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o_guest's profile
Olivia Guest | Ολίβια Γκεστ
Olivia Guest | Ολίβια Γκεστ
Olivia Guest | Ολίβια Γκεστ
@o_guest

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Olivia Guest | Ολίβια Γκεστ

@o_guest

• goth gremlin • computational cognitive/neuroscience modeling • geek & techish Cypriot • plant aficionada • came up with #bropenscience • http://neuroplausible.com  •

Τότεναμ, Λονδίνο & Cyprus
olivia.science
Joined October 2015

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    Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
    • Report Tweet

    What's the best way to calculate pairwise distances for #bigdata in #python? Using scipy is giving me memory errors, but I have 64GB RAM. 😅

    11:43 AM - 21 Feb 2017
    • 2 Retweets
    • 7 Likes
    • Eiko Fried Remi Gau John Flournoy Dr Veronika CH Jonathan Dekhtiar Chris Madan 🐘🧠💻 Christophe Tricot
    9 replies 2 retweets 7 likes
      1. New conversation
      2.  🐸‏ @froggleston 22 Feb 2017
        • Report Tweet
        Replying to @o_guest

        Map reducable? Or do you need to retain context for all-vs-all at all times?

        1 reply 0 retweets 0 likes
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 22 Feb 2017
        • Report Tweet
        Replying to @froggleston

        I have been given a solution that samples the distances and this does the job — I do not (yet) understand the code very much.

        1 reply 0 retweets 0 likes
      4. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 22 Feb 2017
        • Report Tweet
        Replying to @o_guest @froggleston

        I understood enough to pluck from where it was, fix the globals (naughty naughty), and use it on dummy data & compare w pdist.

        1 reply 0 retweets 0 likes
      5. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 22 Feb 2017
        • Report Tweet
        Replying to @o_guest @froggleston

        It's v obv sampling using a step, but it possibly can cope w step = 1 (i.e., sample all) as it's written with multiprocessing.

        1 reply 0 retweets 0 likes
      6. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 22 Feb 2017
        • Report Tweet
        Replying to @o_guest @froggleston

        The solution exists because I have taken over the coding bit of project from previous coder/pd.

        0 replies 0 retweets 0 likes
      7. End of conversation
      1. New conversation
      2. Jonathan Dekhtiar‏ @born2data 21 Feb 2017
        • Report Tweet
        Replying to @o_guest

        maybe you should use a different algorithm. Using KNN or any lasy learner is most of time bad for big data... Try SVM or XGBoost

        1 reply 0 retweets 0 likes
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @born2data

        this isn't a neural network... I just need to calculate pairwise distances...

        2 replies 0 retweets 0 likes
      4. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @o_guest @born2data

        I have some x, y, points that's it.

        0 replies 0 retweets 0 likes
      5. End of conversation
      1. New conversation
      2. Ale  😡‏ @aleperalta82 21 Feb 2017
        • Report Tweet
        Replying to @o_guest

        afaik scipy & numpy copy arrays when operating, so maybe try using iterators? https://gist.github.com/alep/603b41674dcb0b1fd5d2b752d386840d …

        1 reply 0 retweets 1 like
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @aleperalta82

        ah good tip! Explains the reason it's running out of memory, I guess. I'll see what I can do. Just 1 call to pdist currently.

        0 replies 0 retweets 2 likes
      4. End of conversation
      1. New conversation
      2. Kevin M Moermⓐn‏ @KMMoerman 22 Feb 2017
        • Report Tweet
        Replying to @o_guest

        had this with MATLAB. n points requires nxn matrix. I use for loop and devide problem in chunks of the max var size eg 10x nx(n/10)

        1 reply 0 retweets 1 like
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 22 Feb 2017
        • Report Tweet
        Replying to @KMMoerman

        basically what I have been given as the solution by somebody else, yep!

        0 replies 0 retweets 0 likes
      4. End of conversation
      1. New conversation
      2. Jonathan Dekhtiar‏ @born2data 21 Feb 2017
        • Report Tweet
        Replying to @o_guest

        you can't use data streaming ou chunk processing?

        1 reply 0 retweets 0 likes
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @born2data

        I probably can, I'll Google how!

        0 replies 0 retweets 1 like
      4. End of conversation
      1. New conversation
      2. Sebastien Dery‏ @SebDery 21 Feb 2017
        • Report Tweet
        Replying to @o_guest

        Erratum, not quite 400Gb (rather 50 ish) but you get my point ;)

        1 reply 0 retweets 0 likes
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @SebDery

        I don't think it used that much of my RAM which can fit 50GB. But I have a solution now — just need to try it out tomorrow.

        0 replies 0 retweets 0 likes
      4. End of conversation
      1. New conversation
      2. Sebastien Dery‏ @SebDery 21 Feb 2017
        • Report Tweet
        Replying to @o_guest

        How many "items" are you computing the distance for? 10k * 10k * 64bits precision float > 400Gb

        1 reply 0 retweets 0 likes
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @SebDery

        tens of millions

        0 replies 0 retweets 0 likes
      4. End of conversation
      1. New conversation
      2. Han Bossier‏ @HBossier 21 Feb 2017
        • Report Tweet
        Replying to @o_guest

        @cMadan or try random sampling pairs from all pairs and iterate

        1 reply 0 retweets 1 like
      3. Olivia Guest | Ολίβια Γκεστ‏ @o_guest 21 Feb 2017
        • Report Tweet
        Replying to @HBossier @cMadan

        any specific package suggestion?

        1 reply 0 retweets 0 likes
      4. Han Bossier‏ @HBossier 21 Feb 2017
        • Report Tweet
        Replying to @o_guest @cMadan

        hm, not that I know, probably need to code it yourself... :P

        0 replies 0 retweets 1 like
      5. End of conversation

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