| --- Log opened Wed May 17 00:00:33 2017 | ||
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| @sukey | Pull Request #3812 "Add global fixture with binary label data" synchronized by MikeLing - https://github.com/shogun-toolbox/shogun/pull/3812 | 05:41 |
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| mikeling | wiking: ping | 08:34 |
| @wiking | pong | 08:35 |
| mikeling | wiking: what's this error for? https://ci.appveyor.com/project/vigsterkr/shogun/build/4.2.736/job/153p5yu4py10h3i8#L6660 | 08:36 |
| mikeling | and on Travis CI, I guess it doesn't build with the latest commit | 08:49 |
| mikeling | the format error is about f101fd9142e0eeeafeaff160456343821c4dcd5a https://travis-ci.org/shogun-toolbox/shogun/jobs/233082415#L531, | 08:50 |
| mikeling | but the latest one is f2ec710cbd354d29bd68676d60bf5213a471c7ab | 08:51 |
| mikeling | and I had check my pr's format locally before I push it. I don't think there are any format issue | 08:51 |
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| @wiking | mikeling, i can try restarting it as it seem some internal error | 09:12 |
| @wiking | mmm there seems to be | 09:12 |
| @wiking | https://travis-ci.org/shogun-toolbox/shogun/jobs/233082415#L536 | 09:12 |
| @wiking | which is this pr? | 09:13 |
| @sukey | Pull Request #3813 "Modify check_format.sh so that it can be used on local environments." merged by vigsterkr - https://github.com/shogun-toolbox/shogun/pull/3813 | 09:14 |
| @sukey | New Commit "Merge pull request #3813 from geektoni/patch-14 | 09:14 |
| @sukey | Modify check_format.sh so that it can be used on local environments." to shogun-toolbox/shogun by vigsterkr: https://github.com/shogun-toolbox/shogun/commit/a0da9f8f60d18c2954d886a42221f2610dec1dcc | 09:14 |
| @sukey | Pull Request #3815 "Minor fix to .clang-format." merged by vigsterkr - https://github.com/shogun-toolbox/shogun/pull/3815 | 09:14 |
| @sukey | New Commit "Merge pull request #3815 from geektoni/patch-16 | 09:14 |
| @sukey | Minor fix to .clang-format." to shogun-toolbox/shogun by vigsterkr: https://github.com/shogun-toolbox/shogun/commit/929c1951d6213256611e0de5a047e11465a33eba | 09:14 |
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| mikeling | wiking: | 09:19 |
| mikeling | but the latest commit is da7b06f29e8141ca9adf0ca08dc605add66a45cd | 09:19 |
| @wiking | checking sorry | 09:19 |
| mikeling | it seems like Travis CI stop synchronizing the pr | 09:23 |
| @wiking | ok but that one has again some formating error | 09:23 |
| @wiking | mmm lemme close open | 09:23 |
| @wiking | :) | 09:23 |
| @sukey | Pull Request #3812 "Add global fixture with binary label data" closed by vigsterkr - https://github.com/shogun-toolbox/shogun/pull/3812 | 09:24 |
| @sukey | Pull Request #3812 "Add global fixture with binary label data" reopened by vigsterkr - https://github.com/shogun-toolbox/shogun/pull/3812 | 09:24 |
| @wiking | mmm | 09:24 |
| @wiking | didn't help the trigger | 09:24 |
| @wiking | ok i'll do it manually on travis | 09:24 |
| @wiking | oh no it triggerd | 09:24 |
| @wiking | ok rebuilding | 09:24 |
| @wiking | but this is wrong no? | 09:25 |
| @wiking | ah no | 09:25 |
| @wiking | it's ok | 09:25 |
| mikeling | wiking: thank you! | 09:25 |
| @wiking | let's see | 09:25 |
| @wiking | nw | 09:25 |
| @sukey | Pull Request #3812 "Add global fixture with binary label data" synchronized by MikeLing - https://github.com/shogun-toolbox/shogun/pull/3812 | 09:27 |
| @wiking | mm | 09:32 |
| @wiking | ah you've just pushed something | 09:32 |
| @wiking | :))) | 09:32 |
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| mikeling | yep, because I found there are some conflict with the pr you just merged | 09:33 |
| @wiking | kk | 09:34 |
| @wiking | it's trying to build it | 09:34 |
| mikeling | not actually a conflict | 09:34 |
| mikeling | not actually a conflict | 09:34 |
| mikeling | but it has some overlap part with the merged pr on clang-format | 09:35 |
| mikeling | so I just pull rebase and push it again :) | 09:35 |
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| mikeling | Do we need to retrigger it now? again? | 09:36 |
| @wiking | no | 09:37 |
| @wiking | it triggered itself | 09:37 |
| @sukey | Pull Request #3816 "Refactor Some<> to make it a bit more standalone. " opened by geektoni - https://github.com/shogun-toolbox/shogun/pull/3816 | 10:20 |
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| mikeling | wiking: so it still doesn't work for the clang format :( | 11:03 |
| mikeling | https://travis-ci.org/shogun-toolbox/shogun/jobs/233127560#L535 | 11:03 |
| @wiking | yes | 11:03 |
| mikeling | but latest one is b8c08f24a787e19010bfe92b5ea8305ed870e901 https://github.com/shogun-toolbox/shogun/commit/3d4b581ac21def962499cc17616dd49bbf0ab267 | 11:03 |
| @wiking | the question is that have you ran that locally? | 11:03 |
| @wiking | ?? | 11:04 |
| @wiking | your latest is this | 11:04 |
| @wiking | https://github.com/shogun-toolbox/shogun/pull/3812/commits/b8c08f24a787e19010bfe92b5ea8305ed870e901 | 11:04 |
| mikeling | yep https://pastebin.mozilla.org/9021966 | 11:04 |
| @wiking | for me based on the error | 11:04 |
| @wiking | it looks as if you are using spaces maybe | 11:04 |
| @wiking | instead of tab? | 11:05 |
| @wiking | but actually | 11:06 |
| mikeling | I just check it and yes. But it's auto modified by clang-format :/ | 11:06 |
| @wiking | your formatting based on the eror | 11:06 |
| @wiking | *error is wrong | 11:06 |
| @wiking | :) | 11:06 |
| @wiking | the diff clearly states it | 11:07 |
| @wiking | -protected: | 11:07 |
| @wiking | - std::shared_ptr<BinaryLabelDatas> mBinaryLabelData; | 11:07 |
| @wiking | +protected: | 11:07 |
| @wiking | +std::shared_ptr<BinaryLabelDatas> mBinaryLabelData; | 11:07 |
| @wiking | }; | 11:07 |
| mikeling | mmmm, so just use 'git clang-format-3.8 --commit --binary /usr/bin/clang-format-3.8' wasn't necessary to fix the format error | 11:10 |
| @wiking | i mean what is required | 11:12 |
| @wiking | that you run clang-format | 11:12 |
| @wiking | on your code | 11:12 |
| @wiking | and see if there's any error | 11:12 |
| @wiking | mikeling, have you seen this: https://github.com/shogun-toolbox/shogun/pull/3814/files | 11:16 |
| @wiking | ./scripts/check_format.sh "feature/BRANCH_NAME" "develop" | 11:16 |
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| @wiking | anybody here worked with kalman filters in the past? | 11:20 |
| @wiking | i have some very simple questions :) | 11:21 |
| @iglesiasg | wiking: let's talk about it | 11:24 |
| @wiking | ok so i'm wodnering that say you have 2 signals | 11:25 |
| @wiking | or random variables right | 11:25 |
| @wiking | and i wanna train a kalman filter | 11:25 |
| @wiking | for that state space | 11:25 |
| @wiking | where | 11:25 |
| @wiking | the states of the filter is going to be the parameters of the linear model no? | 11:26 |
| @iglesiasg | usually state refers to the hidden variables | 11:27 |
| @wiking | yeah | 11:27 |
| @wiking | but those hidden vars | 11:27 |
| @wiking | are actually the params of a linear model | 11:27 |
| @wiking | no? | 11:27 |
| @wiking | i mean the kalman filter assumes linearity and gaussian noise | 11:28 |
| @wiking | right? | 11:28 |
| @iglesiasg | I think with parameters people normally refer to the transition and measurement models | 11:28 |
| @iglesiasg | so you have something like | 11:28 |
| @iglesiasg | x_k = F*x_{k-1} + v_k | 11:29 |
| @iglesiasg | y_k = G*x_k + w_k | 11:29 |
| @wiking | yeah | 11:29 |
| @wiking | v_k and w_k are the gaussian noise | 11:29 |
| @wiking | right? | 11:29 |
| @iglesiasg | correct | 11:29 |
| @iglesiasg | zero-mean Gaussian noise | 11:29 |
| @wiking | yeah | 11:29 |
| @iglesiasg | parameterized by covariance matrices | 11:29 |
| @wiking | F is the transition matrix right? | 11:30 |
| @iglesiasg | those covariance matrices, together with the transition matrix F and the measurement matrix G are usually called model parameters | 11:30 |
| @wiking | so how do you transfer from state k-1 -> k | 11:30 |
| @iglesiasg | yes | 11:30 |
| @iglesiasg | I suppose if you want to apply learning in a Kalman filtering context so want to use some data to estimate F, G, and the covariance matrices of v and w | 11:31 |
| @wiking | mmmm for v and w i have ideas | 11:31 |
| @iglesiasg | ok! | 11:31 |
| @wiking | but yeah i'm just wondering about F and G | 11:31 |
| @iglesiasg | oh I see | 11:31 |
| @wiking | but on the end of the story | 11:32 |
| @wiking | using the learnt model/filter | 11:32 |
| @wiking | you'll get x_k | 11:32 |
| @wiking | right? | 11:32 |
| @wiking | your sate | 11:32 |
| @wiking | *state | 11:32 |
| @wiking | so i k time you have the kth state of x | 11:32 |
| @iglesiasg | in the standard filtering setting (Kalman is optimal in the linear-Gaussian case), all those are given (not to be estimated/learnt). The filtering algorithm estimates x over time based on y | 11:32 |
| @iglesiasg | yeah, right | 11:33 |
| @iglesiasg | there are some methods that do the more complicated problem of filtering together with learning | 11:33 |
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| @HeikoS | EM | 11:36 |
| @wiking | yeah em | 11:36 |
| @HeikoS | works well | 11:37 |
| @HeikoS | just need to re-run a few times | 11:37 |
| @iglesiasg | particle mcmc are very nice too, suitable for harder problems | 11:39 |
| @HeikoS | you can even use kernel particle smc :D | 11:40 |
| @HeikoS | and cite my papers muhahahaha | 11:40 |
| @HeikoS | but I would rather ran EM | 11:40 |
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| @wiking | :) | 11:43 |
| @wiking | HeikoS, so you resurrect day after tomorrow? | 11:43 |
| @HeikoS | sunday | 11:44 |
| @HeikoS | firday evening is deadline | 11:44 |
| @HeikoS | sat I am away | 11:44 |
| @HeikoS | but then :D | 11:44 |
| @wiking | :>> | 11:44 |
| @wiking | ok | 11:44 |
| @wiking | HeikoS, godspeed | 11:44 |
| @HeikoS | thanks | 11:45 |
| @HeikoS | and sorry for long outtime | 11:45 |
| @wiking | HeikoS, dont https://www.youtube.com/watch?v=OR6jEdq2Bew | 11:45 |
| @wiking | :) | 11:45 |
| @wiking | may 28th is the concert ... fly over :) | 11:45 |
| @wiking | (psy rock) | 11:46 |
| @HeikoS | haha ... | 11:46 |
| @HeikoS | Im in Berlin then :) | 11:46 |
| @wiking | btw | 11:50 |
| @wiking | this is from scijs: | 11:50 |
| @wiking | [07:15] <Bondifrench> Hi, noob here at using javascript ndarrays | 11:50 |
| @wiking | [07:16] <Bondifrench> to do pca (principal component analysis) using ndarray, what's the best procedure/package? | 11:50 |
| @wiking | i.e. we need JS wrapper :) | 11:50 |
| @HeikoS | jes! | 11:52 |
| @HeikoS | definitely! | 11:52 |
| @HeikoS | did I ever mention how much python sucks ? | 11:52 |
| @wiking | :>>>>>>>>>>>>>>>>>>>> | 11:52 |
| @HeikoS | I am really sick of this | 11:53 |
| @HeikoS | time for a new language | 11:53 |
| @HeikoS | for me | 11:53 |
| @HeikoS | but dont know what | 11:53 |
| @wiking | julia :) | 11:53 |
| @wiking | llvm is cool | 11:53 |
| @HeikoS | maybe Ill do that | 11:54 |
| @HeikoS | sigh | 11:54 |
| @HeikoS | need to write so much code from scratch then :/ | 11:54 |
| @wiking | :< | 11:55 |
| @HeikoS | also I have the feeling that this might be at the same point in a few years time | 11:56 |
| @HeikoS | given the package managment they do, and all the writing all the software from scratch again | 11:56 |
| @HeikoS | by scientists mostly | 11:56 |
| @HeikoS | ok coffee break | 11:57 |
| @HeikoS | see you later | 11:57 |
| @wiking | HeikoS, heheh but py and js packaging | 11:57 |
| @wiking | is like back in 1980s | 11:57 |
| @wiking | :) | 11:57 |
| @iglesiasg | HeikoS: return to matlab? ^_^ | 11:58 |
| @wiking | :D | 11:59 |
| @wiking | they dont even try to have packaging | 11:59 |
| @wiking | :)))) | 11:59 |
| @wiking | it's either in matlab | 11:59 |
| @wiking | or you are fucked | 11:59 |
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| @sukey | Issue #3817 "Thread safety with trace memory allocs" opened by iglesias - https://github.com/shogun-toolbox/shogun/issues/3817 | 13:11 |
| @sukey | Issue #3817 "Thread safety with trace memory allocs" assigned to: iglesias by iglesias - https://github.com/shogun-toolbox/shogun/issues/3817 | 13:11 |
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| @sukey | Pull Request #3812 "Add global fixture with binary label data" synchronized by MikeLing - https://github.com/shogun-toolbox/shogun/pull/3812 | 13:36 |
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| @iglesiasg | TingMiao: Hey! | 13:54 |
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| @iglesiasg | TingMiao: might be interesting for your project: https://twitter.com/imadali/status/864277309314019329 | 13:55 |
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| @sukey | Issue #3817 "Thread safety with trace memory allocs" assigned to: vigsterkr by iglesias - https://github.com/shogun-toolbox/shogun/issues/3817 | 14:10 |
| @iglesiasg | wiking: ^ it is beating me so far | 14:10 |
| @wiking | :) | 14:11 |
| @sukey | Pull Request #3812 "Add global fixture with binary label data" synchronized by MikeLing - https://github.com/shogun-toolbox/shogun/pull/3812 | 14:35 |
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| geektoni | hey! Does anybody here use Ubuntu to develop Shogun? :P | 15:38 |
| @wiking | yes | 15:38 |
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| geektoni | wiking: oh nice! :D which IDE do you usually use? | 15:39 |
| @wiking | vim | 15:39 |
| @wiking | no ide | 15:40 |
| geektoni | hardcore developer? ;) | 15:40 |
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| @wiking | :D | 15:41 |
| geektoni | how can you be productive with THAT? | 15:42 |
| geektoni | I mean | 15:42 |
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| geektoni | VIM is *the* editor | 15:42 |
| geektoni | but I can't imagine to work on a huge project with it. | 15:43 |
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| @wiking | :) | 15:49 |
| @wiking | it's a matter of opinion | 15:49 |
| @wiking | so feel free to use some other tool of course :) | 15:49 |
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| lisitsyn | YUUUUUGEEE | 15:50 |
| @wiking | :>>>>>>>>>>>> | 15:50 |
| @wiking | huge | 15:50 |
| @wiking | :) | 15:50 |
| lisitsyn | I can't imagine working on yuuuge project with IDE | 15:50 |
| lisitsyn | porque they die :P | 15:50 |
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| @wiking | :D | 15:51 |
| mikeling | geektoni: I use visual studio code BTW:) | 15:52 |
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| geektoni | I was searching for good code refactoring tools, actually. ;) | 15:59 |
| @wiking | cline | 16:00 |
| @wiking | or what | 16:00 |
| @wiking | try that :) | 16:00 |
| geektoni | mikeling: thanks! I'll take a look :D | 16:00 |
| geektoni | lisitsyn: wat ? xD | 16:01 |
| lisitsyn | refactoring for C++? | 16:02 |
| lisitsyn | :P | 16:02 |
| geektoni | lisistsyn: yes, since I will do mostly refactoring activities I would like to have a tool which can help me speed up the job. | 16:04 |
| geektoni | lisitsyn ^ | 16:04 |
| lisitsyn | I am not optimistic about that | 16:05 |
| lisitsyn | probably all the available tools can do only trivial things | 16:05 |
| geektoni | yeah, sure. | 16:11 |
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| olinguyen | I have a question regarding development environment. The MIMIC database runs on a PostgreSQL server (it is quite large). I've got the server running independently, and Shogun working with Docker. [11:07] <olinguyen> Do you have any experience integrating the two? | 17:10 |
| @HeikoS | olinguyen: so the way to input data into shogun atm is via the features class | 17:11 |
| @HeikoS | wiking: how is the re-factored csv reader going? | 17:11 |
| @HeikoS | olinguyen: there are a few file formats shogun can read, but there was a problem I remember | 17:11 |
| @HeikoS | olinguyen: I guess you will have to write some gluing code | 17:11 |
| @HeikoS | i.e. extract data from your server, and store it either in files that shogun can read, or write a file-loader that can talk to such databases in shogun (much cooler) | 17:12 |
| @HeikoS | olinguyen: how much data are we talking about? | 17:13 |
| olinguyen | Let me double check | 17:13 |
| olinguyen | The entire dataset (MIMIC-II) is over 100 GB. | 17:15 |
| @HeikoS | olinguyen: do you already have a plan what parts of that you want to use? | 17:16 |
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| @HeikoS | since all might be a bit ambituous? ;) | 17:16 |
| olinguyen | Yea, i have a rough idea. It will probably be simplest to take a subset of the data and store that in a easier to use format | 17:17 |
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| @HeikoS | olinguyen: I think that is a good start | 17:18 |
| @HeikoS | but we might want to run some larger models on larger amounts of data (shogun can do some amount of streaming) | 17:19 |
| @HeikoS | so good to think about that | 17:19 |
| olinguyen | Thanks! I'll start that way but keep that in mind | 17:19 |
| @HeikoS | olinguyen: it would be really useful if you could write a summary of the data you want to use for (a) proof of concept (b) during the project and (c) optionally more if time allows | 17:19 |
| @HeikoS | both in terms of number of data and features to use | 17:19 |
| olinguyen | Sounds good ;)! | 17:21 |
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| @sukey | Pull Request #3816 "Refactor Some<> to make it a bit more standalone. " merged by vigsterkr - https://github.com/shogun-toolbox/shogun/pull/3816 | 19:01 |
| @sukey | New Commit "Merge pull request #3816 from geektoni/patch-17 | 19:01 |
| @sukey | Refactor Some<> to make it a bit more standalone." to shogun-toolbox/shogun by vigsterkr: https://github.com/shogun-toolbox/shogun/commit/1a24c625612aad0d74b0a8cac99265254293c4f4 | 19:01 |
| lisitsyn | YAY | 19:01 |
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| @wiking | let it rumble | 19:09 |
| @wiking | :) | 19:09 |
| lisitsyn | wiking: this guy geektoni fixed it instead of blaming me :P | 19:09 |
| @wiking | see | 19:10 |
| @wiking | amazing stuff :) | 19:10 |
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| TingMiao | iglesiasg Thank you for the twitter! | 20:29 |
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