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Leveraging Graphs for Better AI
Jennifer Reif
Developer Relations Engineer, Neo4j
@JMHReif
jennifer.reif@neo4j.com
IT’S NOT WHAT
YOU KNOW…
IT’S HOW YOU
ARE CONNECTED.
• Current data science models ignore network structure
• Graphs add highly predictive features to existing ML models
• Otherwise unattainable predictions based on relationships
Novel & More Accurate Predictions

with the Data You Already Have
Machine Learning Pipeline
“The idea is that graph networks are bigger than 

any one machine-learning approach.
Graphs bring an ability to generalize about structure
that the individual neural nets don't have.”
"Where do the graphs
come from that 

graph networks
operate over?”
Financial Crimes Drug Discovery Recommendations
Cybersecurity Predictive Maintenance
Customer Segmentation
Churn Prediction Search/MDM
Graphs Data Science Applications
What does the process
look like?
!6
Building a Graph ML Model
Data Sources Native Graph Platform Machine Learning
Aggregate Disparate
Data and Cleanse
Build Predictive Models
Unify Graphs and
Engineer Features
Parquet JSON
and more…
MLlib
and more…
Spark Graph Native Graph Platform Machine Learning
Example: Spark & Neo4j Workflow
Graph
Transactions
Graph
Analytics
Cypher 9 in Spark 3.0
to create non-
persistent graphs
MLlib to Train Models
Native Graph Algorithms,
Processing, and Storage
Morpheus
integration
Explore Graphs Build Graph Solutions
• Massively scalable
• Powerful data pipelining
• Robust ML Libraries
• Non-persistent, non-native graphs
• Persistent, dynamic graphs
• Graph native query and algorithm
performance
• Constantly growing list of graph
algorithms and embeddings
Where do we start?
!10
Steps Forward in Graph Data Science
Query Based
Knowledge
Graph
Query Based
Feature
Engineering
Graph
Algorithm
Feature
Engineering
Graph
Embeddings
Graph Neural
Networks
Enterprise Delivery
DataScienceComplexity
Knowledge
Graphs
Graph Feature
Engineering
Graph Native Learning
Graph Persistence
Steps Forward in Graph Data Science
Query Based
Knowledge
Graph
Query Based
Feature
Engineering
Graph Algorithm
Feature
Engineering
Graph
Embeddings
Graph Neural
Networks
Enterprise Maturity
DataScienceComplexity
Query-Based Knowledge Graphs

Connecting the Dots
“Using Neo4j someone from our Orion project found information from
the Apollo project that prevented an issue, saving well over two years
of work and one million dollars of taxpayer funds.”
Steps Forward in Graph Data Science
Query Based
Knowledge
Graph
Graph
Algorithm
Feature
Engineering
Graph
Embeddings
Graph Neural
Networks
Query Based
Feature
Engineering
Enterprise Maturity
DataScienceComplexity
HetioNet is a knowledge
graph integrating over 50
years of biomedical data
Leveraged to predict new uses
for drugs by using the graph
topology to create features to
predict new links
Query-Based Feature Engineering

Mining Data for Drug Discovery
het.io
HetioNet is a knowledge
graph integrating over 50
years of biomedical data
Leveraged to predict new uses
for drugs by using the graph
topology to create features to
predict new links
het.io
Query-Based Feature Engineering

Mining Data for Drug Discovery
Query-Based Feature Engineering

Mining Data for Drug Discovery
Spark Graph Native Graph Platform Machine Learning
• Merge distributed data
into DataFrames
• Reshape your tables 

into graphs
• Explore cypher queries
• Move to Neo4j to build
expert queries
• Persist your graph
Knowledge Graphs: 

Getting Started Example with Spark
• Bring query based
graph features to ML
pipeline
Graph
Transactions
Graph
Analytics
Steps Forward in Graph Data Science
Query Based
Feature
Engineering
Graph
Embeddings
Graph Neural
Networks
Query Based
Knowledge
Graph
Graph
Algorithm
Feature
Engineering
Enterprise Maturity
DataScienceComplexity
Feature Engineering is how we combine and process the data to create
new, more meaningful features, such as clustering or connectivity
metrics.
Graph Connected Feature Engineering
Add More Descriptive Features:
- Influence
- Relationships
- Communities
Extraction
!21
Graph Feature Categories & Algorithms
Pathfinding 

& Search
Finds the optimal paths or evaluates 

route availability and quality
Centrality /
Importance
Determines the importance of
distinct nodes in the network
Community
Detection
Detects group clustering or
partition options
Heuristic 

Link Prediction
Estimates the likelihood of nodes 

forming a relationship
Evaluates how alike
nodes are
Similarity Embeddings
Learned representations

of connectivity or topology
• Connected components to identify
disjointed graphs sharing identifiers
• PageRank to measure influence and
transaction volumes
• Louvain to identify communities that
frequently interact
• Jaccard to measure account similarity
Graph Connected Feature Engineering 

Financial Crime: Detecting Fraud
Large financial institutions already have existing pipelines to identify fraud via heuristics and
models

Graph based features improve accuracy:
+48,000 U.S. Patents for 

Graph Fraud / Anomaly Detection 

in the last 10 years
Spark Graph Native Graph Platform Machine Learning
• Merge distributed data
into DataFrames
• Reshape your tables 

into graphs
• Explore cypher queries and
simple algorithms
• Persist your graph
• Create rule based
features
• Run native graph
algorithms and write to
graph or stream
Graph Feature Engineering: 

Getting Started Example with Spark
• Bring graph features to
ML pipeline for training
Graph
Transactions
Graph
Analytics
!25
Graph Algorithms in Neo4J
• Parallel Breadth First Search
• Parallel Depth First Search
• Shortest Path
• Single-Source Shortest Path
• All Pairs Shortest Path
• Minimum Spanning Tree
• A* Shortest Path
• Yen’s K Shortest Path
• K-Spanning Tree (MST)
• Random Walk
• Degree Centrality
• Closeness Centrality
• CC Variations: Harmonic, Dangalchev,
Wasserman & Faust
• Betweenness Centrality
• Approximate Betweenness Centrality
• PageRank
• Personalized PageRank
• ArticleRank
• Eigenvector Centrality
• Triangle Count
• Clustering Coefficients
• Connected Components (Union Find)
• Strongly Connected Components
• Label Propagation
• Louvain Modularity – 1 Step & Multi-Step
• Balanced Triad (identification)
• Euclidean Distance
• Cosine Similarity
• Jaccard Similarity
• Overlap Similarity
• Pearson Similarity
Pathfinding 

& Search
Centrality /
Importance
Community
Detection
Similarity
neo4j.com/docs/

graph-algorithms/current/
Link 

Prediction
• Adamic Adar
• Common Neighbors
• Preferential Attachment
• Resource Allocations
• Same Community
• Total Neighbors
Steps Forward in Graph Data Science
Query Based
Knowledge
Graph
Graph
Algorithm
Feature
Engineering
Graph Neural
Networks
Query Based
Feature
Engineering
Graph
Embeddings
Enterprise Maturity
DataScienceComplexity
Embedding transforms graphs into a feature vector, or set of vectors,
describing topology, connectivity, or attributes of nodes and edges in the
graph
!27
Graph Embeddings
• Vertex/Node embeddings: describe connectivity of each node
• Path embeddings: traversals across the graph
• Graph embeddings: encode an entire graph into a single vector
Explainable Reasoning over Knowledge Graphs for
Recommendation
!28
Graph Embeddings - Recommendations
!29
Graph Embeddings - Recommendations
Explainable Reasoning over Knowledge Graphs for
Recommendation
Spark Graph Native Graph Platform Machine Learning
• Merge distributed data
into DataFrames
• Reshape your tables 

into graphs
• Explore cypher queries and
simple algorithms
• Move to Neo4j to build
expert queries
• Write to persist
• Stay tuned for DeepWalk
and DeepGL algorithms
Graph Feature Engineering-Embedding: 

Getting Started Example with Spark
• Bring graph features to
ML pipeline for training
Graph
Transactions
Graph
Analytics
Steps Forward in Graph Data Science
Query Based
Knowledge
Graph
Graph
Algorithm
Feature
Engineering
Query Based
Feature
Engineering
Graph Neural
Networks
Graph
Embeddings
Enterprise Maturity
DataScienceComplexity
Deep Learning refers to training multi-layer neural networks using
gradient descent
!32
Graph Native Learning
Graph Native Learning refers to deep learning models that take a graph
as an input, performs computations, and return a graph
!33
Graph Native Learning
Battaglia et al, 2018
Example: electron path prediction
Bradshaw et al, 2019
!34
Graph Native Learning
Given reactants and reagents, what will the
products be?
Given reactants and reagents, how do they form
it?
Example: electron path prediction
!35
Graph Native Learning
Progressing in Graph Data Science
Query Based
Knowledge
Graph
Query Based
Feature
Engineering
Graph
Algorithm
Feature
Engineering
Graph
Embeddings
Graph Neural
Networks
Enterprise Maturity
DataScienceComplexity
Knowledge
Graphs
Graph Feature
Engineering
Graph Native Learning
Graph Persistence
Resources
Business
• neo4j.com/use-cases/

artificial-intelligence-analytics/
Data Scientists/Developers
• neo4j.com/sandbox
• neo4j.com/developer/
• community.neo4j.com
jennifer.reif@neo4j.com
@JMHReif
neo4j.com/

graph-algorithms-book

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Leveraging Graphs for Better AI

  • 1. Leveraging Graphs for Better AI Jennifer Reif Developer Relations Engineer, Neo4j @JMHReif jennifer.reif@neo4j.com
  • 2. IT’S NOT WHAT YOU KNOW… IT’S HOW YOU ARE CONNECTED.
  • 3. • Current data science models ignore network structure • Graphs add highly predictive features to existing ML models • Otherwise unattainable predictions based on relationships Novel & More Accurate Predictions
 with the Data You Already Have Machine Learning Pipeline
  • 4. “The idea is that graph networks are bigger than 
 any one machine-learning approach. Graphs bring an ability to generalize about structure that the individual neural nets don't have.” "Where do the graphs come from that 
 graph networks operate over?”
  • 5. Financial Crimes Drug Discovery Recommendations Cybersecurity Predictive Maintenance Customer Segmentation Churn Prediction Search/MDM Graphs Data Science Applications
  • 6. What does the process look like? !6
  • 7. Building a Graph ML Model Data Sources Native Graph Platform Machine Learning Aggregate Disparate Data and Cleanse Build Predictive Models Unify Graphs and Engineer Features Parquet JSON and more… MLlib and more…
  • 8. Spark Graph Native Graph Platform Machine Learning Example: Spark & Neo4j Workflow Graph Transactions Graph Analytics Cypher 9 in Spark 3.0 to create non- persistent graphs MLlib to Train Models Native Graph Algorithms, Processing, and Storage Morpheus integration
  • 9. Explore Graphs Build Graph Solutions • Massively scalable • Powerful data pipelining • Robust ML Libraries • Non-persistent, non-native graphs • Persistent, dynamic graphs • Graph native query and algorithm performance • Constantly growing list of graph algorithms and embeddings
  • 10. Where do we start? !10
  • 11. Steps Forward in Graph Data Science Query Based Knowledge Graph Query Based Feature Engineering Graph Algorithm Feature Engineering Graph Embeddings Graph Neural Networks Enterprise Delivery DataScienceComplexity Knowledge Graphs Graph Feature Engineering Graph Native Learning Graph Persistence
  • 12. Steps Forward in Graph Data Science Query Based Knowledge Graph Query Based Feature Engineering Graph Algorithm Feature Engineering Graph Embeddings Graph Neural Networks Enterprise Maturity DataScienceComplexity
  • 13. Query-Based Knowledge Graphs
 Connecting the Dots “Using Neo4j someone from our Orion project found information from the Apollo project that prevented an issue, saving well over two years of work and one million dollars of taxpayer funds.”
  • 14. Steps Forward in Graph Data Science Query Based Knowledge Graph Graph Algorithm Feature Engineering Graph Embeddings Graph Neural Networks Query Based Feature Engineering Enterprise Maturity DataScienceComplexity
  • 15. HetioNet is a knowledge graph integrating over 50 years of biomedical data Leveraged to predict new uses for drugs by using the graph topology to create features to predict new links Query-Based Feature Engineering
 Mining Data for Drug Discovery het.io
  • 16. HetioNet is a knowledge graph integrating over 50 years of biomedical data Leveraged to predict new uses for drugs by using the graph topology to create features to predict new links het.io Query-Based Feature Engineering
 Mining Data for Drug Discovery
  • 17. Query-Based Feature Engineering
 Mining Data for Drug Discovery
  • 18. Spark Graph Native Graph Platform Machine Learning • Merge distributed data into DataFrames • Reshape your tables 
 into graphs • Explore cypher queries • Move to Neo4j to build expert queries • Persist your graph Knowledge Graphs: 
 Getting Started Example with Spark • Bring query based graph features to ML pipeline Graph Transactions Graph Analytics
  • 19. Steps Forward in Graph Data Science Query Based Feature Engineering Graph Embeddings Graph Neural Networks Query Based Knowledge Graph Graph Algorithm Feature Engineering Enterprise Maturity DataScienceComplexity
  • 20. Feature Engineering is how we combine and process the data to create new, more meaningful features, such as clustering or connectivity metrics. Graph Connected Feature Engineering Add More Descriptive Features: - Influence - Relationships - Communities Extraction
  • 21. !21 Graph Feature Categories & Algorithms Pathfinding 
 & Search Finds the optimal paths or evaluates 
 route availability and quality Centrality / Importance Determines the importance of distinct nodes in the network Community Detection Detects group clustering or partition options Heuristic 
 Link Prediction Estimates the likelihood of nodes 
 forming a relationship Evaluates how alike nodes are Similarity Embeddings Learned representations
 of connectivity or topology
  • 22. • Connected components to identify disjointed graphs sharing identifiers • PageRank to measure influence and transaction volumes • Louvain to identify communities that frequently interact • Jaccard to measure account similarity Graph Connected Feature Engineering 
 Financial Crime: Detecting Fraud Large financial institutions already have existing pipelines to identify fraud via heuristics and models
 Graph based features improve accuracy:
  • 23. +48,000 U.S. Patents for 
 Graph Fraud / Anomaly Detection 
 in the last 10 years
  • 24. Spark Graph Native Graph Platform Machine Learning • Merge distributed data into DataFrames • Reshape your tables 
 into graphs • Explore cypher queries and simple algorithms • Persist your graph • Create rule based features • Run native graph algorithms and write to graph or stream Graph Feature Engineering: 
 Getting Started Example with Spark • Bring graph features to ML pipeline for training Graph Transactions Graph Analytics
  • 25. !25 Graph Algorithms in Neo4J • Parallel Breadth First Search • Parallel Depth First Search • Shortest Path • Single-Source Shortest Path • All Pairs Shortest Path • Minimum Spanning Tree • A* Shortest Path • Yen’s K Shortest Path • K-Spanning Tree (MST) • Random Walk • Degree Centrality • Closeness Centrality • CC Variations: Harmonic, Dangalchev, Wasserman & Faust • Betweenness Centrality • Approximate Betweenness Centrality • PageRank • Personalized PageRank • ArticleRank • Eigenvector Centrality • Triangle Count • Clustering Coefficients • Connected Components (Union Find) • Strongly Connected Components • Label Propagation • Louvain Modularity – 1 Step & Multi-Step • Balanced Triad (identification) • Euclidean Distance • Cosine Similarity • Jaccard Similarity • Overlap Similarity • Pearson Similarity Pathfinding 
 & Search Centrality / Importance Community Detection Similarity neo4j.com/docs/
 graph-algorithms/current/ Link 
 Prediction • Adamic Adar • Common Neighbors • Preferential Attachment • Resource Allocations • Same Community • Total Neighbors
  • 26. Steps Forward in Graph Data Science Query Based Knowledge Graph Graph Algorithm Feature Engineering Graph Neural Networks Query Based Feature Engineering Graph Embeddings Enterprise Maturity DataScienceComplexity
  • 27. Embedding transforms graphs into a feature vector, or set of vectors, describing topology, connectivity, or attributes of nodes and edges in the graph !27 Graph Embeddings • Vertex/Node embeddings: describe connectivity of each node • Path embeddings: traversals across the graph • Graph embeddings: encode an entire graph into a single vector
  • 28. Explainable Reasoning over Knowledge Graphs for Recommendation !28 Graph Embeddings - Recommendations
  • 29. !29 Graph Embeddings - Recommendations Explainable Reasoning over Knowledge Graphs for Recommendation
  • 30. Spark Graph Native Graph Platform Machine Learning • Merge distributed data into DataFrames • Reshape your tables 
 into graphs • Explore cypher queries and simple algorithms • Move to Neo4j to build expert queries • Write to persist • Stay tuned for DeepWalk and DeepGL algorithms Graph Feature Engineering-Embedding: 
 Getting Started Example with Spark • Bring graph features to ML pipeline for training Graph Transactions Graph Analytics
  • 31. Steps Forward in Graph Data Science Query Based Knowledge Graph Graph Algorithm Feature Engineering Query Based Feature Engineering Graph Neural Networks Graph Embeddings Enterprise Maturity DataScienceComplexity
  • 32. Deep Learning refers to training multi-layer neural networks using gradient descent !32 Graph Native Learning
  • 33. Graph Native Learning refers to deep learning models that take a graph as an input, performs computations, and return a graph !33 Graph Native Learning Battaglia et al, 2018
  • 34. Example: electron path prediction Bradshaw et al, 2019 !34 Graph Native Learning Given reactants and reagents, what will the products be? Given reactants and reagents, how do they form it?
  • 35. Example: electron path prediction !35 Graph Native Learning
  • 36. Progressing in Graph Data Science Query Based Knowledge Graph Query Based Feature Engineering Graph Algorithm Feature Engineering Graph Embeddings Graph Neural Networks Enterprise Maturity DataScienceComplexity Knowledge Graphs Graph Feature Engineering Graph Native Learning Graph Persistence
  • 37. Resources Business • neo4j.com/use-cases/
 artificial-intelligence-analytics/ Data Scientists/Developers • neo4j.com/sandbox • neo4j.com/developer/ • community.neo4j.com jennifer.reif@neo4j.com @JMHReif neo4j.com/
 graph-algorithms-book