{"action":"created","issue":{"url":"https://api.github.com/repos/cognoma/machine-learning/issues/25","repository_url":"https://api.github.com/repos/cognoma/machine-learning","labels_url":"https://api.github.com/repos/cognoma/machine-learning/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/cognoma/machine-learning/issues/25/comments","events_url":"https://api.github.com/repos/cognoma/machine-learning/issues/25/events","html_url":"https://github.com/cognoma/machine-learning/pull/25","id":169236539,"number":25,"title":"Using pipeline in the TCGA-MLexample, add feature selection","user":{"login":"yl565","id":15843826,"avatar_url":"https://avatars.githubusercontent.com/u/15843826?v=3","gravatar_id":"","url":"https://api.github.com/users/yl565","html_url":"https://github.com/yl565","followers_url":"https://api.github.com/users/yl565/followers","following_url":"https://api.github.com/users/yl565/following{/other_user}","gists_url":"https://api.github.com/users/yl565/gists{/gist_id}","starred_url":"https://api.github.com/users/yl565/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yl565/subscriptions","organizations_url":"https://api.github.com/users/yl565/orgs","repos_url":"https://api.github.com/users/yl565/repos","events_url":"https://api.github.com/users/yl565/events{/privacy}","received_events_url":"https://api.github.com/users/yl565/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-08-03T21:18:16Z","updated_at":"2016-08-03T22:43:31Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/cognoma/machine-learning/pulls/25","html_url":"https://github.com/cognoma/machine-learning/pull/25","diff_url":"https://github.com/cognoma/machine-learning/pull/25.diff","patch_url":"https://github.com/cognoma/machine-learning/pull/25.patch"},"body":"I modified the example to use the following pipeline:\r\nmedian absolute deviation (MAD) feature selection -> z-score scaling -> Grid_search with SGDClassifier\r\nSince pipeline is used, all the feature extraction steps (feature selection/scaling) are estimated using only x_train. The mask of selected feature and the estimated mean/std (for scaling)  is then applied to x_test.\r\n\r\nTo reduce computation time, I used the top 500 features with the largest MAD. Higher performance may be achieved with more features included (grid search the optimal number of features may also be an option).\r\n\r\n(I noticed in the example x_train and x_test are standardized separately which works fine if x_test contains sufficient samples. From a practical point of view, I think it would works better to estimate the mean/std from x_train and apply it to standardize x_test)\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/cognoma/machine-learning/issues/comments/237398060","html_url":"https://github.com/cognoma/machine-learning/pull/25#issuecomment-237398060","issue_url":"https://api.github.com/repos/cognoma/machine-learning/issues/25","id":237398060,"user":{"login":"yl565","id":15843826,"avatar_url":"https://avatars.githubusercontent.com/u/15843826?v=3","gravatar_id":"","url":"https://api.github.com/users/yl565","html_url":"https://github.com/yl565","followers_url":"https://api.github.com/users/yl565/followers","following_url":"https://api.github.com/users/yl565/following{/other_user}","gists_url":"https://api.github.com/users/yl565/gists{/gist_id}","starred_url":"https://api.github.com/users/yl565/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yl565/subscriptions","organizations_url":"https://api.github.com/users/yl565/orgs","repos_url":"https://api.github.com/users/yl565/repos","events_url":"https://api.github.com/users/yl565/events{/privacy}","received_events_url":"https://api.github.com/users/yl565/received_events","type":"User","site_admin":false},"created_at":"2016-08-03T22:43:31Z","updated_at":"2016-08-03T22:43:31Z","body":"Ok, it takes me a while to setup the environment and commit all the changes. Still learning how to use git.  Is everything working? Also, can I ask what command we should use to commit all changes (including delete some files)"}}
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