Improving Machine Learning using Graph Algorithms
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The document discusses enhancing machine learning (ML) predictions through graph algorithms, emphasizing the importance of relationships in predicting behavior. It highlights features extraction and engineering from graph databases like Neo4j, which provide novel insights and improve ML models by utilizing connected data structures. Various use cases, such as predicting collaboration in academic networks and applications in industries like healthcare and finance, illustrate the advantages of integrating graph algorithms into ML workflows.
![Cypher: Powerful & Expressive Query Language
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Improving Machine Learning using Graph Algorithms
- 1. Improve ML Predictions using Graph Algorithms Mark Needham, Neo4j Amy Hodler, Neo4j May 2019 #Neo4j #GraphAnalytics
- 2. • Graphs for Predictions • Connected Features • Link Prediction • Neo4j + Spark Workflow Amy E. Hodler Graph Analytics & AI Program Manager, Neo4j [email protected] @amyhodler neo4j.com/ graph-algorithms-book Chapter 8: Graph + ML Spark & Neo4j Mark Needham Developer Relations Engineer, Neo4j [email protected] @markHneedham
- 3. What in Common is Predictive?
- 4. Relationships: Strongest Predictors of Behavior! “Increasingly we're learning that you can make better predictions about people by getting all the information from their friends and their friends’ friends than you can from the information you have about the person themselves” James Fowler David Burkus James Fowler Albert-Laszlo Barabasi
- 5. Native Graph Platforms are Designed for Connected Data TRADITIONAL PLATFORMS BIG DATA TECHNOLOGY Store and retrieve data Aggregate and filter data Connections in data Real time storage & retrieval Real-Time Connected Insights Long running queries aggregation & filtering “Our Neo4j solution is literally thousands of times faster than the prior MySQL solution, with queries that require 10-100 times less code” Volker Pacher, Senior Developer Max # of hops ~3 Millions
- 6. Graph Database Surging in Popularity Trends since Jan 2013 DB-Engines.com
- 8. Graph Data Science Applications
- 9. • Current data science models ignore network structure & complex relationships • 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
- 12. Connection-related metrics about our graph, such as the number of relationships going into or out of nodes, a count of potential triangles, or neighbors in common. 14c What Are Connected Features?
- 13. Query (e.g. Cypher) Real-time, local decisioning and pattern matching Graph Algorithms Libraries Global analysis and iterations You know what you’re looking for and making a decision You’re learning the overall structure of a network, updating data, and predicting Local Patterns Global Computation Deriving Connected Features
- 14. Connected Feature Engineering Feature Engineering is how we combine and process the data to create new, more meaningful features, such as clustering or connectivity metrics. Add More Descriptive Features: - Influence - Relationships - Communities Extraction
- 15. 17 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
- 16. Link Prediction
- 17. 19 Can we infer new interactions in the future? What unobserved facts we’re missing?
- 18. + 50 years of biomedical data integrated in a knowledge graph Predicting new uses for drugs by using the graph structure to create features for link prediction Example: het.io
- 19. Example: het.io
- 20. Methods for Link Prediction Algorithm Measures Run targeted algorithms and score outcomes Set a threshold value used to predict a link between nodes Machine Learning Use the measures as features to train an ML model Community Detection Link Prediction Similarity 1st Node 2nd Node Common Neighbors Preferential Attachment label 1 2 4 15 1 3 4 7 12 1 5 6 1 1 0 Centrality
- 22. • Citation Network Dataset - Research Dataset – “ArnetMiner: Extraction and Mining of Academic Social Networks”, by J. Tang et al – Used a subset with 52K papers, 80K authors, 140K author relationships and 29K citation relationships • Neo4j – Create a co-authorship graph and connected feature engineering • Spark and MLlib – Train and test our model using a random forest classifier 24 Predicting Collaboration with a Graph Enhanced ML Model
- 23. Our Link Prediction Workflow Import Data Create Co-Author Graph Extract Data & Store as Graph Explore, Clean, Modify Prepare for Machine Learning Train Models Evaluate Results Productionize
- 25. Our Link Prediction Workflow Import Data Create Co-Author Graph Extract Data & Store as Graph Explore, Clean, Modify Prepare for Machine Learning Train Models Evaluate Results Productionize Identified sparse feature areas Feature Engineering: New graphy features
- 26. Graph Algorithms Used for Feature Engineering (few examples) Preferential Attachment measure the closeness of nodes based on shared neighbors Common Neighbors measures the number of possible neighbors (triadic closure) Illustration be.amazd.com/link-prediction/
- 27. Graph Algorithms Used for Feature Engineering (few examples) Triangle counting and clustering coefficients measure the density of connections around nodes Louvain Modularity identifies interacting communities and hierarchies
- 28. Our Link Prediction Workflow Import Data Create Co-Author Graph Extract Data & Store as Graph Explore, Clean, Modify Prepare for Machine Learning Train Models Evaluate Results Productionize Identified sparse feature areas Feature Engineering: New graphy features Train / Test Split Resample: Downsampled for proportional representation
- 29. 31
- 30. 32 Test/Train Split 1st Node 2nd Node Common Neighbors Preferential Attachment label 1 2 4 15 1 3 4 7 12 1 5 6 1 1 0 2 12 3 3 0 4 9 4 8 1 7 10 12 36 1 8 11 2 3 0
- 31. 33 Test/Train Split 1st Node 2nd Node Common Neighbors Preferential Attachment label 1 2 4 15 1 3 4 7 12 1 5 6 1 1 0 2 12 3 3 0 4 9 4 8 1 7 10 12 36 1 8 11 2 3 0 Train Test
- 32. OMG I’m Good! Data Leakage! Graph metric computation for the train set touches data from the test set. Did you get really high accuracy on your first run without tuning?
- 33. Train and Test Graphs: Time Based Split 1st Node 2nd Node Common Neighbors Preferential Attachment label 1 2 4 15 1 3 4 7 12 1 5 6 1 1 0 Train Test 1st Node 2nd Node Common Neighbors Preferential Attachment label 2 12 3 3 0 4 9 4 8 1 7 10 12 36 1 < 2006 >= 2006
- 34. Train and Test Graphs: Time Based Split 1st Node 2nd Node Common Neighbors Preferential Attachment label 1 2 4 15 1 3 4 7 12 1 5 6 1 1 0 Train Test 1st Node 2nd Node Common Neighbors Preferential Attachment label 2 12 3 3 0 4 9 4 8 1 7 10 12 36 1
- 36. There are significantly more negative examples than positive ones: # negative examples = (# nodes)² - (# relationships) - (# nodes) 38 Class Imbalance
- 37. A very high accuracy model could predict that a pair of nodes are not linked. 39 Class Imbalance
- 38. Class Imbalance
- 39. Our Link Prediction Workflow Import Data Create Co-Author Graph Extract Data & Store as Graph Explore, Clean, Modify Prepare for Machine Learning Train Models Evaluate Results Productionize Identified sparse feature areas Feature Engineering: New graphy features Train / Test Split Resample: Downsampled for proportional representation Model Selection: Random Forest Ensemble method
- 41. Training Our Model This is one decision tree in our Random Forest used as a binary classifier to learn how to classify a pair: predicting either linked or not linked.
- 42. 4 Models Trained with Multiple Graph Features Graph Features: • Common Authors “Graphy” Model Common Authors Model Triangles Model Community Model Graph Features: • Preferential Attachment • Total Neighbors Graph Features: • Min & Max Triangles • Min & Max Clustering Coefficient Graph Features: • Label Propagation • Louvain Modularity
- 43. Our Link Prediction Workflow Import Data Create Co-Author Graph Extract Data & Store as Graph Explore, Clean, Modify Prepare for Machine Learning Train Models Evaluate Results Productionize Identified sparse feature areas Feature Engineering: New graphy features Train / Test Split Resample: Downsampled for proportional representation Precision, Accuracy, Recall ROC Curve & AUC Model Selection: Random Forest Ensemble method
- 44. Measures Accuracy Proportion of total correct predictions. Beware of skewed data! Precision Proportion of positive predictions that are correct. Low score = more false positives Recall / True Positive Rate Proportion of actual positives that are correct. Low score = more false negatives False Positive Rate Proportion of incorrect positives ROC Curve & AUC X-Y Chart mapping above 2 metrics (TPR and FPR) with area under curve
- 45. Result: First Model ROC & AUC Problematic False Positives! Common Authors Model 1
- 46. Result: All Models Common Authors Model 1 Community Model 4
- 47. Iteration & Tuning: Feature Influence For feature importance, the Spark random forest averages the reduction in impurity across all trees in the forest Feature rankings are in comparison to the group of features evaluated Also try PageRank! Try removing different features (LabelPropagation)
- 48. Graph Machine Learning Workflow Data aggregation Create and store graphs Extract Data & Store as Graph Explore, Clean, Modify Prepare for Machine Learning Train Models Evaluate Results Productionize Identify uninteresting features Cleanse (outliers+) Feature engineering/ extraction Train / Test split Resample for meaningful representation (proportional, etc.) Precision, accuracy, recall (ROC curve & AUC) SME Review Cross-validation Model & variable selection Hyperparameter tuning Ensemble methods
- 49. Resources • neo4j.com/sandbox • neo4j.com/developer/ graph-algorithms/ • community.neo4j.com Data & Code: • This example from O’Reilly book bit.ly/2FPgGVV (ML Folder) [email protected] @amyhodler neo4j.com/ graph-algorithms-book
- 50. Q&A/Extra Stuff to delete 52
- 51. 53 Connected Feature Extraction Feature Extraction is how when we change the shape or format of the data to be usable in a machine learning pipeline. For example, from a graph, we extract the relevant subset of the data into a tabular format for model building.
- 52. Connected Feature Selection Feature Selection is how we reduce the number of features used in a model to a relevant subset. This can be done algorithmically or based on domain expertise, but the objective is to maximize the predictive power of your model while minimizing overfitting.
- 53. 720+ 7/10 12/2 5 8/10 53K+ 100+ 300+ 450+ Adoption Top Retail Firms Top Financial Firms Top Software Vendors Customers Partners • Creator of the Neo4j Graph Platform • ~250 employees • HQ in Silicon Valley, other offices include London, Munich, Paris and Malmö Sweden • $80M new funding led by Morgan Stanley & One Peak. Total $160M from Fidelity, Sunstone, Conor, Creandum, and Greenbridge Capital • Over 15M+ downloads & container pulls • 325+ enterprise subscription customers with over half with >$1B in revenue Ecosystem Startups in program Enterprise customers Partners Meet up members Events per year Industry’s Largest Dedicated Investment in Graphs Neo4j - The Graph Company
- 54. Strictly ConfidentialStrictly Confidential 56 Helping The World To Make Sense of Data ICIJ used Neo4j to uncover the world’s largest journalistic leak to date, The Panama Papers NASA uses Neo4j for a “Lessons Learned” database to improve effectiveness in search missions in space Neo4j is used to graph the human body, map correlations, identify cause & effect and search for the cure for cancer SAVING DEMOCRACY MISSION TO MARS CURING CANCER
- 55. Graph and ML Algorithms in Neo4j • Parallel Breadth First Search & DFS • 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/ Updated April 2019 Link Prediction • Adamic Adar • Common Neighbors • Preferential Attachment • Resource Allocations • Same Community • Total Neighbors
- 56. Conceive Code Compute Store Non-Native Graph DBNative Graph DB RDBM S Optimized for graph workloads Connectedness Differentiates Neo4j
- 57. Neo4j is an enterprise-grade native graph platform that enables you to: • Store, reveal and query data relationships • Traverse and analyze any levels of depth in real-time • Add context and connect new data on the fly 59 Who We Are: Leader in Graph Innovations • Performance • ACID Transactions • Schema-free Agility • Graph Algorithms Designed, built and tested natively for graphs from the start for: • Developer Productivity • Hardware Efficiency • Global Scale • Graph Adoption Graph Transactions Graph Analytics Data Integration Development & Admin Analytics Tooling Drivers & APIs Discovery & Visualization
- 58. 60 • Record “Cyber Monday” sales • About 35M daily transactions • Each transaction is 3-22 hops • Queries executed in 4ms or less • Replaced IBM Websphere commerce • 300M pricing operations per day • 10x transaction throughput on half the hardware compared to Oracle • Replaced Oracle database • Large postal service with over 500k employees • Neo4j routes 7M+ packages daily at peak, with peaks of 5,000+ routing operations per second. Handling Large Graph Work Loads for Enterprises Real-time promotion recommendations Marriott’s Real-time Pricing Engine Handling Package Routing in Real-Time
- 59. Recommendations Dynamic Pricing IoT-applicationsFraud Detection Real-Time Transaction Applications Generate and Protect Revenue Customer Engagement Metadata and Advanced Analytics Data Lake Integration Knowledge Graphs for AI Risk Mitigation Generate Actionable Insights Network Management Supply Chain Efficiency Identity and Access Management Internal Business Processes Improve Efficiency and Cut Costs Graph Use Cases by Value Proposition
- 60. Softwar e Financial Services Teleco m Retail & Consumer Goods Media & Entertainment Other Industries Airbus 62 Copyright © 2017 Neo4j, Inc. Company Confidential
- 61. Graph Transactions Graph Analytics Data Integration Development & Admin Analytics Tooling Drivers & APIs Discovery & Visualization Developers Admins Applications Business Users Data Analysts Data Scientists Enterprise Data Hub Native Graph Platform: Tools for Many Users
- 62. Collections-Focused Multi-Model, Documents, Columns & Simple Tables, Joins Neo4j is designed for data relationships Different Paradigms NoSQL Relational DBMS Neo4j Graph Platform Connections-Focused Focused on Data Relationships Development Benefits Easy model maintenance Easy query Deployment Benefits Ultra high performance Minimal resource usage
- 63. How Neo4j Fits — Common Architecture Patterns From Disparate Silos To Cross-Silo Connections From Tabular Data To Connected Data From Data Lake Analytics to Real-Time Operations
- 64. Cypher: Powerful & Expressive Query Language MATCH (:Person { name:“Dan”} ) -[:MARRIED_TO]-> (spouse) MARRIED_TO Dan Ann NODE RELATIONSHIP TYPE LABEL PROPERTY VARIABLE
- 65. Neo4j Bloom 67 • High fidelity • Scene navigation • Property views • Search suggestions • Saved phrase history • Property editor • Schema perspectives • Bloom chart type • Visualize • Communicate • Discover • Navigate • Isolate • Edit • Share
- 66. 68 Real-Time Recommendations Fraud Detection Network & IT Operations Master Data Management Knowledge Graph Identity & Access Management Common Graph Technology Use Cases AirBnb
- 67. Graphs Drive Innovation 69 Context Paths Auto-Graphs Graph Layers 1st Graph Cross- Connect Cross-tech applications Internet of Things operations Transparent Neural Networks Blockchain-managed systems Adjacent graph layers inspire new innovations Metadata / Risk Management Knowledge Graphs AI- Powered Customer Experiences Connect unlike objects such as people to products, locations Mobile app explosion Recommendation engines Fraud detectors Desire for more context to follow connections Connects like objects People, computer networks, telco, etc
- 68. Business Problem • Find relationships between people, accounts, shell companies and offshore accounts • Journalists are non-technical • Biggest “Snowden-Style” document leak ever; 11.5 million documents, 2.6TB of data Solution and Benefits • Pulitzer Prize winning investigation resulted in robust coverage of fraud and corruption • PM of Iceland & Pakistan resigned, exposed Putin, Prime Ministers, gangsters, celebrities (Messi) • Led to assassination of journalist in Malta Background • International Consortium of Investigative Journalists (ICIJ), small team of data journalists • International investigative team specializing in cross-border crime, corruption and accountability of power • Works regularly with leaks and large datasets ICIJ Panama Papers INVESTIGATIVE JOURNALISM Fraud Detection / Knowledge Graph70
- 69. Thomson Reuters Graph 71 • Data Fusion for Portfolio Managers • Graph layers
- 70. Background • Personal shopping assistant • Converses with buyer via text, picture and voice to provide real-time recommendations • Combines AI and natural language understanding (NLU) in Neo4j Knowledge Graph • First of many apps in eBay's AI Platform Business Problem • Improve personal context in online shopping • Transform buyer-provided context into ideal purchase recommendations over social platforms • "Feels like talking to a friend" Solution and Benefits • 3 developers, 8M nodes, 20M relationships • Needed high-performance traversals to respond to live customer requests • Easy to train new algorithms and grow model • Generating revenue since launch eBay for Google Assistant ONLINE RETAIL Knowledge Graph powers Real-Time Recommendations72 EE Customer since 2016 Q3
- 71. Background • Over 7M citizens suffer from Diabetes • Connecting over 400 researchers • Incorporates over 50 databases, 100k’s of Excel workbooks, 30 database of biological samples • Sought to examine disease from as many angles as possible. Business Problem • Genes are connected by proteins or to metabolites, and patients are connected with their diets, etc… • Needed to improve the utilization of immensely technical data • Needed to cater to doctors and researchers with simple navigation, communication and connections of the graph. Solution and Benefits • Dr. Alexander Jarasch, Head of Bioinformatics and Data Management • Scientists can conduct parallel research without asking the same questions or repeating tests • Built views like a liver sample knowledge graph DZD - German Center for Diabetes Research Medical Genomic Research73 EE Customer since 2016 Q4