DBSCAN clustering is not working even on 40k data but working on 10k data using python and sklearn

Question

I am trying to cluster my dataset. I have 700k rows in my data set. I took 40k from it and tried DBSCAN clustering in python and sklearn. I ran on 32 GB ram. The algorithm ran the whole night but it didn't finish and I stopped the program then manually.

But when I tried with 10k data set it was running.

Is there any limitation of DBSCAN in the case of dataset size?

I used below code:

clustering = DBSCAN().fit(df)
pred_y = clustering.labels_

and also below version:

clustering = DBSCAN(eps=9.7, min_samples=2, algorithm='ball_tree', metric='minkowski', leaf_size=90, p=2).fit(df)
pred_y = clustering.labels_

How can I use DBSCAN clustering in my dataset?

Answer 1

[UPDATED]

How many columns are we talking about here? From my experience with DBSCAN it's the number of columns that impacts performance more than the number of rows. I tend to use PCA before fitting the data into DBSCAN to reduce the dimensionallity - this significantly speeds up the clustering process.

Based on the additional info you provided I did a simple repro (warning: With current params it will run for looooong time):

import numpy as np

data_1k = np.random.random((1000, 4))
data_5k = np.random.random((5000, 4))
data_10k = np.random.random((10000, 4))
data_40k = np.random.random((40000, 4))

from sklearn.cluster import DBSCAN

clustering = DBSCAN(eps=9.7, min_samples=2, algorithm='ball_tree', metric='minkowski', leaf_size=90, p=2).fit(data_40k)
np.unique(clustering.labels_)

Above code will execute in just several seconds for 10k dataset but for 40k it will be processing it for super long time and it is caused by a really high value for eps param. Are you absolutely sure that it's the "right" value for your data?
For the example I provided above, simply lowering down eps value (eg to 0.08 ) speeds up the process to just ~3 seconds.

In case eps=9.7 is truly the required value for your data I would consider using some scalers or something that would maybe help reduce the values range? (and lower down eps value)