diff --git a/CHANGELOG.md b/CHANGELOG.md index 390b32e26..73f962d03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,9 @@ ## Next +### Added +- Added a new semantic match resolver to the KG Builder for entity resolution based on spaCy embeddings and cosine similarities so that nodes with similar textual properties get merged. + ## 1.6.0 ### Added diff --git a/docs/source/api.rst b/docs/source/api.rst index f27bf3af7..034ef615a 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -104,6 +104,11 @@ SinglePropertyExactMatchResolver .. autoclass:: neo4j_graphrag.experimental.components.resolver.SinglePropertyExactMatchResolver :members: run +SpaCySemanticMatchResolver +================================ + +.. autoclass:: neo4j_graphrag.experimental.components.resolver.SpaCySemanticMatchResolver + :members: run .. _pipeline-section: diff --git a/docs/source/index.rst b/docs/source/index.rst index ae8c25d6c..f36e884c5 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -99,7 +99,8 @@ List of extra dependencies: - **qdrant**: store vectors in Qdrant - **experimental**: experimental features mainly from the Knowledge Graph creation pipelines. - Warning: this requires `pygraphviz`. Installation instructions can be found `here `_. - +- nlp: + - **spaCy**: load spaCy trained models for nlp pipelines, used by `SpaCySemanticMatchResolver` component from the Knowledge Graph creation pipelines. ******** Examples diff --git a/docs/source/user_guide_kg_builder.rst b/docs/source/user_guide_kg_builder.rst index 20a7db63f..5bbe11095 100644 --- a/docs/source/user_guide_kg_builder.rst +++ b/docs/source/user_guide_kg_builder.rst @@ -1028,22 +1028,28 @@ without making assumptions about entity similarity. The Entity Resolver is responsible for refining the created knowledge graph by merging entity nodes that represent the same real-world object. -In practice, this package implements a simple resolver that merges nodes -with the same label and identical "name" property. +In practice, this package implements two resolvers: + +- a simple resolver that merges nodes with the same label and identical "name" property; +- a semantic match resolver that merges nodes with the same label and similar set of textual properties (by default it uses the "name" property). +So far, the semantic matching is based on spaCy embeddings and cosine similarities of embedding vectors. .. warning:: - The `SinglePropertyExactMatchResolver` **replaces** the nodes created by the KG writer. + - The `SinglePropertyExactMatchResolver` and `SpaCySemanticMatchResolver` **replace** the nodes created by the KG writer. + + - Check the :ref:`installation` section to make sure you have the required dependencies installed when using `SpaCySemanticMatchResolver`. -It can be used like this: +The resolvers can be used like this: .. code:: python from neo4j_graphrag.experimental.components.resolver import ( SinglePropertyExactMatchResolver, ) - resolver = SinglePropertyExactMatchResolver(driver) + resolver = SinglePropertyExactMatchResolver(driver) # exact match resolver + # resolver = SpaCySemanticMatchResolver(driver) # semantic match with spaCy res = await resolver.run() .. warning:: diff --git a/examples/README.md b/examples/README.md index 3dd6ee65c..e4759a456 100644 --- a/examples/README.md +++ b/examples/README.md @@ -126,8 +126,8 @@ are listed in [the last section of this file](#customize). - [Neo4j writer](./customize/build_graph/components/writers/neo4j_writer.py) - [Custom](./customize/build_graph/components/writers/custom_writer.py) - Entity Resolver: - - [SinglePropertyExactMatchResolver](./customize/build_graph/components/resolvers/simple_entity_resolver.py) - [SinglePropertyExactMatchResolver with pre-filter](./customize/build_graph/components/resolvers/simple_entity_resolver_pre_filter.py) + - [SpaCySemanticMatchResolver with pre-filter](./customize/build_graph/components/resolvers/spacy_entity_resolver_pre_filter.py) - [Custom resolver](./customize/build_graph/components/resolvers/custom_resolver.py) - [Custom component](./customize/build_graph/components/custom_component.py) diff --git a/examples/customize/build_graph/components/resolvers/simple_entity_resolver.py b/examples/customize/build_graph/components/resolvers/simple_entity_resolver.py deleted file mode 100644 index 49a4da398..000000000 --- a/examples/customize/build_graph/components/resolvers/simple_entity_resolver.py +++ /dev/null @@ -1,25 +0,0 @@ -"""The SinglePropertyExactMatchResolver merge nodes with same label -and exact same property value (by default using the "name" property). - -WARNING: this process is destructive, initial nodes are deleted and replaced -by the resolved ones, but all relationships are kept. -See apoc.refactor.mergeNodes documentation for more details. -""" - -import neo4j -from neo4j_graphrag.experimental.components.resolver import ( - SinglePropertyExactMatchResolver, -) -from neo4j_graphrag.experimental.components.types import ResolutionStats - - -async def main(driver: neo4j.Driver) -> None: - resolver = SinglePropertyExactMatchResolver( - driver, - # optionally, change the property used for resolution (default is "name") - # resolve_property="name", - # and the neo4j database where data is updated - # neo4j_database="neo4j", - ) - res: ResolutionStats = await resolver.run() - print(res) diff --git a/examples/customize/build_graph/components/resolvers/spacy_entity_resolver_pre_filter.py b/examples/customize/build_graph/components/resolvers/spacy_entity_resolver_pre_filter.py new file mode 100644 index 000000000..2da7ed062 --- /dev/null +++ b/examples/customize/build_graph/components/resolvers/spacy_entity_resolver_pre_filter.py @@ -0,0 +1,37 @@ +"""The SpaCySemanticMatchResolver merges nodes with same label +and similar textual properties (by default using the "name" property) based on spaCy +embeddings and cosine similarities of embedding vectors. + +If the resolution is intended to be applied only on some nodes, for instance nodes that +belong to a specific document, a "WHERE" query can be added. The only variable in the +query scope is "entity". + +WARNING: this process is destructive, initial nodes are deleted and replaced +by the resolved ones, but all relationships are kept. +See apoc.refactor.mergeNodes documentation for more details. +""" + +import neo4j +from neo4j_graphrag.experimental.components.resolver import ( + SpaCySemanticMatchResolver, +) +from neo4j_graphrag.experimental.components.types import ResolutionStats + + +async def main(driver: neo4j.Driver) -> None: + resolver = SpaCySemanticMatchResolver( + driver, + # let's filter all entities that belong to a certain docId + filter_query="WHERE (entity)-[:FROM_CHUNK]->(:Chunk)-[:FROM_DOCUMENT]->(doc:" + "Document {id = 'docId'}", + # optionally, change the properties used for resolution (default is "name") + # resolve_properties=["name", "ssn"], + # the similarity threshold (default is 0.8) + # similarity_threshold=0.9 + # the spaCy trained model (default is "en_core_web_lg") + # spacy_model="en_core_web_sm" + # and the neo4j database where data is updated + # neo4j_database="neo4j", + ) + res: ResolutionStats = await resolver.run() + print(res) diff --git a/poetry.lock b/poetry.lock index 9f3b1f7a3..e6d2c2296 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,104 +1,104 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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See the License for the specific language governing permissions and # limitations under the License. import abc -from typing import Any, Optional +import logging +from itertools import combinations +from typing import Any, Optional, List import neo4j +import numpy as np +from numpy.typing import NDArray +import spacy +from spacy.language import Language +from spacy.cli.download import download as spacy_download from neo4j_graphrag.experimental.components.types import ResolutionStats from neo4j_graphrag.experimental.pipeline import Component from neo4j_graphrag.utils import driver_config +logger = logging.getLogger(__name__) + class EntityResolver(Component, abc.ABC): """Entity resolution base class @@ -137,3 +146,181 @@ async def run(self) -> ResolutionStats: number_of_nodes_to_resolve=number_of_nodes_to_resolve, number_of_created_nodes=number_of_created_nodes, ) + + +class SpaCySemanticMatchResolver(EntityResolver): + """ + Resolve entities with same label and similar set of textual properties (default is + ["name"]) based on spaCy's static embeddings and cosine similarities. + + Args: + driver (neo4j.Driver): The Neo4j driver to connect to the database. + filter_query (Optional[str]): Optional Cypher WHERE clause to reduce the resolution scope. + resolve_properties (Optional[List[str]]): The list of properties to consider for embeddings Defaults to ["name"]. + similarity_threshold (float): The similarity threshold above which nodes are merged. Defaults to 0.8. + spacy_model (str): The name of the spaCy model to load. Defaults to "en_core_web_lg". + neo4j_database (Optional[str]): The name of the Neo4j database. If not provided, this defaults to the server's default database ("neo4j" by default) (`see reference to documentation `_). + + Example: + + .. code-block:: python + + from neo4j import GraphDatabase + from neo4j_graphrag.experimental.components.resolver import SinglePropertyExactMatchResolver + + URI = "neo4j://localhost:7687" + AUTH = ("neo4j", "password") + DATABASE = "neo4j" + + driver = GraphDatabase.driver(URI, auth=AUTH) + resolver = SinglePropertyExactMatchResolver(driver=driver, neo4j_database=DATABASE) + await resolver.run() # no expected parameters + + """ + + def __init__( + self, + driver: neo4j.Driver, + filter_query: Optional[str] = None, + resolve_properties: Optional[List[str]] = None, + similarity_threshold: float = 0.8, + spacy_model: str = "en_core_web_lg", + neo4j_database: Optional[str] = None, + ) -> None: + super().__init__(driver, filter_query) + self.resolve_properties = resolve_properties or ["name"] + self.similarity_threshold = similarity_threshold + self.neo4j_database = neo4j_database + self.nlp = self._load_or_download_spacy_model(spacy_model) + + async def run(self) -> ResolutionStats: + """Resolve entities based on the following rules: + For each entity label, entities with similar 'resolve_properties' + (cosine similarity on embedding vectors) are merged into a single node. + + See apoc.refactor.mergeNodes documentation for more details. + """ + match_query = "MATCH (entity:__Entity__)" + if self.filter_query: + match_query += f" {self.filter_query}" + + # generate a dynamic map of requested properties, e.g. "name: entity.name, description: entity.description, ..." + props_map_list = [f"{prop}: entity.{prop}" for prop in self.resolve_properties] + props_map = ", ".join(props_map_list) + + # Cypher query: + # matches extracted entities + # filters entities if filter_query is provided + # unwinds labels to skip reserved ones + # collects all properties needed for embeddings + query = f""" + {match_query} + UNWIND labels(entity) AS lab + WITH lab, entity + WHERE NOT lab IN ['__Entity__', '__KGBuilder__'] + WITH lab, collect({{ id: id(entity), {props_map} }}) AS labelCluster + RETURN lab, labelCluster + """ + + records, _, _ = self.driver.execute_query(query, database_=self.neo4j_database) + + total_entities_embedded = 0 + total_merged_nodes = 0 + + # for each row, 'lab' is the label, 'labelCluster' is a list of dicts (id + textual properties) + for row in records: + entities = row["labelCluster"] + + # build node embeddings + node_embeddings = {} + for ent in entities: + # concatenate all textual properties (if non-null) into a single string + texts = [ + str(ent[p]) for p in self.resolve_properties if p in ent and ent[p] + ] + combined_text = " ".join(texts).strip() + if combined_text: + node_embeddings[ent["id"]] = self.nlp(combined_text).vector + total_entities_embedded += len(node_embeddings) + + # identify pairs to merge + pairs_to_merge = [] + for (id1, emb1), (id2, emb2) in combinations(node_embeddings.items(), 2): + sim = self._cosine_similarity( + np.asarray(emb1, dtype=np.float64), + np.asarray(emb2, dtype=np.float64), + ) + if sim >= self.similarity_threshold: + pairs_to_merge.append({id1, id2}) + + # consolidate overlapping sets of node IDs + resolved_sets = self._consolidate_sets(pairs_to_merge) + + # perform merges in the db using APOC + merged_count = 0 + for node_id_set in resolved_sets: + if len(node_id_set) > 1: + merge_query = ( + "MATCH (n) WHERE id(n) IN $ids " + "WITH collect(n) AS nodes " + "CALL apoc.refactor.mergeNodes(nodes, {properties: 'discard', mergeRels: true}) " + "YIELD node RETURN id(node)" + ) + result, _, _ = self.driver.execute_query( + merge_query, + {"ids": list(node_id_set)}, + database_=self.neo4j_database, + ) + merged_count += len(result) + + total_merged_nodes += merged_count + + return ResolutionStats( + number_of_nodes_to_resolve=total_entities_embedded, + number_of_created_nodes=total_merged_nodes, + ) + + @staticmethod + def _consolidate_sets(pairs: List[set[str]]) -> List[set[str]]: + """Consolidate overlapping sets of node pairs into unique sets.""" + consolidated: List[set[str]] = [] + for pair in pairs: + merged = False + for cons in consolidated: + # if there is any intersection, unify them + if pair & cons: + cons.update(pair) + merged = True + break + if not merged: + consolidated.append(set(pair)) + return consolidated + + @staticmethod + def _cosine_similarity( + vec1: NDArray[np.float64], vec2: NDArray[np.float64] + ) -> float: + """Calculate cosine similarity between two embedding vectors.""" + dot_product = np.dot(vec1, vec2) + norm1 = np.linalg.norm(vec1) + norm2 = np.linalg.norm(vec2) + if not norm1 or not norm2: + return 0.0 + return float(dot_product / (norm1 * norm2)) + + @staticmethod + def _load_or_download_spacy_model(model_name: str) -> Language: + """ + Attempt to load the specified spaCy model by name. + If not installed, automatically download and then load it. + """ + try: + return spacy.load(model_name) + except OSError as e: + # handling cases where the spaCy model is not yet downloaded: + if "doesn't seem to be a Python package or a valid path" in str(e): + logger.info(f"Model '{model_name}' not found. Downloading...") + spacy_download(model_name) + return spacy.load(model_name) + else: + raise e diff --git a/tests/unit/experimental/components/test_resolver.py b/tests/unit/experimental/components/test_resolver.py index 558b23f5d..fded67d0e 100644 --- a/tests/unit/experimental/components/test_resolver.py +++ b/tests/unit/experimental/components/test_resolver.py @@ -18,6 +18,7 @@ import pytest from neo4j_graphrag.experimental.components.resolver import ( SinglePropertyExactMatchResolver, + SpaCySemanticMatchResolver, ) from neo4j_graphrag.experimental.components.types import ResolutionStats @@ -57,3 +58,105 @@ async def test_simple_resolver_custom_filter(driver: MagicMock) -> None: ) ] ) + + +@pytest.mark.asyncio +async def test_spacy_resolver_match_on_name_property(driver: MagicMock) -> None: + driver.execute_query.side_effect = [ + ( + [ + neo4j.Record( + { + "lab": "Person", + "labelCluster": [ + {"id": 1, "name": "Alice"}, + {"id": 2, "name": "Alice"}, + ], + } + ) + ], + None, + None, + ), + ( + [neo4j.Record({"id(node)": 1})], + None, + None, + ), + ] + + resolver = SpaCySemanticMatchResolver(driver=driver) + + res = await resolver.run() + assert isinstance(res, ResolutionStats) + assert res.number_of_nodes_to_resolve == 2 + assert res.number_of_created_nodes == 1 + + assert driver.execute_query.call_count == 2 + + +@pytest.mark.asyncio +async def test_spacy_resolver_no_merge(driver: MagicMock) -> None: + driver.execute_query.side_effect = [ + ( + [ + neo4j.Record( + { + "lab": "Person", + "labelCluster": [ + {"id": 1, "name": "Alice"}, + {"id": 2, "name": "Bob"}, + ], + } + ) + ], + None, + None, + ), + ] + + resolver = SpaCySemanticMatchResolver(driver=driver) + + res = await resolver.run() + assert res.number_of_nodes_to_resolve == 2 + assert res.number_of_created_nodes == 0 + + assert driver.execute_query.call_count == 1 + + +@pytest.mark.asyncio +async def test_spacy_resolver_match_on_multiple_text_properties( + driver: MagicMock, +) -> None: + driver.execute_query.side_effect = [ + ( + [ + neo4j.Record( + { + "lab": "Person", + "labelCluster": [ + {"id": 10, "name": "John Smith", "ssn": "23-45-6789"}, + {"id": 11, "name": "Jonathan Smith", "ssn": "23-45-6789"}, + ], + } + ) + ], + None, + None, + ), + ( + [neo4j.Record({"id(node)": 10})], + None, + None, + ), + ] + + resolver = SpaCySemanticMatchResolver( + driver=driver, resolve_properties=["name", "ssn"] + ) + res = await resolver.run() + assert isinstance(res, ResolutionStats) + assert res.number_of_nodes_to_resolve == 2 + assert res.number_of_created_nodes == 1 + + assert driver.execute_query.call_count == 2