build_communities_v1
Analyzes paper-entity relationships to identify research topic communities using graph clustering algorithms, helping researchers discover thematic connections in academic literature.
Instructions
构建主题社区
从 Paper->Entity 关系构建共现图，使用 Leiden 算法聚类。
Args: level: 社区层级，"macro" 或 "micro" min_df: 节点至少出现在 N 篇 paper，默认 3 resolution: Leiden 分辨率参数，默认 1.0 max_nodes: 最大节点数，默认 20000 rebuild: 是否重建（清除同 level 旧结果），默认 False
Returns: 社区列表，每个包含 comm_id、大小和 top entities
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| level | No | macro | |
| min_df | No | ||
| resolution | No | ||
| max_nodes | No | ||
| rebuild | No |
Implementation Reference
- The @mcp.tool()-decorated function build_communities_v1 that implements the core logic: builds co-occurrence graph from paper-entity relations, filters nodes by document frequency, applies Leiden clustering with igraph/leidenalg, and stores communities/members in the database.
@mcp.tool() def build_communities_v1( level: str = "macro", min_df: int = 3, resolution: float = 1.0, max_nodes: int = 20000, rebuild: bool = False, ) -> dict[str, Any]: """构建主题社区 从 Paper->Entity 关系构建共现图，使用 Leiden 算法聚类。 Args: level: 社区层级，"macro" 或 "micro" min_df: 节点至少出现在 N 篇 paper，默认 3 resolution: Leiden 分辨率参数，默认 1.0 max_nodes: 最大节点数，默认 20000 rebuild: 是否重建（清除同 level 旧结果），默认 False Returns: 社区列表，每个包含 comm_id、大小和 top entities """ try: # 尝试导入社区发现库 try: import igraph as ig import leidenalg except ImportError: return BuildCommunitiesOut( error=MCPErrorModel( code="DEPENDENCY_ERROR", message="igraph and leidenalg are required. Install with: pip install igraph leidenalg" ), ).model_dump() with get_db() as conn: # 如果 rebuild，先清除旧结果 if rebuild: with conn.cursor() as cur: cur.execute( """ DELETE FROM community_members WHERE comm_id IN (SELECT comm_id FROM communities WHERE level = %s) """, (level,) ) cur.execute( """ DELETE FROM community_summaries WHERE comm_id IN (SELECT comm_id FROM communities WHERE level = %s) """, (level,) ) cur.execute( "DELETE FROM communities WHERE level = %s", (level,) ) # 1. 获取 Paper->Entity 关系 relations = query_all( """ SELECT p.entity_id AS paper_eid, p.canonical_key AS doc_id, x.entity_id AS node_eid, x.type AS node_type, x.canonical_name FROM relations r JOIN entities p ON p.entity_id = r.subj_entity_id AND p.type = 'Paper' JOIN entities x ON x.entity_id = r.obj_entity_id WHERE r.predicate IN ( 'PAPER_HAS_TOPIC', 'PAPER_USES_MEASURE', 'PAPER_IDENTIFIES_WITH', 'PAPER_IN_SETTING', 'PAPER_USES_DATA' ) AND x.type = ANY(%s) """, (COMMUNITY_ENTITY_TYPES,) ) if not relations: return BuildCommunitiesOut( communities=[], error=MCPErrorModel(code="NOT_FOUND", message="No Paper->Entity relations found"), ).model_dump() # 2. 计算节点 document frequency paper_to_nodes: dict[str, set[int]] = defaultdict(set) node_info: dict[int, dict] = {} for r in relations: paper_to_nodes[r["doc_id"]].add(r["node_eid"]) if r["node_eid"] not in node_info: node_info[r["node_eid"]] = { "entity_id": r["node_eid"], "type": r["node_type"], "canonical_name": r["canonical_name"], } # 计算 df node_df: dict[int, int] = defaultdict(int) for doc_id, nodes in paper_to_nodes.items(): for node_id in nodes: node_df[node_id] += 1 # 3. 过滤低频节点 valid_nodes = {nid for nid, df in node_df.items() if df >= min_df} if not valid_nodes: return BuildCommunitiesOut( communities=[], error=MCPErrorModel( code="NOT_FOUND", message=f"No nodes with df >= {min_df}" ), ).model_dump() # 限制节点数量 if len(valid_nodes) > max_nodes: # 保留 df 最高的节点 sorted_nodes = sorted(valid_nodes, key=lambda x: node_df[x], reverse=True) valid_nodes = set(sorted_nodes[:max_nodes]) # 4. 构建共现边 edge_counts: dict[tuple[int, int], float] = defaultdict(float) for doc_id, nodes in paper_to_nodes.items(): valid_doc_nodes = [n for n in nodes if n in valid_nodes] # 两两配对 for i, n1 in enumerate(valid_doc_nodes): for n2 in valid_doc_nodes[i+1:]: if n1 < n2: key = (n1, n2) else: key = (n2, n1) # 获取边权重 weight = get_edge_weight( node_info[n1]["type"], node_info[n2]["type"] ) edge_counts[key] += weight if not edge_counts: return BuildCommunitiesOut( communities=[], error=MCPErrorModel(code="NOT_FOUND", message="No edges found"), ).model_dump() # 5. 构建 igraph 图 # 创建节点映射 node_list = sorted(valid_nodes) node_to_idx = {nid: idx for idx, nid in enumerate(node_list)} edges = [] weights = [] for (n1, n2), w in edge_counts.items(): edges.append((node_to_idx[n1], node_to_idx[n2])) weights.append(w) g = ig.Graph(n=len(node_list), edges=edges, directed=False) g.es["weight"] = weights # 6. Leiden 聚类 partition = leidenalg.find_partition( g, leidenalg.RBConfigurationVertexPartition, weights="weight", resolution_parameter=resolution, ) # 7. 写入数据库 communities_result: list[CommunityBrief] = [] # 收集每个社区的成员 community_members_map: dict[int, list[tuple[int, float]]] = defaultdict(list) for node_idx, comm_idx in enumerate(partition.membership): node_id = node_list[node_idx] # 使用 df 作为权重 weight = float(node_df[node_id]) community_members_map[comm_idx].append((node_id, weight)) # 写入社区 with conn.cursor() as cur: for comm_idx, members in community_members_map.items(): if len(members) < 2: # 跳过太小的社区 continue # 创建社区 cur.execute( """ INSERT INTO communities(level, method, params) VALUES (%s, 'leiden', %s::jsonb) RETURNING comm_id """, (level, json.dumps({ "resolution": resolution, "min_df": min_df, "original_community_idx": comm_idx, })) ) result = cur.fetchone() comm_id = result["comm_id"] # 写入成员 for node_id, weight in members: cur.execute( """ INSERT INTO community_members(comm_id, entity_id, role, weight) VALUES (%s, %s, 'member', %s) """, (comm_id, node_id, weight) ) # 排序获取 top entities sorted_members = sorted(members, key=lambda x: x[1], reverse=True) top_entities = [] for node_id, weight in sorted_members[:20]: info = node_info.get(node_id, {}) top_entities.append({ "entity_id": node_id, "type": info.get("type", ""), "canonical_name": info.get("canonical_name", ""), "weight": weight, }) communities_result.append(CommunityBrief( comm_id=comm_id, size=len(members), top_entities=top_entities, )) # 按大小排序 communities_result.sort(key=lambda x: x.size, reverse=True) return BuildCommunitiesOut( communities=communities_result, ).model_dump() except Exception as e: return BuildCommunitiesOut( error=MCPErrorModel(code="DB_CONN_ERROR", message=str(e)), ).model_dump() - Pydantic models defining input schema (BuildCommunitiesIn with params like level, min_df, resolution), supporting CommunityBrief, and output schema BuildCommunitiesOut.
# build_communities_v1 工具模型 # ============================================================ class BuildCommunitiesIn(BaseModel): """build_communities_v1 输入""" level: Literal["macro", "micro"] = "macro" min_df: int = 3 # 节点至少出现在 N 篇 paper resolution: float = 1.0 # Leiden resolution max_nodes: int = 20000 rebuild: bool = False # 是否清除同 level 旧结果 class CommunityBrief(BaseModel): """社区简要信息""" comm_id: int size: int top_entities: list[dict[str, Any]] # [{entity_id, type, canonical_name, weight}, ...] class BuildCommunitiesOut(BaseModel): """build_communities_v1 输出""" communities: list[CommunityBrief] = Field(default_factory=list) error: Optional[MCPErrorModel] = None - src/paperlib_mcp/server.py:42-42 (registration)Top-level registration call register_graph_community_tools(mcp) in the MCP server entrypoint, which defines and registers the tool.
register_graph_community_tools(mcp) - Helper constants (COMMUNITY_ENTITY_TYPES, EDGE_WEIGHTS) and get_edge_weight function used for graph construction and weighting.
# v1 参与社区构建的实体类型 COMMUNITY_ENTITY_TYPES = [ EntityType.Topic.value, EntityType.MeasureProxy.value, EntityType.IdentificationStrategy.value, EntityType.Setting.value, EntityType.DataSource.value, ] # 边权重配置 EDGE_WEIGHTS = { (EntityType.Topic.value, EntityType.MeasureProxy.value): 2.0, (EntityType.Topic.value, EntityType.IdentificationStrategy.value): 2.0, (EntityType.MeasureProxy.value, EntityType.IdentificationStrategy.value): 1.5, (EntityType.Topic.value, EntityType.Setting.value): 1.0, (EntityType.IdentificationStrategy.value, EntityType.Setting.value): 1.0, } def get_edge_weight(type1: str, type2: str) -> float: """获取两种实体类型之间的边权重""" key = (type1, type2) if key in EDGE_WEIGHTS: return EDGE_WEIGHTS[key] key = (type2, type1) if key in EDGE_WEIGHTS: return EDGE_WEIGHTS[key] return 1.0 - src/paperlib_mcp/tools/graph_community.py:58-60 (registration)The register_graph_community_tools function definition that uses @mcp.tool() decorator to register build_communities_v1.
def register_graph_community_tools(mcp: FastMCP) -> None: """注册 GraphRAG 社区构建工具"""