Graph Based Machine Learning on Relational Data
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This document discusses approaches for performing machine learning on graph-structured relational data stored in databases. It describes how machine learning is iterative like graph traversal. Common domains like healthcare and finance can be modeled as graphs stored in databases. Three approaches are described: 1) extract-transform-load methods to synchronize an external analytics system with the database, 2) storing the graph natively in the database, and 3) using a graph query language to translate queries to the database. Each approach has advantages and disadvantages regarding performance, ability to leverage the database, and flexibility to explore graph structures in the data.
![Iterative PageRank in Python
def pageRank(G, s = .85, maxerr = .001):
n = G.shape[0]
# transform G into markov matrix M
M = csc_matrix(G,dtype=np.float)
rsums = np.array(M.sum(1))[:,0]
ri, ci = M.nonzero()
M.data /= rsums[ri]
sink = rsums==0 # bool array of sink states
# Compute pagerank r until we converge
ro, r = np.zeros(n), np.ones(n)
while np.sum(np.abs(r-ro)) > maxerr:
ro = r.copy()
for i in xrange(0,n):
Ii = np.array(M[:,i].todense())[:,0] # inlinks of state i
Si = sink / float(n) # account for sink states
Ti = np.ones(n) / float(n) # account for teleportation
r[i] = ro.dot( Ii*s + Si*s + Ti*(1-s) )
return r/sum(r) # return normalized pagerank](https://image.slidesharecdn.com/graph-basedanalysisofrelationaldata-presentation-150507161658-lva1-app6892/85/Graph-Based-Machine-Learning-on-Relational-Data-8-320.jpg)
![Graph-Based PageRank in Gremlin
pagerank = [:].withDefault{0}
size = uris.size();
uris.each{
count = it.outE.count();
if(count == 0 || rand.nextDouble() > 0.85) {
rank = pagerank[it]
uris.each {
pagerank[it] = pagerank[it] / uris.size()
}
}
rank = pagerank[it] / it.outE.count();
it.out.each{
pagerank[it] = pagerank[it] + rank;
}
}](https://image.slidesharecdn.com/graph-basedanalysisofrelationaldata-presentation-150507161658-lva1-app6892/85/Graph-Based-Machine-Learning-on-Relational-Data-9-320.jpg)
Graph Based Machine Learning on Relational Data
- 1. Graph Based Machine Learning on Relational Data Problems and Methods
- 2. Machine Learning using Graphs
- 3. Machine Learning using Graphs - Machine Learning is iterative but iteration can also be seen as traversal.
- 4. Machine Learning using Graphs - Machine Learning is iterative but iteration can also be seen as traversal. - Many domains have structures already modeled as graphs (health records, finance)
- 5. Machine Learning using Graphs - Machine Learning is iterative but iteration can also be seen as traversal. - Many domains have structures already modeled as graphs (health records, finance) - Important analyses are graph algorithms: clusters, influence propagation, centrality.
- 6. Machine Learning using Graphs - Machine Learning is iterative but iteration can also be seen as traversal. - Many domains have structures already modeled as graphs (health records, finance) - Important analyses are graph algorithms: clusters, influence propagation, centrality. - Performance benefits on sparse data
- 7. Machine Learning using Graphs - Machine Learning is iterative but iteration can also be seen as traversal. - Many domains have structures already modeled as graphs (health records, finance) - Important analyses are graph algorithms: clusters, influence propagation, centrality. - Performance benefits on sparse data - More understandable implementation
- 8. Iterative PageRank in Python def pageRank(G, s = .85, maxerr = .001): n = G.shape[0] # transform G into markov matrix M M = csc_matrix(G,dtype=np.float) rsums = np.array(M.sum(1))[:,0] ri, ci = M.nonzero() M.data /= rsums[ri] sink = rsums==0 # bool array of sink states # Compute pagerank r until we converge ro, r = np.zeros(n), np.ones(n) while np.sum(np.abs(r-ro)) > maxerr: ro = r.copy() for i in xrange(0,n): Ii = np.array(M[:,i].todense())[:,0] # inlinks of state i Si = sink / float(n) # account for sink states Ti = np.ones(n) / float(n) # account for teleportation r[i] = ro.dot( Ii*s + Si*s + Ti*(1-s) ) return r/sum(r) # return normalized pagerank
- 9. Graph-Based PageRank in Gremlin pagerank = [:].withDefault{0} size = uris.size(); uris.each{ count = it.outE.count(); if(count == 0 || rand.nextDouble() > 0.85) { rank = pagerank[it] uris.each { pagerank[it] = pagerank[it] / uris.size() } } rank = pagerank[it] / it.outE.count(); it.out.each{ pagerank[it] = pagerank[it] + rank; } }
- 10. Learning by Example - Machine Learning requires many instances with which to fit a model to make predictions.
- 11. Learning by Example - Machine Learning requires many instances with which to fit a model to make predictions. - Current large scale analytical methods (Pregel, Giraph, GraphLab) are in-memory without data storage components.
- 12. Learning by Example - Machine Learning requires many instances with which to fit a model to make predictions. - Current large scale analytical methods (Pregel, Giraph, GraphLab) are in-memory with data storage components - And while Neo4j, OrientDB, and Titan are ok...
- 13. Learning by Example - Machine Learning requires many instances with which to fit a model to make predictions. - Current large scale analytical methods (Pregel, Giraph, GraphLab) are in-memory with data storage components - And while Neo4j, OrientDB, and Titan are ok... - Most (active) data sits in relational databases where users interact with it in real time via transactions in web applications.
- 14. Is it because relational data is a legacy system we must support? Is it purely because of inertia?
- 15. NO! It’s because Relational Data is awesome! Awesome sauce relational data of the future.
- 16. - Ability to express queries/algorithms using a declarative, graph-domain specific language like SQL, or at the very least via UDFs. Requirements
- 17. Requirements - Ability to express queries/algorithms using a declarative, graph-domain specific language like SQL, or at the very least via UDFs. - Ability to explore and identify hidden or implicit graphs in the database.
- 18. Requirements - Ability to express queries/algorithms using a declarative, graph-domain specific language like SQL, or at the very least via UDFs. - Ability to explore and identify hidden or implicit graphs in the database. - Combine in-memory analytics with some disk storage facility that is transactional.
- 19. Approach 1: ETL Methods t = 0 t > 0 extract transform load synchronize analyze
- 20. Approach 1: ETL Methods The Good - Processing is not physical layer dependent - Relational data storage with real time interaction - Analytics can scale in size to Hadoop or in speed to in- memory computation frameworks. The Bad - Must know structure of graph in relational database ahead of time, no exploration. - Synchronization can cause inconsistency. - OLAP processes incur resource penalty (I/O or CPU depending on location).
- 21. Approach 1: ETL Methods The Good - Processing is not physical layer dependent - Relational data storage with real time interaction - Analytics can scale in size to Hadoop or in speed to in- memory computation frameworks. The Bad - Must know structure of graph in relational database ahead of time, no exploration. - Synchronization can cause inconsistency. - OLAP processes incur resource penalty (I/O or CPU depending on location).
- 22. Approach 2: Store Graph in RDBMS
- 23. Approach 2: Store Graph in RDBMS The Good - Can utilize relational devices like indices and parallel joins for graph-specific queries on existing data. - Simply use SQL for the data access mechanism. - Transactional storage of the data. The Bad - Constrained to graph-specific schema. - Many joins required for traversal. - Depending on storage mechanisms there may be too few or too many tables in the database for applications. - Must convert existing database to this structure.
- 24. Approach 2: Store Graph in RDBMS The Good - Can utilize relational devices like indices and parallel joins for graph-specific queries on existing data. - Simply use SQL for the data access mechanism. - Transactional storage of the data. The Bad - Constrained to graph-specific schema. - Many joins required for traversal. - Depending on storage mechanisms there may be too few or too many tables in the database for applications. - Must convert existing database to this structure.
- 25. Approach 3: Use Graph Query Language API Optimizer Query Result Query Translator SQL Queries Final SQL Queries Graph DSL Query
- 26. Approach 3: Use Graph Query Language The Good - DSL in the graph domain that easily expresses graph analytics but also relational semantics. - Can use existing relational schemas; allows for exploration and identification of graphs. - Computation is offloaded into in-memory processing The Bad - Many graphs or big graphs can cause too many joins without optimal query translation. - User is required to facilitate definition of relational structure into a graph representation. - May not leverage relational resources.
- 27. Approach 3: Use Graph Query Language The Good - DSL in the graph domain that easily expresses graph analytics but also relational semantics. - Can use existing relational schemas; allows for exploration and identification of graphs. - Computation is offloaded into in-memory processing The Bad - Many graphs or big graphs can cause too many joins without optimal query translation. - User is required to facilitate definition of relational structure into a graph representation. - May not leverage relational resources.
- 28. Any Questions?
- 29. Thank you! Presented By: Konstantinos Xirogiannopoulos <[email protected]> Benjamin Bengfort <[email protected]> May 7, 2015
Editor's Notes
- #2: Hi, my name is Kostas and this is Ben. Today we’re going to present the research challenges and existing methods of using graph analyses on relational data stores. [SLIDE CHANGE] Today I’d like to talk a little bit about conducting Graph Based Machine Learning on Relational Data
- #3: As we’ve read and discussed in class - graphs are a valuable data structure, well suited for a range of non-trivial analyses and machine learning tasks. [SLIDE CHANGE] So as we’ve recently read about and talked about in class, graphs are an interesting data structure that is actually well suited not only for trivial graph analyses as well as complex machine learning tasks.
- #4: To motivate the usage of graphs and graph oriented frameworks even further
- #6: Analyses like finding clusters, influence propagation by means of Pagerank for example, or centrality, are in essence graph algorithms.
- #8: But more importantly, graph, and graph specific languages and frameworks provide a substantially more comprehensible way of implementing algorithms
- #9: https://gist.github.com/diogojc/1338222 G = np.array([[0,0,1,0,0,0,0], [0,1,1,0,0,0,0], [1,0,1,1,0,0,0], [0,0,0,1,1,0,0], [0,0,0,0,0,0,1], [0,0,0,0,0,1,1], [0,0,0,1,1,0,1]])
- #10: https://groups.google.com/forum/#!topic/gremlin-users/LAm4mzzg8NY Expressing graph algorithms through this framework is a lot more intuitive!
- #11: So hopefully I’ve convinced you about why we’d want to use Graphs for these types of analyses. Now we also know that Machine learning...
- #14: Most actuve data actually sits inside relational databases , where users interact with it in real time via transactions in the web applications that we use every day
- #15: Now why is it that we don’t move on? A rusting old jalopy in Hackberry, a small Arizona town just outside the middle of nowhere. https://flic.kr/p/dqG9Ad
- #16: 1996 McLaren F1 GTR https://flic.kr/p/oc8gUh Awesome because : Strong semantics (durability, fault tolerance, integrity constraints) They support truly ACID Transactions They provide assurance because mature