Saturday, 29 March 2014

Using Neo4j to Manage and Calculate Hierarchies

I recently had a number of extremely interesting conversations with a company that wants to use Neo4j for managing hierarchical data. This use case is so common, that I decided to write up my findings and experiments and share over here. Hierarchical data is extremely common in many different situations - let's just mention a few:
Conceptually and mathematically, hierarchies are nothing more than a particular type of graph. Therefore, I would automatically think that finding things in or calculating things over a hierarchy would be a great application for a graph database like neo4j - and that's what this post is about.

Generating a Product Hierarchy

In order to start looking at this, I needed an appropriately sized hierarchy to work with. My normal way of working would be to do something in a spreadsheet and then generate the graph from there - but My dear friend Michael recently wrote a blogpost that inspired me to skip that step. In fact, I can quickly generate a hierarchy myself using Cypher only. Let's talk a look at the following statements:

//Let's create the top of the tree, the PRODUCT
create (n1:PRODUCT {id:1});

//Let's create 100 children of the PRODUCT, COST_GROUPS connected to the top of the tree
match (n1:PRODUCT {id:1})
with range(1,100) as RANGE, n1
foreach (r in RANGE | create (n2:COST_GROUP {id:r})-[:PART_OF {quantity:round(rand()*100)}]->(n1) );

The first query creates the top of the hierarchy, eg. a product. Underneath that we could then create the first level (100 nodes in this example) by iterating through the range and assigning a random identifier to the node and a "quantity" to the "PART_OF" relationship. Semantically, this would mean that the node at Level 1 would be composed of 100 nodes at level 2, using a given quantity of each of the nodes - mentioned on the relationship. In fact, we are building a hierarchy like this one:

So in fact we need to generate another 4 levels underneath the two existing ones, using the same technique as above:

//for every COST_GROUP, let's connect 100 children at a 3rd level, the COST_TYPEs
match (n2:COST_GROUP)
with range(1,100) as RANGE, n2
foreach (r in RANGE | create (n3:COST_TYPE {id:r})-[:PART_OF {quantity:round(rand()*100)}]->(n2) );

//for every COST_TYPE, connect 10 COST_SUBTYPEs 
match (n3:COST_TYPE)
with range(1,10) as RANGE, n3
foreach (r in RANGE | create (n4:COST_SUBTYPE {id:r})-[:PART_OF {quantity:round(rand()*100)}]->(n3) );

//for every COST_SUBTYPE, connect 5 different COSTs
match (n4:COST_SUBTYPE)
with range(1,5) as RANGE, n4
foreach (r in RANGE | create (n5:COST {id:r})-[:PART_OF {quantity:round(rand()*100)}]->(n4) );

So now we already have a graph of 1*100*100*10*5 =500000 nodes. To add the sixth, lowest level of this hierarchy, I actually needed to run three separate queries, as my machine would run out of memory otherwise - the transaction would just be too big:

//for every COST, connect 3 COST_COMPONENTs
match (n5:COST)
create (n6:COST_COMPONENT {id:1,price:round(rand()*1000)})-[:PART_OF {quantity:round(rand()*100)}]->(n5);
match (n5:COST)
create (n6:COST_COMPONENT {id:2,price:round(rand()*1000)})-[:PART_OF {quantity:round(rand()*100)}]->(n5);
match (n5:COST)
create (n6:COST_COMPONENT {id:3,price:round(rand()*1000)})-[:PART_OF {quantity:round(rand()*100)}]->(n5);

As you can see, the sixth level of the hierarchy is a bit different than the ones above, as it includes actual pricing information for the lowest component of the product that we are building. Creating this entire structure on my machine (a 2012 MBP with 8Gbyte of RAM) took about 5minutes, which is not bad in my opinion - it's not a tiny little graph: 2110101 nodes in total.

We can take a look at the browser and see the hierarchy:

So that was already interesting :) ... but now let's see how we can work with these hierarchies, how we can do some interesting queries.

Querying and recalculating the hierarchy - a "graph global" approach

The first scenario that I wanted to explore is to see how fast neo4j would be able to (re)calculate the price of this "complex" (in the sense that it contains millions of parts) product if I would change the price (or the quantity for that matter) of one of the underlying components.  In order to do that, my initial approach was to walk the graph from top to bottom, evaluating the "quantity" property on every relationship, and multiplying that with the price of the COST_COMPONENT at the bottom. Summing all of that would then yield the total price of the product:

//calculating price based on full sweep of the tree
match (n1:PRODUCT {id:1})<-[r1]-(:COST_GROUP)<-[r2]-(:COST_TYPE)<-[r3]-(:COST_SUBTYPE)<-[r4]-(:COST)<-[r5]-(n6:COST_COMPONENT)
return sum(r1.quantity*r2.quantity*r3.quantity*r4.quantity*r5.quantity*n6.price);

One massive advantage of this approach is its simplicity. Cypher is just so great at these types of recursive operations and simplifying the notation for it in a 2 line query. The result comes back in a very reasonable time (43 seconds):
Note that I at first had forgotten to add directions to the relationships, and that this had a massive impact on performance (factor 5 approximately).

What this little test shows, in my humble opinion, and without having done any kind of optimisation of my machine/setup, neo4j is immediately very good at this - it essentially grabs the entire tree, hops along all the 2.1M nodes and relationships to grab the price and the quantities.

Doing some intermediate price calculations

One way of optimizing this kind of operation, of course, is to do some intermediate calculations at every level of the hierarchy. Essentially adding the price at every node as the sum of the prices of the underlying nodes, multiplied by the quantities on the connecting relationships. Let's set that up with the following queries:

//calculate intermediate pricing at the COST level
match (n5:COST)<-[r5]-(n6:COST_COMPONENT)
with n5, sum(r5.quantity*n6.price) as Sum
set n5.price=Sum;

//calculate intermediate pricing at the COST-SUBTYPE level
match (n4:COST_SUBTYPE)<-[r4]-(n5:COST)
with n4,sum(r4.quantity*n5.price) as Sum
set n4.price=Sum;

//calculate intermediate pricing at the COST-TYPE level
match (n3:COST_TYPE)<-[r3]-(n4:COST_SUBTYPE)
with n3,sum(r3.quantity*n4.price) as Sum
set n3.price=Sum;

//calculate intermediate pricing at the COST-GROUP level
match (n2:COST_GROUP)<-[r2]-(n3:COST_TYPE)
with n2,sum(r2.quantity*n3.price) as Sum
set n2.price=Sum;

//calculate intermediate pricing at the PRODUCT level
match (n1:PRODUCT)<-[r1]-(n2:COST_GROUP)
with n1, sum(r1.quantity*n2.price) as Sum
set n1.price=Sum;

Running these queries is really fast:
The advantage of having these intermediate pricing is of course that calculating the price of the product can now be done at every one of the levels. Let's look at two levels: if we use the intermediate pricing at COST-GROUP level, we run this query

//calculate pricing using intermediate pricing levels at the COST-GROUP level
match (n1:PRODUCT {id:1})<-[r1]-(n2:COST_GROUP)
return sum(r1.quantity*n2.price);

and the result is there instantaneously:
Running the same query at the COST-TYPE level takes a bit longer

//calculate pricing using intermediate pricing levels at the COST-TYPE level
match (n1:PRODUCT {id:1})<-[r1]-(n2:COST_GROUP)<-[r2]-(n3:COST_TYPE)
return sum(r1.quantity*r2.quantity*n3.price);

but gives the same result, fortunately:
Interesting. But what would happen if we would change one or more prices of COST_COMPONENTS? How would that affect the hierarchy/graph? Would it perform?

Doing simulations on the hierarchy - recalculating price

If we change something in the price of one of the nodes at the lowest level of the hierarchy, then that would obviously affect the price of the product at the top of the hierarchy. So how can we recalculate price? The "brute force" way is of course to re-run the sweeping query above, and run through the entire hierarchy again. But now that we have the intermediate prices, we can do this much more intelligently.

Essentially what we will do is, when we do the update of the price of the COST_COMPONENT, we will at the same time also update all of the intermediate prices above it. And, consequently, also recalculate the price of the top-level of the hierarchy, the PRODUCT level.

Here's the query that I wrote:

//Changing the price of ONE COST_COMPONENT
with n6, n6.price as OLDPRICE limit 1
set n6.price = n6.price*10
with n6.price-OLDPRICE as PRICEDIFF,n6
match n6-[r5:PART_OF]->(n5:COST)-[r4:PART_OF]->(n4:COST_SUBTYPE)-[r3:PART_OF]->(n3:COST_TYPE)-[r2:PART_OF]->(n2:COST_GROUP)-[r1:PART_OF]-(n1:PRODUCT)
set n5.price=n5.price+(PRICEDIFF*r5.quantity),
return PRICEDIFF, n1.price;

It basically does a couple of things:

  • it takes 1 COST_COMPONENT, and extracts the price (OLDPRICE)
  • it changes the price of that COST_COMPONENT to *10 as expensive
  • it stores the price difference between old and new price in a PRICEDIFF variable
  • it then runs through all the levels ABOVE the COST_COMPONENT involved, and changes the intermediate pricing of those nodes. By doing so, we get the new price at the top of the hierarchy.

the result of that changes is also there instantaneously:
We can do the same thing for a hundred COST_COMPONENTS at a time, and still get instantaneous responses. In the following query we increase the pricing of 100 COST_COMPONENTS with 5%:

//Changing the price of ONE HUNDRED COST_COMPONENTS
with n6, n6.price as OLDPRICE limit 100
set n6.price = round(n6.price*1.05)
with n6.price-OLDPRICE as PRICEDIFF,n6
match n6-[r5:PART_OF]->(n5:COST)-[r4:PART_OF]->(n4:COST_SUBTYPE)-[r3:PART_OF]->(n3:COST_TYPE)-[r2:PART_OF]->(n2:COST_GROUP)-[r1:PART_OF]-(n1:PRODUCT)
set n5.price=n5.price+(PRICEDIFF*r5.quantity),
return PRICEDIFF, n1.price;

And the result is there immediately (160ms):

According to the intermediate pricing, the pricing should now be as follows:
If we do another sweeping price calculation then we see that this approach is indeed correct.


All of the queries that I wrote for this blogpost are available in the gist over here. If you would run them in your neo4j instance you would be able to create a hierarchy yourself and take a look at the results. Just beware that the hierarchy that I created is quite big, and that some of the transactions involve hundreds of thousands of updates to neo4j in one transaction - and your machine has to be able to do that (mine bombed out on a number of occasions).

Aside from that, I took a away many different things from this weekend exploration of hierarchies in neo4j.

  • First of all, without any manipulation of intermediate calculations, neo4j performs fantastically for these types of hierarchical operations. Don't forget, we were looking at a truly large "Product" definition (2.1 millions nodes and relationships for 1 product), and we were recalculating the pricing in under a minute. 
  • Secondly, I found that if you would apply the traditional technique of "precalculating" parts of the hierarchy in neo4j (which is what we would always do in relational systems to maintain some kind of performance), the model would become a bit more complicated - but the speed would become AMAZING. 

So there you go - another fantastic use case for neo4j. Anything to do with hierarchies really should be modeled as a graph :) ...

Hope this is useful.




  1. Rik, this is fantastic. I work in the CAD/CAM/PLM area and product hierarchies for products are as you point out every where - but connecting between hierarchies (eg requirements to modules/ submodules, product 'attributes' to modules, etc etc) is hard. Your observation (and something I have concluded myself is) that graphs are useful in these more (but not completely structured) situations, is so true. BOM systems. CAD assembly hierarchies - when represented also usefully only have implicit relations between children.

    I would also like to point out that Neo4j is also better more allowing the hierarchy 'schema/model' for want of a better term to emerge and evolve. If anyone else is interested in developing in this 'product' development support area (tangible and non tangible product areas - let me know.

    1. I am currently working on a piece of software for a large manufacturing company that is interested in analyzing the impact to "cost" and "flow-time" by modifying the "precedence-task-network" of activities required to complete a product (or sub-system of a product) by constraining this "model" on various attributes like: quantity of resources available to perform work, space requirements (how many resources can fit in an area where the tasks are located), and many more. I started out by taking the approach of a graph of data without really knowing that graph db's existed - and then I found Neo4j :-) I would be very interested to learn about others that are interested in working on these types of problems and/or what other work has been done in this area so I don't re-invent the wheel :-)

      Fascinating stuff!!

  2. Very cool and I agree completely on the flexibility stuff...

    Had not made the link with CAD/CAM... would love to know what you are working on - ping me if you want to have a chat?


  3. Excellent study of hierarchy use case. This use case is very pertinent in my field. Thank you very much for this entry.

    When I get to creating the sixth level node creation, I get the "disconnected from server" error.
    I thought it was the jvm setting and so I increased the VM size to 8 GB. It did not make any difference.

    In the messages log, I do see a lot of

    GC Monitor: Application threads blocked for 9999ms WARNING messages.

    If you have any suggestions, I would surely appreciate it.



    1. Mmmm that's weird. What version of Neo4j are you using? As you can tell this post is a bit old, so there may be a bit of a different behaviour on the latest versions... Let me know and I will give it a go myself on the 3.0 series...

    2. Hi Rik,

      Wow... didn't expect a response. I suspect that there is a problem with the 2.3.2 release on Mac. I poked around the installation directory and saw the following in i4jlauncher.config :

      1019=The JVM found at {0} is damaged.\r\nPlease reinstall or define EXE4J_JAVA_HOME\r\nto point to an installed 32-bit JDK or JRE.
      1018=The {0} environment variable does not\r\npoint to a working 64-bit JDK or JRE.
      1017=The {0} environment variable does not\r\npoint to a working 32-bit JDK or JRE.
      1016=No JVM could be found on your system.\r\nPlease define EXE4J_JAVA_HOME\r\nto point to an installed {0}-bit JDK or JRE or download a JRE from

      So, I suspect it might be the package, but I am not sure.
      Having said this, I installed Neo4J on a Ubuntu 14 and it worked superbly.... Sorta.

      In the Community Edition 2.3.2 is that your queries on the stored intermediary do not return the same results.:

      match (n1:PRODUCT {id:1})<-[r1]-(:COST_GROUP)<-[r2]-(:COST_TYPE)<-[r3]-(:COST_SUBTYPE)<-[r4]-(:COST)<-[r5]-(n6:COST_COMPONENT)
      return sum(r1.quantity*r2.quantity*r3.quantity*r4.quantity*r5.quantity*n6.price);


      generate intermediary results per this blog...

      match (n1:PRODUCT {id:1})<-[r1]-(n2:COST_GROUP)<-[r2]-(n3:COST_TYPE) return sum(r1.quantity*r2.quantity*n3.price);


      match (n1:PRODUCT {id:1})<-[r1]-(n2:COST_GROUP) return sum(r1.quantity*n2.price);

      This is more disturbing in my opinion.

      Thanks for your kind response.



    3. For some reason I never saw this comment - only saw it just now when another reader commented...

      So did you solve this? I was not able to reproduce the above... Have you tried with a recent version of Neo4j?


  4. Hi
    Interesting discussion. I spent some time on Neo4j, it is great. Was there any success in implementing Neo4J for Product Structures in PLM.

    1. Yeah there's some very large projects happening / in production in that domain. Ping me and we can have a chat about them?