OntoLearner 1.4.9__py3-none-any.whl → 1.4.11__py3-none-any.whl

ontolearner/VERSION

@@ -1 +1 @@
-1.4.9
+1.4.11

ontolearner/base/learner.py

@@ -18,6 +18,7 @@ from transformers import AutoModelForCausalLM, AutoTokenizer
 import torch
 import torch.nn.functional as F
 from sentence_transformers import SentenceTransformer
+from collections import defaultdict
 
 class AutoLearner(ABC):
     """
@@ -70,6 +71,7 @@ class AutoLearner(ABC):
                  - "term-typing": Predict semantic types for terms
                  - "taxonomy-discovery": Identify hierarchical relationships
                  - "non-taxonomy-discovery": Identify non-hierarchical relationships
+                 - "text2onto" : Extract ontology terms and their semantic types from documents
 
         Raises:
             NotImplementedError: If not implemented by concrete class.
@@ -81,6 +83,8 @@ class AutoLearner(ABC):
             self._taxonomy_discovery(train_data, test=False)
         elif task == 'non-taxonomic-re':
             self._non_taxonomic_re(train_data, test=False)
+        elif task == 'text2onto':
+            self._text2onto(train_data, test=False)
         else:
             raise ValueError(f"{task} is not a valid task.")
 
@@ -103,6 +107,7 @@ class AutoLearner(ABC):
             - term-typing: List of predicted types for each term
             - taxonomy-discovery: Boolean predictions for relationships
             - non-taxonomy-discovery: Predicted relation types
+            - text2onto : Extract ontology terms and their semantic types from documents
 
         Raises:
             NotImplementedError: If not implemented by concrete class.
@@ -115,6 +120,8 @@ class AutoLearner(ABC):
             return self._taxonomy_discovery(eval_data, test=True)
         elif task == 'non-taxonomic-re':
             return self._non_taxonomic_re(eval_data, test=True)
+        elif task == 'text2onto':
+            return self._text2onto(eval_data, test=True)
         else:
             raise ValueError(f"{task} is not a valid task.")
 
@@ -147,6 +154,9 @@ class AutoLearner(ABC):
     def _non_taxonomic_re(self, data: Any, test: bool = False) -> Optional[Any]:
         pass
 
+    def _text2onto(self, data: Any, test: bool = False) -> Optional[Any]:
+        pass
+
     def tasks_data_former(self, data: Any, task: str, test: bool = False) -> List[str | Dict[str, str]]:
         formatted_data = []
         if task == "term-typing":
@@ -171,6 +181,7 @@ class AutoLearner(ABC):
             non_taxonomic_types = list(set(non_taxonomic_types))
             non_taxonomic_res = list(set(non_taxonomic_res))
             formatted_data = {"types": non_taxonomic_types, "relations": non_taxonomic_res}
+
         return formatted_data
 
     def tasks_ground_truth_former(self, data: Any, task: str) -> List[Dict[str, str]]:
@@ -186,6 +197,26 @@ class AutoLearner(ABC):
                 formatted_data.append({"head": non_taxonomic_triplets.head,
                                        "tail": non_taxonomic_triplets.tail,
                                        "relation": non_taxonomic_triplets.relation})
+        if task == "text2onto":
+            terms2docs = data.get("terms2docs", {}) or {}
+            terms2types = data.get("terms2types", {}) or {}
+
+            # gold doc→terms
+            gold_terms = []
+            for term, doc_ids in terms2docs.items():
+                for doc_id in doc_ids or []:
+                    gold_terms.append({"doc_id": doc_id, "term": term})
+
+            # gold doc→types derived via doc→terms + term→types
+            doc2types = defaultdict(set)
+            for term, doc_ids in terms2docs.items():
+                for doc_id in doc_ids or []:
+                    for ty in (terms2types.get(term, []) or []):
+                        if isinstance(ty, str) and ty.strip():
+                            doc2types[doc_id].add(ty.strip())
+            gold_types = [{"doc_id": doc_id, "type": ty} for doc_id, tys in doc2types.items() for ty in tys]
+            return {"terms": gold_terms, "types": gold_types}
+
         return formatted_data
 
 class AutoLLM(ABC):
@@ -201,7 +232,7 @@ class AutoLLM(ABC):
         tokenizer: The tokenizer associated with the model.
     """
 
-    def __init__(self, label_mapper: Any, device: str='cpu', token: str="") -> None:
+    def __init__(self, label_mapper: Any, device: str='cpu', token: str="", max_length: int = 256) -> None:
         """
         Initialize the LLM component.
 
@@ -213,6 +244,7 @@ class AutoLLM(ABC):
         self.device=device
         self.model: Optional[Any] = None
         self.tokenizer: Optional[Any] = None
+        self.max_length = max_length
 
 
     def load(self, model_id: str) -> None:
@@ -236,10 +268,8 @@ class AutoLLM(ABC):
         self.tokenizer = AutoTokenizer.from_pretrained(model_id, padding_side='left', token=self.token)
         self.tokenizer.pad_token = self.tokenizer.eos_token
         if self.device == "cpu":
-            # device_map = "cpu"
             self.model = AutoModelForCausalLM.from_pretrained(
                 model_id,
-                # device_map=device_map,
                 torch_dtype=torch.bfloat16,
                 token=self.token
             )
@@ -248,8 +278,8 @@ class AutoLLM(ABC):
             self.model = AutoModelForCausalLM.from_pretrained(
                 model_id,
                 device_map=device_map,
-                torch_dtype=torch.bfloat16,
-                token=self.token
+                token=self.token,
+                trust_remote_code=True,
             )
         self.label_mapper.fit()
 
@@ -276,29 +306,20 @@ class AutoLLM(ABC):
             List of generated text responses, one for each input prompt.
             Responses include the original input plus generated continuation.
         """
-        # Tokenize inputs and move to device
         encoded_inputs = self.tokenizer(inputs,
                                         return_tensors="pt",
-                                        padding=True,
+                                        max_length=self.max_length,
                                         truncation=True).to(self.model.device)
         input_ids = encoded_inputs["input_ids"]
         input_length = input_ids.shape[1]
-
-        # Generate output
         outputs = self.model.generate(
             **encoded_inputs,
             max_new_tokens=max_new_tokens,
-            pad_token_id=self.tokenizer.eos_token_id
+            pad_token_id=self.tokenizer.eos_token_id,
+            eos_token_id=self.tokenizer.eos_token_id
         )
-
-        # Extract only the newly generated tokens (excluding prompt)
         generated_tokens = outputs[:, input_length:]
-
-        # Decode only the generated part
         decoded_outputs = [self.tokenizer.decode(g, skip_special_tokens=True).strip() for g in generated_tokens]
-        print(decoded_outputs)
-        print(self.label_mapper.predict(decoded_outputs))
-        # Map the decoded text to labels
         return self.label_mapper.predict(decoded_outputs)
 
 class AutoRetriever(ABC):

ontolearner/base/ontology.py

@@ -372,7 +372,7 @@ class BaseOntology(ABC):
         # Save updated metrics
         df.to_excel(metrics_file_path, index=False)
 
-    def is_valid_label(label: str) -> Any:
+    def is_valid_label(self, label: str) -> Any:
         invalids = ['root', 'thing']
         if label.lower() in invalids:
             return None
@@ -522,7 +522,7 @@ class BaseOntology(ABC):
                 return True
         return False
 
-    def _is_anonymous_id(label: str) -> bool:
+    def _is_anonymous_id(self, label: str) -> bool:
         """Check if a label represents an anonymous class identifier."""
         if not label:
             return True

ontolearner/evaluation/metrics.py

@@ -11,44 +11,84 @@
 # 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 List, Dict, Tuple, Set
+from typing import List, Dict, Tuple, Set, Any, Union
 
 SYMMETRIC_RELATIONS = {"equivalentclass", "sameas", "disjointwith"}
 
-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:
+def text2onto_metrics(
+    y_true: Dict[str, Any],
+    y_pred: Dict[str, Any],
+    similarity_threshold: float = 0.8
+) -> Dict[str, Any]:
+    """
+    Expects:
+      y_true = {"terms": [{"doc_id": str, "term": str}, ...],
+               "types": [{"doc_id": str, "type": str}, ...]}
+      y_pred = same shape
+
+    Returns:
+      {"terms": {...}, "types": {...}}
+    """
+
+    def jaccard_similarity(text_a: str, text_b: str) -> float:
+        tokens_a = set(text_a.lower().split())
+        tokens_b = set(text_b.lower().split())
+        if not tokens_a and not tokens_b:
             return 1.0
-        return len(set_a & set_b) / len(set_a | set_b)
-
-    matched_gt_indices = set()
-    matched_pred_indices = set()
-    for i, pred_label in enumerate(y_pred):
-        for j, gt_label in enumerate(y_true):
-            if j in matched_gt_indices:
-                continue
-            sim = jaccard_similarity(pred_label, gt_label)
-            if sim >= similarity_threshold:
-                matched_pred_indices.add(i)
-                matched_gt_indices.add(j)
-                break  # each gt matched once
-
-    total_correct = len(matched_pred_indices)
-    total_predicted = len(y_pred)
-    total_ground_truth = len(y_true)
+        return len(tokens_a & tokens_b) / len(tokens_a | tokens_b)
+
+    def pairs_to_strings(rows: List[Dict[str, str]], value_key: str) -> List[str]:
+        paired_strings: List[str] = []
+        for row in rows or []:
+            doc_id = (row.get("doc_id") or "").strip()
+            value = (row.get(value_key) or "").strip()
+            if doc_id and value:
+                # keep doc association + allow token Jaccard
+                paired_strings.append(f"{doc_id} {value}")
+        return paired_strings
+
+    def score_list(ground_truth_items: List[str], predicted_items: List[str]) -> Dict[str, Union[float, int]]:
+        matched_ground_truth_indices: Set[int] = set()
+        matched_predicted_indices: Set[int] = set()
+
+        for predicted_index, predicted_item in enumerate(predicted_items):
+            for ground_truth_index, ground_truth_item in enumerate(ground_truth_items):
+                if ground_truth_index in matched_ground_truth_indices:
+                    continue
+
+                if jaccard_similarity(predicted_item, ground_truth_item) >= similarity_threshold:
+                    matched_predicted_indices.add(predicted_index)
+                    matched_ground_truth_indices.add(ground_truth_index)
+                    break
+
+        total_correct = len(matched_predicted_indices)
+        total_predicted = len(predicted_items)
+        total_ground_truth = len(ground_truth_items)
+
+        precision = total_correct / total_predicted if total_predicted else 0.0
+        recall = total_correct / total_ground_truth if total_ground_truth else 0.0
+        f1 = (2 * precision * recall / (precision + recall)) if (precision + recall) else 0.0
+
+        return {
+            "f1_score": f1,
+            "precision": precision,
+            "recall": recall,
+            "total_correct": total_correct,
+            "total_predicted": total_predicted,
+            "total_ground_truth": total_ground_truth,
+        }
+
+    ground_truth_terms = pairs_to_strings(y_true.get("terms", []), "term")
+    predicted_terms = pairs_to_strings(y_pred.get("terms", []), "term")
+    ground_truth_types = pairs_to_strings(y_true.get("types", []), "type")
+    predicted_types = pairs_to_strings(y_pred.get("types", []), "type")
+
+    terms_metrics = score_list(ground_truth_terms, predicted_terms)
+    types_metrics = score_list(ground_truth_types, predicted_types)
 
-    precision = total_correct / total_predicted if total_predicted > 0 else 0
-    recall = total_correct / total_ground_truth if total_ground_truth > 0 else 0
-    f1_score = 2 * precision * recall / (precision + recall) if (precision + recall) > 0 else 0
     return {
-        "f1_score": f1_score,
-        "precision": precision,
-        "recall": recall,
-        "total_correct": total_correct,
-        "total_predicted": total_predicted,
-        "total_ground_truth": total_ground_truth
+        "terms": terms_metrics,
+        "types": types_metrics,
     }
 
 def term_typing_metrics(y_true: List[Dict[str, List[str]]], y_pred: List[Dict[str, List[str]]]) -> Dict[str, float | int]:

ontolearner/learner/__init__.py

@@ -14,6 +14,6 @@
 
 from .llm import AutoLLMLearner, FalconLLM, MistralLLM
 from .retriever import AutoRetrieverLearner, LLMAugmentedRetrieverLearner
-from .rag import AutoRAGLearner
+from .rag import AutoRAGLearner, LLMAugmentedRAGLearner
 from .prompt import StandardizedPrompting
 from .label_mapper import LabelMapper

ontolearner/learner/label_mapper.py

@@ -31,7 +31,7 @@ class LabelMapper:
                  ngram_range: Tuple=(1, 1),
                  label_dict: Dict[str, List[str]]=None,
                  analyzer: str = 'word',
-                 iterator_no: int = 100):
+                 iterator_no: int = 1000):
         """
         Initializes the TFIDFLabelMapper with a specified classifier and TF-IDF configuration.
 

ontolearner/learner/prompt.py

@@ -17,15 +17,50 @@ from ..base import AutoPrompt
 class StandardizedPrompting(AutoPrompt):
     def __init__(self, task: str = None):
         if task == "term-typing":
-            prompt_template = """Determine whether the given term can be categorized as an instance of the specified high-level type. Answer with `yes` if it is otherwise answer with `no`. Do not explain.
+            prompt_template = """You are performing term typing.
+
+Determine whether the given term is a clear and unambiguous instance of the specified high-level type.
+
+Rules:
+- Answer "yes" only if the term commonly and directly belongs to the type.
+- Answer "no" if the term does not belong to the type, is ambiguous, or only weakly related.
+- Use the most common meaning of the term.
+- Do not explain your answer.
+
 Term: {term}
 Type: {type}
-Answer: """
+Answer (yes or no):"""
         elif task == "taxonomy-discovery":
-            prompt_template = """Is {parent} a direct or indirect superclass (or parent concept) of {child} in a conceptual hierarchy? Answer with yes or no.
-Answer: """
+            prompt_template =  """You are identifying taxonomic (is-a) relationships.
+
+Question:
+Is "{parent}" a superclass (direct or indirect) of "{child}" in a standard conceptual or ontological hierarchy?
+
+Rules:
+- A superclass means: "{child}" is a type or instance of "{parent}".
+- Answer "yes" only if the relationship is a true is-a relationship.
+- Answer "no" for part-of, related-to, or associative relationships.
+- Use general world knowledge.
+- Do not explain.
+
+Parent: {parent}
+Child: {child}
+Answer (yes or no):"""
         elif task == "non-taxonomic-re":
-            prompt_template = """Given the conceptual types `{head}` and `{tail}`, does a `{relation}` relation exist between them? Respond with "yes" if it does, otherwise respond with "no"."""
+            prompt_template = """You are identifying non-taxonomic conceptual relationships.
+
+Given two conceptual types, determine whether the specified relation typically holds between them.
+
+Rules:
+- Answer "yes" only if the relation commonly and meaningfully applies.
+- Answer "no" if the relation is rare, indirect, or context-dependent.
+- Do not infer relations that require specific situations.
+- Do not explain.
+
+Head type: {head}
+Tail type: {tail}
+Relation: {relation}
+Answer (yes or no):"""
         else:
             raise ValueError("Unknown task! Current tasks are: 'term-typing', 'taxonomy-discovery', 'non-taxonomic-re'")
         super().__init__(prompt_template)

ontolearner/learner/rag/__init__.py

@@ -0,0 +1,14 @@
+# Copyright (c) 2025 SciKnowOrg
+#
+# Licensed under the MIT License (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://opensource.org/licenses/MIT
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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 .rag import AutoRAGLearner, LLMAugmentedRAGLearner

ontolearner/learner/{rag.py → rag/rag.py}

@@ -14,8 +14,7 @@
 
 import warnings
 from typing import Any
-from ..base import AutoLearner
-
+from ...base import AutoLearner
 
 class AutoRAGLearner(AutoLearner):
     def __init__(self,
@@ -87,3 +86,9 @@ class AutoRAGLearner(AutoLearner):
             return self.llm._non_taxonomic_re_predict(dataset=dataset)
         else:
             warnings.warn("No requirement for fiting the non-taxonomic-re model, the predict module will use the input data to do the fit as well.")
+
+
+class LLMAugmentedRAGLearner(AutoRAGLearner):
+
+    def set_augmenter(self, augmenter):
+        self.retriever.set_augmenter(augmenter=augmenter)

ontolearner/learner/retriever/__init__.py

@@ -16,4 +16,4 @@ from .crossencoder import CrossEncoderRetriever
 from .embedding import GloveRetriever, Word2VecRetriever
 from .ngram import NgramRetriever
 from .learner import AutoRetrieverLearner, LLMAugmentedRetrieverLearner
-from .llm_retriever import LLMAugmenterGenerator, LLMAugmenter, LLMAugmentedRetriever
+from .augmented_retriever import LLMAugmenterGenerator, LLMAugmenter, LLMAugmentedRetriever

ontolearner/learner/retriever/{llm_retriever.py → augmented_retriever.py}

@@ -17,6 +17,8 @@ from typing import Any, List, Dict
 from openai import OpenAI
 import time
 from tqdm import tqdm
+import torch
+import torch.nn.functional as F
 
 from ...base import AutoRetriever
 from ...utils import load_json
@@ -125,7 +127,6 @@ class LLMAugmenterGenerator(ABC):
             except Exception:
                 print("sleep for 5 seconds")
                 time.sleep(5)
-
         return inference
 
     def tasks_data_former(self, data: Any, task: str) -> List[str] | Dict[str, List[str]]:
@@ -298,21 +299,12 @@ class LLMAugmentedRetriever(AutoRetriever):
     Attributes:
         augmenter: An augmenter instance that provides transform() and top_n_candidate.
     """
-
-    def __init__(self) -> None:
-        """
-        Initialize the augmented retriever with no augmenter attached.
-        """
+    def __init__(self, threshold: float = 0.0, cutoff_rate: float = 100.0) -> None:
         super().__init__()
-        self.augmenter = None
+        self.threshold = threshold
+        self.cutoff_rate = cutoff_rate
 
     def set_augmenter(self, augmenter):
-        """
-        Attach an augmenter instance.
-
-        Args:
-            augmenter: An object providing `transform(query, task)` and `top_n_candidate`.
-        """
         self.augmenter = augmenter
 
     def retrieve(self, query: List[str], top_k: int = 5, batch_size: int = -1, task: str = None) -> List[List[str]]:
@@ -328,29 +320,46 @@ class LLMAugmentedRetriever(AutoRetriever):
         Returns:
             list[list[str]]: A list of document lists, one per input query.
         """
-        parent_retrieve = super(LLMAugmentedRetriever, self).retrieve
-
-        if task == 'taxonomy-discovery':
-            query_sets = []
-            for idx in range(self.augmenter.top_n_candidate):
-                query_set = []
-                for qu in query:
-                    query_set.append(self.augmenter.transform(qu, task=task)[idx])
-                query_sets.append(query_set)
-
-            retrieves = [
-                parent_retrieve(query=query_set, top_k=top_k, batch_size=batch_size)
-                for query_set in query_sets
-            ]
-
-            results = []
-            for qu_idx, qu in enumerate(query):
-                qu_result = []
-                for top_idx in range(self.augmenter.top_n_candidate):
-                    qu_result += retrieves[top_idx][qu_idx]
-                results.append(list(set(qu_result)))
-
-            return results
-
-        else:
-            return parent_retrieve(query=query, top_k=top_k, batch_size=batch_size)
+        if task != 'taxonomy-discovery':
+            return super().retrieve(query=query, top_k=top_k, batch_size=batch_size)
+        return self.augmented_retrieve(query, top_k=top_k, batch_size=batch_size, task=task)
+
+    def augmented_retrieve(self, query: List[str], top_k: int = 5, batch_size: int = -1, task: str = None):
+        if self.embeddings is None:
+            raise RuntimeError("Retriever model must index documents before prediction.")
+
+        augmented_queries, index_map = [], []
+        for qu_idx, qu in enumerate(query):
+            augmented = self.augmenter.transform(qu, task=task)
+            for aug in augmented:
+                augmented_queries.append(aug)
+                index_map.append(qu_idx)
+
+        doc_norm = F.normalize(self.embeddings, p=2, dim=1)
+        results = [dict() for _ in range(len(query))]
+
+        if batch_size == -1:
+            batch_size = len(augmented_queries)
+
+        for start in range(0, len(augmented_queries), batch_size):
+            batch_aug = augmented_queries[start:start + batch_size]
+            batch_embeddings = self.embedding_model.encode(batch_aug, convert_to_tensor=True)
+            batch_norm = F.normalize(batch_embeddings, p=2, dim=1)
+            similarity_matrix = torch.matmul(batch_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)
+
+            for i, (doc_indices, sim_scores) in enumerate(zip(topk_indices, topk_similarities)):
+                original_query_idx = index_map[start + i]
+
+                for doc_idx, score in zip(doc_indices.tolist(), sim_scores.tolist()):
+                    if score >= self.threshold:
+                        doc = self.documents[doc_idx]
+                        prev = results[original_query_idx].get(doc, 0.0)
+                        results[original_query_idx][doc] = prev + score
+
+        final_results = []
+        for doc_score_map in results:
+            sorted_docs = sorted(doc_score_map.items(), key=lambda x: x[1], reverse=True)
+            final_results.append([doc for doc, _ in sorted_docs])
+        return final_results

ontolearner/learner/retriever/learner.py

@@ -122,7 +122,6 @@ class AutoRetrieverLearner(AutoLearner):
             warnings.warn("No requirement for fiting the non-taxonomic RE model, the predict module will use the input data to do the fit as well..")
 
 
-
 class LLMAugmentedRetrieverLearner(AutoRetrieverLearner):
 
     def set_augmenter(self, augmenter):
@@ -160,9 +159,9 @@ class LLMAugmentedRetrieverLearner(AutoRetrieverLearner):
             taxonomic_pairs = [{"parent": candidate, "child": query}
                                for query, candidates in zip(data, candidates_lst)
                                for candidate in candidates if candidate.lower() != query.lower()]
-            taxonomic_pairs += [{"parent": query, "child": candidate}
-                                for query, candidates in zip(data, candidates_lst)
-                                for candidate in candidates if candidate.lower() != query.lower()]
+            # taxonomic_pairs += [{"parent": query, "child": candidate}
+            #                    for query, candidates in zip(data, candidates_lst)
+            #                    for candidate in candidates if candidate.lower() != query.lower()]
             unique_taxonomic_pairs, seen = [], set()
             for pair in taxonomic_pairs:
                 key = (pair["parent"].lower(), pair["child"].lower())  # Directional key (parent, child)

ontolearner/learner/text2onto/__init__.py

@@ -12,5 +12,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .alexbek import AlexbekFewShotLearner
+from .alexbek import AlexbekRAGFewShotLearner
 from .sbunlp import SBUNLPFewShotLearner