Remove unused node embedding functionality from graph storage

- Deleted embed_nodes() method implementations

lightrag/kg/age_impl.py

@@ -6,7 +6,6 @@ import sys
 from contextlib import asynccontextmanager
 from dataclasses import dataclass
 from typing import Any, Dict, List, NamedTuple, Optional, Union, final
-import numpy as np
 import pipmaster as pm
 from lightrag.types import KnowledgeGraph, KnowledgeGraphNode, KnowledgeGraphEdge
 
@@ -668,21 +667,6 @@ class AGEStorage(BaseGraphStorage):
                 logger.error(f"Error during edge deletion: {str(e)}")
                 raise
 
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        """Embed nodes using the specified algorithm
-
-        Args:
-            algorithm: Name of the embedding algorithm
-
-        Returns:
-            tuple: (embedding matrix, list of node identifiers)
-        """
-        if algorithm not in self._node_embed_algorithms:
-            raise ValueError(f"Node embedding algorithm {algorithm} not supported")
-        return await self._node_embed_algorithms[algorithm]()
-
     async def get_all_labels(self) -> list[str]:
         """Get all node labels in the database
 

lightrag/kg/gremlin_impl.py

@@ -6,9 +6,6 @@ import pipmaster as pm
 from dataclasses import dataclass
 from typing import Any, Dict, List, final
 
-import numpy as np
-
-
 from tenacity import (
     retry,
     retry_if_exception_type,
@@ -419,27 +416,6 @@ class GremlinStorage(BaseGraphStorage):
             logger.error(f"Error during node deletion: {str(e)}")
             raise
 
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        """
-        Embed nodes using the specified algorithm.
-        Currently, only node2vec is supported but never called.
-
-        Args:
-            algorithm: The name of the embedding algorithm to use
-
-        Returns:
-            A tuple of (embeddings, node_ids)
-
-        Raises:
-            NotImplementedError: If the specified algorithm is not supported
-            ValueError: If the algorithm is not supported
-        """
-        if algorithm not in self._node_embed_algorithms:
-            raise ValueError(f"Node embedding algorithm {algorithm} not supported")
-        return await self._node_embed_algorithms[algorithm]()
-
     async def get_all_labels(self) -> list[str]:
         """
         Get all node entity_names in the graph

lightrag/kg/mongo_impl.py

@@ -663,20 +663,6 @@ class MongoGraphStorage(BaseGraphStorage):
         # Remove the node doc
         await self.collection.delete_one({"_id": node_id})
 
-    #
-    # -------------------------------------------------------------------------
-    # EMBEDDINGS (NOT IMPLEMENTED)
-    # -------------------------------------------------------------------------
-    #
-
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        """
-        Placeholder for demonstration, raises NotImplementedError.
-        """
-        raise NotImplementedError("Node embedding is not used in lightrag.")
-
     #
     # -------------------------------------------------------------------------
     # QUERY

lightrag/kg/neo4j_impl.py

@@ -2,8 +2,7 @@ import inspect
 import os
 import re
 from dataclasses import dataclass
-from typing import Any, final
-import numpy as np
+from typing import final
 import configparser
 
 
@@ -1126,11 +1125,6 @@ class Neo4JStorage(BaseGraphStorage):
                 logger.error(f"Error during edge deletion: {str(e)}")
                 raise
 
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        raise NotImplementedError
-
     async def drop(self) -> dict[str, str]:
         """Drop all data from storage and clean up resources
 

lightrag/kg/networkx_impl.py

@@ -1,7 +1,6 @@
 import os
 from dataclasses import dataclass
-from typing import Any, final
-import numpy as np
+from typing import final
 
 from lightrag.types import KnowledgeGraph, KnowledgeGraphNode, KnowledgeGraphEdge
 from lightrag.utils import logger
@@ -16,7 +15,6 @@ if not pm.is_installed("graspologic"):
     pm.install("graspologic")
 
 import networkx as nx
-from graspologic import embed
 from .shared_storage import (
     get_storage_lock,
     get_update_flag,
@@ -42,40 +40,6 @@ class NetworkXStorage(BaseGraphStorage):
         )
         nx.write_graphml(graph, file_name)
 
-    # TODO：deprecated, remove later
-    @staticmethod
-    def _stabilize_graph(graph: nx.Graph) -> nx.Graph:
-        """Refer to https://github.com/microsoft/graphrag/index/graph/utils/stable_lcc.py
-        Ensure an undirected graph with the same relationships will always be read the same way.
-        """
-        fixed_graph = nx.DiGraph() if graph.is_directed() else nx.Graph()
-
-        sorted_nodes = graph.nodes(data=True)
-        sorted_nodes = sorted(sorted_nodes, key=lambda x: x[0])
-
-        fixed_graph.add_nodes_from(sorted_nodes)
-        edges = list(graph.edges(data=True))
-
-        if not graph.is_directed():
-
-            def _sort_source_target(edge):
-                source, target, edge_data = edge
-                if source > target:
-                    temp = source
-                    source = target
-                    target = temp
-                return source, target, edge_data
-
-            edges = [_sort_source_target(edge) for edge in edges]
-
-        def _get_edge_key(source: Any, target: Any) -> str:
-            return f"{source} -> {target}"
-
-        edges = sorted(edges, key=lambda x: _get_edge_key(x[0], x[1]))
-
-        fixed_graph.add_edges_from(edges)
-        return fixed_graph
-
     def __post_init__(self):
         self._graphml_xml_file = os.path.join(
             self.global_config["working_dir"], f"graph_{self.namespace}.graphml"
@@ -191,24 +155,6 @@ class NetworkXStorage(BaseGraphStorage):
         else:
             logger.warning(f"Node {node_id} not found in the graph for deletion.")
 
-    # TODO: NOT USED
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        if algorithm not in self._node_embed_algorithms:
-            raise ValueError(f"Node embedding algorithm {algorithm} not supported")
-        return await self._node_embed_algorithms[algorithm]()
-
-    # TODO: NOT USED
-    async def _node2vec_embed(self):
-        graph = await self._get_graph()
-        embeddings, nodes = embed.node2vec_embed(
-            graph,
-            **self.global_config["node2vec_params"],
-        )
-        nodes_ids = [graph.nodes[node_id]["id"] for node_id in nodes]
-        return embeddings, nodes_ids
-
     async def remove_nodes(self, nodes: list[str]):
         """Delete multiple nodes
 

lightrag/kg/postgres_impl.py

@@ -1485,24 +1485,6 @@ class PGGraphStorage(BaseGraphStorage):
         labels = [result["label"] for result in results]
         return labels
 
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        """
-        Generate node embeddings using the specified algorithm.
-
-        Args:
-            algorithm (str): The name of the embedding algorithm to use.
-
-        Returns:
-            tuple[np.ndarray[Any, Any], list[str]]: A tuple containing the embeddings and the corresponding node IDs.
-        """
-        if algorithm not in self._node_embed_algorithms:
-            raise ValueError(f"Unsupported embedding algorithm: {algorithm}")
-
-        embed_func = self._node_embed_algorithms[algorithm]
-        return await embed_func()
-
     async def get_knowledge_graph(
         self,
         node_label: str,

lightrag/kg/tidb_impl.py

@@ -800,13 +800,6 @@ class TiDBGraphStorage(BaseGraphStorage):
         }
         await self.db.execute(merge_sql, data)
 
-    async def embed_nodes(
-        self, algorithm: str
-    ) -> tuple[np.ndarray[Any, Any], list[str]]:
-        if algorithm not in self._node_embed_algorithms:
-            raise ValueError(f"Node embedding algorithm {algorithm} not supported")
-        return await self._node_embed_algorithms[algorithm]()
-
     # Query
 
     async def has_node(self, node_id: str) -> bool: