml_pipeline_sqs.py +122 -6
  84. workbench/scripts/training_test.py +85 -0
  85. workbench/themes/dark/custom.css +59 -0
  86. workbench/themes/dark/plotly.json +5 -5
  87. workbench/themes/light/custom.css +153 -40
  88. workbench/themes/light/plotly.json +9 -9
  89. workbench/themes/midnight_blue/custom.css +59 -0
  90. workbench/utils/aws_utils.py +0 -1
  91. workbench/utils/chem_utils/fingerprints.py +87 -46
  92. workbench/utils/chem_utils/mol_descriptors.py +18 -7
  93. workbench/utils/chem_utils/mol_standardize.py +80 -58
  94. workbench/utils/chem_utils/projections.py +16 -6
  95. workbench/utils/chem_utils/vis.py +25 -27
  96. workbench/utils/chemprop_utils.py +141 -0
  97. workbench/utils/config_manager.py +2 -6
  98. workbench/utils/endpoint_utils.py +5 -7
  99. workbench/utils/license_manager.py +2 -6
  100. workbench/utils/markdown_utils.py +57 -0
  101. workbench/utils/meta_model_simulator.py +499 -0
  102. workbench/utils/metrics_utils.py +256 -0
  103. workbench/utils/model_utils.py +274 -87
  104. workbench/utils/pipeline_utils.py +0 -1
  105. workbench/utils/plot_utils.py +159 -34
  106. workbench/utils/pytorch_utils.py +87 -0
  107. workbench/utils/shap_utils.py +11 -57
  108. workbench/utils/theme_manager.py +95 -30
  109. workbench/utils/xgboost_local_crossfold.py +267 -0
  110. workbench/utils/xgboost_model_utils.py +127 -220
  111. workbench/web_interface/components/experiments/outlier_plot.py +0 -1
  112. workbench/web_interface/components/model_plot.py +16 -2
  113. workbench/web_interface/components/plugin_unit_test.py +5 -3
  114. workbench/web_interface/components/plugins/ag_table.py +2 -4
  115. workbench/web_interface/components/plugins/confusion_matrix.py +3 -6
  116. workbench/web_interface/components/plugins/model_details.py +48 -80
  117. workbench/web_interface/components/plugins/scatter_plot.py +192 -92
  118. workbench/web_interface/components/settings_menu.py +184 -0
  119. workbench/web_interface/page_views/main_page.py +0 -1
  120. {workbench-0.8.174.dist-info → workbench-0.8.227.dist-info}/METADATA +31 -17
  121. {workbench-0.8.174.dist-info → workbench-0.8.227.dist-info}/RECORD +125 -111
  122. {workbench-0.8.174.dist-info → workbench-0.8.227.dist-info}/entry_points.txt +4 -0
  123. {workbench-0.8.174.dist-info → workbench-0.8.227.dist-info}/licenses/LICENSE +1 -1
  124. workbench/core/cloud_platform/aws/aws_df_store.py +0 -404
  125. workbench/core/cloud_platform/aws/aws_parameter_store.py +0 -280
  126. workbench/model_scripts/custom_models/meta_endpoints/example.py +0 -53
  127. workbench/model_scripts/custom_models/proximity/generated_model_script.py +0 -138
  128. workbench/model_scripts/custom_models/proximity/proximity.py +0 -384
  129. workbench/model_scripts/custom_models/uq_models/generated_model_script.py +0 -393
  130. workbench/model_scripts/custom_models/uq_models/mapie.template +0 -502
  131. workbench/model_scripts/custom_models/uq_models/meta_uq.template +0 -386
  132. workbench/model_scripts/custom_models/uq_models/proximity.py +0 -384
  133. workbench/model_scripts/ensemble_xgb/generated_model_script.py +0 -279
  134. workbench/model_scripts/quant_regression/quant_regression.template +0 -279
  135. workbench/model_scripts/quant_regression/requirements.txt +0 -1
  136. workbench/themes/quartz/base_css.url +0 -1
  137. workbench/themes/quartz/custom.css +0 -117
  138. workbench/themes/quartz/plotly.json +0 -642
  139. workbench/themes/quartz_dark/base_css.url +0 -1
  140. workbench/themes/quartz_dark/custom.css +0 -131
  141. workbench/themes/quartz_dark/plotly.json +0 -642
  142. workbench/utils/fast_inference.py +0 -167
  143. workbench/utils/resource_utils.py +0 -39
  144. {workbench-0.8.174.dist-info → workbench-0.8.227.dist-info}/WHEEL +0 -0
  145. {workbench-0.8.174.dist-info → workbench-0.8.227.dist-info}/top_level.txt +0 -0
@@ -1,477 +1,445 @@
1
- # Imports for XGB Model
2
- import xgboost as xgb
3
- import awswrangler as wr
1
+ # XGBoost Model Template for Workbench
2
+ #
3
+ # This template handles both classification and regression models with:
4
+ # - K-fold cross-validation ensemble training (or single train/val split)
5
+ # - Out-of-fold predictions for validation metrics
6
+ # - Uncertainty quantification for regression models
7
+ # - Sample weights support
8
+ # - Categorical feature handling
9
+ # - Compressed feature decompression
10
+ #
11
+ # NOTE: Imports are structured to minimize serverless endpoint startup time.
12
+ # Heavy imports (sklearn, awswrangler) are deferred to training time.
13
+
14
+ import json
15
+ import os
16
+
17
+ import joblib
4
18
  import numpy as np
19
+ import pandas as pd
20
+ import xgboost as xgb
5
21
 
6
- # Model Performance Scores
7
- from sklearn.metrics import (
8
- mean_absolute_error,
9
- r2_score,
10
- root_mean_squared_error,
11
- precision_recall_fscore_support,
12
- confusion_matrix,
22
+ from model_script_utils import (
23
+ convert_categorical_types,
24
+ decompress_features,
25
+ expand_proba_column,
26
+ input_fn,
27
+ match_features_case_insensitive,
28
+ output_fn,
29
+ )
30
+ from uq_harness import (
31
+ compute_confidence,
32
+ load_uq_models,
33
+ predict_intervals,
13
34
  )
14
35
 
15
- # Classification Encoder
16
- from sklearn.preprocessing import LabelEncoder
36
+ # =============================================================================
37
+ # Default Hyperparameters
38
+ # =============================================================================
39
+ DEFAULT_HYPERPARAMETERS = {
40
+ # Training parameters
41
+ "n_folds": 5, # Number of CV folds (1 = single train/val split)
42
+ # Core tree parameters
43
+ "n_estimators": 300,
44
+ "max_depth": 7,
45
+ "learning_rate": 0.05,
46
+ # Sampling parameters (less aggressive - ensemble provides regularization)
47
+ "subsample": 0.8,
48
+ "colsample_bytree": 0.8,
49
+ # Regularization (lighter - ensemble averaging reduces overfitting)
50
+ "min_child_weight": 3,
51
+ "gamma": 0.1,
52
+ "reg_alpha": 0.1,
53
+ "reg_lambda": 1.0,
54
+ # Random seed
55
+ "seed": 42,
56
+ }
17
57
 
18
- # Scikit Learn Imports
19
- from sklearn.model_selection import train_test_split
58
+ # Workbench-specific parameters (not passed to XGBoost)
59
+ WORKBENCH_PARAMS = {"n_folds"}
20
60
 
21
- from io import StringIO
22
- import json
23
- import argparse
24
- import joblib
25
- import os
26
- import pandas as pd
27
- from typing import List, Tuple
61
+ # Regression-only parameters (filtered out for classifiers)
62
+ REGRESSION_ONLY_PARAMS = {"objective"}
28
63
 
29
- # Template Parameters
64
+ # Template parameters (filled in by Workbench)
30
65
  TEMPLATE_PARAMS = {
31
66
  "model_type": "{{model_type}}",
32
67
  "target": "{{target_column}}",
33
68
  "features": "{{feature_list}}",
69
+ "id_column": "{{id_column}}",
34
70
  "compressed_features": "{{compressed_features}}",
35
71
  "model_metrics_s3_path": "{{model_metrics_s3_path}}",
36
- "train_all_data": "{{train_all_data}}"
72
+ "hyperparameters": "{{hyperparameters}}",
37
73
  }
38
74
 
39
- # Function to check if dataframe is empty
40
- def check_dataframe(df: pd.DataFrame, df_name: str) -> None:
41
- """
42
- Check if the provided dataframe is empty and raise an exception if it is.
43
-
44
- Args:
45
- df (pd.DataFrame): DataFrame to check
46
- df_name (str): Name of the DataFrame
47
- """
48
- if df.empty:
49
- msg = f"*** The training data {df_name} has 0 rows! ***STOPPING***"
50
- print(msg)
51
- raise ValueError(msg)
52
-
53
-
54
- def expand_proba_column(df: pd.DataFrame, class_labels: List[str]) -> pd.DataFrame:
55
- """
56
- Expands a column in a DataFrame containing a list of probabilities into separate columns.
57
-
58
- Args:
59
- df (pd.DataFrame): DataFrame containing a "pred_proba" column
60
- class_labels (List[str]): List of class labels
61
-
62
- Returns:
63
- pd.DataFrame: DataFrame with the "pred_proba" expanded into separate columns
64
- """
65
-
66
- # Sanity check
67
- proba_column = "pred_proba"
68
- if proba_column not in df.columns:
69
- raise ValueError('DataFrame does not contain a "pred_proba" column')
70
-
71
- # Construct new column names with '_proba' suffix
72
- proba_splits = [f"{label}_proba" for label in class_labels]
73
-
74
- # Expand the proba_column into separate columns for each probability
75
- proba_df = pd.DataFrame(df[proba_column].tolist(), columns=proba_splits)
76
-
77
- # Drop any proba columns and reset the index in prep for the concat
78
- df = df.drop(columns=[proba_column]+proba_splits, errors="ignore")
79
- df = df.reset_index(drop=True)
80
-
81
- # Concatenate the new columns with the original DataFrame
82
- df = pd.concat([df, proba_df], axis=1)
83
- print(df)
84
- return df
85
-
86
-
87
- def match_features_case_insensitive(df: pd.DataFrame, model_features: list) -> pd.DataFrame:
88
- """
89
- Matches and renames DataFrame columns to match model feature names (case-insensitive).
90
- Prioritizes exact matches, then case-insensitive matches.
91
-
92
- Raises ValueError if any model features cannot be matched.
93
- """
94
- df_columns_lower = {col.lower(): col for col in df.columns}
95
- rename_dict = {}
96
- missing = []
97
- for feature in model_features:
98
- if feature in df.columns:
99
- continue # Exact match
100
- elif feature.lower() in df_columns_lower:
101
- rename_dict[df_columns_lower[feature.lower()]] = feature
102
- else:
103
- missing.append(feature)
104
-
105
- if missing:
106
- raise ValueError(f"Features not found: {missing}")
107
-
108
- # Rename the DataFrame columns to match the model features
109
- return df.rename(columns=rename_dict)
110
-
111
75
 
112
- def convert_categorical_types(df: pd.DataFrame, features: list, category_mappings={}) -> tuple:
113
- """
114
- Converts appropriate columns to categorical type with consistent mappings.
115
-
116
- Args:
117
- df (pd.DataFrame): The DataFrame to process.
118
- features (list): List of feature names to consider for conversion.
119
- category_mappings (dict, optional): Existing category mappings. If empty dict, we're in
120
- training mode. If populated, we're in inference mode.
121
-
122
- Returns:
123
- tuple: (processed DataFrame, category mappings dictionary)
124
- """
125
- # Training mode
126
- if category_mappings == {}:
127
- for col in df.select_dtypes(include=["object", "string"]):
128
- if col in features and df[col].nunique() < 20:
129
- print(f"Training mode: Converting {col} to category")
130
- df[col] = df[col].astype("category")
131
- category_mappings[col] = df[col].cat.categories.tolist() # Store category mappings
132
-
133
- # Inference mode
76
+ # =============================================================================
77
+ # Model Loading (for SageMaker inference)
78
+ # =============================================================================
79
+ def model_fn(model_dir: str) -> dict:
80
+ """Load XGBoost ensemble from the specified directory."""
81
+ # Load ensemble metadata
82
+ metadata_path = os.path.join(model_dir, "ensemble_metadata.json")
83
+ if os.path.exists(metadata_path):
84
+ with open(metadata_path) as f:
85
+ metadata = json.load(f)
86
+ n_ensemble = metadata["n_ensemble"]
134
87
  else:
135
- for col, categories in category_mappings.items():
136
- if col in df.columns:
137
- print(f"Inference mode: Applying categorical mapping for {col}")
138
- df[col] = pd.Categorical(df[col], categories=categories) # Apply consistent categorical mapping
139
-
140
- return df, category_mappings
88
+ n_ensemble = 1 # Legacy single model
141
89
 
90
+ # Load ensemble models
91
+ ensemble_models = []
92
+ for i in range(n_ensemble):
93
+ model_path = os.path.join(model_dir, f"xgb_model_{i}.joblib")
94
+ if not os.path.exists(model_path):
95
+ model_path = os.path.join(model_dir, "xgb_model.joblib") # Legacy fallback
96
+ ensemble_models.append(joblib.load(model_path))
142
97
 
143
- def decompress_features(df: pd.DataFrame, features: List[str], compressed_features: List[str]) -> Tuple[pd.DataFrame, List[str]]:
144
- """Prepare features for the XGBoost model
98
+ print(f"Loaded {len(ensemble_models)} model(s)")
145
99
 
146
- Args:
147
- df (pd.DataFrame): The features DataFrame
148
- features (List[str]): Full list of feature names
149
- compressed_features (List[str]): List of feature names to decompress (bitstrings)
150
-
151
- Returns:
152
- pd.DataFrame: DataFrame with the decompressed features
153
- List[str]: Updated list of feature names after decompression
100
+ # Load label encoder (classifier only)
101
+ label_encoder = None
102
+ encoder_path = os.path.join(model_dir, "label_encoder.joblib")
103
+ if os.path.exists(encoder_path):
104
+ label_encoder = joblib.load(encoder_path)
105
+
106
+ # Load category mappings
107
+ category_mappings = {}
108
+ category_path = os.path.join(model_dir, "category_mappings.json")
109
+ if os.path.exists(category_path):
110
+ with open(category_path) as f:
111
+ category_mappings = json.load(f)
112
+
113
+ # Load UQ models (regression only)
114
+ uq_models, uq_metadata = None, None
115
+ uq_path = os.path.join(model_dir, "uq_metadata.json")
116
+ if os.path.exists(uq_path):
117
+ uq_models, uq_metadata = load_uq_models(model_dir)
118
+
119
+ return {
120
+ "ensemble_models": ensemble_models,
121
+ "n_ensemble": n_ensemble,
122
+ "label_encoder": label_encoder,
123
+ "category_mappings": category_mappings,
124
+ "uq_models": uq_models,
125
+ "uq_metadata": uq_metadata,
126
+ }
127
+
128
+
129
+ # =============================================================================
130
+ # Inference (for SageMaker inference)
131
+ # =============================================================================
132
+ def predict_fn(df: pd.DataFrame, model_dict: dict) -> pd.DataFrame:
133
+ """Make predictions with XGBoost ensemble."""
134
+ model_dir = os.environ.get("SM_MODEL_DIR", "/opt/ml/model")
135
+ with open(os.path.join(model_dir, "feature_columns.json")) as f:
136
+ features = json.load(f)
137
+ print(f"Model Features: {features}")
154
138
 
155
- Raises:
156
- ValueError: If any missing values are found in the specified features
157
- """
139
+ # Extract model components
140
+ ensemble_models = model_dict["ensemble_models"]
141
+ label_encoder = model_dict.get("label_encoder")
142
+ category_mappings = model_dict.get("category_mappings", {})
143
+ uq_models = model_dict.get("uq_models")
144
+ uq_metadata = model_dict.get("uq_metadata")
145
+ compressed_features = TEMPLATE_PARAMS["compressed_features"]
158
146
 
159
- # Check for any missing values in the required features
160
- missing_counts = df[features].isna().sum()
161
- if missing_counts.any():
162
- missing_features = missing_counts[missing_counts > 0]
163
- print(
164
- f"WARNING: Found missing values in features: {missing_features.to_dict()}. "
165
- "WARNING: You might want to remove/replace all NaN values before processing."
166
- )
147
+ # Prepare features
148
+ matched_df = match_features_case_insensitive(df, features)
149
+ matched_df, _ = convert_categorical_types(matched_df, features, category_mappings)
167
150
 
168
- # Decompress the specified compressed features
169
- decompressed_features = features
170
- for feature in compressed_features:
171
- if (feature not in df.columns) or (feature not in features):
172
- print(f"Feature '{feature}' not in the features list, skipping decompression.")
173
- continue
151
+ if compressed_features:
152
+ print("Decompressing features for prediction...")
153
+ matched_df, features = decompress_features(matched_df, features, compressed_features)
174
154
 
175
- # Remove the feature from the list of features to avoid duplication
176
- decompressed_features.remove(feature)
155
+ X = matched_df[features]
177
156
 
178
- # Handle all compressed features as bitstrings
179
- bit_matrix = np.array([list(bitstring) for bitstring in df[feature]], dtype=np.uint8)
180
- prefix = feature[:3]
157
+ # Collect ensemble predictions
158
+ all_preds = [m.predict(X) for m in ensemble_models]
159
+ ensemble_preds = np.stack(all_preds, axis=0)
181
160
 
182
- # Create all new columns at once - avoids fragmentation
183
- new_col_names = [f"{prefix}_{i}" for i in range(bit_matrix.shape[1])]
184
- new_df = pd.DataFrame(bit_matrix, columns=new_col_names, index=df.index)
161
+ if label_encoder is not None:
162
+ # Classification: average probabilities, then argmax
163
+ all_probs = [m.predict_proba(X) for m in ensemble_models]
164
+ avg_probs = np.mean(np.stack(all_probs, axis=0), axis=0)
165
+ class_preds = np.argmax(avg_probs, axis=1)
185
166
 
186
- # Add to features list
187
- decompressed_features.extend(new_col_names)
167
+ df["prediction"] = label_encoder.inverse_transform(class_preds)
168
+ df["pred_proba"] = [p.tolist() for p in avg_probs]
169
+ df = expand_proba_column(df, label_encoder.classes_)
170
+ else:
171
+ # Regression: average predictions
172
+ df["prediction"] = np.mean(ensemble_preds, axis=0)
173
+ df["prediction_std"] = np.std(ensemble_preds, axis=0)
188
174
 
189
- # Drop original column and concatenate new ones
190
- df = df.drop(columns=[feature])
191
- df = pd.concat([df, new_df], axis=1)
175
+ # Add UQ intervals if available
176
+ if uq_models and uq_metadata:
177
+ df = predict_intervals(df, X, uq_models, uq_metadata)
178
+ df = compute_confidence(df, uq_metadata["median_interval_width"], "q_10", "q_90")
192
179
 
193
- return df, decompressed_features
180
+ print(f"Inference complete: {len(df)} predictions, {len(ensemble_models)} ensemble members")
181
+ return df
194
182
 
195
183
 
184
+ # =============================================================================
185
+ # Training
186
+ # =============================================================================
196
187
  if __name__ == "__main__":
197
- """The main function is for training the XGBoost model"""
188
+ # -------------------------------------------------------------------------
189
+ # Training-only imports (deferred to reduce serverless startup time)
190
+ # -------------------------------------------------------------------------
191
+ import argparse
192
+
193
+ import awswrangler as wr
194
+ from sklearn.model_selection import KFold, StratifiedKFold, train_test_split
195
+ from sklearn.preprocessing import LabelEncoder
196
+
197
+ from model_script_utils import (
198
+ check_dataframe,
199
+ compute_classification_metrics,
200
+ compute_regression_metrics,
201
+ print_classification_metrics,
202
+ print_confusion_matrix,
203
+ print_regression_metrics,
204
+ )
205
+ from uq_harness import (
206
+ save_uq_models,
207
+ train_uq_models,
208
+ )
198
209
 
199
- # Harness Template Parameters
210
+ # -------------------------------------------------------------------------
211
+ # Setup: Parse arguments and load data
212
+ # -------------------------------------------------------------------------
213
+ parser = argparse.ArgumentParser()
214
+ parser.add_argument("--model-dir", type=str, default=os.environ.get("SM_MODEL_DIR", "/opt/ml/model"))
215
+ parser.add_argument("--train", type=str, default=os.environ.get("SM_CHANNEL_TRAIN", "/opt/ml/input/data/train"))
216
+ parser.add_argument("--output-data-dir", type=str, default=os.environ.get("SM_OUTPUT_DATA_DIR", "/opt/ml/output/data"))
217
+ args = parser.parse_args()
218
+
219
+ # Extract template parameters
200
220
  target = TEMPLATE_PARAMS["target"]
201
221
  features = TEMPLATE_PARAMS["features"]
202
222
  orig_features = features.copy()
223
+ id_column = TEMPLATE_PARAMS["id_column"]
203
224
  compressed_features = TEMPLATE_PARAMS["compressed_features"]
204
225
  model_type = TEMPLATE_PARAMS["model_type"]
205
226
  model_metrics_s3_path = TEMPLATE_PARAMS["model_metrics_s3_path"]
206
- train_all_data = TEMPLATE_PARAMS["train_all_data"]
207
- validation_split = 0.2
208
-
209
- # Script arguments for input/output directories
210
- parser = argparse.ArgumentParser()
211
- parser.add_argument("--model-dir", type=str, default=os.environ.get("SM_MODEL_DIR", "/opt/ml/model"))
212
- parser.add_argument("--train", type=str, default=os.environ.get("SM_CHANNEL_TRAIN", "/opt/ml/input/data/train"))
213
- parser.add_argument(
214
- "--output-data-dir", type=str, default=os.environ.get("SM_OUTPUT_DATA_DIR", "/opt/ml/output/data")
215
- )
216
- args = parser.parse_args()
227
+ hyperparameters = {**DEFAULT_HYPERPARAMETERS, **(TEMPLATE_PARAMS["hyperparameters"] or {})}
217
228
 
218
- # Read the training data into DataFrames
219
- training_files = [
220
- os.path.join(args.train, file)
221
- for file in os.listdir(args.train)
222
- if file.endswith(".csv")
223
- ]
229
+ # Load training data
230
+ training_files = [os.path.join(args.train, f) for f in os.listdir(args.train) if f.endswith(".csv")]
224
231
  print(f"Training Files: {training_files}")
225
-
226
- # Combine files and read them all into a single pandas dataframe
227
- all_df = pd.concat([pd.read_csv(file, engine="python") for file in training_files])
228
-
229
- # Check if the dataframe is empty
232
+ all_df = pd.concat([pd.read_csv(f, engine="python") for f in training_files])
230
233
  check_dataframe(all_df, "training_df")
231
234
 
232
- # Features/Target output
233
235
  print(f"Target: {target}")
234
- print(f"Features: {str(features)}")
236
+ print(f"Features: {features}")
237
+ print(f"Hyperparameters: {hyperparameters}")
235
238
 
236
- # Convert any features that might be categorical to 'category' type
239
+ # -------------------------------------------------------------------------
240
+ # Preprocessing: Categorical features and decompression
241
+ # -------------------------------------------------------------------------
237
242
  all_df, category_mappings = convert_categorical_types(all_df, features)
238
243
 
239
- # If we have compressed features, decompress them
240
244
  if compressed_features:
241
- print(f"Decompressing features {compressed_features}...")
245
+ print(f"Decompressing features: {compressed_features}")
242
246
  all_df, features = decompress_features(all_df, features, compressed_features)
243
247
 
244
- # Do we want to train on all the data?
245
- if train_all_data:
246
- print("Training on ALL of the data")
247
- df_train = all_df.copy()
248
- df_val = all_df.copy()
249
-
250
- # Does the dataframe have a training column?
251
- elif "training" in all_df.columns:
252
- print("Found training column, splitting data based on training column")
253
- df_train = all_df[all_df["training"]]
254
- df_val = all_df[~all_df["training"]]
255
- else:
256
- # Just do a random training Split
257
- print("WARNING: No training column found, splitting data with random state=42")
258
- df_train, df_val = train_test_split(
259
- all_df, test_size=validation_split, random_state=42
260
- )
261
- print(f"FIT/TRAIN: {df_train.shape}")
262
- print(f"VALIDATION: {df_val.shape}")
263
-
264
- # Now spin up our XGB Model
248
+ # -------------------------------------------------------------------------
249
+ # Classification setup
250
+ # -------------------------------------------------------------------------
251
+ label_encoder = None
265
252
  if model_type == "classifier":
266
- xgb_model = xgb.XGBClassifier(enable_categorical=True)
267
-
268
- # Encode the target column
269
253
  label_encoder = LabelEncoder()
270
- df_train[target] = label_encoder.fit_transform(df_train[target])
271
- df_val[target] = label_encoder.transform(df_val[target])
254
+ all_df[target] = label_encoder.fit_transform(all_df[target])
255
+ print(f"Class labels: {label_encoder.classes_.tolist()}")
272
256
 
273
- else:
274
- xgb_model = xgb.XGBRegressor(enable_categorical=True)
275
- label_encoder = None # We don't need this for regression
276
-
277
- # Grab our Features, Target and Train the Model
278
- y_train = df_train[target]
279
- X_train= df_train[features]
280
- xgb_model.fit(X_train, y_train)
281
-
282
- # Make Predictions on the Validation Set
283
- print(f"Making Predictions on Validation Set...")
284
- y_validate = df_val[target]
285
- X_validate = df_val[features]
286
- preds = xgb_model.predict(X_validate)
287
- if model_type == "classifier":
288
- # Also get the probabilities for each class
289
- print("Processing Probabilities...")
290
- probs = xgb_model.predict_proba(X_validate)
291
- df_val["pred_proba"] = [p.tolist() for p in probs]
292
-
293
- # Expand the pred_proba column into separate columns for each class
294
- print(df_val.columns)
295
- df_val = expand_proba_column(df_val, label_encoder.classes_)
296
- print(df_val.columns)
297
-
298
- # Decode the target and prediction labels
299
- y_validate = label_encoder.inverse_transform(y_validate)
300
- preds = label_encoder.inverse_transform(preds)
301
-
302
- # Save predictions to S3 (just the target, prediction, and '_proba' columns)
303
- df_val["prediction"] = preds
304
- output_columns = [target, "prediction"]
305
- output_columns += [col for col in df_val.columns if col.endswith("_proba")]
306
- wr.s3.to_csv(
307
- df_val[output_columns],
308
- path=f"{model_metrics_s3_path}/validation_predictions.csv",
309
- index=False,
310
- )
257
+ # -------------------------------------------------------------------------
258
+ # Cross-validation setup
259
+ # -------------------------------------------------------------------------
260
+ n_folds = hyperparameters["n_folds"]
261
+ xgb_params = {k: v for k, v in hyperparameters.items() if k not in WORKBENCH_PARAMS}
311
262
 
312
- # Report Performance Metrics
313
- if model_type == "classifier":
314
- # Get the label names and their integer mapping
315
- label_names = label_encoder.classes_
316
-
317
- # Calculate various model performance metrics
318
- scores = precision_recall_fscore_support(
319
- y_validate, preds, average=None, labels=label_names
320
- )
321
-
322
- # Put the scores into a dataframe
323
- score_df = pd.DataFrame(
324
- {
325
- target: label_names,
326
- "precision": scores[0],
327
- "recall": scores[1],
328
- "fscore": scores[2],
329
- "support": scores[3],
330
- }
331
- )
332
-
333
- # We need to get creative with the Classification Metrics
334
- metrics = ["precision", "recall", "fscore", "support"]
335
- for t in label_names:
336
- for m in metrics:
337
- value = score_df.loc[score_df[target] == t, m].iloc[0]
338
- print(f"Metrics:{t}:{m} {value}")
339
-
340
- # Compute and output the confusion matrix
341
- conf_mtx = confusion_matrix(y_validate, preds, labels=label_names)
342
- for i, row_name in enumerate(label_names):
343
- for j, col_name in enumerate(label_names):
344
- value = conf_mtx[i, j]
345
- print(f"ConfusionMatrix:{row_name}:{col_name} {value}")
263
+ # Map 'seed' to 'random_state' for XGBoost
264
+ if "seed" in xgb_params:
265
+ xgb_params["random_state"] = xgb_params.pop("seed")
346
266
 
267
+ # Handle objective: filter regression-only params for classifiers, set default for regressors
268
+ if model_type == "classifier":
269
+ xgb_params = {k: v for k, v in xgb_params.items() if k not in REGRESSION_ONLY_PARAMS}
347
270
  else:
348
- # Calculate various model performance metrics (regression)
349
- rmse = root_mean_squared_error(y_validate, preds)
350
- mae = mean_absolute_error(y_validate, preds)
351
- r2 = r2_score(y_validate, preds)
352
- print(f"RMSE: {rmse:.3f}")
353
- print(f"MAE: {mae:.3f}")
354
- print(f"R2: {r2:.3f}")
355
- print(f"NumRows: {len(df_val)}")
356
-
357
- # Now save the model to the standard place/name
358
- xgb_model.save_model(os.path.join(args.model_dir, "xgb_model.json"))
359
- if label_encoder:
360
- joblib.dump(label_encoder, os.path.join(args.model_dir, "label_encoder.joblib"))
361
-
362
- # Save the features (this will validate input during predictions)
363
- with open(os.path.join(args.model_dir, "feature_columns.json"), "w") as fp:
364
- json.dump(orig_features, fp) # We save the original features, not the decompressed ones
365
-
366
- # Save the category mappings
367
- with open(os.path.join(args.model_dir, "category_mappings.json"), "w") as fp:
368
- json.dump(category_mappings, fp)
369
-
370
-
371
- def model_fn(model_dir):
372
- """Deserialize and return fitted XGBoost model"""
373
-
374
- model_path = os.path.join(model_dir, "xgb_model.json")
375
-
376
- with open(model_path, "r") as f:
377
- model_json = json.load(f)
378
-
379
- sklearn_data = model_json['learner']['attributes']['scikit_learn']
380
- model_type = json.loads(sklearn_data)['_estimator_type']
271
+ # Default to MAE (reg:absoluteerror) for regression if not specified
272
+ xgb_params.setdefault("objective", "reg:absoluteerror")
381
273
 
382
- model_class = xgb.XGBClassifier if model_type == "classifier" else xgb.XGBRegressor
383
- model = model_class(enable_categorical=True)
384
- model.load_model(model_path)
385
-
386
- return model
274
+ print(f"XGBoost params: {xgb_params}")
387
275
 
276
+ if n_folds == 1:
277
+ # Single train/val split
278
+ if "training" in all_df.columns:
279
+ print("Using 'training' column for train/val split")
280
+ train_idx = np.where(all_df["training"])[0]
281
+ val_idx = np.where(~all_df["training"])[0]
282
+ else:
283
+ print("WARNING: No 'training' column found, using random 80/20 split")
284
+ indices = np.arange(len(all_df))
285
+ train_idx, val_idx = train_test_split(indices, test_size=0.2, random_state=42)
286
+ folds = [(train_idx, val_idx)]
287
+ else:
288
+ # K-fold cross-validation
289
+ if model_type == "classifier":
290
+ kfold = StratifiedKFold(n_splits=n_folds, shuffle=True, random_state=42)
291
+ folds = list(kfold.split(all_df, all_df[target]))
292
+ else:
293
+ kfold = KFold(n_splits=n_folds, shuffle=True, random_state=42)
294
+ folds = list(kfold.split(all_df))
388
295
 
389
- def input_fn(input_data, content_type):
390
- """Parse input data and return a DataFrame."""
391
- if not input_data:
392
- raise ValueError("Empty input data is not supported!")
296
+ print(f"Training {'single model' if n_folds == 1 else f'{n_folds}-fold ensemble'}...")
393
297
 
394
- # Decode bytes to string if necessary
395
- if isinstance(input_data, bytes):
396
- input_data = input_data.decode("utf-8")
298
+ # -------------------------------------------------------------------------
299
+ # Training loop
300
+ # -------------------------------------------------------------------------
301
+ # Initialize out-of-fold storage
302
+ oof_predictions = np.full(len(all_df), np.nan, dtype=np.float64)
303
+ if model_type == "classifier":
304
+ num_classes = len(label_encoder.classes_)
305
+ oof_proba = np.full((len(all_df), num_classes), np.nan, dtype=np.float64)
306
+ else:
307
+ oof_proba = None
308
+
309
+ # Check for sample weights
310
+ has_sample_weights = "sample_weight" in all_df.columns
311
+ if has_sample_weights:
312
+ sw = all_df["sample_weight"]
313
+ print(f"Using sample weights: min={sw.min():.2f}, max={sw.max():.2f}, mean={sw.mean():.2f}")
314
+
315
+ # Train ensemble
316
+ ensemble_models = []
317
+ for fold_idx, (train_idx, val_idx) in enumerate(folds):
318
+ print(f"\n{'='*50}")
319
+ print(f"Fold {fold_idx + 1}/{len(folds)} - Train: {len(train_idx)}, Val: {len(val_idx)}")
320
+ print(f"{'='*50}")
321
+
322
+ # Prepare fold data
323
+ X_train = all_df.iloc[train_idx][features]
324
+ y_train = all_df.iloc[train_idx][target]
325
+ X_val = all_df.iloc[val_idx][features]
326
+ sample_weights = all_df.iloc[train_idx]["sample_weight"] if has_sample_weights else None
327
+
328
+ # Create model with fold-specific random state for diversity
329
+ fold_params = {**xgb_params, "random_state": xgb_params.get("random_state", 42) + fold_idx}
330
+ if model_type == "classifier":
331
+ model = xgb.XGBClassifier(enable_categorical=True, **fold_params)
332
+ else:
333
+ model = xgb.XGBRegressor(enable_categorical=True, **fold_params)
334
+
335
+ # Train
336
+ model.fit(X_train, y_train, sample_weight=sample_weights)
337
+ ensemble_models.append(model)
338
+
339
+ # Out-of-fold predictions
340
+ oof_predictions[val_idx] = model.predict(X_val)
341
+ if model_type == "classifier":
342
+ oof_proba[val_idx] = model.predict_proba(X_val)
343
+
344
+ print(f"\nTraining complete! Trained {len(ensemble_models)} model(s).")
345
+
346
+ # -------------------------------------------------------------------------
347
+ # Prepare validation results
348
+ # -------------------------------------------------------------------------
349
+ if n_folds == 1:
350
+ # Single fold: only validation rows
351
+ val_mask = ~np.isnan(oof_predictions)
352
+ df_val = all_df[val_mask].copy()
353
+ predictions = oof_predictions[val_mask]
354
+ if oof_proba is not None:
355
+ oof_proba = oof_proba[val_mask]
356
+ else:
357
+ # K-fold: all rows have out-of-fold predictions
358
+ df_val = all_df.copy()
359
+ predictions = oof_predictions
397
360
 
398
- if "text/csv" in content_type:
399
- return pd.read_csv(StringIO(input_data))
400
- elif "application/json" in content_type:
401
- return pd.DataFrame(json.loads(input_data)) # Assumes JSON array of records
361
+ # Decode labels for classification
362
+ if model_type == "classifier":
363
+ df_val[target] = label_encoder.inverse_transform(df_val[target].astype(int))
364
+ df_val["prediction"] = label_encoder.inverse_transform(predictions.astype(int))
365
+ if oof_proba is not None:
366
+ df_val["pred_proba"] = [p.tolist() for p in oof_proba]
367
+ df_val = expand_proba_column(df_val, label_encoder.classes_)
402
368
  else:
403
- raise ValueError(f"{content_type} not supported!")
369
+ df_val["prediction"] = predictions
404
370
 
371
+ # -------------------------------------------------------------------------
372
+ # Compute and print metrics
373
+ # -------------------------------------------------------------------------
374
+ y_true = df_val[target].values
375
+ y_pred = df_val["prediction"].values
405
376
 
406
- def output_fn(output_df, accept_type):
407
- """Supports both CSV and JSON output formats."""
408
- if "text/csv" in accept_type:
409
- csv_output = output_df.fillna("N/A").to_csv(index=False) # CSV with N/A for missing values
410
- return csv_output, "text/csv"
411
- elif "application/json" in accept_type:
412
- return output_df.to_json(orient="records"), "application/json" # JSON array of records (NaNs -> null)
377
+ if model_type == "classifier":
378
+ label_names = label_encoder.classes_
379
+ score_df = compute_classification_metrics(y_true, y_pred, label_names, target)
380
+ print_classification_metrics(score_df, target, label_names)
381
+ print_confusion_matrix(y_true, y_pred, label_names)
413
382
  else:
414
- raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
383
+ metrics = compute_regression_metrics(y_true, y_pred)
384
+ print_regression_metrics(metrics)
385
+
386
+ # Compute ensemble prediction_std
387
+ if n_folds > 1:
388
+ all_preds = np.stack([m.predict(all_df[features]) for m in ensemble_models])
389
+ df_val["prediction_std"] = np.std(all_preds, axis=0)
390
+ print(f"Ensemble std - mean: {df_val['prediction_std'].mean():.4f}, max: {df_val['prediction_std'].max():.4f}")
391
+ else:
392
+ df_val["prediction_std"] = 0.0
393
+
394
+ # Train UQ models for uncertainty quantification
395
+ print("\n" + "=" * 50)
396
+ print("Training UQ Models")
397
+ print("=" * 50)
398
+ uq_models, uq_metadata = train_uq_models(
399
+ all_df[features], all_df[target], df_val[features], y_true
400
+ )
401
+ df_val = predict_intervals(df_val, df_val[features], uq_models, uq_metadata)
402
+ df_val = compute_confidence(df_val, uq_metadata["median_interval_width"])
415
403
 
404
+ # -------------------------------------------------------------------------
405
+ # Save validation predictions to S3
406
+ # -------------------------------------------------------------------------
407
+ output_columns = []
408
+ if id_column in df_val.columns:
409
+ output_columns.append(id_column)
410
+ output_columns += [target, "prediction"]
416
411
 
417
- def predict_fn(df, model) -> pd.DataFrame:
418
- """Make Predictions with our XGB Model
412
+ if model_type != "classifier":
413
+ output_columns.append("prediction_std")
414
+ output_columns += [c for c in df_val.columns if c.startswith("q_") or c == "confidence"]
419
415
 
420
- Args:
421
- df (pd.DataFrame): The input DataFrame
422
- model: The model use for predictions
416
+ output_columns += [c for c in df_val.columns if c.endswith("_proba")]
423
417
 
424
- Returns:
425
- pd.DataFrame: The DataFrame with the predictions added
426
- """
427
- compressed_features = TEMPLATE_PARAMS["compressed_features"]
418
+ wr.s3.to_csv(df_val[output_columns], f"{model_metrics_s3_path}/validation_predictions.csv", index=False)
428
419
 
429
- # Grab our feature columns (from training)
430
- model_dir = os.environ.get("SM_MODEL_DIR", "/opt/ml/model")
431
- with open(os.path.join(model_dir, "feature_columns.json")) as fp:
432
- features = json.load(fp)
433
- print(f"Model Features: {features}")
434
-
435
- # Load the category mappings (from training)
436
- with open(os.path.join(model_dir, "category_mappings.json")) as fp:
437
- category_mappings = json.load(fp)
420
+ # -------------------------------------------------------------------------
421
+ # Save model artifacts
422
+ # -------------------------------------------------------------------------
423
+ for idx, m in enumerate(ensemble_models):
424
+ joblib.dump(m, os.path.join(args.model_dir, f"xgb_model_{idx}.joblib"))
425
+ print(f"Saved {len(ensemble_models)} model(s)")
438
426
 
439
- # Load our Label Encoder if we have one
440
- label_encoder = None
441
- if os.path.exists(os.path.join(model_dir, "label_encoder.joblib")):
442
- label_encoder = joblib.load(os.path.join(model_dir, "label_encoder.joblib"))
427
+ with open(os.path.join(args.model_dir, "ensemble_metadata.json"), "w") as f:
428
+ json.dump({"n_ensemble": len(ensemble_models), "n_folds": n_folds}, f)
443
429
 
444
- # We're going match features in a case-insensitive manner, accounting for all the permutations
445
- # - Model has a feature list that's any case ("Id", "taCos", "cOunT", "likes_tacos")
446
- # - Incoming data has columns that are mixed case ("ID", "Tacos", "Count", "Likes_Tacos")
447
- matched_df = match_features_case_insensitive(df, features)
430
+ with open(os.path.join(args.model_dir, "feature_columns.json"), "w") as f:
431
+ json.dump(orig_features, f)
448
432
 
449
- # Detect categorical types in the incoming DataFrame
450
- matched_df, _ = convert_categorical_types(matched_df, features, category_mappings)
433
+ with open(os.path.join(args.model_dir, "category_mappings.json"), "w") as f:
434
+ json.dump(category_mappings, f)
451
435
 
452
- # If we have compressed features, decompress them
453
- if compressed_features:
454
- print("Decompressing features for prediction...")
455
- matched_df, features = decompress_features(matched_df, features, compressed_features)
436
+ with open(os.path.join(args.model_dir, "hyperparameters.json"), "w") as f:
437
+ json.dump(hyperparameters, f, indent=2)
456
438
 
457
- # Predict the features against our XGB Model
458
- X = matched_df[features]
459
- predictions = model.predict(X)
460
-
461
- # If we have a label encoder, decode the predictions
462
439
  if label_encoder:
463
- predictions = label_encoder.inverse_transform(predictions)
464
-
465
- # Set the predictions on the DataFrame
466
- df["prediction"] = predictions
467
-
468
- # Does our model have a 'predict_proba' method? If so we will call it and add the results to the DataFrame
469
- if getattr(model, "predict_proba", None):
470
- probs = model.predict_proba(matched_df[features])
471
- df["pred_proba"] = [p.tolist() for p in probs]
440
+ joblib.dump(label_encoder, os.path.join(args.model_dir, "label_encoder.joblib"))
472
441
 
473
- # Expand the pred_proba column into separate columns for each class
474
- df = expand_proba_column(df, label_encoder.classes_)
442
+ if model_type != "classifier":
443
+ save_uq_models(uq_models, uq_metadata, args.model_dir)
475
444
 
476
- # All done, return the DataFrame with new columns for the predictions
477
- return df
445
+ print(f"\nModel training complete! Artifacts saved to {args.model_dir}")