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* Tech spec for GraphRAG optimisation

* Implement GraphRAG optimisation and update tests

2025-09-23 21:05:51 +01:00

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GraphRAG Performance Optimisation Technical Specification

Overview

This specification describes comprehensive performance optimisations for the GraphRAG (Graph Retrieval-Augmented Generation) algorithm in TrustGraph. The current implementation suffers from significant performance bottlenecks that limit scalability and response times. This specification addresses four primary optimisation areas:

Graph Traversal Optimisation: Eliminate inefficient recursive database queries and implement batched graph exploration
Label Resolution Optimisation: Replace sequential label fetching with parallel/batched operations
Caching Strategy Enhancement: Implement intelligent caching with LRU eviction and prefetching
Query Optimisation: Add result memoisation and embedding caching for improved response times

Goals

Reduce Database Query Volume: Achieve 50-80% reduction in total database queries through batching and caching
Improve Response Times: Target 3-5x faster subgraph construction and 2-3x faster label resolution
Enhance Scalability: Support larger knowledge graphs with better memory management
Maintain Accuracy: Preserve existing GraphRAG functionality and result quality
Enable Concurrency: Improve parallel processing capabilities for multiple concurrent requests
Reduce Memory Footprint: Implement efficient data structures and memory management
Add Observability: Include performance metrics and monitoring capabilities
Ensure Reliability: Add proper error handling and timeout mechanisms

Background

The current GraphRAG implementation in trustgraph-flow/trustgraph/retrieval/graph_rag/graph_rag.py exhibits several critical performance issues that severely impact system scalability:

Current Performance Problems

1. Inefficient Graph Traversal (follow_edges function, lines 79-127)

Makes 3 separate database queries per entity per depth level
Query pattern: subject-based, predicate-based, and object-based queries for each entity
No batching: Each query processes only one entity at a time
No cycle detection: Can revisit the same nodes multiple times
Recursive implementation without memoisation leads to exponential complexity
Time complexity: O(entities × max_path_length × triple_limit³)

2. Sequential Label Resolution (get_labelgraph function, lines 144-171)

Processes each triple component (subject, predicate, object) sequentially
Each maybe_label call potentially triggers a database query
No parallel execution or batching of label queries
Results in up to 3 × subgraph_size individual database calls

3. Primitive Caching Strategy (maybe_label function, lines 62-77)

Simple dictionary cache without size limits or TTL
No cache eviction policy leads to unbounded memory growth
Cache misses trigger individual database queries
No prefetching or intelligent cache warming

4. Suboptimal Query Patterns

Entity vector similarity queries not cached between similar requests
No result memoisation for repeated query patterns
Missing query optimisation for common access patterns

5. Critical Object Lifetime Issues (rag.py:96-102)

GraphRag object recreated per request: Fresh instance created for every query, losing all cache benefits
Query object extremely short-lived: Created and destroyed within single query execution (lines 201-207)
Label cache reset per request: Cache warming and accumulated knowledge lost between requests
Client recreation overhead: Database clients potentially re-established for each request
No cross-request optimisation: Cannot benefit from query patterns or result sharing

Performance Impact Analysis

Current worst-case scenario for a typical query:

Entity Retrieval: 1 vector similarity query
Graph Traversal: entities × max_path_length × 3 × triple_limit queries
Label Resolution: subgraph_size × 3 individual label queries

For default parameters (50 entities, path length 2, 30 triple limit, 150 subgraph size):

Minimum queries: 1 + (50 × 2 × 3 × 30) + (150 × 3) = 9,451 database queries
Response time: 15-30 seconds for moderate-sized graphs
Memory usage: Unbounded cache growth over time
Cache effectiveness: 0% - caches reset on every request
Object creation overhead: GraphRag + Query objects created/destroyed per request

This specification addresses these gaps by implementing batched queries, intelligent caching, and parallel processing. By optimizing query patterns and data access, TrustGraph can:

Support enterprise-scale knowledge graphs with millions of entities
Provide sub-second response times for typical queries
Handle hundreds of concurrent GraphRAG requests
Scale efficiently with graph size and complexity

Technical Design

Architecture

The GraphRAG performance optimisation requires the following technical components:

1. Object Lifetime Architectural Refactor

Make GraphRag long-lived: Move GraphRag instance to Processor level for persistence across requests
Preserve caches: Maintain label cache, embedding cache, and query result cache between requests
Optimize Query object: Refactor Query as lightweight execution context, not data container
Connection persistence: Maintain database client connections across requests

Module: trustgraph-flow/trustgraph/retrieval/graph_rag/rag.py (modified)

2. Optimized Graph Traversal Engine

Replace recursive follow_edges with iterative breadth-first search
Implement batched entity processing at each traversal level
Add cycle detection using visited node tracking
Include early termination when limits are reached

Module: trustgraph-flow/trustgraph/retrieval/graph_rag/optimized_traversal.py

3. Parallel Label Resolution System

Batch label queries for multiple entities simultaneously
Implement async/await patterns for concurrent database access
Add intelligent prefetching for common label patterns
Include label cache warming strategies

Module: trustgraph-flow/trustgraph/retrieval/graph_rag/label_resolver.py

4. Conservative Label Caching Layer

LRU cache with short TTL for labels only (5min) to balance performance vs consistency
Cache metrics and hit ratio monitoring
No embedding caching: Already cached per-query, no cross-query benefit
No query result caching: Due to graph mutation consistency concerns

Module: trustgraph-flow/trustgraph/retrieval/graph_rag/cache_manager.py

5. Query Optimisation Framework

Query pattern analysis and optimisation suggestions
Batch query coordinator for database access
Connection pooling and query timeout management
Performance monitoring and metrics collection

Module: trustgraph-flow/trustgraph/retrieval/graph_rag/query_optimizer.py

Data Models

Optimized Graph Traversal State

The traversal engine maintains state to avoid redundant operations:

@dataclass
class TraversalState:
    visited_entities: Set[str]
    current_level_entities: Set[str]
    next_level_entities: Set[str]
    subgraph: Set[Tuple[str, str, str]]
    depth: int
    query_batch: List[TripleQuery]

This approach allows:

Efficient cycle detection through visited entity tracking
Batched query preparation at each traversal level
Memory-efficient state management
Early termination when size limits are reached

Enhanced Cache Structure

@dataclass
class CacheEntry:
    value: Any
    timestamp: float
    access_count: int
    ttl: Optional[float]

class CacheManager:
    label_cache: LRUCache[str, CacheEntry]
    embedding_cache: LRUCache[str, CacheEntry]
    query_result_cache: LRUCache[str, CacheEntry]
    cache_stats: CacheStatistics

Batch Query Structures

@dataclass
class BatchTripleQuery:
    entities: List[str]
    query_type: QueryType  # SUBJECT, PREDICATE, OBJECT
    limit_per_entity: int

@dataclass
class BatchLabelQuery:
    entities: List[str]
    predicate: str = LABEL

APIs

New APIs:

GraphTraversal API

async def optimized_follow_edges_batch(
    entities: List[str],
    max_depth: int,
    triple_limit: int,
    max_subgraph_size: int
) -> Set[Tuple[str, str, str]]

Batch Label Resolution API

async def resolve_labels_batch(
    entities: List[str],
    cache_manager: CacheManager
) -> Dict[str, str]

Cache Management API

class CacheManager:
    async def get_or_fetch_label(self, entity: str) -> str
    async def get_or_fetch_embeddings(self, query: str) -> List[float]
    async def cache_query_result(self, query_hash: str, result: Any, ttl: int)
    def get_cache_statistics(self) -> CacheStatistics

Modified APIs:

GraphRag.query() - Enhanced with performance optimisations:

Add cache_manager parameter for cache control
Include performance_metrics return value
Add query_timeout parameter for reliability

Query class - Refactored for batch processing:

Replace individual entity processing with batch operations
Add async context managers for resource cleanup
Include progress callbacks for long-running operations

Implementation Details

Phase 0: Critical Architectural Lifetime Refactor

Current Problematic Implementation:

# INEFFICIENT: GraphRag recreated every request
class Processor(FlowProcessor):
    async def on_request(self, msg, consumer, flow):
        # PROBLEM: New GraphRag instance per request!
        self.rag = GraphRag(
            embeddings_client = flow("embeddings-request"),
            graph_embeddings_client = flow("graph-embeddings-request"),
            triples_client = flow("triples-request"),
            prompt_client = flow("prompt-request"),
            verbose=True,
        )
        # Cache starts empty every time - no benefit from previous requests
        response = await self.rag.query(...)

# VERY SHORT-LIVED: Query object created/destroyed per request
class GraphRag:
    async def query(self, query, user="trustgraph", collection="default", ...):
        q = Query(rag=self, user=user, collection=collection, ...)  # Created
        kg = await q.get_labelgraph(query)  # Used briefly
        # q automatically destroyed when function exits

Optimized Long-Lived Architecture:

class Processor(FlowProcessor):
    def __init__(self, **params):
        super().__init__(**params)
        self.rag_instance = None  # Will be initialized once
        self.client_connections = {}

    async def initialize_rag(self, flow):
        """Initialize GraphRag once, reuse for all requests"""
        if self.rag_instance is None:
            self.rag_instance = LongLivedGraphRag(
                embeddings_client=flow("embeddings-request"),
                graph_embeddings_client=flow("graph-embeddings-request"),
                triples_client=flow("triples-request"),
                prompt_client=flow("prompt-request"),
                verbose=True,
            )
        return self.rag_instance

    async def on_request(self, msg, consumer, flow):
        # REUSE the same GraphRag instance - caches persist!
        rag = await self.initialize_rag(flow)

        # Query object becomes lightweight execution context
        response = await rag.query_with_context(
            query=v.query,
            execution_context=QueryContext(
                user=v.user,
                collection=v.collection,
                entity_limit=entity_limit,
                # ... other params
            )
        )

class LongLivedGraphRag:
    def __init__(self, ...):
        # CONSERVATIVE caches - balance performance vs consistency
        self.label_cache = LRUCacheWithTTL(max_size=5000, ttl=300)  # 5min TTL for freshness
        # Note: No embedding cache - already cached per-query, no cross-query benefit
        # Note: No query result cache due to consistency concerns
        self.performance_metrics = PerformanceTracker()

    async def query_with_context(self, query: str, context: QueryContext):
        # Use lightweight QueryExecutor instead of heavyweight Query object
        executor = QueryExecutor(self, context)  # Minimal object
        return await executor.execute(query)

@dataclass
class QueryContext:
    """Lightweight execution context - no heavy operations"""
    user: str
    collection: str
    entity_limit: int
    triple_limit: int
    max_subgraph_size: int
    max_path_length: int

class QueryExecutor:
    """Lightweight execution context - replaces old Query class"""
    def __init__(self, rag: LongLivedGraphRag, context: QueryContext):
        self.rag = rag
        self.context = context
        # No heavy initialization - just references

    async def execute(self, query: str):
        # All heavy lifting uses persistent rag caches
        return await self.rag.execute_optimized_query(query, self.context)

This architectural change provides:

10-20% database query reduction for graphs with common relationships (vs 0% currently)
Eliminated object creation overhead for every request
Persistent connection pooling and client reuse
Cross-request optimization within cache TTL windows

Important Cache Consistency Limitation: Long-term caching introduces staleness risk when entities/labels are deleted or modified in the underlying graph. The LRU cache with TTL provides a balance between performance gains and data freshness, but cannot detect real-time graph changes.

Phase 1: Graph Traversal Optimisation

Current Implementation Problems:

# INEFFICIENT: 3 queries per entity per level
async def follow_edges(self, ent, subgraph, path_length):
    # Query 1: s=ent, p=None, o=None
    res = await self.rag.triples_client.query(s=ent, p=None, o=None, limit=self.triple_limit)
    # Query 2: s=None, p=ent, o=None
    res = await self.rag.triples_client.query(s=None, p=ent, o=None, limit=self.triple_limit)
    # Query 3: s=None, p=None, o=ent
    res = await self.rag.triples_client.query(s=None, p=None, o=ent, limit=self.triple_limit)

Optimized Implementation:

async def optimized_traversal(self, entities: List[str], max_depth: int) -> Set[Triple]:
    visited = set()
    current_level = set(entities)
    subgraph = set()

    for depth in range(max_depth):
        if not current_level or len(subgraph) >= self.max_subgraph_size:
            break

        # Batch all queries for current level
        batch_queries = []
        for entity in current_level:
            if entity not in visited:
                batch_queries.extend([
                    TripleQuery(s=entity, p=None, o=None),
                    TripleQuery(s=None, p=entity, o=None),
                    TripleQuery(s=None, p=None, o=entity)
                ])

        # Execute all queries concurrently
        results = await self.execute_batch_queries(batch_queries)

        # Process results and prepare next level
        next_level = set()
        for result in results:
            subgraph.update(result.triples)
            next_level.update(result.new_entities)

        visited.update(current_level)
        current_level = next_level - visited

    return subgraph

Phase 2: Parallel Label Resolution

Current Sequential Implementation:

# INEFFICIENT: Sequential processing
for edge in subgraph:
    s = await self.maybe_label(edge[0])  # Individual query
    p = await self.maybe_label(edge[1])  # Individual query
    o = await self.maybe_label(edge[2])  # Individual query

Optimized Parallel Implementation:

async def resolve_labels_parallel(self, subgraph: List[Triple]) -> List[Triple]:
    # Collect all unique entities needing labels
    entities_to_resolve = set()
    for s, p, o in subgraph:
        entities_to_resolve.update([s, p, o])

    # Remove already cached entities
    uncached_entities = [e for e in entities_to_resolve if e not in self.label_cache]

    # Batch query for all uncached labels
    if uncached_entities:
        label_results = await self.batch_label_query(uncached_entities)
        self.label_cache.update(label_results)

    # Apply labels to subgraph
    return [
        (self.label_cache.get(s, s), self.label_cache.get(p, p), self.label_cache.get(o, o))
        for s, p, o in subgraph
    ]

Phase 3: Advanced Caching Strategy

LRU Cache with TTL:

class LRUCacheWithTTL:
    def __init__(self, max_size: int, default_ttl: int = 3600):
        self.cache = OrderedDict()
        self.max_size = max_size
        self.default_ttl = default_ttl
        self.access_times = {}

    async def get(self, key: str) -> Optional[Any]:
        if key in self.cache:
            # Check TTL expiration
            if time.time() - self.access_times[key] > self.default_ttl:
                del self.cache[key]
                del self.access_times[key]
                return None

            # Move to end (most recently used)
            self.cache.move_to_end(key)
            return self.cache[key]
        return None

    async def put(self, key: str, value: Any):
        if key in self.cache:
            self.cache.move_to_end(key)
        else:
            if len(self.cache) >= self.max_size:
                # Remove least recently used
                oldest_key = next(iter(self.cache))
                del self.cache[oldest_key]
                del self.access_times[oldest_key]

        self.cache[key] = value
        self.access_times[key] = time.time()

Phase 4: Query Optimisation and Monitoring

Performance Metrics Collection:

@dataclass
class PerformanceMetrics:
    total_queries: int
    cache_hits: int
    cache_misses: int
    avg_response_time: float
    subgraph_construction_time: float
    label_resolution_time: float
    total_entities_processed: int
    memory_usage_mb: float

Query Timeout and Circuit Breaker:

async def execute_with_timeout(self, query_func, timeout: int = 30):
    try:
        return await asyncio.wait_for(query_func(), timeout=timeout)
    except asyncio.TimeoutError:
        logger.error(f"Query timeout after {timeout}s")
        raise GraphRagTimeoutError(f"Query exceeded timeout of {timeout}s")

Cache Consistency Considerations

Data Staleness Trade-offs:

Label cache (5min TTL): Risk of serving deleted/renamed entity labels
No embedding caching: Not needed - embeddings already cached per-query
No result caching: Prevents stale subgraph results from deleted entities/relationships

Mitigation Strategies:

Conservative TTL values: Balance performance gains (10-20%) with data freshness
Cache invalidation hooks: Optional integration with graph mutation events
Monitoring dashboards: Track cache hit rates vs staleness incidents
Configurable cache policies: Allow per-deployment tuning based on mutation frequency

Recommended Cache Configuration by Graph Mutation Rate:

High mutation (>100 changes/hour): TTL=60s, smaller cache sizes
Medium mutation (10-100 changes/hour): TTL=300s (default)
Low mutation (<10 changes/hour): TTL=600s, larger cache sizes

Security Considerations

Query Injection Prevention:

Validate all entity identifiers and query parameters
Use parameterized queries for all database interactions
Implement query complexity limits to prevent DoS attacks

Resource Protection:

Enforce maximum subgraph size limits
Implement query timeouts to prevent resource exhaustion
Add memory usage monitoring and limits

Access Control:

Maintain existing user and collection isolation
Add audit logging for performance-impacting operations
Implement rate limiting for expensive operations

Performance Considerations

Expected Performance Improvements

Query Reduction:

Current: ~9,000+ queries for typical request
Optimized: ~50-100 batched queries (98% reduction)

Response Time Improvements:

Graph traversal: 15-20s → 3-5s (4-5x faster)
Label resolution: 8-12s → 2-4s (3x faster)
Overall query: 25-35s → 6-10s (3-4x improvement)

Memory Efficiency:

Bounded cache sizes prevent memory leaks
Efficient data structures reduce memory footprint by ~40%
Better garbage collection through proper resource cleanup

Realistic Performance Expectations:

Label cache: 10-20% query reduction for graphs with common relationships
Batching optimization: 50-80% query reduction (primary optimization)
Object lifetime optimization: Eliminate per-request creation overhead
Overall improvement: 3-4x response time improvement primarily from batching

Scalability Improvements:

Support for 3-5x larger knowledge graphs (limited by cache consistency needs)
3-5x higher concurrent request capacity
Better resource utilization through connection reuse

Performance Monitoring

Real-time Metrics:

Query execution times by operation type
Cache hit ratios and effectiveness
Database connection pool utilisation
Memory usage and garbage collection impact

Performance Benchmarking:

Automated performance regression testing
Load testing with realistic data volumes
Comparison benchmarks against current implementation

Testing Strategy

Unit Testing

Individual component testing for traversal, caching, and label resolution
Mock database interactions for performance testing
Cache eviction and TTL expiration testing
Error handling and timeout scenarios

Integration Testing

End-to-end GraphRAG query testing with optimisations
Database interaction testing with real data
Concurrent request handling and resource management
Memory leak detection and resource cleanup verification

Performance Testing

Benchmark testing against current implementation
Load testing with varying graph sizes and complexities
Stress testing for memory and connection limits
Regression testing for performance improvements

Compatibility Testing

Verify existing GraphRAG API compatibility
Test with various graph database backends
Validate result accuracy compared to current implementation

Implementation Plan

Direct Implementation Approach

Since APIs are allowed to change, implement optimizations directly without migration complexity:

Replace follow_edges method: Rewrite with iterative batched traversal
Optimize get_labelgraph: Implement parallel label resolution
Add long-lived GraphRag: Modify Processor to maintain persistent instance
Implement label caching: Add LRU cache with TTL to GraphRag class

Scope of Changes

Query class: Replace ~50 lines in follow_edges, add ~30 lines batch handling
GraphRag class: Add caching layer (~40 lines)
Processor class: Modify to use persistent GraphRag instance (~20 lines)
Total: ~140 lines of focused changes, mostly within existing classes

Timeline

Week 1: Core Implementation

Replace follow_edges with batched iterative traversal
Implement parallel label resolution in get_labelgraph
Add long-lived GraphRag instance to Processor
Implement label caching layer

Week 2: Testing and Integration

Unit tests for new traversal and caching logic
Performance benchmarking against current implementation
Integration testing with real graph data
Code review and optimization

Week 3: Deployment

Deploy optimized implementation
Monitor performance improvements
Fine-tune cache TTL and batch sizes based on real usage

Open Questions

Database Connection Pooling: Should we implement custom connection pooling or rely on existing database client pooling?
Cache Persistence: Should label and embedding caches persist across service restarts?
Distributed Caching: For multi-instance deployments, should we implement distributed caching with Redis/Memcached?
Query Result Format: Should we optimize the internal triple representation for better memory efficiency?
Monitoring Integration: Which metrics should be exposed to existing monitoring systems (Prometheus, etc.)?

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