| --- Log opened Mon Apr 22 00:00:28 2013 | ||
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| shogun-buildbot | build #369 of nightly_default is complete: Failure [failed test] Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_default/builds/369 | 04:28 |
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| gsomix | good morning | 08:48 |
| @iglesiasg | good morning gsomix | 08:49 |
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| deerishi | @iglesiasg: hi | 09:34 |
| deerishi | i have implemented the scikit kpca example | 09:34 |
| deerishi | http://scikit-learn.org/dev/auto_examples/decomposition/plot_kernel_pca.html | 09:34 |
| deerishi | https://github.com/deerishi/KernelPCA-test-check/commit/743d3d9bc373aa36b0ea4bb7065ed36ba8706a93#commitcomment-3057022 | 09:35 |
| deerishi | @iglesiasg: could u have a look at it | 09:38 |
| deerishi | ? | 09:38 |
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| @iglesiasg | deerishi: let me see | 10:00 |
| @iglesiasg | ok | 10:01 |
| deerishi | can i do a pull request regarding the kernel pca test check | 10:03 |
| @iglesiasg | deerishi: it could be maybe somethign to merge in graphical examples | 10:04 |
| @iglesiasg | something* | 10:04 |
| @iglesiasg | deerishi: there are some things that look a bit messy in circle_data.py though | 10:06 |
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| deerishi | @iglesiasg: could you eleborate a bit more? | 10:07 |
| @iglesiasg | deerishi: well, just in general the creation of the data | 10:09 |
| @iglesiasg | you are just creating data or plotting two circunferences, aren't you? | 10:10 |
| @iglesiasg | that's something like x^2+y^2=r^2 | 10:11 |
| @iglesiasg | I have the intuition that it should be easier to create that data | 10:11 |
| deerishi | i am actuaaly creating the data | 10:15 |
| deerishi | *actually | 10:15 |
| deerishi | i am storing the values of the circle in a 2 dimensional array | 10:17 |
| deerishi | then i am concatenating the 2 arrays by hstack for kpca data | 10:18 |
| @iglesiasg | ok | 10:19 |
| deerishi | @iglesiasg : where is the graphical examples folder? | 10:37 |
| -!- HeikoS [~heiko@nat-182-85.internal.eduroam.ucl.ac.uk] has joined #shogun | 10:39 | |
| deerishi | hello HeikoS | 10:40 |
| HeikoS | hi deerishi | 10:40 |
| deerishi | i did solve the scikit kpca example | 10:41 |
| deerishi | :) | 10:41 |
| HeikoS | deerishi: finally :) | 10:41 |
| HeikoS | cool | 10:41 |
| HeikoS | Ill have a look at the code | 10:41 |
| deerishi | https://github.com/deerishi/KernelPCA-test-check/commit/743d3d9bc373aa36b0ea4bb7065ed36ba8706a93 | 10:41 |
| HeikoS | deerishi: nice, so this makes sense now! | 10:42 |
| deerishi | yes!! | 10:42 |
| HeikoS | so what I suggest now is that you merge this code into the existing kpca example | 10:42 |
| HeikoS | note that input arguments | 10:43 |
| HeikoS | there is a list that is used for integration testing | 10:43 |
| HeikoS | for the python_modular example, please remove all plotting code and return the transformation matrix and the transformed features and the preprocessor object | 10:43 |
| HeikoS | but I would also suggest to add you plotting example under the graphical examples | 10:43 |
| HeikoS | since it looks very nice | 10:44 |
| HeikoS | please pimp it a bit and then add as graphical example | 10:44 |
| HeikoS | if you have questions on the integration tests, let me know | 10:44 |
| @lisitsyn | something is unhealthy with normalization | 10:45 |
| HeikoS | lisitsyn: ah good that you see that! | 10:45 |
| HeikoS | what is it? | 10:45 |
| @lisitsyn | IIRC kPCA preserves the scale | 10:45 |
| @lisitsyn | HeikoS: check axes, they are e-10 | 10:45 |
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| HeikoS | lisitsyn: I see | 10:45 |
| HeikoS | I dont know | 10:46 |
| HeikoS | if kpca does this | 10:46 |
| HeikoS | better check | 10:46 |
| @lisitsyn | HeikoS: kpca with linear is pca | 10:46 |
| @lisitsyn | or mds | 10:46 |
| @lisitsyn | they are all the same for linear kernel | 10:46 |
| HeikoS | lisitsyn: yes right its linear kernel | 10:46 |
| HeikoS | I forgot | 10:46 |
| @lisitsyn | so scale should be preserved | 10:46 |
| HeikoS | well, then we should see same scalling | 10:46 |
| @lisitsyn | I am not sure if it is kpca that is wrong | 10:46 |
| @lisitsyn | but something is wrong for sure | 10:47 |
| HeikoS | lisitsyn: maybe we should have a unit test which compares KPCA with PCA | 10:47 |
| HeikoS | lisitsyn: haveing this example is good already | 10:47 |
| HeikoS | since we can detect these things | 10:47 |
| @lisitsyn | HeikoS: yeah | 10:48 |
| sijin | @lisitsyn, I just found tapkee KPCA and kernel PCA in shogun gives different result | 10:48 |
| HeikoS | here we go :) | 10:48 |
| wiking | mornin' | 10:48 |
| HeikoS | wiking: hi! | 10:49 |
| sijin | I project features using Kernel PCA in Shogun, and compare it with the embedding result of tapkee KPCA, | 10:49 |
| @lisitsyn | sijin ha! | 10:50 |
| @lisitsyn | sijin: how significant? | 10:50 |
| @lisitsyn | either of them has a bug haha | 10:50 |
| sijin | when target dimension is 1, the difference is 1e-3 | 10:50 |
| sijin | however, when target_dimension is greater than 1, their ouput looks totally different | 10:51 |
| @lisitsyn | sijin: could you plot it? | 10:51 |
| sijin | you mean printing the result in text? | 10:52 |
| @lisitsyn | sijin: no, just compare 2d results | 10:52 |
| sijin | not yet. I am not familiar with shogun's plot function, any suggestion? or I send you the output of them? | 10:54 |
| @lisitsyn | sijin: there is no plot function in shogun - what have you used to compare? | 10:54 |
| sijin | I just print it output.(I use small matrix for testing) | 10:55 |
| @lisitsyn | I see | 10:55 |
| sijin | can I paste the output here( matrix size = 10x5)? | 10:58 |
| wiking | sijin: pastbin | 10:59 |
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| sijin | @wiking thx, | 11:02 |
| sijin | here is the result http://pastebin.com/Dkys8UPX | 11:02 |
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| sijin | Here is the result with target_dim = 2 http://pastebin.com/ffe5m6gU | 11:06 |
| sijin | As you can see, the output of shogun kernel pca is consistent. (I mean the output for target_dim ==3 is the "subset" of that of target_dim == 2) | 11:14 |
| sijin | sorry, the output with target_dim ==2 is the subset of result with target_dim == 3 | 11:15 |
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| sijin | @lisitsyn Is there any special "normalization" in tapkee kpca ? | 11:18 |
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| sijin | @listsyn I plot 2d output of kpca(shogun, blue) and kpca(tapkee, red) http://ctrlv.in/182191 | 11:41 |
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| wiking | xfingerz this works | 12:10 |
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| shogun-notifier- | shogun: Viktor Gal :develop * 026a413 / .travis.yml,src/Makefile: https://github.com/shogun-toolbox/shogun/commit/026a413de78c36484e2de21dc6d0f70a3857e96e | 12:10 |
| shogun-notifier- | shogun: Travis: run unit tests when building libshogun interface | 12:10 |
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| wiking | deerishi: see my comment for your prs | 12:18 |
| deerishi | seen . | 12:20 |
| deerishi | :) | 12:20 |
| wiking | so please redo your prs | 12:20 |
| wiking | as these ones are going to be ignored/closed automatically | 12:20 |
| deerishi | wiking: k. will do in a few minutes. | 12:22 |
| wiking | no worries | 12:22 |
| wiking | thnx | 12:22 |
| wiking | heheh | 12:29 |
| wiking | https://api.travis-ci.org/shogun-toolbox/shogun.png?branch=develop | 12:29 |
| wiking | ;) | 12:29 |
| shogun-notifier- | shogun: Viktor Gal :develop * c1f397c / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/c1f397cc3088881a896356a3e141827674eba3e0 | 12:31 |
| shogun-notifier- | shogun: Fix typo in .travis.yml | 12:31 |
| shogun-notifier- | shogun: Viktor Gal :develop * e83dd28 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/e83dd28c731ab0585506b5380ae58fce9ef6f333 | 12:40 |
| shogun-notifier- | shogun: Travis: fix gmock/gtest location | 12:40 |
| wiking | HeikoS: have u checked/fixed bug #925 and #926? | 12:50 |
| HeikoS | wiking: nope | 12:51 |
| HeikoS | not yet | 12:51 |
| wiking | HeikoS: okey, then i guess they are still leaking :P | 12:51 |
| HeikoS | yes ;) | 12:51 |
| wiking | ok let's see if finally i've managed to get unit testing working on travis... | 12:52 |
| wiking | then the only thing that remains is that stupid python_modular error we keep getting... | 12:52 |
| wiking | and it should be fixed before gsoc kicks off | 12:52 |
| wiking | so that PRs can be safely merged | 12:52 |
| wiking | if it's indicated 'good' by travis | 12:52 |
| HeikoS | wiking: yes | 12:53 |
| HeikoS | very good that the unit-tests are working, great work! :) | 12:54 |
| @sonney2k | wiking, which one still fails? | 12:54 |
| @sonney2k | we better blacklist the particular test if we cannot figure out what's wrong | 12:55 |
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| travis-ci | [travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/6531164 | 12:56 |
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| wiking | sonney2k: it's something general... | 13:03 |
| wiking | sonney2k: pickle and /tmp | 13:03 |
| wiking | sonney2k: i have no idea why that is an error atm | 13:04 |
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| wiking | sonney2k: /usr/lib/python2.7/pickle.py:1217: RuntimeWarning: [WARN] Could not read `labels/values' from `/tmp/fileG5ZWUc'! | 13:05 |
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| wiking | sonney2k: i dont even know who's calling it :( | 13:06 |
| wiking | sonney2k: this is weird... | 13:09 |
| wiking | first it succeeds, but then when it's called within this test it fails | 13:09 |
| wiking | cd ../../../tests/integration/python_modular && \ | 13:09 |
| wiking | ( LD_LIBRARY_PATH=//usr/local/lib \ | 13:09 |
| wiking | PYTHONPATH="//usr/local/lib/python2.7/dist-packages" python tester.py ) | 13:09 |
| wiking | sonney2k: ideas? | 13:09 |
| wiking | HeikoS: not yet... hope the next build with travis succeeds ;P | 13:10 |
| wiking | sonney2k: i think it's something with integration script ./tester.py | 13:12 |
| wiking | tests/integration/python_modular/tester.py | 13:12 |
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| travis-ci | [travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/6531564 | 13:12 |
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| wiking | HeikoS: does the integration test run for you? | 13:14 |
| * wiking is not building with python_modular interface... | 13:14 | |
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| @sonney2k | wiking, the tester runs all scripts from the very same python instance | 13:18 |
| @sonney2k | wiking, it is fast this way but if one of the test calls some stuff that underneath massacres memory consecutive test may fail | 13:19 |
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| wiking | sonney2k: mmmm the first test fails right away with that pickle error (classifier_averaged_perceptron_modular.py) | 13:22 |
| deerishi | HeikoS :I submitted my pull request. now i am working on Global Alignment kernels issue 866 | 13:22 |
| wiking | but then some succeeds | 13:22 |
| HeikoS | deerishi: nice, will comment/review soon! | 13:23 |
| wiking | hahahaha oh | 13:26 |
| wiking | i see | 13:26 |
| @sonney2k | HeikoS, wiking, did someone change anything on labels? | 13:26 |
| @sonney2k | wi? | 13:26 |
| wiking | HeikoS sonney2k http://www.shogun-toolbox.org/buildbot/builders/nightly_default/builds/369/steps/test/logs/stdio | 13:26 |
| @sonney2k | wiking, ? | 13:26 |
| wiking | sonney2k: it fails on nightly as well | 13:26 |
| wiking | so this is something unrelated to travis | 13:26 |
| @sonney2k | wiking, sure it is | 13:27 |
| wiking | sonney2k: HeikoS done some changes | 13:27 |
| @sonney2k | so just find out which version worked last | 13:27 |
| @sonney2k | and then we have it | 13:27 |
| @sonney2k | ok friday everything was still fine | 13:28 |
| wiking | it started to crash with this commit: https://github.com/shogun-toolbox/shogun/commit/d30f20557e0282e8bd8580608b8583aa2586b1a7 | 13:28 |
| wiking | HeikoS: this is your work ;) | 13:28 |
| wiking | or let's say it started to crash after this https://github.com/shogun-toolbox/shogun/commit/d53a8982fa51e129a1e08df11089f8212fca7fa6 | 13:28 |
| wiking | i reckon it's somewhere here: https://github.com/shogun-toolbox/shogun/commit/65da3fd2646dc13e2d36baaca314c5f7f2e36411 | 13:31 |
| wiking | ? | 13:31 |
| @sonney2k | HeikoS, http://shogun-toolbox.org/demos/gp/entrance | 13:31 |
| wiking | sonney2k: lol | 13:32 |
| wiking | niiice | 13:32 |
| HeikoS | hey guys | 13:33 |
| HeikoS | sorry | 13:33 |
| HeikoS | was out for lunch | 13:33 |
| HeikoS | so whats happening? | 13:33 |
| @sonney2k | HeikoS, this | 13:34 |
| @sonney2k | http://shogun-toolbox.org/demos/gp/entrance | 13:34 |
| @sonney2k | and then the build bot failure | 13:34 |
| wiking | HeikoS: i think you've broken integration test with fixing the labels :S | 13:34 |
| @sonney2k | see just the few lines above | 13:34 |
| @sonney2k | seems like | 13:34 |
| HeikoS | sonney2k: the GP demo is ultra cool | 13:34 |
| HeikoS | now it needs heatmaps for the predictive distribution | 13:34 |
| wiking | sonney2k: tweeted ;) | 13:35 |
| HeikoS | sonney2k: ah | 13:36 |
| HeikoS | I see | 13:36 |
| HeikoS | I added a parameter | 13:36 |
| HeikoS | register | 13:36 |
| HeikoS | did I push this to master or to develop? Currently confused about where the buildbot runs | 13:36 |
| wiking | HeikoS: develop | 13:36 |
| HeikoS | ok, let me fix it | 13:36 |
| wiking | HeikoS: nightly buildbot runs on develop | 13:36 |
| HeikoS | wiking: ah ok | 13:36 |
| @sonney2k | wiking, hmmhh shouldn't the other buildbot also run on develop? | 13:37 |
| @sonney2k | I thougth we changed that | 13:37 |
| wiking | sonney2k: not yet :P | 13:37 |
| @sonney2k | wiking, nice one with the matrix :) | 13:37 |
| @sonney2k | wiking, no I think I did | 13:37 |
| wiking | sonney2k: hahaha yeah htat was fridayafternoon rushtime ;) | 13:38 |
| wiking | sonney2k: well they are not building afaik | 13:38 |
| wiking | see for example: http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/711 | 13:38 |
| @sonney2k | it says branch='develop' | 13:38 |
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| wiking | sonney2k: yeah | 13:39 |
| wiking | sonney2k: what i dont understand for exmaple | 13:39 |
| wiking | is why the last build then is april 07 | 13:39 |
| wiking | http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun | 13:39 |
| wiking | or | 13:39 |
| wiking | http://www.shogun-toolbox.org/buildbot/builders/deb1%20-%20libshogun | 13:39 |
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| wiking | april 5 | 13:39 |
| -!- shogun-buildbot_ [~shogun-bu@7nn.de] has joined #shogun | 13:39 | |
| wiking | and that's still on master branch | 13:39 |
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| @sonney2k | shogun-buildbot, status | 13:40 |
| shogun-buildbot | bsd1 - libshogun: idle, last build 359h58m40s ago: build successful | 13:40 |
| shogun-buildbot | cyg1 - libshogun: idle, last build 163h03m46s ago: build successful | 13:40 |
| shogun-buildbot | deb1 - libshogun: idle, last build 416h38m00s ago: build successful | 13:40 |
| shogun-buildbot | deb2 - static_interfaces: idle, last build 299h58m08s ago: build successful | 13:40 |
| shogun-buildbot | deb3 - modular_interfaces: idle, last build 138h33m54s ago: build successful | 13:40 |
| shogun-buildbot | nightly_all: idle, last build 10h00m23s ago: build successful | 13:40 |
| shogun-buildbot | nightly_default: idle, last build 9h11m58s ago: failed test | 13:40 |
| shogun-buildbot | nightly_none: idle, last build 10h25m02s ago: build successful | 13:40 |
| shogun-buildbot | rpm1 - libshogun: idle, last build 162h11m15s ago: build successful | 13:40 |
| shogun-buildbot | ubu1 - libshogun: offline | 13:40 |
| wiking | ok i've started ubu1 | 13:40 |
| @sonney2k | it is weird | 13:40 |
| wiking | but yeah apart from nightly | 13:40 |
| @sonney2k | it certainly lists develop in there | 13:40 |
| wiking | they are not building | 13:40 |
| @sonney2k | so I guess sth is wrong | 13:41 |
| @sonney2k | the poller uses develop | 13:41 |
| @sonney2k | and the fetcher too | 13:41 |
| @sonney2k | weird | 13:41 |
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| HeikoS | sonney2k: when is the parameter version increased? | 13:42 |
| HeikoS | upon release? | 13:42 |
| HeikoS | since I need to tell the thing when the parameter was added but PARAM_VERSION is still at one | 13:42 |
| HeikoS | mmh, this stuff was broken, thats why we did not increase, I remember | 13:43 |
| HeikoS | at some point this should be fixed, we always break compitability with previous version otherwise when we change classes | 13:43 |
| @sonney2k | HeikoS, then increase it now | 13:43 |
| HeikoS | sonney2k: problem is then serialization stops working | 13:43 |
| wiking | that's weird | 13:43 |
| HeikoS | remember the bug? | 13:43 |
| @sonney2k | HeikoS, no | 13:44 |
| wiking | that last none-nightly build was Apr 16 | 13:44 |
| @sonney2k | sry but got the catch a plane | 13:44 |
| wiking | by deb3 - modular_interfaces | 13:44 |
| HeikoS | sonney2k: we had this discussion | 13:44 |
| @sonney2k | cu | 13:44 |
| HeikoS | sonney2k: bye | 13:44 |
| wiking | and ever since then it's not building | 13:44 |
| wiking | cya | 13:44 |
| saket | hi | 13:45 |
| saket | SG_PRINT("1") ; m_temp_lhs = CDenseFeatures<float64_t>(p1, m_dimensions, 1); SG_PRINT("2") ; m_temp_rhs = CDenseFeatures<float64_t>(p2, m_dimensions, 1); SG_PRINT("3") ; m_distance->init(&m_temp_lhs, &m_temp_rhs) ; SG_PRINT("4") ; return m_distance->distance(0, 0) ; | 13:45 |
| wiking | okeeey let's see if unittesting will run | 13:45 |
| saket | I am getting Segmentation fault in m_distance->init(...) .any idea why? | 13:46 |
| saket | p1 and p2 are float64_t * | 13:46 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * 74c1f6a / src/shogun/labels/DenseLabels.cpp: https://github.com/shogun-toolbox/shogun/commit/74c1f6abb2ec3633f4c3239776ab1aab7bed2348 | 13:48 |
| shogun-notifier- | shogun: removed parameter from class to make tests work again | 13:48 |
| shogun-notifier- | shogun: Heiko Strathmann :develop * c1d2bdf / src/shogun/labels/DenseLabels.cpp: https://github.com/shogun-toolbox/shogun/commit/c1d2bdf32e4e98b91b74780e7a54a74748487e5f | 13:48 |
| shogun-notifier- | shogun: Merge pull request #1002 from karlnapf/develop | 13:48 |
| shogun-notifier- | shogun: | 13:48 |
| shogun-notifier- | shogun: fix integration tests | 13:48 |
| HeikoS | wiking: this fixed the integration tests locally here | 13:49 |
| HeikoS | sorry for the mess | 13:49 |
| wiking | HeikoS: ok lets see how that effects travis :P | 13:49 |
| HeikoS | wiking: indeed :) | 13:49 |
| wiking | HeikoS: ok unit testing works | 13:51 |
| HeikoS | wiking: aweseom! | 13:51 |
| HeikoS | e | 13:51 |
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| votjakovr | Hi everyone :) | 14:02 |
| wiking | yo | 14:02 |
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| travis-ci | [travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/6531733 | 14:04 |
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| wiking | mmm i think i'll have to hack something with ruby... | 14:06 |
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| votjakovr | Looking through the code of GP framework, I don't understand the idea, why base class CLikelihoodModel has a protected field m_df (degrees of freedom)... I think it's better to declare it, where it really needs (for example in CStudentsTLikelihood). What do you think about that? | 14:10 |
| @iglesiasg | votjakovr: better in what sense? | 14:11 |
| @iglesiasg | I don't know much about the GP framework we have, so just asking out of curiosity | 14:12 |
| wiking | jacob wrote that code... but i haven't seen him around ever since gsoc'12 finished | 14:14 |
| votjakovr | iglesiasg: I think that base class should contain properties, which are common for all derived. | 14:14 |
| votjakovr | But degrees of freedom aren't used in GaussianLikelihood, for example | 14:17 |
| @iglesiasg | votjakovr: yeah, that makes sense. But if all the derived classes have some degrees of freedom, doesn't it make sense to have it there? Even if the number of degrees of freedom is different among them | 14:17 |
| @iglesiasg | votjakovr: aham I see | 14:17 |
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| gsomix | hi | 14:21 |
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| travis-ci | [travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/6533291 | 14:23 |
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| vikram360 | Hi, I'm just curious to know what the git workflow of some of the veteran shogun developers is. | 14:33 |
| votjakovr | iglesiasg: If all derived classes from has degrees of freedom field, I think it's better to have it in base class. But it's not true in our case. | 14:33 |
| @iglesiasg | votjakovr: ok | 14:39 |
| votjakovr | iglesiasg: So, I'd like to remove it from base class and declare in derived. What do you think? | 14:39 |
| @iglesiasg | votjakovr: how many derived classes are there that use that member? | 14:40 |
| votjakovr | iglesiasg: just one | 14:40 |
| @iglesiasg | votjakovr: then yeah, it could make sense to have it as you are saying | 14:41 |
| votjakovr | iglesiasg: thanks, then i'll do it in next PR :) | 14:42 |
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| saket | lisitsyn: Hi, yesterday we talked out multiple v_array classes in the package ... we resolved it using a deeper namespace... but then each time i do "sudo make install" I have to add changes to auto-generated file /src/interfaces/modshoung_wrap.cxx about the namespaces | 15:00 |
| saket | lisitsyn: do you know how to avoid this ? | 15:00 |
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| @lisitsyn | saket: no, not really | 15:00 |
| @iglesiasg | saket: have you tried doing make clean and building all over again? | 15:01 |
| @iglesiasg | sometimes that helps | 15:01 |
| saket | yes i tried | 15:01 |
| saket | didn;'t work | 15:01 |
| @lisitsyn | saket: where the second one v_array is used? | 15:02 |
| saket | in /classifer/vw/somefiles here | 15:02 |
| saket | I think there were a few more .. I am unable to recall now .. was fixing them as and when they showed in the errors | 15:03 |
| @iglesiasg | see you later guys | 15:03 |
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| vgorbati | lisitsyn: hello, did you have time to review the PR? | 15:04 |
| @lisitsyn | vgorbati: no sorry | 15:04 |
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| saket | lisitsyn: /io/AsciiFile.h too | 15:04 |
| @lisitsyn | saket: would that make sense to remove it from jlcovertree? | 15:05 |
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| saket | I think the other(jlcov...) is also used in other files | 15:06 |
| vgorbati | lisitsyn: for what?) btw, what about the issue "Develop an adapter for t-SNE" - I am planning to start working on it today? I mean, is it still open? | 15:07 |
| @lisitsyn | vgorbati: what for what? | 15:07 |
| vgorbati | lisitsyn: sorry for what?) | 15:08 |
| vgorbati | lisitsyn: it isn't actually a question) | 15:09 |
| @lisitsyn | vgorbati: that I hadn't find time for that yet | 15:09 |
| vgorbati | lisitsyn: I meant to say that its okay) | 15:09 |
| saket | lisitsyn: Apart, @iglesias said you will be able to tell better for the PR(https://github.com/shogun-toolbox/shogun/pull/994 ) in the third last comment | 15:09 |
| @lisitsyn | sorry guys quite overwhelmed right now - will have some time tonight | 15:10 |
| saket | lisitsyn: I sent a new one on develop branch as per chat with @sonney2k ..can you please look into it too (https://github.com/shogun-toolbox/shogun/pull/995 ) | 15:10 |
| saket | lisitsyn: okay... will catch you after some time :-) | 15:11 |
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| wiking | HeikoS: ok we are back at square one: serialization_complex_example.py setting 1/2 | 15:55 |
| wiking | fails | 15:55 |
| HeikoS | wiking: this was the state we were in before right? :) | 15:55 |
| HeikoS | serialisation needs a fix in order for us to be able to add new parameters to classes | 15:55 |
| HeikoS | there are things broken | 15:56 |
| HeikoS | but at least now we can detect things | 15:56 |
| HeikoS | which makes it much easier to fix | 15:56 |
| wiking | HeikoS: ok but how to detect this error, since as far as i understand it fails only on travis :S | 15:57 |
| HeikoS | wiking: oh really? | 15:57 |
| wiking | or anybody else gets this error? | 15:57 |
| HeikoS | I talked about the other problems | 15:57 |
| HeikoS | no idea | 15:57 |
| wiking | HeikoS: does it fail for you? in the integration test? | 15:57 |
| HeikoS | lemecheck | 15:57 |
| wiking | serialization_complex_example.py setting 1/2 | 15:58 |
| wiking | in integration test | 15:58 |
| HeikoS | I dont have json installed so yes fails | 15:58 |
| wiking | it's a json test? | 15:59 |
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| wiking | is it tests/serialization_complex_example0.txt or tests/serialization_complex_example1.txt | 16:02 |
| wiking | or it's none of that? | 16:04 |
| wiking | i really dont get what's happening in that testsuite :P | 16:04 |
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| towelenee | hello, I would like to know do you need any contribution in decision trees? | 17:28 |
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| @sonney2k | hurray I am back online :D | 19:03 |
| @iglesiasg | the captain is back \o/ | 19:03 |
| @sonney2k | iglesiasg, I am more close to you than ever now | 19:04 |
| @sonney2k | direct view to the eiffel tower | 19:04 |
| @iglesiasg | sonney2k: where are you? | 19:04 |
| @iglesiasg | you know I am not in Spain right? | 19:04 |
| @iglesiasg | nor in France hehe | 19:04 |
| @sonney2k | iglesiasg, ah forgot | 19:05 |
| @iglesiasg | :-) | 19:05 |
| @sonney2k | but if you were paris is closer to spain than berlin :D | 19:05 |
| @iglesiasg | indeed | 19:05 |
| @sonney2k | so I cann assume I am more close to dvalcarce now | 19:05 |
| @iglesiasg | you are close to dvalcarce | 19:05 |
| @iglesiasg | yeah exactly, if he is in coru?a I mean | 19:06 |
| @sonney2k | wiking, HeikoS - it shouldn't be a json thing | 19:07 |
| @sonney2k | IIRC I disabled json altogether | 19:07 |
| towelenee | ping | 19:24 |
| @iglesiasg | pong | 19:26 |
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| HeikoS | sonney2k: its just on my computer, I dont have json installed so the integration tests fails complaining about not finding json | 19:39 |
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| HeikoS | sonney2k: btw my name is now registered with the nickserver | 19:45 |
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| @HeikoS | ah | 19:46 |
| @HeikoS | not logged in : | 19:47 |
| @HeikoS | :) | 19:47 |
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| gsomix | hi | 20:10 |
| gsomix | sonney2k, but you are farther from Russia. Go back sooner. :) | 20:16 |
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| saket | hi | 20:16 |
| saket | random question: is there a way other than using SG_PRINT to debug the code ? | 20:16 |
| gsomix | saket, gdb, valgrind >:3 | 20:16 |
| saket | gsomix: for using gdb what parameters i need to pass to make ? | 20:17 |
| gsomix | saket, I dunno. I just did "gdb example_that_covers_my_code". | 20:20 |
| saket | gsomix: which interface do you use ? | 20:21 |
| gsomix | saket, native c++. :) | 20:21 |
| saket | gsomix: okhay, thanks :) anyidea if we can debug through python interface ? | 20:23 |
| gsomix | saket, pdb, maybe. http://docs.python.org/2/library/pdb.html | 20:24 |
| saket | gsomix: thanks will ave a look | 20:24 |
| saket | *have | 20:24 |
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| vgorbati_ | lisitsyn: hello, are you here? | 20:36 |
| @lisitsyn | vgorbati_: yes | 20:36 |
| vgorbati_ | lisitsyn: where can I take a look at tapkee implementation of t-SNE? | 20:36 |
| @lisitsyn | vgorbati_: it is not merged yet I think | 20:37 |
| @lisitsyn | vgorbati_: okay about your PR | 20:37 |
| @lisitsyn | vgorbati_: does it work? | 20:37 |
| vgorbati_ | lisitsyn: the test passes, if you are talking about it) | 20:37 |
| @lisitsyn | what is the intersection rate? | 20:38 |
| @lisitsyn | okay let me merge latest tapkee now | 20:38 |
| vgorbati_ | lisitsyn: wait a second | 20:38 |
| vgorbati_ | lisitsyn: when initial n_dimension=4, target=3, neigbor_count=40 (total_samples=100), the minimal intersection rate is 25/40 | 20:42 |
| vgorbati_ | lisitsyn: average is about 30/40 | 20:42 |
| @lisitsyn | alright that looks more or less ok for me | 20:42 |
| vgorbati_ | have you looked at PR already? | 20:43 |
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| @lisitsyn | vgorbati_: I have a major issue there - you didn't set up your git properly | 20:46 |
| vgorbati_ | what did I missed? | 20:47 |
| @lisitsyn | vgorbati_: ah no sorry | 20:47 |
| @lisitsyn | that looked like an email | 20:48 |
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| @lisitsyn | vgorbati_: didn't you reinvent http://www.cplusplus.com/reference/algorithm/set_intersection/ ? | 20:49 |
| vgorbati_ | lisitsyn: I thought of it, but then decided to optimize a little) I mean, set_intersection would have required a temporary set.. | 20:50 |
| @lisitsyn | I see | 20:50 |
| vgorbati_ | it would me more readable though) | 20:51 |
| vgorbati_ | should I change to set_intersection? | 20:51 |
| @lisitsyn | no, that's ok for me | 20:51 |
| @lisitsyn | I am a bit concerned with the randomization of that test | 20:52 |
| vgorbati_ | n_gaussians=1? | 20:52 |
| @lisitsyn | it is out of kinda 3 sigmas of course but it may fail | 20:52 |
| @lisitsyn | I mean there is somewhat may be 1e-5 probability of failure | 20:53 |
| vgorbati_ | ah, you mean that the min_similarity level is close to min matches | 20:53 |
| vgorbati_ | ? | 20:53 |
| @lisitsyn | yes | 20:53 |
| @lisitsyn | and in general | 20:53 |
| @lisitsyn | the graph *may* get a few connected components | 20:53 |
| vgorbati_ | so that neighborhood graph won't be connected? | 20:54 |
| @lisitsyn | yes | 20:54 |
| @lisitsyn | it may happen with non-zero Pr | 20:55 |
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| vgorbati_ | can you please explain me (if it is not too long to explain), what does 'neighborhood graph is not connected' means when we are talking about vectors? | 20:56 |
| @lisitsyn | just imagine a graph that has edge from i to j if and only if jth vector is in k nearest neighborhood of ith vector | 20:56 |
| vgorbati_ | got it, so if we have to clusters with lets say 2*k points in each, that are far from each other - it would be two connected components? | 20:58 |
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| @lisitsyn | ye | 20:58 |
| @lisitsyn | s | 20:58 |
| vgorbati_ | two cluster* | 20:58 |
| @lisitsyn | and we are in trouble like in taylor swift song | 20:58 |
| @lisitsyn | http://www.youtube.com/watch?feature=player_detailpage&v=bgNjzCrR3fw | 20:59 |
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| vgorbati_ | :) okay, than should I change the test to predefined values? | 20:59 |
| @lisitsyn | vgorbati_: no I think we are ok currently | 21:00 |
| vgorbati_ | lisitsyn: so what do you suggest? Leaving the test as it is? | 21:01 |
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| @lisitsyn | vgorbati_: yeah we can improve later I think | 21:01 |
| vgorbati_ | so, can the issue https://github.com/shogun-toolbox/shogun/issues/882 be considered as closed? | 21:02 |
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| shogun-notifier- | shogun: vladislav.horbatiuk@gmail.com :develop * 7dbc220 / tests/unit/converter/LocallyLinearEmbedding_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/7dbc2200a4280eaec07cf2ea41cec034bde59c21 | 21:03 |
| shogun-notifier- | shogun: Added unit test for locally linear embedding method, that checks, whether it preserves neighbors (according to https://github.com/shogun-toolbox/shogun/issues/882) | 21:03 |
| shogun-notifier- | shogun: vladislav.horbatiuk@gmail.com :develop * c20178b / tests/unit/Makefile: https://github.com/shogun-toolbox/shogun/commit/c20178b7fccea1fe4a1a4ba3046183d7d521a56b | 21:03 |
| shogun-notifier- | shogun: Modified unit tests makefile, so that it adds GTEST_DIR and GMOCK_DIR to include paths, when compiling unit tests - since they do include gtest and gmock files. | 21:03 |
| shogun-notifier- | shogun: vladislav.horbatiuk@gmail.com :develop * 2d7d574 / / (7 files): https://github.com/shogun-toolbox/shogun/commit/2d7d5744afab843af1b3adb0e289b659d9114aa2 | 21:03 |
| shogun-notifier- | shogun: Merge branch 'develop' of https://github.com/shogun-toolbox/shogun into vgorbati-develop | 21:03 |
| shogun-notifier- | shogun: vladislav.horbatiuk@gmail.com :develop * eb32fa6 / / (8 files): https://github.com/shogun-toolbox/shogun/commit/eb32fa68d181990b3523ab81d56f410c1db6632d | 21:03 |
| shogun-notifier- | shogun: Merge branch 'develop' of https://github.com/shogun-toolbox/shogun into vgorbati-develop | 21:03 |
| shogun-notifier- | shogun: vladislav.horbatiuk@gmail.com :develop * 4786c8c / tests/unit/converter/LocallyLinearEmbedding_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/4786c8c366c1fda98a2268cdaefdc24506068977 | 21:03 |
| @lisitsyn | vgorbati_: closed, merged | 21:03 |
| shogun-notifier- | shogun: Modified unit test for Locally Linear Embedding, so that it allows 'misses' of neighbors before and after the dimensionality reduction. | 21:03 |
| shogun-notifier- | shogun: Sergey Lisitsyn :develop * 6debd28 / tests/unit/Makefile,tests/unit/converter/LocallyLinearEmbedding_unittest.cc: https://github.com/shogun-toolbox/shogun/commit/6debd2867b5196478e100fbb57d1ffd6255699b5 | 21:03 |
| shogun-notifier- | shogun: Merge pull request #990 from vladislav-horbatiuk/vgorbati-develop | 21:03 |
| vgorbati_ | wow, so many lines) | 21:03 |
| vgorbati_ | lisitsyn: about t-SNE: I looked at https://github.com/lisitsyn/tapkee/blob/master/include/tapkee_methods.hpp (embedtDistributedStochasticNeighborEmbedding method) - is that the method that will be used? | 21:05 |
| @lisitsyn | vgorbati_: exactly | 21:05 |
| @lisitsyn | vgorbati_: I am now merging the latest code and then you can go | 21:05 |
| vgorbati_ | lisitsyn: great | 21:05 |
| vgorbati_ | lisitsyn: also wanted to ask: do you have some method of finding the distance between strings in shogun? I did looked a bit at distance folder, but still not sure | 21:07 |
| @lisitsyn | vgorbati_: the usual way is to use kernel distance | 21:07 |
| @lisitsyn | vgorbati_: simples is exp{-k(x,x')/width} | 21:08 |
| @lisitsyn | simplest* | 21:08 |
| @lisitsyn | vgorbati_: one may use the hamming distance of course | 21:08 |
| @lisitsyn | bah! proposals are now accepted | 21:09 |
| vgorbati_ | :) | 21:09 |
| vgorbati_ | what about sequence alignment? | 21:09 |
| vgorbati_ | when we have the penalty for mismatched letter and the penalty for inserting a gap | 21:10 |
| vgorbati_ | and find the optimal way to insert gaps in both strings | 21:11 |
| vgorbati_ | then the resulting penalty would be a distance | 21:11 |
| @lisitsyn | vgorbati_: you are talking about some alignment kernel I guess | 21:11 |
| @lisitsyn | I am not an expert in that unfortunately as I am more into the computer vision | 21:12 |
| vgorbati_ | I just recently have heard about the algorithm, so I decided to pretend smart:) | 21:13 |
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| vgorbati_ | however, the algorithm is quadratic in a maximum length of both strings, so I am not sure whether its suitable | 21:14 |
| @lisitsyn | vgorbati_: check shogun/kernel/string if you are interested | 21:15 |
| @lisitsyn | vgorbati_: it plays its role in bioinformatics | 21:15 |
| vgorbati_ | yeah, its used for DNA sequences alignment | 21:16 |
| vgorbati_ | wow, that's quite a lot of kernels) | 21:16 |
| @lisitsyn | vgorbati_: just as an example - genes are interrupted by introns in RNA of such creatures like humans | 21:17 |
| @lisitsyn | err DNA | 21:17 |
| @lisitsyn | whatever :D | 21:17 |
| @lisitsyn | like | 21:17 |
| @lisitsyn | [gene region] [kawabanga! intron] [gene region continued] | 21:17 |
| @lisitsyn | I am afraid to let sonney2k die from laugh with my lame things but it is kind of that IIRC | 21:18 |
| naywhayare | sonney2k: quick GSoC question that I can't seem to find an answer to: is it possible that a person can sign up to be a mentor, but end up without a student because nobody was interested in his particular project? | 21:18 |
| naywhayare | it would seem unreasonable if that weren't the case, but I can't seem to find it in writing anywhere... | 21:18 |
| @lisitsyn | naywhayare: I think you'd have to ask carol directly | 21:19 |
| vgorbati_ | lisitsyn: :) sonney2k is biologist? | 21:19 |
| naywhayare | lisitsyn: you think so? I imagine this would be a fairly commonplace situation | 21:19 |
| @lisitsyn | naywhayare: ahh sorry | 21:19 |
| @lisitsyn | I misread | 21:19 |
| @lisitsyn | naywhayare: I thought you asked about mentor -> student transformation | 21:19 |
| @lisitsyn | :) | 21:19 |
| @lisitsyn | vgorbati_: former bioinformatician yes | 21:20 |
| naywhayare | nope, not in this case :) | 21:20 |
| @lisitsyn | naywhayare: yes that's totally ok | 21:20 |
| @lisitsyn | he won't be a mentor though | 21:20 |
| @lisitsyn | won't receive t-shirt etc :) | 21:20 |
| naywhayare | I figured. I have some people who would like to be mentors, but only for the right student and the right project | 21:20 |
| @lisitsyn | naywhayare: we have 14 mentors - you know we won't receive 14 slots :) | 21:21 |
| naywhayare | wow, 14? nice. | 21:21 |
| @lisitsyn | naywhayare: btw what's up with your project? how is it going? | 21:22 |
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| travis-ci | [travis-ci] it's Sergey Lisitsyn's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/6544478 | 21:26 |
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| naywhayare | lisitsyn: it's going pretty well. it takes a lot of time to answer all the emails I get | 21:27 |
| @lisitsyn | naywhayare: hah I feel your pai | 21:27 |
| @lisitsyn | n | 21:27 |
| naywhayare | mlpack is not a particularly mature project, so, in some ways it hasn't really developed a community, so the influx of GSoC applicants is quite a shock | 21:28 |
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| naywhayare | I don't work on weekends, so Mondays have been pretty brutal; I show up and I have like 20 emails to answer... | 21:29 |
| @lisitsyn | naywhayare: yeah I had to answer somewhat 10 on sunday | 21:30 |
| vgorbati_ | I found it - https://github.com/shogun-toolbox/shogun/blob/master/src/shogun/kernel/string/LocalAlignmentStringKernel.h :) | 21:31 |
| naywhayare | I'd probably have an easier time if I answered them on weekends too, but I find it's really good for my stress levels to do completely different things on weekends | 21:32 |
| vgorbati_ | lisitsyn: still there? | 21:54 |
| @lisitsyn | naywhayare: yes | 21:54 |
| @lisitsyn | oops | 21:54 |
| @lisitsyn | vgorbati_: yes | 21:54 |
| @sonney2k | naywhayare, sure that can happen | 21:56 |
| vgorbati_ | lisitsyn: I am trying to write a documentation for getter and setter for perplexity parameter in t-SNE embedding class. Am I right that perplexity determines the width of gaussian 'bell' around each data point? | 21:56 |
| @sonney2k | naywhayare, you then just don't officially mentor | 21:56 |
| @sonney2k | vgorbati, sure - want to know where your genes are? | 21:57 |
| naywhayare | sonney2k: thanks. that's what I figured -- I was just making sure that my mentors aren't commiting themselves to something they might now want to do | 21:57 |
| vgorbati_ | sonney2k: you mean where are they located?) | 21:57 |
| @lisitsyn | vgorbati_: kind of | 21:58 |
| @lisitsyn | let me cite | 21:58 |
| @lisitsyn | "The perplexity can be interpreted as a smooth measure of the effective number of neighbors" | 21:58 |
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| vgorbati_ | lisitsyn: :) "Note that the perplexity increases monotonically with the variance" | 21:58 |
| wiking | wtf is that 1/2 test for serialization | 21:58 |
| @sonney2k | naywhayare, it will work like this: once you have your student applications in | 21:59 |
| @sonney2k | mentors can say 'I want to mentor this project' | 21:59 |
| @sonney2k | so you can have multiple mentors / project | 21:59 |
| @sonney2k | or none | 21:59 |
| vgorbati_ | lisitsyn: ok, but how to write this in function specification? Or i can just leave 'setter for perplexity', 'getter for perplexity'? | 21:59 |
| @lisitsyn | vgorbati_: yes that's ok | 22:00 |
| @sonney2k | wiking, yes that is crazy | 22:00 |
| @sonney2k | it should work yes / no | 22:00 |
| @sonney2k | wiking, only thing I see we can do is print out the different objects before failing | 22:00 |
| @sonney2k | vgorbati, yes | 22:00 |
| wiking | sonney2k: but what does actually happen in that script? | 22:00 |
| @sonney2k | vgorbati, where on DNA | 22:01 |
| @sonney2k | wiking, what do you mean? | 22:01 |
| @sonney2k | wiking, the big picture? | 22:01 |
| wiking | sonney2k: in that exact script | 22:01 |
| wiking | lisitsyn: wtf man | 22:01 |
| wiking | lisitsyn: https://github.com/shogun-toolbox/shogun/pull/990/files | 22:01 |
| @sonney2k | wiking, generator.py just runs the different settings | 22:01 |
| wiking | lisitsyn: BAD | 22:01 |
| wiking | lisitsyn: should not merge! | 22:01 |
| @sonney2k | it is calling that function in each python script | 22:01 |
| @lisitsyn | wiking: makefile? | 22:01 |
| @sonney2k | with all the parameter settings in that script | 22:02 |
| @sonney2k | for each parameter setting it is just python.pickling the results | 22:02 |
| wiking | lisitsyn: see my comment | 22:02 |
| @sonney2k | then tester.py is doing the same again - and loads the serialized reference data from disk comparing things | 22:02 |
| wiking | lisitsyn: https://github.com/shogun-toolbox/shogun/pull/990/files | 22:02 |
| wiking | https://github.com/shogun-toolbox/shogun/pull/990/files#r3903403 | 22:03 |
| wiking | lisitsyn: so somebody fix this | 22:03 |
| @lisitsyn | wiking: I see - I thought it was missed | 22:03 |
| wiking | ASAP | 22:03 |
| wiking | lisitsyn: it was not | 22:03 |
| wiking | who's vladislav-horbatiuk | 22:03 |
| wiking | ? | 22:03 |
| vgorbati_ | wiking: are you sure? When I tried it without -I GTEST_DIR ..., it gave me an error: 'gtest/gtest.h' - not found | 22:03 |
| wiking | vgorbati_: that was *your* fault | 22:03 |
| vgorbati_ | wiking: its me | 22:03 |
| wiking | vgorbati_: should have checked those variables before doing this patch | 22:04 |
| wiking | vgorbati_: r u sure ./configure found your gmock and gtest src? | 22:04 |
| wiking | from the configure: | 22:05 |
| wiking | COMPFLAGS_GTEST_CPP="-I$GTEST_HEADER_PATH" | 22:05 |
| wiking | so i'm pretty sure that it was there | 22:05 |
| wiking | and since for everybody else who uses gmock/gtest this was working | 22:05 |
| shogun-notifier- | shogun: Sergey Lisitsyn :develop * f2dae9d / tests/unit/Makefile: https://github.com/shogun-toolbox/shogun/commit/f2dae9dbaa0b8fbf34b01c5bb53a3108986e4184 | 22:05 |
| shogun-notifier- | shogun: Removed unnecessary compilation include paths | 22:05 |
| wiking | i'm pretty sure that there is something wrong at your end | 22:05 |
| vgorbati_ | wiking: I did not put my gtest/gmock at default paths | 22:05 |
| @lisitsyn | wiking: alright solved | 22:06 |
| wiking | vgorbati_: then you should have told that to the configure script, right? | 22:06 |
| wiking | lisitsyn: thnx | 22:06 |
| wiking | vgorbati_: ./configure --gmock=... --gtest=... | 22:06 |
| wiking | and check what configure's output is actually for gmock and gtest | 22:06 |
| wiking | i.e. if it finds it or not | 22:06 |
| vgorbati_ | wiking: now I get it, sorry for that much text | 22:06 |
| @lisitsyn | outrageous wiking with an axe is killing people | 22:07 |
| gsomix | sonney2k, there? how long are you going to stay in France? | 22:07 |
| wiking | sonney2k: ok so am i right if i assume that it fails with this particular serialized model: data/testsuite/tests/serialization_complex_example0.txt? | 22:08 |
| @sonney2k | gsomix, until wednesday | 22:08 |
| wiking | lisitsyn: indeed | 22:08 |
| @sonney2k | wiking, yes | 22:08 |
| gsomix | sonney2k, ok, thanks. | 22:08 |
| wiking | sonney2k: mmmhm... i'll try to somehow reproduce this error :S | 22:08 |
| wiking | sonney2k: which part of .fr? | 22:09 |
| @lisitsyn | wiking: he is looking at the eiffel tower | 22:10 |
| @sonney2k | and if one runs tester.py -d serialization_complex_example.py it would give you a python shell when things deviate | 22:10 |
| @sonney2k | so you have two variables a and b then | 22:10 |
| @sonney2k | which are lists of what got returned | 22:10 |
| @sonney2k | wiking, the problem is that I cannot reproduce the issue here | 22:10 |
| @sonney2k | wiking, paris | 22:10 |
| @sonney2k | yeah I am at this event here | 22:10 |
| @sonney2k | https://research.microsoft.com/en-us/um/cambridge/events/mls2013/default.aspx | 22:11 |
| vgorbati_ | lisitsyn: theta and perplexity are the only parameters for t-SNE, aren't they? | 22:11 |
| @lisitsyn | vgorbati_: yes | 22:11 |
| @lisitsyn | theta is even not the t-sne but barnes-hut-sne | 22:11 |
| @iglesiasg | sonney2k: nice event! | 22:11 |
| naywhayare | sonney2k: okay, thanks for the info | 22:11 |
| wiking | sonney2k: ah cool! although paris i hate :P | 22:12 |
| @lisitsyn | haha I put russian elections 2011 to the t-SNE | 22:12 |
| wiking | lisitsyn: :DDDDDD | 22:12 |
| wiking | LOL | 22:12 |
| wiking | sonney2k: have u managed to figure out wtf is going on with the buildbots? or no time | 22:12 |
| @sonney2k | no time and internet connection of this hotel is too unstable | 22:13 |
| wiking | heheheh | 22:13 |
| @lisitsyn | wiking: https://dl.dropboxusercontent.com/u/10139213/share/elections.png | 22:13 |
| wiking | internet in a hotel in .fr is always shiat | 22:14 |
| vgorbati_ | lisitsyn: I thought theta is basically parameter of all gradient-descend-like methods | 22:14 |
| @sonney2k | not sure if there is some boring session tomorrow - then I would fix it | 22:14 |
| wiking | lisitsyn: that's a brain? :DDD | 22:14 |
| @lisitsyn | wiking: usual picture for t-sne | 22:14 |
| @lisitsyn | vgorbati_: yes, theta=0 is t-sne | 22:18 |
| @lisitsyn | theta \ne 0 is barnes-hut | 22:18 |
| vgorbati_ | so for t-SNE there's only one parameter - perplexity? | 22:20 |
| vgorbati_ | ah, we are actually using 'barnes-hut' in the end, so theta is used | 22:21 |
| @lisitsyn | vgorbati_: yes for pure t-sne only perplexity matters | 22:22 |
| @lisitsyn | it is kind of exact | 22:22 |
| vgorbati_ | lisitsyn: ok, going to sleep now, hope will finish it by tomorrow | 22:24 |
| @lisitsyn | vgorbati_: alright | 22:24 |
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| travis-ci | [travis-ci] it's Sergey Lisitsyn's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/6546082 | 22:40 |
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| van51 | hello all | 23:13 |
| @iglesiasg | hey van51 | 23:13 |
| van51 | i am trying to tackle an entry task | 23:13 |
| van51 | can you tell if it is possible to do a partial build? | 23:13 |
| van51 | and if yes, how? | 23:14 |
| @iglesiasg | van51: what do you mean with a partial build_ | 23:15 |
| @iglesiasg | not to build all shogun modules_ | 23:15 |
| @iglesiasg | _ -> ? | 23:15 |
| van51 | yes | 23:15 |
| van51 | to re-build just the components that I have changed | 23:15 |
| @iglesiasg | no, unfortunately we have not such an option | 23:16 |
| @iglesiasg | well, if you are talking about re-building | 23:16 |
| @iglesiasg | as long as you have not modified headers, make will do that automatically | 23:16 |
| van51 | oh ok | 23:16 |
| van51 | I had modified a header last time and that's why it did it all over again I guess | 23:16 |
| @iglesiasg | if you configure with --disable-optimization | 23:16 |
| @iglesiasg | it compiles faster too | 23:17 |
| @iglesiasg | and also using a compiler cache | 23:17 |
| van51 | nice, good to know! | 23:17 |
| @iglesiasg | van51: yeah, that's the case when you modify a header | 23:17 |
| van51 | thanks! | 23:17 |
| @iglesiasg | van51: I really want to see cmake integration in shogun so we could manage this partial builds nicely | 23:17 |
| van51 | iglesiasg: I wish I knew what you were talking about :p | 23:18 |
| van51 | it's my first time "developing" on such a large scale framework | 23:18 |
| @iglesiasg | hehe :) | 23:18 |
| @iglesiasg | have you heard of cmake? | 23:18 |
| van51 | I believe I have used it | 23:19 |
| @iglesiasg | ok | 23:19 |
| van51 | but I was just copying commands | 23:19 |
| @iglesiasg | so the partial buil issue you were talking about | 23:19 |
| @iglesiasg | can be handled well with cmake | 23:19 |
| @iglesiasg | see for example PCL (another open source project) | 23:19 |
| @iglesiasg | what you do there instead of doing a configure | 23:19 |
| @iglesiasg | you do cmake | 23:19 |
| @iglesiasg | and that creates the Makefile | 23:20 |
| @iglesiasg | also you can configure cmake with its cousin ccmake | 23:20 |
| @iglesiasg | ccmake gets you to a nice ncurses interface | 23:20 |
| @iglesiasg | and you may be able to choose options, such as the modules you want to build | 23:20 |
| van51 | I see | 23:21 |
| van51 | and would it be difficult to make this transition? | 23:21 |
| @iglesiasg | let's say not easy :) | 23:21 |
| van51 | hehe | 23:22 |
| @iglesiasg | I guess one would require to learn some cmake first | 23:22 |
| van51 | It could be an upcoming project | 23:22 |
| @iglesiasg | and study shogun structure to some depth | 23:22 |
| van51 | thank you for the information | 23:24 |
| @iglesiasg | np :) | 23:24 |
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| --- Log closed Tue Apr 23 00:00:28 2013 | ||
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