Neo4j Query Tuning Skill

When to Use

• Query takes unexpectedly long; need root-cause analysis
• EXPLAIN/PROFILE output in hand — needs interpretation
• Identifying which index is missing or unused
• Deciding between slotted / pipelined / parallel runtimes
• Monitoring live queries: SHOW QUERIES, SHOW TRANSACTIONS
• Cardinality estimates wrong (plan replanning needed)

When NOT to Use

• Writing Cypher from scratch → neo4j-cypher-skill
• GDS algorithm performance → neo4j-gds-skill
• Schema design / data modelling → neo4j-modeling-skill

EXPLAIN vs PROFILE

| | EXPLAIN | PROFILE |

|---|---|---|

| Executes query? | No | Yes |

| Returns data? | No | Yes |

| Shows rows (actual) | No | Yes |

| Shows dbHits (actual) | No | Yes |

| Shows estimatedRows | Yes | Yes |

| Cost | Zero | Full query cost |

Run PROFILE twice — first run warms page cache; second gives representative metrics.

EXPLAIN MATCH (p:Person {email: $email}) RETURN p.name
PROFILE MATCH (p:Person {email: $email}) RETURN p.name

Query API alternative (no driver):

curl -X POST https://<host>/db/<db>/query/v2 \
  -u <user>:<pass> -H "Content-Type: application/json" \
  -d '{"statement": "EXPLAIN MATCH (p:Person {email: $email}) RETURN p.name", "parameters": {"email": "[email protected]"}}'

Key Plan Metrics

| Metric | Good | Investigate if |

|---|---|---|

| dbHits | Low; drops after index added | High relative to rows |

| rows | Shrinks early in plan | Large until final operator |

| estimatedRows | Close to rows | >10× divergence from actual |

| pageCacheHitRatio | >0.99 | <0.90 (disk I/O bottleneck) |

| pageCacheHits | High | — |

| pageCacheMisses | Near 0 | Rising (page cache too small) |

Read plans bottom-up — leaf operators at bottom initiate data retrieval.

Operator Reference

| Operator | Good/Bad | Meaning | Fix |

|---|---|---|---|

| NodeIndexSeek | ✓ | Exact match via RANGE/LOOKUP index | — |

| NodeUniqueIndexSeek | ✓ | Unique constraint index hit | — |

| NodeIndexContainsScan | ✓ | TEXT index CONTAINS / STARTS WITH | — |

| NodeIndexScan | ~ | Full index scan (no predicate) | Add WHERE predicate or composite index |

| NodeByLabelScan | ✗ | Scans all nodes of label | Add RANGE index on lookup property |

| AllNodesScan | ✗✗ | Scans entire node store | Add label + index to MATCH |

| Expand(All) | ~ | Traverse relationships from node | Normal; limit with LIMIT or WHERE |

| Expand(Into) | ~ | Find rels between two matched nodes | Normal for known-endpoint joins |

| Filter | ~ | Predicate applied after scan | Move predicate into WHERE with index |

| CartesianProduct | ✗ | No join predicate between two MATCH | Add WHERE join or use WITH between MATCHes |

| NodeHashJoin | ~ | Hash join on node IDs | Normal; planner chose hash join |

| ValueHashJoin | ~ | Hash join on values | Normal; watch memory for large inputs |

| EagerAggregation | ~ | Full aggregation (ORDER BY, count(*)) | Normal for aggregates |

| Aggregation | ✓ | Streaming aggregation | — |

| Eager | ✗ | Read/write conflict; materialises all rows | See Eager fix strategies below |

| Sort | ~ | Full sort — O(n log n) | Add LIMIT before Sort; push LIMIT earlier |

| Top | ✓ | Sort+Limit combined — O(n log k) | Preferred over Sort+Limit |

| Limit | ✓ | Truncates rows early | Push as early as possible |

| Skip | ~ | Offset pagination | Use keyset pagination on large graphs |

| ProduceResults | — | Final output operator | Root of tree |

| UndirectedRelationshipByIdSeekPipe | ~ | Lookup by relationship ID | Avoid id(r) — use elementId(r) |

Full operator reference → references/plan-operators.md

Diagnostic Workflow (Agent Runbook)

Step 1 — Baseline Plan

EXPLAIN <query>

Scan output for AllNodesScan, NodeByLabelScan, CartesianProduct, Eager.

Step 2 — Check Indexes

SHOW INDEXES YIELD name, type, labelsOrTypes, properties, state
WHERE state = 'ONLINE'

Find whether the label/property from the bad operator has an index.

Step 3 — Create Missing Index

// RANGE index for equality/range predicates:
CREATE INDEX person_email IF NOT EXISTS FOR (n:Person) ON (n.email)
// TEXT index for CONTAINS/ENDS WITH:
CREATE TEXT INDEX person_bio IF NOT EXISTS FOR (n:Person) ON (n.bio)
// Composite for multi-property lookup:
CREATE INDEX order_status_date IF NOT EXISTS FOR (n:Order) ON (n.status, n.createdAt)

Wait for state = 'ONLINE' before measuring.

Step 4 — Profile After Fix

PROFILE <query>

Compare dbHits and elapsed ms before/after. Target: NodeIndexSeek replaces scan operators.

Step 5 — Stale Statistics (if estimatedRows wildly off)

CALL db.prepareForReplanning()
// or resample a specific index:
CALL db.resampleIndex("person_email")
// or resample all outdated:
CALL db.resampleOutdatedIndexes()

Config: dbms.cypher.statistics_divergence_threshold (default 0.75 — plan expires when stat changes >75%).

Fixing Common Plan Problems

Missing Index → NodeByLabelScan / AllNodesScan

// Force index hint when planner ignores it:
MATCH (p:Person {email: $email})
USING INDEX p:Person(email)
RETURN p.name
// Force label scan (sometimes faster for high selectivity):
MATCH (p:Person {email: $email})
USING SCAN p:Person
RETURN p.name

Wrong Anchor — Planner Picks Wrong Starting Node

Reorder MATCH or use hints:

// Force join at specific node:
MATCH (a:Author)-[:WROTE]->(b:Book)-[:IN_CATEGORY]->(c:Category {name: $cat})
USING JOIN ON b
RETURN a.name, b.title

CartesianProduct — Two Unconnected MATCHes

// Bad (Cartesian product):
MATCH (a:Author {id: $aid})
MATCH (b:Book  {id: $bid})
RETURN a.name, b.title

// Good (explicit join or WITH):
MATCH (a:Author {id: $aid})-[:WROTE]->(b:Book {id: $bid})
RETURN a.name, b.title
// Or: WITH between them to reset planning context

Eager — Read/Write Conflict

Three strategies (pick simplest):

• Add specific labels to MATCH nodes so planner distinguishes read/write sets
• Collect-then-write: WITH collect(n) AS nodes UNWIND nodes AS n SET n.x = 1
• CALL IN TRANSACTIONS: isolates each batch in its own transaction

CYPHER 25
MATCH (p:Person) WHERE p.score > 100
CALL (p) { SET p.tier = 'gold' } IN TRANSACTIONS OF 1000 ROWS

Expensive CONTAINS / ENDS WITH

// Needs TEXT index (RANGE does NOT support these):
CREATE TEXT INDEX person_bio IF NOT EXISTS FOR (n:Person) ON (n.bio)
MATCH (p:Person) WHERE p.bio CONTAINS $keyword RETURN p.name

Over-Traversal — Push LIMIT Early

// Bad: LIMIT after expensive join
MATCH (a:Author)-[:WROTE]->(b:Book)-[:REVIEWED_BY]->(r:Review)
RETURN a.name, b.title, r.text LIMIT 10

// Good: anchor limit before fan-out
MATCH (a:Author)-[:WROTE]->(b:Book)
WITH a, b LIMIT 10
MATCH (b)-[:REVIEWED_BY]->(r:Review)
RETURN a.name, b.title, r.text

Cypher Runtime Selection

| Runtime | Select | Best For | Avoid When |

|---|---|---|---|

| pipelined | CYPHER runtime=pipelined | Default OLTP; streaming, low memory | Unsupported operators fall back to slotted |

| slotted | CYPHER runtime=slotted | Guaranteed stable behavior; debug | Performance-critical OLTP |

| parallel | CYPHER 25 runtime=parallel | Large analytical scans; aggregations | OLTP, writes, short queries, Aura Free |

Pipelined is default for most queries. Parallel requires dbms.cypher.parallel.worker_limit configured; available on Enterprise and Aura Pro 2025+.

// Force parallel for large aggregation:
CYPHER 25 runtime=parallel
MATCH (n:Transaction) WHERE n.amount > 1000
RETURN n.currency, count(*), sum(n.amount)

Query Monitoring Commands

// Live queries + resource usage:
SHOW QUERIES YIELD query, queryId, elapsedTimeMillis, allocatedBytes, status, username

// Running transactions:
SHOW TRANSACTIONS YIELD transactionId, currentQuery, currentQueryProgress, elapsedTime, status, username, cpuTime, activeLockCount  // currentQueryProgress added [2026.03]

// Kill a specific transaction:
TERMINATE TRANSACTION $transactionId

// Kill a query:
TERMINATE QUERY $queryId

// Graph count stats (node/rel counts by label/type — feed into planner):
CALL db.stats.retrieve('GRAPH COUNTS') YIELD section, data RETURN section, data

// Token stats (label/property/rel-type IDs):
CALL db.stats.retrieve('TOKENS') YIELD section, data RETURN section, data

Full monitoring reference → references/stats-and-monitoring.md

Checklist

• [ ] Run EXPLAIN first — identifies plan problems without execution cost
• [ ] Check for AllNodesScan / NodeByLabelScan — missing index
• [ ] Check for CartesianProduct — missing join predicate
• [ ] Check for Eager — read/write conflict
• [ ] SHOW INDEXES — confirm relevant index exists and state = 'ONLINE'
• [ ] Create missing index; wait for ONLINE
• [ ] Run PROFILE twice — first warms cache, second is representative
• [ ] Compare dbHits before/after fix
• [ ] If estimatedRows wildly off → CALL db.prepareForReplanning()
• [ ] Push LIMIT / WITH n LIMIT k before high-fanout operations
• [ ] For CONTAINS/ENDS WITH — TEXT index, not RANGE
• [ ] For large analytical queries — consider runtime=parallel
• [ ] Kill long-running queries with TERMINATE TRANSACTION