Building a large distance matrix
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I am trying to build a distance matrix for around 600,000 locations for which I have the latitudes and longitudes. I want to use this distance matrix for agglomerative clustering. Since this is a large set of locations, calculating the distance matrix is an extremely heavy operation. Is there any way to opimize this process while keeping in mind that I am going to use this matrix for clustering later. Below is the code I am using.
from scipy.spatial.distance import pdist
import time
start = time.time()
# dist is a custom distance function that I wrote
y = pdist(locations[['Latitude', 'Longitude']].values, metric=dist)
end = time.time()
print(end - start)
python clustering distance
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
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Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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$begingroup$
I am trying to build a distance matrix for around 600,000 locations for which I have the latitudes and longitudes. I want to use this distance matrix for agglomerative clustering. Since this is a large set of locations, calculating the distance matrix is an extremely heavy operation. Is there any way to opimize this process while keeping in mind that I am going to use this matrix for clustering later. Below is the code I am using.
from scipy.spatial.distance import pdist
import time
start = time.time()
# dist is a custom distance function that I wrote
y = pdist(locations[['Latitude', 'Longitude']].values, metric=dist)
end = time.time()
print(end - start)
python clustering distance
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
$endgroup$
add a comment |
$begingroup$
I am trying to build a distance matrix for around 600,000 locations for which I have the latitudes and longitudes. I want to use this distance matrix for agglomerative clustering. Since this is a large set of locations, calculating the distance matrix is an extremely heavy operation. Is there any way to opimize this process while keeping in mind that I am going to use this matrix for clustering later. Below is the code I am using.
from scipy.spatial.distance import pdist
import time
start = time.time()
# dist is a custom distance function that I wrote
y = pdist(locations[['Latitude', 'Longitude']].values, metric=dist)
end = time.time()
print(end - start)
python clustering distance
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
$endgroup$
I am trying to build a distance matrix for around 600,000 locations for which I have the latitudes and longitudes. I want to use this distance matrix for agglomerative clustering. Since this is a large set of locations, calculating the distance matrix is an extremely heavy operation. Is there any way to opimize this process while keeping in mind that I am going to use this matrix for clustering later. Below is the code I am using.
from scipy.spatial.distance import pdist
import time
start = time.time()
# dist is a custom distance function that I wrote
y = pdist(locations[['Latitude', 'Longitude']].values, metric=dist)
end = time.time()
print(end - start)
python clustering distance
python clustering distance
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
asked 6 mins ago
Karthik KatragaddaKarthik Katragadda
113
113
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Karthik Katragadda is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
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