linkml-store 0.1.13__py3-none-any.whl → 0.1.14__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of linkml-store might be problematic. Click here for more details.

@@ -0,0 +1,145 @@
1
+ import logging
2
+ from dataclasses import dataclass
3
+ from typing import Any, Optional
4
+
5
+ import yaml
6
+ from llm import get_key
7
+
8
+ from linkml_store.api.collection import OBJECT, Collection
9
+ from linkml_store.inference.inference_config import Inference, InferenceConfig, LLMConfig
10
+ from linkml_store.inference.inference_engine import InferenceEngine
11
+
12
+ logger = logging.getLogger(__name__)
13
+
14
+ SYSTEM_PROMPT = """
15
+ You are a {llm_config.role}, your task is to inference the YAML
16
+ object output given the YAML object input. I will provide you
17
+ with a collection of examples that will provide guidance both
18
+ on the desired structure of the response, as well as the kind
19
+ of content.
20
+
21
+ You should return ONLY valid YAML in your response.
22
+ """
23
+
24
+
25
+ @dataclass
26
+ class RAGInferenceEngine(InferenceEngine):
27
+ """
28
+ AI Retrieval Augmented Generation (RAG) based predictor.
29
+
30
+
31
+ >>> from linkml_store.api.client import Client
32
+ >>> from linkml_store.utils.format_utils import Format
33
+ >>> from linkml_store.inference.inference_config import LLMConfig
34
+ >>> client = Client()
35
+ >>> db = client.attach_database("duckdb", alias="test")
36
+ >>> db.import_database("tests/input/countries/countries.jsonl", Format.JSONL, collection_name="countries")
37
+ >>> db.list_collection_names()
38
+ ['countries']
39
+ >>> collection = db.get_collection("countries")
40
+ >>> features = ["name"]
41
+ >>> targets = ["code", "capital", "continent", "languages"]
42
+ >>> llm_config = LLMConfig(model_name="gpt-4o-mini",)
43
+ >>> config = InferenceConfig(target_attributes=targets, feature_attributes=features, llm_config=llm_config)
44
+ >>> ie = RAGInferenceEngine(config=config)
45
+ >>> ie.load_and_split_data(collection)
46
+ >>> ie.initialize_model()
47
+ >>> prediction = ie.derive({"name": "Uruguay"})
48
+ >>> prediction.predicted_object
49
+ {'capital': 'Montevideo', 'code': 'UY', 'continent': 'South America', 'languages': ['Spanish']}
50
+
51
+ """
52
+
53
+ classifier: Any = None
54
+ encoders: dict = None
55
+ _model: "llm.Model" = None # noqa: F821
56
+
57
+ rag_collection: Collection = None
58
+
59
+ def __post_init__(self):
60
+ if not self.config:
61
+ self.config = InferenceConfig()
62
+ if not self.config.llm_config:
63
+ self.config.llm_config = LLMConfig()
64
+
65
+ @property
66
+ def model(self) -> "llm.Model": # noqa: F821
67
+ import llm
68
+
69
+ if self._model is None:
70
+ self._model = llm.get_model(self.config.llm_config.model_name)
71
+ if self._model.needs_key:
72
+ key = get_key(None, key_alias=self._model.needs_key)
73
+ self._model.key = key
74
+
75
+ return self._model
76
+
77
+ def initialize_model(self, **kwargs):
78
+ td = self.training_data
79
+ s = td.slice
80
+ if not s[0] and not s[1]:
81
+ rag_collection = td.collection
82
+ else:
83
+ base_collection = td.collection
84
+ objs = base_collection.find({}, offset=s[0], limit=s[1] - s[0]).rows
85
+ db = base_collection.parent
86
+ rag_collection = db.get_collection(f"{base_collection.alias}__rag_{s[0]}_{s[1]}", create_if_not_exists=True)
87
+ rag_collection.insert(objs)
88
+ rag_collection.attach_indexer("llm", auto_index=False)
89
+ self.rag_collection = rag_collection
90
+
91
+ def object_to_text(self, object: OBJECT) -> str:
92
+ return yaml.dump(object)
93
+
94
+ def derive(self, object: OBJECT) -> Optional[Inference]:
95
+ import llm
96
+ from tiktoken import encoding_for_model
97
+
98
+ from linkml_store.utils.llm_utils import get_token_limit, render_formatted_text
99
+
100
+ model: llm.Model = self.model
101
+ model_name = self.config.llm_config.model_name
102
+ feature_attributes = self.config.feature_attributes
103
+ target_attributes = self.config.target_attributes
104
+ num_examples = self.config.llm_config.number_of_few_shot_examples or 5
105
+ query_text = self.object_to_text(object)
106
+ if not self.rag_collection.indexers:
107
+ raise ValueError("RAG collection must have an indexer attached")
108
+ rs = self.rag_collection.search(query_text, limit=num_examples, index_name="llm")
109
+ examples = rs.rows
110
+ if not examples:
111
+ raise ValueError(f"No examples found for {query_text}; size = {self.rag_collection.size()}")
112
+ prompt_clauses = []
113
+ for example in examples:
114
+ input_obj = {k: example.get(k, None) for k in feature_attributes}
115
+ output_obj = {k: example.get(k, None) for k in target_attributes}
116
+ prompt_clause = (
117
+ "---\nExample:\n"
118
+ f"## INPUT:\n{self.object_to_text(input_obj)}\n"
119
+ f"## OUTPUT:\n{self.object_to_text(output_obj)}\n"
120
+ )
121
+ prompt_clauses.append(prompt_clause)
122
+ query_obj = {k: object.get(k, None) for k in feature_attributes}
123
+ query_text = self.object_to_text(query_obj)
124
+ prompt_end = "---\nQuery:\n" f"## INPUT:\n{query_text}\n" "## OUTPUT:\n"
125
+ system_prompt = SYSTEM_PROMPT.format(llm_config=self.config.llm_config)
126
+
127
+ def make_text(texts):
128
+ return "\n".join(prompt_clauses) + prompt_end
129
+
130
+ try:
131
+ encoding = encoding_for_model(model_name)
132
+ except KeyError:
133
+ encoding = encoding_for_model("gpt-4")
134
+ token_limit = get_token_limit(model_name)
135
+ prompt = render_formatted_text(make_text, prompt_clauses, encoding, token_limit)
136
+ logger.info(f"Prompt: {prompt}")
137
+ response = model.prompt(prompt, system_prompt)
138
+ yaml_str = response.text()
139
+ logger.info(f"Response: {yaml_str}")
140
+ try:
141
+ predicted_object = yaml.safe_load(yaml_str)
142
+ return Inference(predicted_object=predicted_object)
143
+ except yaml.parser.ParserError as e:
144
+ logger.error(f"Error parsing response: {yaml_str}\n{e}")
145
+ return None
@@ -0,0 +1,158 @@
1
+ import logging
2
+ from copy import copy
3
+ from dataclasses import dataclass
4
+ from io import StringIO
5
+ from pathlib import Path
6
+ from typing import Any, ClassVar, Dict, List, Optional, Union
7
+
8
+ import yaml
9
+ from linkml_map.utils.eval_utils import eval_expr
10
+ from linkml_runtime import SchemaView
11
+ from linkml_runtime.linkml_model.meta import AnonymousClassExpression, ClassRule
12
+ from linkml_runtime.utils.formatutils import underscore
13
+ from pydantic import BaseModel
14
+
15
+ from linkml_store.api.collection import OBJECT, Collection
16
+ from linkml_store.inference.inference_config import Inference
17
+ from linkml_store.inference.inference_engine import InferenceEngine, ModelSerialization
18
+
19
+ logger = logging.getLogger(__name__)
20
+
21
+
22
+ def expression_matches(ce: AnonymousClassExpression, object: OBJECT) -> bool:
23
+ """
24
+ Check if a class expression matches an object.
25
+
26
+ :param ce: The class expression
27
+ :param object: The object
28
+ :return: True if the class expression matches the object
29
+ """
30
+ if ce.any_of:
31
+ if not any(expression_matches(subce, object) for subce in ce.any_of):
32
+ return False
33
+ if ce.all_of:
34
+ if not all(expression_matches(subce, object) for subce in ce.all_of):
35
+ return False
36
+ if ce.none_of:
37
+ if any(expression_matches(subce, object) for subce in ce.none_of):
38
+ return False
39
+ if ce.slot_conditions:
40
+ for slot in ce.slot_conditions.values():
41
+ slot_name = slot.name
42
+ v = object.get(slot_name, None)
43
+ if slot.equals_string is not None:
44
+ if slot.equals_string != str(v):
45
+ return False
46
+ if slot.equals_integer is not None:
47
+ if slot.equals_integer != v:
48
+ return False
49
+ if slot.equals_expression is not None:
50
+ eval_v = eval_expr(slot.equals_expression, **object)
51
+ if v != eval_v:
52
+ return False
53
+ return True
54
+
55
+
56
+ def apply_rule(rule: ClassRule, object: OBJECT):
57
+ """
58
+ Apply a rule to an object.
59
+
60
+ Mutates the object
61
+
62
+ :param rule: The rule to apply
63
+ :param object: The object to apply the rule to
64
+ """
65
+ for condition in rule.preconditions:
66
+ if expression_matches(condition, object):
67
+ for postcondition in rule.postconditions:
68
+ all_of = [x for x in postcondition.all_of] + [postcondition]
69
+ for pc in all_of:
70
+ sc = pc.slot_condition
71
+ if sc:
72
+ if sc.equals_string:
73
+ object[sc.name] = sc.equals_string
74
+ if sc.equals_integer:
75
+ object[sc.name] = sc.equals_integer
76
+ if sc.equals_expression:
77
+ object[sc.name] = eval_expr(sc.equals_expression, **object)
78
+ return object
79
+
80
+
81
+ @dataclass
82
+ class RuleBasedInferenceEngine(InferenceEngine):
83
+ """
84
+ TODO
85
+
86
+ """
87
+
88
+ class_rules: Optional[List[ClassRule]] = None
89
+ slot_rules: Optional[Dict[str, List[ClassRule]]] = None
90
+ slot_expressions: Optional[Dict[str, str]] = None
91
+
92
+ PERSIST_COLS: ClassVar = ["config", "class_rules", "slot_rules", "slot_expressions"]
93
+
94
+ def initialize_model(self, **kwargs):
95
+ td = self.training_data
96
+ collection: Collection = td.collection
97
+ cd = collection.class_definition()
98
+ sv: SchemaView = collection.parent.schema_view
99
+ class_rules = cd.rules
100
+ if class_rules:
101
+ self.class_rules = class_rules
102
+ for slot in sv.class_induced_slots(cd.name):
103
+ if slot.equals_expression:
104
+ self.slot_expressions[slot.name] = slot.equals_expression
105
+
106
+ def derive(self, object: OBJECT) -> Optional[Inference]:
107
+ object = copy(object)
108
+ if self.class_rules:
109
+ for rule in self.class_rules:
110
+ apply_rule(rule, object)
111
+ object = {underscore(k): v for k, v in object.items()}
112
+ if self.slot_expressions:
113
+ for slot, expr in self.slot_expressions.items():
114
+ print(f"EVAL {object}")
115
+ v = eval_expr(expr, **object)
116
+ if v is not None:
117
+ object[slot] = v
118
+ return Inference(predicted_object=object)
119
+
120
+ def import_model_from(self, inference_engine: InferenceEngine, **kwargs):
121
+ io = StringIO()
122
+ inference_engine.export_model(io, model_serialization=ModelSerialization.LINKML_EXPRESSION)
123
+ config = inference_engine.config
124
+ if len(config.target_attributes) != 1:
125
+ raise ValueError("Can only import models with a single target attribute")
126
+ target_attribute = config.target_attributes[0]
127
+ if self.slot_expressions is None:
128
+ self.slot_expressions = {}
129
+ self.slot_expressions[target_attribute] = io.getvalue()
130
+
131
+ def save_model(self, output: Union[str, Path]) -> None:
132
+ """
133
+ Save the trained model and related data to a file.
134
+
135
+ :param output: Path to save the model
136
+ """
137
+
138
+ def _serialize_value(v: Any) -> Any:
139
+ if isinstance(v, BaseModel):
140
+ return v.model_dump(exclude_unset=True)
141
+ return v
142
+
143
+ model_data = {k: _serialize_value(getattr(self, k)) for k in self.PERSIST_COLS}
144
+ with open(output, "w", encoding="utf-8") as f:
145
+ yaml.dump(model_data, f)
146
+
147
+ @classmethod
148
+ def load_model(cls, file_path: Union[str, Path]) -> "RuleBasedInferenceEngine":
149
+ model_data = yaml.safe_load(open(file_path))
150
+
151
+ engine = cls(config=model_data["config"])
152
+ for k, v in model_data.items():
153
+ if k == "config":
154
+ continue
155
+ setattr(engine, k, v)
156
+
157
+ logger.info(f"Model loaded from {file_path}")
158
+ return engine
@@ -0,0 +1,290 @@
1
+ import logging
2
+ from dataclasses import dataclass, field
3
+ from pathlib import Path
4
+ from typing import Any, ClassVar, Dict, List, Optional, TextIO, Type, Union
5
+
6
+ import numpy as np
7
+ import pandas as pd
8
+ from sklearn.model_selection import cross_val_score
9
+ from sklearn.preprocessing import LabelEncoder, MultiLabelBinarizer, OneHotEncoder
10
+ from sklearn.tree import DecisionTreeClassifier
11
+
12
+ from linkml_store.api.collection import OBJECT
13
+ from linkml_store.inference.implementations.rule_based_inference_engine import RuleBasedInferenceEngine
14
+ from linkml_store.inference.inference_config import Inference, InferenceConfig
15
+ from linkml_store.inference.inference_engine import InferenceEngine, ModelSerialization
16
+ from linkml_store.utils.sklearn_utils import tree_to_nested_expression, visualize_decision_tree
17
+
18
+ logger = logging.getLogger(__name__)
19
+
20
+
21
+ @dataclass
22
+ class SklearnInferenceEngine(InferenceEngine):
23
+ config: InferenceConfig
24
+ classifier: Any = None
25
+ encoders: Dict[str, Any] = field(default_factory=dict)
26
+ transformed_features: List[str] = field(default_factory=list)
27
+ transformed_targets: List[str] = field(default_factory=list)
28
+ skip_features: List[str] = field(default_factory=list)
29
+ categorical_encoder_class: Optional[Type[Union[OneHotEncoder, MultiLabelBinarizer]]] = None
30
+ maximum_proportion_distinct_features: float = 0.2
31
+ confidence: float = 0.0
32
+
33
+ strict: bool = False
34
+
35
+ PERSIST_COLS: ClassVar = [
36
+ "config",
37
+ "classifier",
38
+ "encoders",
39
+ "transformed_features",
40
+ "transformed_targets",
41
+ "skip_features",
42
+ "confidence",
43
+ ]
44
+
45
+ def _get_encoder(self, v: Union[List[Any], Any]) -> Any:
46
+ if isinstance(v, list):
47
+ if all(isinstance(x, list) for x in v):
48
+ return MultiLabelBinarizer()
49
+ elif all(isinstance(x, str) for x in v):
50
+ return OneHotEncoder(sparse_output=False, handle_unknown="ignore")
51
+ elif all(isinstance(x, (int, float)) for x in v):
52
+ return None
53
+ else:
54
+ raise ValueError("Mixed data types in the list are not supported")
55
+ else:
56
+ if hasattr(v, "dtype"):
57
+ if v.dtype == "object" or v.dtype.name == "category":
58
+ if isinstance(v.iloc[0], list):
59
+ return MultiLabelBinarizer()
60
+ elif self.categorical_encoder_class:
61
+ return self.categorical_encoder_class(handle_unknown="ignore")
62
+ else:
63
+ return OneHotEncoder(sparse_output=False, handle_unknown="ignore")
64
+ elif v.dtype.kind in "biufc":
65
+ return None
66
+ raise ValueError("Unable to determine appropriate encoder for the input data")
67
+
68
+ def _is_complex_column(self, column: pd.Series) -> bool:
69
+ """Check if the column contains complex data types like lists or dicts."""
70
+ # MV_TYPE = (list, dict)
71
+ MV_TYPE = (list,)
72
+ return (column.dtype == "object" or column.dtype == "category") and any(
73
+ isinstance(x, MV_TYPE) for x in column.dropna()
74
+ )
75
+
76
+ def _get_unique_values(self, column: pd.Series) -> set:
77
+ """Get unique values from a column, handling list-type data."""
78
+ if self._is_complex_column(column):
79
+ # For columns with lists, flatten the lists and get unique values
80
+ return set(
81
+ item for sublist in column.dropna() for item in (sublist if isinstance(sublist, list) else [sublist])
82
+ )
83
+ else:
84
+ return set(column.unique())
85
+
86
+ def initialize_model(self, **kwargs):
87
+ logger.info(f"Initializing model with config: {self.config}")
88
+ df = self.training_data.as_dataframe(flattened=True)
89
+ logger.info(f"Training data shape: {df.shape}")
90
+ target_cols = self.config.target_attributes
91
+ feature_cols = self.config.feature_attributes
92
+ if len(target_cols) != 1:
93
+ raise ValueError("Only one target column is supported")
94
+ if not feature_cols:
95
+ feature_cols = df.columns.difference(target_cols).tolist()
96
+ self.config.feature_attributes = feature_cols
97
+ target_col = target_cols[0]
98
+ logger.info(f"Feature columns: {feature_cols}")
99
+ X = df[feature_cols].copy()
100
+ logger.info(f"Target column: {target_col}")
101
+ y = df[target_col].copy()
102
+
103
+ # find list of features to skip (categorical with > N categories)
104
+ skip_features = []
105
+ for col in X.columns:
106
+ unique_values = self._get_unique_values(X[col])
107
+ if len(unique_values) > self.maximum_proportion_distinct_features * len(X[col]):
108
+ skip_features.append(col)
109
+ if False and (X[col].dtype == "object" or X[col].dtype.name == "category"):
110
+ if len(X[col].unique()) > self.maximum_proportion_distinct_features * len(X[col]):
111
+ skip_features.append(col)
112
+ self.skip_features = skip_features
113
+ X = X.drop(skip_features, axis=1)
114
+ logger.info(f"Skipping features: {skip_features}")
115
+
116
+ # Encode features
117
+ encoded_features = []
118
+ for col in X.columns:
119
+ logger.info(f"Checking whether to encode: {col}")
120
+ col_encoder = self._get_encoder(X[col])
121
+ if col_encoder:
122
+ self.encoders[col] = col_encoder
123
+ if isinstance(col_encoder, OneHotEncoder):
124
+ encoded = col_encoder.fit_transform(X[[col]])
125
+ feature_names = col_encoder.get_feature_names_out([col])
126
+ encoded_df = pd.DataFrame(encoded, columns=feature_names, index=X.index)
127
+ X = pd.concat([X.drop(col, axis=1), encoded_df], axis=1)
128
+ encoded_features.extend(feature_names)
129
+ elif isinstance(col_encoder, MultiLabelBinarizer):
130
+ encoded = col_encoder.fit_transform(X[col])
131
+ feature_names = [f"{col}_{c}" for c in col_encoder.classes_]
132
+ encoded_df = pd.DataFrame(encoded, columns=feature_names, index=X.index)
133
+ X = pd.concat([X.drop(col, axis=1), encoded_df], axis=1)
134
+ encoded_features.extend(feature_names)
135
+ else:
136
+ X[col] = col_encoder.fit_transform(X[col])
137
+ encoded_features.append(col)
138
+ else:
139
+ encoded_features.append(col)
140
+
141
+ self.transformed_features = encoded_features
142
+ logger.info(f"Encoded features: {self.transformed_features}")
143
+ logger.info(f"Number of features after encoding: {len(self.transformed_features)}")
144
+
145
+ # Encode target
146
+ # y_encoder = LabelEncoder()
147
+ y_encoder = self._get_encoder(y)
148
+ if isinstance(y_encoder, OneHotEncoder):
149
+ y_encoder = LabelEncoder()
150
+ # self.encoders[target_col] = y_encoder
151
+ if y_encoder:
152
+ self.encoders[target_col] = y_encoder
153
+ y = y_encoder.fit_transform(y.values.ravel()) # Convert to 1D numpy array
154
+ self.transformed_targets = y_encoder.classes_
155
+
156
+ logger.info(f"Fitting model with features: {X.columns}")
157
+ clf = DecisionTreeClassifier(random_state=42)
158
+ clf.fit(X, y)
159
+ self.classifier = clf
160
+ logger.info("Model fit complete")
161
+ cv_scores = cross_val_score(self.classifier, X, y, cv=5)
162
+ self.confidence = cv_scores.mean()
163
+ logger.info(f"Cross-validation scores: {cv_scores}")
164
+
165
+ def derive(self, object: OBJECT) -> Optional[Inference]:
166
+ object = self._normalize(object)
167
+ new_X = pd.DataFrame([object])
168
+
169
+ # Apply encodings
170
+ encoded_features = {}
171
+ for col in self.config.feature_attributes:
172
+ if col in self.skip_features:
173
+ continue
174
+ if col in self.encoders:
175
+ encoder = self.encoders[col]
176
+ if isinstance(encoder, OneHotEncoder):
177
+ encoded = encoder.transform(new_X[[col]])
178
+ feature_names = encoder.get_feature_names_out([col])
179
+ for i, name in enumerate(feature_names):
180
+ encoded_features[name] = encoded[0, i]
181
+ elif isinstance(encoder, MultiLabelBinarizer):
182
+ encoded = encoder.transform(new_X[col])
183
+ feature_names = [f"{col}_{c}" for c in encoder.classes_]
184
+ for i, name in enumerate(feature_names):
185
+ encoded_features[name] = encoded[0, i]
186
+ else: # LabelEncoder or similar
187
+ encoded_features[col] = encoder.transform(new_X[col].astype(str))[0]
188
+ else:
189
+ encoded_features[col] = new_X[col].iloc[0]
190
+
191
+ # Ensure all expected features are present and in the correct order
192
+ final_features = []
193
+ for feature in self.transformed_features:
194
+ if feature in encoded_features:
195
+ final_features.append(encoded_features[feature])
196
+ else:
197
+ final_features.append(0) # or some other default value
198
+
199
+ # Create the final input array
200
+ new_X_array = np.array(final_features).reshape(1, -1)
201
+
202
+ logger.info(f"Input features: {self.transformed_features}")
203
+ logger.info(f"Number of input features: {len(self.transformed_features)}")
204
+
205
+ predictions = self.classifier.predict(new_X_array)
206
+ target_attribute = self.config.target_attributes[0]
207
+ y_encoder = self.encoders.get(target_attribute)
208
+
209
+ if y_encoder:
210
+ v = y_encoder.inverse_transform(predictions)
211
+ else:
212
+ v = predictions
213
+
214
+ predicted_object = {target_attribute: v[0]}
215
+ logger.info(f"Predicted object: {predicted_object}")
216
+ return Inference(predicted_object=predicted_object, confidence=self.confidence)
217
+
218
+ def _normalize(self, object: OBJECT) -> OBJECT:
219
+ return {k: object.get(k, None) for k in self.config.feature_attributes}
220
+
221
+ def export_model(
222
+ self, output: Optional[Union[str, Path, TextIO]], model_serialization: ModelSerialization = None, **kwargs
223
+ ):
224
+ def as_file():
225
+ if isinstance(output, (str, Path)):
226
+ return open(output, "w")
227
+ return output
228
+
229
+ if model_serialization is None:
230
+ if isinstance(output, (str, Path)):
231
+ model_serialization = ModelSerialization.from_filepath(output)
232
+ if model_serialization is None:
233
+ model_serialization = ModelSerialization.JOBLIB
234
+
235
+ if model_serialization == ModelSerialization.LINKML_EXPRESSION:
236
+ expr = tree_to_nested_expression(
237
+ self.classifier,
238
+ self.transformed_features,
239
+ self.encoders.keys(),
240
+ feature_encoders=self.encoders,
241
+ target_encoder=self.encoders.get(self.config.target_attributes[0]),
242
+ )
243
+ as_file().write(expr)
244
+ elif model_serialization == ModelSerialization.JOBLIB:
245
+ self.save_model(output)
246
+ elif model_serialization == ModelSerialization.RULE_BASED:
247
+ rbie = RuleBasedInferenceEngine(config=self.config)
248
+ rbie.import_model_from(self)
249
+ rbie.save_model(output)
250
+ elif model_serialization == ModelSerialization.PNG:
251
+ visualize_decision_tree(self.classifier, self.transformed_features, self.transformed_targets, output)
252
+ else:
253
+ raise ValueError(f"Unsupported model serialization: {model_serialization}")
254
+
255
+ def save_model(self, output: Union[str, Path]) -> None:
256
+ """
257
+ Save the trained model and related data to a file.
258
+
259
+ :param output: Path to save the model
260
+ """
261
+ import joblib
262
+
263
+ if self.classifier is None:
264
+ raise ValueError("Model has not been trained. Call initialize_model() first.")
265
+
266
+ # Use self.PERSIST_COLS
267
+ model_data = {k: getattr(self, k) for k in self.PERSIST_COLS}
268
+
269
+ joblib.dump(model_data, output)
270
+
271
+ @classmethod
272
+ def load_model(cls, file_path: Union[str, Path]) -> "SklearnInferenceEngine":
273
+ """
274
+ Load a trained model and related data from a file.
275
+
276
+ :param file_path: Path to the saved model
277
+ :return: SklearnInferenceEngine instance with loaded model
278
+ """
279
+ import joblib
280
+
281
+ model_data = joblib.load(file_path)
282
+
283
+ engine = cls(config=model_data["config"])
284
+ for k, v in model_data.items():
285
+ if k == "config":
286
+ continue
287
+ setattr(engine, k, v)
288
+
289
+ logger.info(f"Model loaded from {file_path}")
290
+ return engine
@@ -0,0 +1,62 @@
1
+ import logging
2
+ from typing import List, Optional, Tuple
3
+
4
+ from pydantic import BaseModel, ConfigDict, Field
5
+
6
+ from linkml_store.api.collection import OBJECT
7
+ from linkml_store.utils.format_utils import Format, load_objects
8
+
9
+ logger = logging.getLogger(__name__)
10
+
11
+
12
+ class LLMConfig(BaseModel, extra="forbid"):
13
+ """
14
+ Configuration for the LLM indexer.
15
+ """
16
+
17
+ model_config = ConfigDict(protected_namespaces=())
18
+
19
+ model_name: str = "gpt-4o-mini"
20
+ token_limit: Optional[int] = None
21
+ number_of_few_shot_examples: Optional[int] = None
22
+ role: str = "Domain Expert"
23
+ cached_embeddings_database: Optional[str] = None
24
+ cached_embeddings_collection: Optional[str] = None
25
+ text_template: Optional[str] = None
26
+ text_template_syntax: Optional[str] = None
27
+
28
+
29
+ class InferenceConfig(BaseModel, extra="forbid"):
30
+ """
31
+ Configuration for inference engines.
32
+ """
33
+
34
+ target_attributes: Optional[List[str]] = None
35
+ feature_attributes: Optional[List[str]] = None
36
+ train_test_split: Optional[Tuple[float, float]] = None
37
+ llm_config: Optional[LLMConfig] = None
38
+
39
+ @classmethod
40
+ def from_file(cls, file_path: str, format: Optional[Format] = None) -> "InferenceConfig":
41
+ """
42
+ Load an inference config from a file.
43
+
44
+ :param file_path: Path to the file.
45
+ :param format: Format of the file (YAML is recommended).
46
+ :return: InferenceConfig
47
+ """
48
+ if format and format.is_xsv():
49
+ logger.warning("XSV format is not recommended for inference config files")
50
+ objs = load_objects(file_path, format=format)
51
+ if len(objs) != 1:
52
+ raise ValueError(f"Expected 1 object, got {len(objs)}")
53
+ return cls(**objs[0])
54
+
55
+
56
+ class Inference(BaseModel, extra="forbid"):
57
+ """
58
+ Result of an inference derivation.
59
+ """
60
+
61
+ predicted_object: OBJECT = Field(..., description="The predicted object.")
62
+ confidence: Optional[float] = Field(default=None, description="The confidence of the prediction.", le=1.0, ge=0.0)