How to cluster nodes together in Neo4j - neo4j

My graph is 1M nodes. The data model is intentionally simple. There are Entities and IDType nodes. A single Entity may have 1:many IDType nodes. And an IDType node may be connected to 1:many Entities. This forms the graph.
The goal is to find all clusters of IDType's and Entities that are connected together into what I call a cluster of nodes (subgraph I guess some call it). Imagine if we had 1M nodes. I would like to find "clusters" like this in the graph data, I'm trying to figure out how to do that. I've written the cypher query that I believe does it, but it's not clear to me if it's doing what is intended.
The question: how do I efficiently traverse my graph and cluster together nodes so that there is a single row or group of rows that I can return as a row-based result set to my python driver program to then operate over that cluster. While this doesn't need to be the exact structure of my result, this is a sense of what I'm looking for.
cluster|nodes
1|2,3,4,5,6,7
2|10,11,12,13
3|15,17,19,20,21,25,27,28,33
Where the "cluster" is some arbitrary clustering of the list of nodes (frankly if I have a single line that's just a collection of clusters or some other way of telling they are all related, then I'm golden). The "nodes" number represents a unique integer-based property that we tag to every Entity node.
The query is below. The concept is that an "Entity" node can have 1 or many "ID" nodes and I'm trying to get all "Entity" and "ID" that are related to each other through the relationship "HAS_ID".
Conceptually, if there is a relationship that exists in the data like this Entity1-->ID1<--Entity2-->ID2<--Entity3-->ID3<--Entity4-->ID4<--Entity5 then I want to "cluster" them together so that I can create a unique number that represents this group of nodes. With my example, there are 5 entities, but there could just as easily be 2 entities, or 50 entities, which are all related to one another, that's why I'm thinking the variable length path is what I need.
The below is my attempt to do this in the graph. But 1) is it correct? 2) is it efficient because it seems to runs indefinitely 3) how do i best "group" these together?
match
(n:Entity)-[e1:HAS_ID*]-(o)
where n.key <> o.key
return *
limit 10
;
I've also tried
match (n:Entity)-[e1:HAS_ID*]-(o)
where n.key <> o.key
with distinct n.key as key_1, o.key as key_2
return key_1, collect(key_2)
limit 100
;
This seems to do close to what I want, but I'm still not getting a single group for a given key, in other words, I can have 5 rows returned but they are all still related, which I'd rather have 1 row in that case... He's an example, you can see that key "49518" is on the first and second row, I'd rather have one row that grouped them all together.
49518 [49004, 49871, 49940, 50525, 49101, 49625, 50165, 50017, 49098, 50383]
49940 [49088, 49706, 50292, 50470, 49140, 49258, 49216, 49559, 50004, 50346, 49237, 49518, 49894, 49101, 49625, 50165, 50017, 49098, 50383]

Well, for one, your query doesn't match the relationship pattern you described.
Each of your arrows in your pattern is a [:HAS_ID] relationship, so if entities and IDs are always alternating between each relationship, then your current query would only match patterns like this:
(:Entity)-[:HAS_ID]->(:ID)<-[:HAS_ID]-(:Entity)-[:HAS_ID]->(:ID)<-[:HAS_ID]-(:Entity)
3 entities, 2 IDs, 4 relationships. That doesn't match your example pattern of 5 entities, 4 IDs, and 8 relationships. So at the very least, you'll want to alter your pattern to use *8.
As for efficiency...the thing you're trying to do seems rather inefficient, as it must attempt to find this pattern on every single :Entity node in your graph, trying every single :HAS_ID relationship it finds. If your entire graph is made of this same pattern of :Entity and :ID and :HAS_ID, then your query is going to be traversing your entire graph, not once but multiple times.
You are going to get duplicate results. Even if we assume that your entire graph is made up of isolated 5 entity / 4 ID / 8 relationship chains like a snake, as in your example (an entity either being at the end of the chain with one link to an ID, or somewhere in the middle with links to 2 IDs), then you'll be getting 2 matches for that same group of nodes, one matching from one end of the chain, the other matching the other end. And that's the simple case...I'm guessing your graph could be much more complex than this, allowing even more possibilities for many different patterns to match on the exact same group of nodes. A unique path using your pattern does not equate to a unique grouping of nodes.
At the very least, you'll probably want to match on a pattern and use RETURN DISTINCT NODES(p) to enforce unique sets of nodes, but I still think the matching may take quite a bit of time.

Related

NEO4J - Matching a path where middle node might exist or not

I have the following graph:
I would look to get all contractors and subcontractors and clients, starting from David.
So I thought of a query likes this:
MATCH (a:contractor)-[*0..1]->(b)-[w:works_for]->(c:client) return a,b,c
This would return:
(0:contractor {name:"David"}) (0:contractor {name:"David"}) (56:client {name:"Sarah"})
(0:contractor {name:"David"}) (1:subcontractor {name:"John"}) (56:client {name:"Sarah"})
Which returns the desired result. The issue here is performance.
If the DB contains millions of records and I leave (b) without a label, the query will take forever. If I add a label to (b) such as (b:subcontractor) I won't hit millions of rows but I will only get results with subcontractors:
(0:contractor {name:"David"}) (1:subcontractor {name:"John"}) (56:client {name:"Sarah"})
Is there a more efficient way to do this?
link to graph example: https://console.neo4j.org/r/pry01l
There are some things to consider with your query.
The relationship type is not specified- is it the case that the only relationships from contractor nodes are works_for and hired? If not, you should constrain the relationship types being matched in your query. For example
MATCH (a:contractor)-[:works_for|:hired*0..1]->(b)-[w:works_for]->(c:client)
RETURN a,b,c
The fact that (b) is unlabelled does not mean that every node in the graph will be matched. It will be reached either as a result of traversing the works_for or hired relationships if specified, or any relationship from :contractor, or via the works_for relationship.
If you do want to label it, and you have a hierarchy of types, you can assign multiple labels to nodes and just use the most general one in your query. For example, you could have a label such as ExternalStaff as the generic label, and then further add Contractor or SubContractor to distinguish individual nodes. Then you can do something like
MATCH (a:contractor)-[:works_for|:hired*0..1]->(b:ExternalStaff)-[w:works_for]->(c:client)
RETURN a,b,c
Depends really on your use cases.

Neo4j and Cypher - How can I create/merge chained sequential node relationships (and even better time-series)?

To keep things simple, as part of the ETL on my time-series data, I added a sequence number property to each row corresponding to 0..370365 (370,366 nodes, 5,555,490 properties - not that big). I later added a second property and named it "outeseq" (original) and "ineseq" (second) to see if an outright equivalence to base the relationship on might speed things up a bit.
I can get both of the following queries to run properly on up to ~30k nodes (LIMIT 30000) but past that, its just an endless wait. My JVM has 16g max (if it can even use it on a windows box):
MATCH (a:BOOK),(b:BOOK)
WHERE a.outeseq=b.outeseq-1
MERGE (a)-[s:FORWARD_SEQ]->(b)
RETURN s;
or
MATCH (a:BOOK),(b:BOOK)
WHERE a.outeseq=b.ineseq
MERGE (a)-[s:FORWARD_SEQ]->(b)
RETURN s;
I also added these in hopes of speeding things up:
CREATE CONSTRAINT ON (a:BOOK)
ASSERT a.outeseq IS UNIQUE
CREATE CONSTRAINT ON (b:BOOK)
ASSERT b.ineseq IS UNIQUE
I can't get the relationships created for the entire data set! Help!
Alternatively, I can also get bits of the relationships built with parameters, but haven't figured out how to parameterize the sequence over all of the node-to-node sequential relationships, at least not in a semantically general enough way to do this.
I profiled the query, but did't see any reason for it to "blow-up".
Another question: I would like each relationship to have a property to represent the difference in the time-stamps of each node or delta-t. Is there a way to take the difference between the two values in two sequential nodes, and assign it to the relationship?....for all of the relationships at the same time?
The last Q, if you have the time - I'd really like to use the raw data and just chain the directed relationships from one nodes'stamp to the next nearest node with the minimum delta, but didn't run right at this for fear that it cause scanning of all the nodes in order to build each relationship.
Before anyone suggests that I look to KDB or other db's for time series, let me say I have a very specific reason to want to use a DAG representation.
It seems like this should be so easy...it probably is and I'm blind. Thanks!
Creating Relationships
Since your queries work on 30k nodes, I'd suggest to run them page by page over all the nodes. It seems feasible because outeseq and ineseq are unique and numeric so you can sort nodes by that properties and run query against one slice at time.
MATCH (a:BOOK),(b:BOOK)
WHERE a.outeseq = b.outeseq-1
WITH a, b ORDER BY a.outeseq SKIP {offset} LIMIT 30000
MERGE (a)-[s:FORWARD_SEQ]->(b)
RETURN s;
It will take about 13 times to run the query changing {offset} to cover all the data. It would be nice to write a script on any language which has a neo4j client.
Updating Relationship's Properties
You can assign timestamp delta to relationships using SET clause following the MATCH. Assuming that a timestamp is a long:
MATCH (a:BOOK)-[s:FORWARD_SEQ]->(b:BOOK)
SET s.delta = abs(b.timestamp - a.timestamp);
Chaining Nodes With Minimal Delta
When relationships have the delta property inside, the graph becomes a weighted graph. So we can apply this approach to calculate the shortest path using deltas. Then we just save the length of the shortest path (summ of deltas) into the relation between the first and the last node.
MATCH p=(a:BOOK)-[:FORWARD_SEQ*1..]->(b:BOOK)
WITH p AS shortestPath, a, b,
reduce(weight=0, r in relationships(p) : weight+r.delta) AS totalDelta
ORDER BY totalDelta ASC
LIMIT 1
MERGE (a)-[nearest:NEAREST {delta: totalDelta}]->(b)
RETURN nearest;
Disclaimer: queries above are not supposed to be totally working, they just hint possible approaches to the problem.

Neo4j: error in adding relationships among existing nodes

When writing a query to add relationships to existing nodes, it keeps me warning with this message:
"This query builds a cartesian product between disconnected patterns.
If a part of a query contains multiple disconnected patterns, this will build a cartesian product between all those parts. This may produce a large amount of data and slow down query processing. While occasionally intended, it may often be possible to reformulate the query that avoids the use of this cross product, perhaps by adding a relationship between the different parts or by using OPTIONAL MATCH (identifier is: (e))"
If I run the query, it creates no relationships.
The query is:
match
(a{name:"Angela"}),
(b{name:"Carlo"}),
(c{name:"Andrea"}),
(d{name:"Patrizia"}),
(e{name:"Paolo"}),
(f{name:"Roberta"}),
(g{name:"Marco"}),
(h{name:"Susanna"}),
(i{name:"Laura"}),
(l{name:"Giuseppe"})
create
(a)-[:mother]->(b),
(a)-[:grandmother]->(c), (e)-[:grandfather]->(c), (i)-[:grandfather]->(c), (l)-[:grandmother]->(c),
(b)-[:father]->(c),
(e)-[:father]->(b),
(l)-[:father]->(d),
(i)-[:mother]->(d),
(d)-[:mother]->(c),
(c)-[:boyfriend]->(f),
(g)-[:brother]->(f),
(g)-[:brother]->(h),
(f)-[:sister]->(g), (f)-[:sister]->(h)
Can anyone help me?
PS: if I run the same query, but with just one or two relationships (and less nodes in the match clause), it creates the relationships correctly.
What is wrong here?
First of all, as I mentionned in my comments, you don't have any Labels, it's a really bad practice because Labels are useful to match properties in a certains dataset (if you match "name" property, you don't want to match it on a node who doesn't have a name, Labels are here for that.
The second problem is that your query doesn't know how many nodes it will get before it does. It means that if you have 500 000 nodes having name : "Angela" and 500 000 nodes having name : "Carlo", you will create one relation from each Angela node, going on each Carlo, that's quite a big query (500 000 * 500 000 relations to create if my maths aren't bad). Cypher is giving you a warning for that.
Cypher will still tell you this warning because you aren't using Unique properties to match your nodes, even with Labels, you will still have the warning.
Solution?
Use unique properties to create and match your nodes, so you avoid cartesian product.
Always use labels, Neo4j without labels is like using one giant table in SQL to store all of your data.
If you want to know how your query will run, use PROFILE before your query, here is the profile plan for your query:
Does every single one of those name strings exist? If not then you're not going to get any results because it's all one big match. You could try changing it to a MERGE.
But Supamiu is right, you really should have a label (say Person) and an index on :Person(name).

An Example Showing the Necessity of Relationship Type Index and Related Execution Plan Optimization

Suppose I have a large knowledge base with many relationship types, e.g., hasChild, livesIn, locatedIn, capitalOf, largestCityOf...
The number of capicalOf relationships is relatively small (say, one hundred) compared to that of all nodes and other types of relationships.
I want to fetch any capital which is also the largest city in their country by the following query:
MATCH city-[:capitalOf]->country, city-[:largestCityOf]->country RETURN city
Apparently it would be wise to take the capitalOf type as clue, scan all 100 relationship with this type and refine by [:largestCityOf]. However the current execution plan engine of neo4j would do an AllNodesScan and Expand. Why not consider add an "RelationshipByTypeScan" operator into the current query optimization engine, like what NodeByLabelScan does?
I know that I can transform relationship types to relationship properties, index it using the legacy index and manually indicate
START r=relationship:rels(rtype = "capitalOf")
to tell neo4j how to make it efficient. But for a more complicated pattern query with many relationship types but no node id/label/property to start from, it is clearly a duty of the optimization engine to decide which relationship type to start with.
I saw many questions asking the same problem but getting answers like "negative... a query TYPICALLY starts from nodes... ". I just want to use the above typical scenario to ask why once more.
Thanks!
A relationship is local to its start and end node - there is no global relationship dictionary. An operation like "give me globally all relationships of type x" is therefore an expensive operation - you need to go through all nodes and collect matching relationships.
There are 2 ways to deal with this:
1) use a manual index on relationships as you've sketched
2) assign labels to your nodes. Assume all the country nodes have a Country label. Your can rewrite your query:
MATCH (city)-[:capitalOf]->(country:Country), (city)-[:largestCityOf]->(country) RETURN city
The AllNodesScan is now a NodeByLabelScan. The query grabs all countries and matches to the cities. Since every country does have one capital and one largest city this is efficient and scales independently of the rest of your graph.
If you put all relationships into one index and try to grab to ~100 capitalOf relationships that operation scales logarithmically with the total number of relationships in your graph.

Is a DFS Cypher Query possible?

My database contains about 300k nodes and 350k relationships.
My current query is:
start n=node(3) match p=(n)-[r:move*1..2]->(m) where all(r2 in relationships(p) where r2.GameID = STR(id(n))) return m;
The nodes touched in this query are all of the same kind, they are different positions in a game. Each of the relationships contains a property "GameID", which is used to identify the right relationship if you want to pass the graph via a path. So if you start traversing the graph at a node and follow the relationship with the right GameID, there won't be another path starting at the first node with a relationship that fits the GameID.
There are nodes that have hundreds of in and outgoing relationships, some others only have a few.
The problem is, that I don't know how to tell Cypher how to do this. The above query works for a depth of 1 or 2, but it should look like [r:move*] to return the whole path, which is about 20-200 hops.
But if i raise the values, the querys won't finish. I think that Cypher looks at each outgoing relationship at every single path depth relating to the start node, but as I already explained, there is only one right path. So it should do some kind of a DFS search instead of a BFS search. Is there a way to do so?
I would consider configuring a relationship index for the GameID property. See http://docs.neo4j.org/chunked/milestone/auto-indexing.html#auto-indexing-config.
Once you have done that, you can try a query like the following (I have not tested this):
START n=node(3), r=relationship:rels(GameID = 3)
MATCH (n)-[r*1..]->(m)
RETURN m;
Such a query would limit the relationships considered by the MATCH cause to just the ones with the GameID you care about. And getting that initial collection of relationships would be fast, because of the indexing.
As an aside: since neo4j reuses its internally-generated IDs (for nodes that are deleted), storing those IDs as GameIDs will make your data unreliable (unless you never delete any such nodes). You may want to generate and use you own unique IDs, and store them in your nodes and use them for your GameIDs; and, if you do this, then you should also create a uniqueness constraint for your own IDs -- this will, as a nice side effect, automatically create an index for your IDs.

Resources