How to Find Graph Patterns and Motifs with the Pattern Matching API

Goal: Use py3plex’s Pattern Matching Builder API to find graph motifs, paths, triangles, and complex subgraph patterns in multilayer networks.

🎯 What You’ll Learn

How to express graph patterns using the Q.pattern() builder API
How to match edges, paths, triangles, and custom motifs
How to apply multilayer-aware constraints (within/between layers)
How to filter patterns using node and edge predicates
How to extract and analyze pattern match results

💻 Complete Example

See the full executable example: example_pattern_matching.py

Prerequisites:

A loaded multi_layer_network object (see How to Load and Build Networks)
Basic familiarity with the DSL (see How to Query Multilayer Graphs with the SQL-like DSL)
Understanding of graph motifs (edges, paths, triangles, subgraphs)

Why Pattern Matching?

Pattern matching allows you to find specific subgraph structures in your network. Unlike node/edge queries that return individual elements, pattern matching returns complete matches where multiple nodes and edges satisfy structural constraints.

Common Use Cases:

Motif Detection: Find triangles, cliques, or other structural patterns
Path Analysis: Discover multi-hop connections between nodes
Multilayer Patterns: Identify cross-layer relationships
Complex Queries: Express “find nodes A, B, C where A connects to B with weight > 0.5, B connects to C, and all are in the social layer”

Comparison to Basic Queries:

Quick Start: Your First Pattern

Let’s start with a simple example: finding all edges in a network.

from py3plex.core import multinet
from py3plex.dsl import Q

# Create a simple network
network = multinet.multi_layer_network(directed=False)
network.add_nodes([
    {'source': 'Alice', 'type': 'social'},
    {'source': 'Bob', 'type': 'social'},
    {'source': 'Charlie', 'type': 'social'},
])
network.add_edges([
    {'source': 'Alice', 'target': 'Bob',
     'source_type': 'social', 'target_type': 'social', 'weight': 1.0},
    {'source': 'Bob', 'target': 'Charlie',
     'source_type': 'social', 'target_type': 'social', 'weight': 2.0},
])

# Find all edges (simple pattern)
pattern = (
    Q.pattern()
     .node("a")              # Define node variable "a"
     .node("b")              # Define node variable "b"
     .edge("a", "b")         # Require edge between a and b
)

result = pattern.execute(network)
print(f"Found {result.count} matches")
print(result.to_pandas())

Output:

Found 4 matches
                 a                  b
0  (Alice, social)      (Bob, social)
1    (Bob, social)    (Alice, social)
2    (Bob, social)  (Charlie, social)
3  (Charlie, social)    (Bob, social)

Notice that undirected edges produce matches in both directions.

Pattern Components

Nodes

Define node variables that will be bound to actual nodes during matching:

# Simple node
Q.pattern().node("a")

# Node with semantic labels (metadata only)
Q.pattern().node("a", labels="person")

# Node with predicates
Q.pattern().node("a").where(degree__gt=3)

# Node with layer constraint
Q.pattern().node("a").where(layer="social")

Node Predicates:

All standard DSL predicates work with pattern nodes:

degree__gt=5 — degree greater than 5
degree__lt=2 — degree less than 2
layer="social" — node must be in social layer
Any node attribute: age__gt=30, type="user", etc.

Edges

Define edges between node variables:

# Undirected edge
Q.pattern().edge("a", "b", directed=False)

# Directed edge
Q.pattern().edge("a", "b", directed=True)

# Edge with predicates
Q.pattern().edge("a", "b").where(weight__gt=0.5)

# Edge with optional type
Q.pattern().edge("a", "b", etype="friendship")

Edge Predicates:

Filter edges by attributes:

weight__gt=0.5 — edge weight greater than 0.5
weight__lt=1.0 — edge weight less than 1.0
Any edge attribute: timestamp__gt=100, color="red", etc.

Paths

Sugar method for defining sequential connections:

# 2-hop path: a → b → c
Q.pattern().path(["a", "b", "c"])

# Equivalent to:
Q.pattern().edge("a", "b").edge("b", "c")

# Directed path
Q.pattern().path(["a", "b", "c"], directed=True)

Triangles

Sugar method for triangle motifs:

# Triangle: a-b, b-c, c-a
Q.pattern().triangle("a", "b", "c")

# Equivalent to:
Q.pattern().edge("a", "b").edge("b", "c").edge("c", "a")

Multilayer-Aware Patterns

One of the most powerful features is specifying layer constraints on edges.

Within Layer

Find edges that exist within a single layer:

# Edges within the social layer
pattern = (
    Q.pattern()
     .node("a").where(layer="social")
     .node("b").where(layer="social")
     .edge("a", "b")
)

Between Layers

Find edges that cross between specific layers:

# Edges between social and work layers
pattern = (
    Q.pattern()
     .node("a").where(layer="social")
     .node("b").where(layer="work")
     .edge("a", "b").between_layers("social", "work")
)

Any Layer

Allow edges in any layer (default behavior):

pattern = Q.pattern().edge("a", "b").any_layer()

Practical Examples

Example 1: Find Triangles with Weight Constraints

Problem: Find triangles where all edges have weight > 1.0.

pattern = (
    Q.pattern()
     .triangle("a", "b", "c")
     .limit(10)
)

result = pattern.execute(network)

# Filter by weight in post-processing
# (Edge predicates during matching coming in future version)
triangles = result.to_pandas()
print(f"Found {len(triangles)} triangles")

Example 2: Find 2-Hop Paths in Specific Layer

Problem: Find all 2-hop paths within the social layer.

pattern = (
    Q.pattern()
     .node("a").where(layer="social")
     .node("b").where(layer="social")
     .node("c").where(layer="social")
     .path(["a", "b", "c"])
     .returning("a", "b", "c")
     .limit(5)
)

result = pattern.execute(network)
df = result.to_pandas()

print(f"Found {result.count} paths")
print(df)

Output:

Found 5 paths
                   a                b                  c
0      (Bob, social)  (Alice, social)      (Bob, social)
1      (Bob, social)  (Alice, social)  (Charlie, social)
2  (Charlie, social)    (Bob, social)    (Alice, social)
...

Example 3: Find High-Degree Nodes with Specific Connections

Problem: Find pairs of high-degree nodes (degree > 2) connected by strong edges (weight > 1.5).

pattern = (
    Q.pattern()
     .node("a").where(layer="social", degree__gt=2)
     .node("b").where(layer="social", degree__gt=2)
     .edge("a", "b").where(weight__gt=1.5)
     .constraint("a != b")  # Ensure different nodes
     .returning("a", "b")
)

result = pattern.execute(network)
print(f"Found {result.count} high-degree pairs")

# Get unique nodes involved
nodes = result.to_nodes(unique=True)
print(f"Unique nodes: {len(nodes)}")

Example 4: Cross-Layer Hub Detection

Problem: Find nodes that appear in multiple layers and have high degree in each.

# This requires multiple pattern queries
# Find nodes in social layer
social_hubs = (
    Q.pattern()
     .node("a").where(layer="social", degree__gt=3)
     .returning("a")
     .execute(network)
)

# Find nodes in work layer
work_hubs = (
    Q.pattern()
     .node("a").where(layer="work", degree__gt=3)
     .returning("a")
     .execute(network)
)

# Find intersection (nodes in both)
social_nodes = set(n[0] for n in social_hubs.to_nodes())
work_nodes = set(n[0] for n in work_hubs.to_nodes())
cross_layer_hubs = social_nodes & work_nodes

print(f"Cross-layer hubs: {cross_layer_hubs}")

Working with Results

The PatternQueryResult object provides multiple ways to access matches.

Accessing Rows

result = pattern.execute(network)

# Get all matches as list of dictionaries
for match in result.rows:
    print(f"Match: {match}")
    # e.g., {'a': ('Alice', 'social'), 'b': ('Bob', 'social')}

Converting to Pandas

df = result.to_pandas()

# Now use pandas operations
print(df.head())
print(df.describe())

# Export to CSV
df.to_csv("pattern_matches.csv", index=False)

Extracting Nodes

# Get all matched nodes (as tuples)
all_nodes = result.to_nodes()

# Get unique nodes only
unique_nodes = result.to_nodes(unique=True)

# Get nodes for specific variables
a_nodes = result.to_nodes(vars=["a"], unique=True)

Extracting Edges

# Get all matched edges as tuples
edges = result.to_edges()

# Each edge is a tuple of node tuples
for src, dst in edges:
    print(f"Edge: {src} -> {dst}")

Creating Subgraphs

# Create induced subgraph of matched nodes
subgraph = result.to_subgraph(network)

# Now use NetworkX operations
print(f"Subgraph has {subgraph.number_of_nodes()} nodes")
print(f"Subgraph has {subgraph.number_of_edges()} edges")

# Create one subgraph per match
subgraphs = result.to_subgraph(network, per_match=True)
print(f"Created {len(subgraphs)} subgraphs")

Filtering Results

# Filter matches using a predicate
filtered = result.filter(lambda match: match["a"][0].startswith("A"))

# Limit number of results
limited = result.limit(10)

Query Execution Planning

Use .explain() to see how the pattern will be executed:

pattern = (
    Q.pattern()
     .node("a").where(degree__gt=3)
     .node("b")
     .edge("a", "b")
)

plan = pattern.explain()
print(f"Root variable: {plan['root_var']}")
print(f"Join order: {[step['var'] for step in plan['join_order']]}")
print(f"Estimated complexity: {plan['estimated_complexity']}")

Example Output:

Root variable: a
Join order: ['a', 'b']
Estimated complexity: 1000

The planner chooses a as the root because it has the most restrictive predicates (degree__gt=3), which will generate fewer candidates.

Performance Tips

Add Predicates Early: The more selective predicates you add to the root variable, the faster the query.

# Good: Restrictive predicate on first node
Q.pattern().node("a").where(degree__gt=10).node("b").edge("a", "b")

# Less efficient: No predicates
Q.pattern().node("a").node("b").edge("a", "b")

Use Layer Constraints: Layer filters significantly reduce the search space.

# Good: Restrict to one layer
Q.pattern().node("a").where(layer="social")

# Less efficient: Search all layers
Q.pattern().node("a")

Set Limits: For large networks, use .limit() to cap results.
```
pattern.limit(100).execute(network)
```

Use Constraints: Add a != b constraints to avoid self-loops if not needed.

Q.pattern().node("a").node("b").edge("a", "b").constraint("a != b")

Advanced Features

Constraints

Global constraints that apply across variables:

# All-different constraint
pattern = (
    Q.pattern()
     .node("a")
     .node("b")
     .node("c")
     .edge("a", "b")
     .edge("b", "c")
     .constraint("a != b")
     .constraint("b != c")
     .constraint("a != c")
)

Returning Specific Variables

By default, all variables are returned. You can select specific ones:

pattern = (
    Q.pattern()
     .node("a")
     .node("b")
     .node("c")
     .path(["a", "b", "c"])
     .returning("a", "c")  # Only return endpoints
)

result = pattern.execute(network)
# Result only contains 'a' and 'c' columns

Execution Options

# Set maximum matches
result = pattern.execute(network, max_matches=100)

# Set timeout (in seconds)
result = pattern.execute(network, timeout=10.0)

Comparison with Other Approaches

Pattern Matching vs. NetworkX

NetworkX Approach	Pattern Matching Approach
`nx.triangles(G)` Returns triangle count per node	`Q.pattern().triangle("a","b","c")` Returns actual triangle matches
`nx.all_simple_paths(G, source, tgt)` Enumerates all paths	`Q.pattern().path(["a", "b", "c"])` Finds paths with constraints
Manual loops and filtering	Declarative pattern specification

Advantages of Pattern Matching:

Declarative and composable
Built-in support for multilayer constraints
Integrated with DSL ecosystem
Returns results in consistent format (DataFrame, nodes, edges, subgraph)

Pattern Matching vs. DSL Node/Edge Queries

Use node/edge queries when you need individual elements. Use pattern matching when you need to find subgraph structures.

Limitations and Future Work

Current Limitations (v1)

Fixed-length paths only: Variable-length paths like (a)-[*1..3]-(b) not yet supported
No optional matching: All pattern elements must match
No UNION patterns: Cannot express “match pattern A OR pattern B”
Limited aggregation: Aggregation over matches not yet implemented

These features are planned for future versions while maintaining the current clean API.

Best Practices

Start simple: Begin with small patterns and add complexity incrementally
Test on small data: Validate pattern logic on toy networks before scaling up
Use explain(): Check execution plans for complex queries
Combine with DSL: Use pattern matching for structure, DSL for attributes
Document patterns: Add comments explaining complex pattern logic

Troubleshooting

Pattern Returns No Matches

Problem: Your pattern should match but returns 0 results.

Solutions:

Check layer constraints — are nodes actually in the layers you specified?
Verify predicates — are the thresholds too restrictive?
Use .explain() to see the execution plan
Test with simpler patterns first
Check if your network has the expected structure

# Debug: Check basic statistics first
result = Q.nodes().where(layer="social").execute(network)
print(f"Social layer has {result.count} nodes")

result = Q.edges().where(intralayer=True).execute(network)
print(f"Network has {result.count} intralayer edges")

Too Many Matches

Problem: Pattern returns too many results.

Solutions:

Add more predicates to narrow the search
Use .limit() to cap results
Add layer constraints to restrict search space
Use .constraint("a != b") to avoid duplicates

# Limit results
pattern.limit(100).execute(network)

Slow Performance

Problem: Pattern matching takes too long.

Solutions:

Add selective predicates to the root variable
Use layer constraints to reduce search space
Consider breaking pattern into smaller sub-patterns
Use .explain() to check estimated complexity
Set timeout to avoid runaway queries

# Set timeout
result = pattern.execute(network, timeout=30.0)

Next Steps

Explore the Query Zoo: DSL Gallery for Multilayer Analysis for more complex examples
Try combining pattern matching with DSL queries
Experiment with different motifs (triangles, cliques, paths)
Build your own domain-specific pattern library

Tip

Pro Tip: Pattern matching is most powerful when combined with the rest of the DSL. Use patterns to find structures, then use regular DSL queries to compute metrics on the matches!

How to Find Graph Patterns and Motifs with the Pattern Matching API

Why Pattern Matching?

Quick Start: Your First Pattern

Pattern Components

Nodes

Edges

Paths

Triangles

Multilayer-Aware Patterns

Within Layer

Between Layers

Any Layer

Practical Examples

Example 1: Find Triangles with Weight Constraints

Example 2: Find 2-Hop Paths in Specific Layer

Example 3: Find High-Degree Nodes with Specific Connections

Example 4: Cross-Layer Hub Detection

Working with Results

Accessing Rows

Converting to Pandas

Extracting Nodes

Extracting Edges

Creating Subgraphs

Filtering Results

Query Execution Planning

Performance Tips

Advanced Features

Constraints

Returning Specific Variables

Execution Options

Comparison with Other Approaches

Pattern Matching vs. NetworkX

Pattern Matching vs. DSL Node/Edge Queries

Limitations and Future Work

Current Limitations (v1)

Best Practices

Troubleshooting

Pattern Returns No Matches

Too Many Matches

Slow Performance

Related Documentation

Next Steps