Looks like you have some good changes in your Vectorz branch - any chance
you could tidy up and make a PR?
I like the idea of specialised getSlices and getColumns in particular -
these should be much faster than getting the slices one-by-one if the data
is very sparse.
On Monday, 29 December 2014 09:43:54 UTC+8, Matt Revelle wrote:
>
>
> On Dec 28, 2014, at 7:28 PM, Mike Anderson <mike.r.anderson...@gmail.com>
> wrote:
>
> Interesting idea. The challenge is that I'm not sure how to add
> representation specification in an implementation independent way. It's a
> quirk of vectorz that it has both indexed and hashed storage, I probably
> wouldn't expect any other implementations to have that. Likewise row and
> column oriented storage are fairly obvious choices but I still wouldn't
> expect every implementation to support both.
>
> Any idea how you would specify the API?
>
> I guess we could simply pass an optional map argument of options, but
> behaviour would be completely implementation specific.
>
>
> I think the map is the way to go. You’re probably correct about few other
> implementations having as many options, but adding a map of “preferences”
> seems like a good option. Creating a sparse matrix might then look like:
>
> ;; preferences as a separate arg
> (new-sparse-array [100000 100000] :vectorz {:order :row :indexed true})
>
> ;; an alternative, preferences combined with implementation selection
> (new-sparse-array [100000 100000] {:impl :vectorz :order :row :indexed
> true})
>
> Implementations should throw an exception if they don’t support (or
> understand) the preferences.
>
> On Monday, 29 December 2014 02:12:05 UTC+8, Matt Revelle wrote:
>>
>> Glad to see the addition of new-sparse-array to core.matrix. It looks
>> like it defaults to SparseRowMatrix for the Vectorz implementation? Should
>> the API provide a way to specify which sparse matrix representation (e.g.,
>> row- vs column-based, indexed vs hashed) should be used? I'd suggest a
>> 3-arity new-sparse-array which takes a keyword indicating the
>> representation to use as well as a new function which returns a list of
>> available representations for a specific implementation.
>>
>> I think at this point you incorporated (looks like we have some
>> duplication too, doh) all the changes I had made for sparse matrix support
>> in Vectorz, but will verify.
>>
>
> I definitely haven't covered all the potential code paths - in particular
> a lot of things aren't yet optimised for sparse operations. So any review /
> patches would be appreciated!
>
>
> I did some optimization of sparse ops but the code probably needs to be
> cleaned up before submitting (e.g., generalized and/or moved to the correct
> level in class hierarchy). Those changes were made hastily when I needed to
> quickly get a program running fast.
>
> A branch containing all performance changes based on an older revision of
> the develop branch is available here:
> https://github.com/mattrepl/vectorz/tree/sparse-speed
>
> There is a related sparse-speed branch in my forks of vectorz-clj and
> core.matrix.
>
> We should also look into other sparse array representations for Vectorz
> from: Matlab, MTJ (https://github.com/fommil/matrix-toolkits-java,
> specifically the LinkedSparseMatrix for row and column ops), etc.
>
> -Matt
>
>
>
>>
>> On Saturday, December 27, 2014 4:56:55 AM UTC-5, Mike Anderson wrote:
>>>
>>> Here is a little belated Christmas present for Clojure data aficionados:
>>>
>>> ;; setup
>>> (use 'clojure.core.matrix)
>>> (set-current-implementation :vectorz)
>>>
>>> ;; create a big sparse matrix with a trillion elements (initially zero)
>>> (def A (new-sparse-array [1000000 1000000]))
>>>
>>> ;; we are hopefully smart enough to avoid printing the whole array!
>>> A
>>> => #<SparseRowMatrix Large matrix with shape: [1000000,1000000]>
>>>
>>> ;; mutable setter operations supported so that you can set individual
>>> sparse elements
>>> (dotimes [i 1000]
>>> (mset! A (rand-int 1000000) (rand-int 1000000) (rand-int 100)))
>>>
>>> ;; all standard core.matrix operations supported
>>> (esum A)
>>> => 50479.0
>>>
>>> ;; efficient addition
>>> (time (add A A))
>>> => "Elapsed time: 12.849859 msecs"
>>>
>>> ;; matrix multiplication / inner products actually complete in sensible
>>> time
>>> ;; (i.e. much faster than than the usual O(n^3) which might take a few
>>> thousand years)
>>> (time (mmul A (transpose A)))
>>> => "Elapsed time: 2673.085171 msecs"
>>>
>>>
>>> Some nice things to note about the implementation:
>>> - Everything goes through the core.matrix API, so your code won't have
>>> to change to use sparse matrices :-)
>>> - Sparse matrices are 100% interoperable with non-sparse (dense) matrices
>>> - Sparse arrays are fully mutable. Management of storage / indexing
>>> happens automatically
>>> - It isn't just matrices - you can have sparse vectors, N-dimensional
>>> arrays etc.
>>> - Code is pure JVM - no native dependencies to worry about
>>>
>>> This is all still very much alpha - so any comments / patches / more
>>> rigorous testing much appreciated!
>>>
>>>
>>>
>>>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Numerical Clojure" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/numerical-clojure/LLpq4WHx-k8/unsubscribe
> .
> To unsubscribe from this group and all its topics, send an email to
> numerical-clojure+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>
>
>
--
You received this message because you are subscribed to the Google
Groups "Clojure" group.
To post to this group, send email to clojure@googlegroups.com
Note that posts from new members are moderated - please be patient with your
first post.
To unsubscribe from this group, send email to
clojure+unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/clojure?hl=en
---
You received this message because you are subscribed to the Google Groups
"Clojure" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to clojure+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
