Hi everyone, I'm new to Neo4j.
Let say I have a graph of spectrum, where each spectrum has intensity (an array of numbers) as its property. I want to search a given spectrum against these spectrum to find the spectrum that is most similar. I'm trying k-nearest neighbor algorithm but it is looking for k-nearest-node for each node in the graph, but I want to find the nearest node to a given node only.
Thank you for your help
Hi @ameyasoft Thanks for your reply.
I'm using cosine similarity of two arrays, so for example similarity between [1,2,3] and [2,0,4] = (1x2 + 2x0 + 3x4) / (sqr(1^2 + 2^2 + 3^2)xsqr(2^2+0^2+4^2)). Here is the algorithm I used to find the similaries:
CALL gds.knn.stream('spectrumGraph', {
topK: 1,
nodeProperties: [{Intensities:'COSINE'}],
randomSeed: 1337,
concurrency: 1,
sampleRate: 1.0,
deltaThreshold: 0.0
})
YIELD node1, node2, similarity
RETURN gds.util.asNode(node1).title AS S1, gds.util.asNode(node2).title AS S2, similarity
ORDER BY similarity DESCENDING, S1, S2
I'm copying here to show properties of two nodes (since my array size is kinda large the neo4j desktop doesn't show full screenshot).
Node 1: : 1
Intensities:
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Node 2: : 1
Intensities: [0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0063722641200811584,0.006153010903497263,0.053466462958387126,0.11809743891361771,0.01937084767469783,0.0012389546841883627,0.0016600600684209244,0.0,0.0,0.005216834470781898,0.0,0.0,0.0,0.0,0.003671621325333491,0.0,0.05541538043913287,0.04315460135936994,0.03520232199596992,0.004503391464437476,0.014564677958787357,0.0014651683203463503,0.0018827934947918661,0.0,0.0,0.0,0.0,0.0,0.0030730252419615854,0.0,0.026157256759437458,0.012901137680579385,1.0,0.11479471982571109,0.0517228778550771,0.002902494962396333,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.021368488092462213,0.003998761045315812,0.06760307511336784,0.011679584045326251,0.12340127862907577,0.018124932570935375,0.00956013628501526,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.9085505274257932,0.1672902042535124,0.09603290886374631,0.009640181110117317,0.0017644663620323031,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.007813070971918187,0.0017087830054395678,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.12142451947003365,0.1823351511629121,0.04606405674134036,0.017035626907589987,0.0021264081798850836,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.006838612231545318,0.0013677224463090635,0.0012598359429106386,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.05447920400641751,0.010618120060277233,0.005143750065253933,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]
Thanks for your help!
Personally, I find this as very interesting project and want to help you.
Q: The spectrum intensity values show 0.0 and some non 0.0 numbers. Your example shows for one node. For other nodes the difference occurs in non 0.0 values only or it depends on the position of non 0.0 numbers in the array. If you can post values from two nodes (full images from node properties), I can try something from my end. Thanks
Hi @ameyasoft , It will depend on the position of the non zeroes numbers. I'm using k-nearest-neighbor algorithm. I'm posting the screen shots of two nodes, but it won't show all the numbers since my array has 1000 elements. So I will attach a file for that, but you can try with fewer elements as well. Thank you, I will be waiting for your kind reply.
Here is what I did:
1. Used apoc.coll.dropDuplicateNeighbors to delete duplicate 0.0 values form each node array intensities.
2. Used these truncated arrays to calculate cosine similarity. Since the two arrays above are similar, for my test I moved the first non 0.0 value to the end of the sencond truncated array.
3. Ran cosine similarity
with step 2, I ran the cosine similarity
RETURN gds.similarity.cosine(i1, i2) AS cosineSimilarity
result: 0.17864027595891765
Check and let me know. Thanks
with i1, apoc.coll.dropDuplicateNeighbors(i1) as i2
return size(i1), size(i2), i2
Result:
[0.0, 0.0063722641200811584, 0.006153010903497263, 0.053466462958387126, 0.11809743891361771, 0.01937084767469783, 0.0012389546841883627, 0.0016600600684209244, 0.0, 0.005216834470781898, 0.0, 0.003671621325333491, 0.0, 0.05541538043913287, 0.04315460135936994, 0.03520232199596992, 0.004503391464437476, 0.014564677958787357, 0.0014651683203463503, 0.0018827934947918661, 0.0, 0.0030730252419615854, 0.0, 0.026157256759437458, 0.012901137680579385, 1.0, 0.11479471982571109, 0.0517228778550771, 0.002902494962396333, 0.0, 0.021368488092462213, 0.003998761045315812, 0.06760307511336784, 0.011679584045326251, 0.12340127862907577, 0.018124932570935375, 0.00956013628501526, 0.0, 0.9085505274257932, 0.1672902042535124, 0.09603290886374631, 0.009640181110117317, 0.0017644663620323031, 0.0, 0.007813070971918187, 0.0017087830054395678, 0.0, 0.12142451947003365, 0.1823351511629121, 0.04606405674134036, 0.017035626907589987, 0.0021264081798850836, 0.0, 0.006838612231545318, 0.0013677224463090635, 0.0012598359429106386, 0.0, 0.05447920400641751, 0.010618120060277233, 0.005143750065253933, 0.0].
Originalt size of 1000 reduced to 61
Sorry for the delay. I was on Thanksgiving break. The intensity lists you posted look identical. Please post another list that is different from the posted one. Thanks.
Thank you so much. I will give it a try.
