Fast kNN from python

[Janto Dreijer]

Hi!

I am looking for a Python implementation or bindings to a library that
can quickly find k-Nearest Neighbors given an arbitrary distance
metric between objects. Specifically, I have an "edit distance"
between objects that is written in Python.

I haven't looked at the methods in detail but I think I'm looking for
one of the data structures listed on http://en.wikipedia.org/wiki/Metric_trees
(i.e. vp-trees, cover trees, m-trees or bk trees). But I might be
wrong. An approximate kNN would also work.

If there doesn't exist such an implementation yet, any advice on a
library I can wrap myself would also be appreciated.

Thanks!
Janto

PS Before anyone suggests it, I can't use the library at
http://www.cs.umd.edu/~mount/ANN/ as it assumes Minkowski distance
functions.

[Tim Churches]

Janto Dreijer wrote:

I am looking for a Python implementation or bindings to a library that
can quickly find k-Nearest Neighbors given an arbitrary distance
metric between objects. Specifically, I have an "edit distance"
between objects that is written in Python.

Orange? See http://www.ailab.si/orange/ - not sure about speed, but
quite a few parts of it are written in C, and it does kNN.

Tim C

[Miki]

Hello,

I am looking for a Python implementation or bindings to a library that
can quickly find k-Nearest Neighbors given an arbitrary distance
metric between objects. Specifically, I have an "edit distance"
between objects that is written in Python.

First Google search for "k-Nearest Neighbors python", yielded
http://people.revoledu.com/kardi/tut...resources.html which
pointed to http://biopython.org/DIST/docs/api/p...NN-module.html

HTH,
--
Miki <mi*********@gmail.com>
http://pythonwise.blogspot.com

[Sean Davis]

On Aug 14, 6:16 am, Janto Dreijer <[e-mail]:

Hi!

I am looking for a Python implementation or bindings to a library that
can quickly find k-Nearest Neighbors given an arbitrary distance
metric between objects. Specifically, I have an "edit distance"
between objects that is written in Python.

I haven't looked at the methods in detail but I think I'm looking for
one of the data structures listed onhttp://en.wikipedia.org/wiki/Metric_trees
(i.e. vp-trees, cover trees, m-trees or bk trees). But I might be
wrong. An approximate kNN would also work.

If there doesn't exist such an implementation yet, any advice on a
library I can wrap myself would also be appreciated.

Thanks!
Janto

Have you looked at using Rpy and R? There are probably several knn
implementations that then become accessible to you (although I haven't
checked recently).

Sean

[Janto Dreijer]

On Aug 14, 8:44 pm, Miki <[e-mail]:

Hello,

I am looking for a Python implementation or bindings to a library that
can quickly find k-Nearest Neighbors given an arbitrary distance
metric between objects. Specifically, I have an "edit distance"
between objects that is written in Python.

First Google search for "k-Nearest Neighbors python", yieldedhttp://people.revoledu.com/kardi/tutorial/KNN/resources.html which
pointed tohttp://biopython.org/DIST/docs/api/public/Bio.kNN-module.html

HTH,
--
Miki <[e-mail]>http://pythonwise.blogspot.com

Thanks. Indeed, I did see that page. Unfortunately biopython's knn
does a brute force search for the nearest k and is therefore way too
slow.

Janto

[Janto Dreijer]

On Aug 14, 9:27 pm, Sean Davis <[e-mail]:

On Aug 14, 6:16 am, Janto Dreijer <[e-mail]:

Hi!

I am looking for a Python implementation or bindings to a library that
can quickly find k-Nearest Neighbors given an arbitrary distance
metric between objects. Specifically, I have an "edit distance"
between objects that is written in Python.

I haven't looked at the methods in detail but I think I'm looking for
one of the data structures listed onhttp://en.wikipedia.org/wiki/Metric_trees
(i.e. vp-trees, cover trees, m-trees or bk trees). But I might be
wrong. An approximatekNNwould also work.

If there doesn't exist such an implementation yet, any advice on a
library I can wrap myself would also be appreciated.

Thanks!
Janto

Have you looked at using Rpy and R? There are probably severalknn
implementations that then become accessible to you (although I haven't
checked recently).

Sean

Interesting. I have not looked at that. I can't really find an R
package that does what I want, so any suggestions are appreciated.

Janto