Pass the whole matrix to addItem and getNNs function

[yzizhen]

Pass the whole matrix to addItem and getNNs function

[LTLA]

FWIW the BiocNeighbors::findAnnoy interface and related functions operate on whole matrices.

[yzizhen]

Thanks a lot for the suggestion. I found exactly what I need in BiocNeighbors package. Best Zizhen

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On Wed, Jan 27, 2021 at 2:06 PM Dirk Eddelbuettel ***@***.***> wrote: Please feel free to propose such an addition in pull request. As @LTLA <https://github.com/LTLA> mentioned you may also want to look at the BiocNeighbors package. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#70 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIG5H46NX7FRDAEZESICN43S4CE45ANCNFSM4WUZ6D6Q> .

[eddelbuettel]

Hi @yzizhen that seems like a reasonable suggesion, on the other hand we always ways followed the Python API of annoy itself pretty closely which AFAIK does not have that. And @LTLA is of course spot: maybe his BioConductor package can help you?

[yzizhen]

Hi, Dirk Thanks for the quick response. I would expect looping across all the rows would be a lot faster in C++ than in R, when users have a matrix with millions of rows to process. It might be less of a problem for python. Having these new functionalities could really help adaptation of this package in R community for computationally heavy tasks. Thanks a lot Zizhen

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On Wed, Jan 27, 2021 at 5:12 AM Dirk Eddelbuettel ***@***.***> wrote: Hi @yzizhen <https://github.com/yzizhen> that seems like a reasonable suggesion, on the other hand we always ways followed the Python API of annoy itself pretty closely which AFAIK does not have that. And @LTLA <https://github.com/LTLA> is of course spot: maybe his BioConductor package can help you? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#70 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIG5H4YG65PTNIAMTDGFMJ3S4AGNBANCNFSM4WUZ6D6Q> .

[eddelbuettel]

Please feel free to propose such an addition in pull request. As @LTLA mentioned you may also want to look at the BiocNeighbors package.

[yzizhen]

Just one more thing, could you add Cosine function to the BiocNeighbors package as well? Only Euclidean and Manhattan distance metrics are supported now. Thanks

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On Wed, Jan 27, 2021 at 12:17 AM Aaron Lun ***@***.***> wrote: FWIW the BiocNeighbors::findAnnoy interface and related functions operate on whole matrices. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#70 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIG5H43WMXOVBW32U6HY5VLS37D2DANCNFSM4WUZ6D6Q> .