OntoLearner 1.4.4__py3-none-any.whl → 1.4.6__py3-none-any.whl

ontolearner/VERSION

@@ -1 +1 @@
-1.4.4
+1.4.6

ontolearner/base/learner.py

@@ -13,7 +13,7 @@
 # limitations under the License.
 
 from abc import ABC
-from typing import Any, List, Optional
+from typing import Any, List, Optional, Dict
 from transformers import AutoModelForCausalLM, AutoTokenizer
 import torch
 import torch.nn.functional as F
@@ -147,7 +147,7 @@ class AutoLearner(ABC):
     def _non_taxonomic_re(self, data: Any, test: bool = False) -> Optional[Any]:
         pass
 
-    def tasks_data_former(self, data: Any, task: str, test: bool = False) -> Any:
+    def tasks_data_former(self, data: Any, task: str, test: bool = False) -> List[str | Dict[str, str]]:
         formatted_data = []
         if task == "term-typing":
             for typing in data.term_typings:
@@ -173,7 +173,7 @@ class AutoLearner(ABC):
             formatted_data = {"types": non_taxonomic_types, "relations": non_taxonomic_res}
         return formatted_data
 
-    def tasks_ground_truth_former(self, data: Any, task: str) -> Any:
+    def tasks_ground_truth_former(self, data: Any, task: str) -> List[Dict[str, str]]:
         formatted_data = []
         if task == "term-typing":
             for typing in data.term_typings:
@@ -350,7 +350,7 @@ class AutoRetriever(ABC):
         self.documents = inputs
         self.embeddings = self.embedding_model.encode(inputs, convert_to_tensor=True)
 
-    def retrieve(self, query: List[str], top_k: int = 5) -> List[List[str]]:
+    def retrieve(self, query: List[str], top_k: int = 5, batch_size: int = -1) -> List[List[str]]:
         """
         Retrieve the top-k most similar examples for each query in a list of queries.
 
@@ -363,33 +363,37 @@ class AutoRetriever(ABC):
         """
         if self.embeddings is None:
             raise RuntimeError("Retriever model must index documents before prediction.")
-
-        # Encode all queries at once
         query_embeddings = self.embedding_model.encode(query, convert_to_tensor=True)  # shape: [num_queries, dim]
-
         if query_embeddings.shape[-1] != self.embeddings.shape[-1]:
             raise ValueError(
                 f"Embedding dimension mismatch: query embedding dim={query_embeddings.shape[-1]}, "
                 f"document embedding dim={self.embeddings.shape[-1]}"
             )
-
-        # Normalize embeddings for cosine similarity
-        query_norm = F.normalize(query_embeddings, p=2, dim=1)
         doc_norm = F.normalize(self.embeddings, p=2, dim=1)
+        if batch_size == -1:
+            results = self._retrieve(query_embeddings=query_embeddings, doc_norm=doc_norm, top_k=top_k)
+        else:
+            results = self._batch_retrieve(query_embeddings=query_embeddings, doc_norm=doc_norm, top_k=top_k, batch_size=batch_size)
+        return results
 
-        # Compute cosine similarity: [num_queries, num_docs]
-        similarity_matrix = torch.matmul(query_norm, doc_norm.T)
-
-        # Get top-k indices for each query
-        top_k = min(top_k, len(self.documents))
-        topk_similarities, topk_indices = torch.topk(similarity_matrix, k=top_k, dim=1)
 
-        # Retrieve documents for each query
+    def _retrieve(self, query_embeddings, doc_norm, top_k: int = 5) -> List[List[str]]:
+        query_norm = F.normalize(query_embeddings, p=2, dim=1)
+        similarity_matrix = torch.matmul(query_norm, doc_norm.T)
+        current_top_k = min(top_k, len(self.documents))
+        topk_similarities, topk_indices = torch.topk(similarity_matrix, k=current_top_k, dim=1)
         results = [[self.documents[i] for i in indices] for indices in topk_indices]
-
         return results
 
 
+    def _batch_retrieve(self, query_embeddings, doc_norm, top_k: int = 5, batch_size: int = 1024) -> List[List[str]]:
+        results = []
+        for i in range(0, query_embeddings.size(0), batch_size):
+            batch_queries = query_embeddings[i:i + batch_size]
+            batch_results = self._retrieve(batch_queries, doc_norm, top_k=top_k)
+            results.extend(batch_results)
+        return results
+
 class AutoPrompt(ABC):
     """
     Abstract base class for prompt formatting components.

ontolearner/evaluation/metrics.py

@@ -11,13 +11,12 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-from typing import Dict
+from typing import List, Dict, Tuple, Set
 
 SYMMETRIC_RELATIONS = {"equivalentclass", "sameas", "disjointwith"}
 
-def text2onto_metrics(y_true, y_pred, similarity_threshold: float = 0.8) -> Dict:
-    def jaccard_similarity(a, b):
+def text2onto_metrics(y_true: List[str], y_pred: List[str], similarity_threshold: float = 0.8) -> Dict[str, float | int]:
+    def jaccard_similarity(a: str, b: str) -> float:
         set_a = set(a.lower().split())
         set_b = set(b.lower().split())
         if not set_a and not set_b:
@@ -46,10 +45,13 @@ def text2onto_metrics(y_true, y_pred, similarity_threshold: float = 0.8) -> Dict
     return {
         "f1_score": f1_score,
         "precision": precision,
-        "recall": recall
+        "recall": recall,
+        "total_correct": total_correct,
+        "total_predicted": total_predicted,
+        "total_ground_truth": total_ground_truth
     }
 
-def term_typing_metrics(y_true, y_pred) -> Dict:
+def term_typing_metrics(y_true: List[Dict[str, List[str]]], y_pred: List[Dict[str, List[str]]]) -> Dict[str, float | int]:
     """
     Compute precision, recall, and F1-score for term typing
     using (term, type) pair-level matching instead of ID-based lookups.
@@ -77,13 +79,17 @@ def term_typing_metrics(y_true, y_pred) -> Dict:
     precision = total_correct / total_predicted if total_predicted > 0 else 0.0
     recall = total_correct / total_ground_truth if total_ground_truth > 0 else 0.0
     f1_score = (2 * precision * recall) / (precision + recall) if (precision + recall) > 0 else 0.0
+
     return {
         "f1_score": f1_score,
         "precision": precision,
-        "recall": recall
+        "recall": recall,
+        "total_correct": total_correct,
+        "total_predicted": total_predicted,
+        "total_ground_truth": total_ground_truth
     }
 
-def taxonomy_discovery_metrics(y_true, y_pred) -> Dict:
+def taxonomy_discovery_metrics(y_true: List[Dict[str, str]], y_pred: List[Dict[str, str]]) -> Dict[str, float | int]:
     total_predicted = len(y_pred)
     total_ground_truth = len(y_true)
     # Convert ground truth and predictions to sets of tuples for easy comparison
@@ -102,18 +108,22 @@ def taxonomy_discovery_metrics(y_true, y_pred) -> Dict:
     return {
         "f1_score": f1_score,
         "precision": precision,
-        "recall": recall
+        "recall": recall,
+        "total_correct": total_correct,
+        "total_predicted": total_predicted,
+        "total_ground_truth": total_ground_truth
     }
 
-def non_taxonomic_re_metrics(y_true, y_pred) -> Dict:
-    def normalize_triple(item):
+
+def non_taxonomic_re_metrics(y_true: List[Dict[str, str]], y_pred: List[Dict[str, str]]) -> Dict[str, float | int]:
+    def normalize_triple(item: Dict[str, str]) -> Tuple[str, str, str]:
         return (
             item["head"].strip().lower(),
             item["relation"].strip().lower(),
             item["tail"].strip().lower()
         )
 
-    def expand_symmetric(triples):
+    def expand_symmetric(triples: Set[Tuple[str, str, str]]) -> Set[Tuple[str, str, str]]:
         expanded = set()
         for h, r, t in triples:
             expanded.add((h, r, t))
@@ -136,5 +146,8 @@ def non_taxonomic_re_metrics(y_true, y_pred) -> Dict:
     return {
         "f1_score": f1_score,
         "precision": precision,
-        "recall": recall
+        "recall": recall,
+        "total_correct": total_correct,
+        "total_predicted": total_predicted,
+        "total_ground_truth": total_ground_truth
     }

ontolearner/learner/retriever.py

@@ -17,12 +17,12 @@ from typing import Any, Optional
 import warnings
 
 class AutoRetrieverLearner(AutoLearner):
-    def __init__(self, base_retriever: Any = AutoRetriever(), top_k: int = 5):
+    def __init__(self, base_retriever: Any = AutoRetriever(), top_k: int = 5, batch_size: int = -1):
         super().__init__()
         self.retriever = base_retriever
         self.top_k = top_k
         self._is_term_typing_fit = False
-        self._is_taxonomy_discovery_fit = False
+        self._batch_size = batch_size
 
     def load(self, model_id: str = "sentence-transformers/all-MiniLM-L6-v2"):
         self.retriever.load(model_id=model_id)
@@ -35,7 +35,7 @@ class AutoRetrieverLearner(AutoLearner):
 
     def _retriever_predict(self, data:Any, top_k: int) -> Any:
         if isinstance(data, list):
-            return self.retriever.retrieve(query=data, top_k=top_k)
+            return self.retriever.retrieve(query=data, top_k=top_k, batch_size=self._batch_size)
         if isinstance(data, str):
             return self.retriever.retrieve(query=[data], top_k=top_k)
         raise TypeError(f"Unsupported data type {type(data)}. You should pass a List[str] or a str.")
@@ -63,9 +63,9 @@ class AutoRetrieverLearner(AutoLearner):
         if test:
             self._retriever_fit(data=data)
             candidates_lst =  self._retriever_predict(data=data, top_k=self.top_k + 1)
-            taxonomic_pairs = [{"parent": query, "child": candidate}
+            taxonomic_pairs = [{"parent": candidate, "child": query}
                                for query, candidates in zip(data, candidates_lst)
-                               for candidate in candidates if candidate != query]
+                               for candidate in candidates if candidate.lower() != query.lower()]
             return taxonomic_pairs
         else:
             warnings.warn("No requirement for fiting the taxonomy discovery model, the predict module will use the input data to do the fit as well.")

{ontolearner-1.4.4.dist-info → ontolearner-1.4.6.dist-info}/METADATA

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: OntoLearner
-Version: 1.4.4
+Version: 1.4.6
 Summary: OntoLearner: A Modular Python Library for Ontology Learning with LLMs.
 License: MIT
+License-File: LICENSE
 Author: Hamed Babaei Giglou
 Author-email: hamedbabaeigiglou@gmail.com
 Requires-Python: >=3.10,<3.14.0

{ontolearner-1.4.4.dist-info → ontolearner-1.4.6.dist-info}/RECORD

@@ -1,9 +1,9 @@
-ontolearner/VERSION,sha256=0D2LJotBcTKKwkWM6MqC1pof3jhGnU5PquT4-o2KXjU,6
+ontolearner/VERSION,sha256=Vj1cgMVOd-L4RU7NXBQ4j5qzr3ftxztvRzatpkUnlSw,6
 ontolearner/__init__.py,sha256=E4yukFv2PV4uyztTPDWljCySY9AVDcDDzabuvxfabYE,1889
 ontolearner/_learner.py,sha256=2CRQvpsz8akIOdxTs2-KLJ-MssULrjpK-QDD3QXUJXI,5297
 ontolearner/_ontology.py,sha256=W1mp195SImqLKwaj4ueEaBWuLJg2jUdx1JT20Ds3fmQ,6950
 ontolearner/base/__init__.py,sha256=5pf-ltxzGp32xhEcPdbtm11wXJrYJMUeWG-mbcAYD8Q,705
-ontolearner/base/learner.py,sha256=DVWp7OHlhTYU3Es7Q6CWCOeL7Y5LTbjWilTri_DNExs,17897
+ontolearner/base/learner.py,sha256=J9-Oi2P_UA5Jdbh8muBN0VgH8HGi1uyhEi2LZmCv_rk,18543
 ontolearner/base/ontology.py,sha256=JbMJ1-WUyHWQiNJL-DeaqcriUimLdqN3_ESROgqOPTQ,24772
 ontolearner/base/text2onto.py,sha256=iUXYZoqnwgebQuQzM-XSGTVRfHLlhjUK_z5XUvhRICc,5388
 ontolearner/data_structure/__init__.py,sha256=1HiKvk8FKjhYeI92RHnJXxyQbUJBi3JFytjQjthsY_s,599
@@ -11,13 +11,13 @@ ontolearner/data_structure/data.py,sha256=jUUDfqsOZcEqIR83SRboiKibPdA_JquI1uOEiQ
 ontolearner/data_structure/metric.py,sha256=4QKkZ5L1YK6hDTU-N5Z9I9Ha99DVHmGfYxK7N2qdhfc,7589
 ontolearner/evaluation/__init__.py,sha256=4BZr3BUXjQDTj4Aqlqy4THa80lZPsMuh1EBTCyi9Wig,842
 ontolearner/evaluation/evaluate.py,sha256=NYCVcmPqpyIxYZrMAim37gL-erdh698RD3t3eNTTgZc,1163
-ontolearner/evaluation/metrics.py,sha256=jk-80kQZfWldYV9Lzhq3lZvWE8YT5ywqtzhIfmTm664,5378
+ontolearner/evaluation/metrics.py,sha256=3Aw6ycJ3_Q6xfj4tMBJP6QcexUei0G16H0ZQWt87aRU,6286
 ontolearner/learner/__init__.py,sha256=ZS816XCPb2K7azTlK2032A6ozZNoijlPLDOwcgu3-8g,745
 ontolearner/learner/label_mapper.py,sha256=-XW8MHafm4ix3e9u-RRwDePJ71D804DNuKzdf1zudtk,3789
 ontolearner/learner/llm.py,sha256=bwCoeR7z3YgYrkKyjDM-MRHZAuDzpUt8f-A0bDUbtGM,7151
 ontolearner/learner/prompt.py,sha256=0ckH7xphIDKczPe7G-rwiOxFGZ7RsLnpPlNW92b-31U,1574
 ontolearner/learner/rag.py,sha256=eysB2RvcWkVo53s8-kSbZtJv904YVTmdtxplM4ukUKM,4283
-ontolearner/learner/retriever.py,sha256=FIsvutDXvrr9N6AMu35TNJHdiQGbmRQ4TTGfRRdHdYo,4931
+ontolearner/learner/retriever.py,sha256=GDXr6l0m_prxnctxQzBpm75xL4jW2Q4b91iyePFcDAs,4988
 ontolearner/ontology/__init__.py,sha256=F9Ta1qCX9mOxIK5CPRypEoglQNkpJ6SJpqziz73xKQE,1328
 ontolearner/ontology/agriculture.py,sha256=ZaXHNEFjbtsMH8M7HQ8ypnfJS4TUQy_as16fwv-kOKA,5903
 ontolearner/ontology/arts_humanities.py,sha256=K4ceDJL6PfIfSJZ86uQUkUXOVoiERG6ItgvVE2lhLKk,3996
@@ -53,7 +53,7 @@ ontolearner/tools/visualizer.py,sha256=cwijl4yYaS1SCLM5wbvRTEcbQj9Bjo4fHzZR6q6o8
 ontolearner/utils/__init__.py,sha256=pSEyU3dlPMADBqygqaaid44RdWf0Lo3Fvz-K_rQ7_Bw,733
 ontolearner/utils/io.py,sha256=3DqGK2p7c0onKi0Xxs16WB08uHfHUId3bW0dDKwyS0g,2110
 ontolearner/utils/train_test_split.py,sha256=Zlm42eT6QGWwlySyomCPIiTGmGqeN_h4z4xBY2EAOR8,11530
-ontolearner-1.4.4.dist-info/LICENSE,sha256=krXMLuMKgzX-UgaufgfJdm9ojIloZot7ZdvJUnNxl4I,1067
-ontolearner-1.4.4.dist-info/METADATA,sha256=Uf9twY6zgfxNZbgmtCqIhYJ1nnzzwe-TzC5_bztEV_U,13999
-ontolearner-1.4.4.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-ontolearner-1.4.4.dist-info/RECORD,,
+ontolearner-1.4.6.dist-info/METADATA,sha256=S756f3Kes6TKDwU59ft3TU3GSkffQh6sjptJswr5orw,14021
+ontolearner-1.4.6.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+ontolearner-1.4.6.dist-info/licenses/LICENSE,sha256=krXMLuMKgzX-UgaufgfJdm9ojIloZot7ZdvJUnNxl4I,1067
+ontolearner-1.4.6.dist-info/RECORD,,

{ontolearner-1.4.4.dist-info → ontolearner-1.4.6.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any