{"action":"created","issue":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/939","repository_url":"https://api.github.com/repos/markovmodel/PyEMMA","labels_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/939/labels{/name}","comments_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/939/comments","events_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/939/events","html_url":"https://github.com/markovmodel/PyEMMA/issues/939","id":178553283,"number":939,"title":"Using partial_fit with TICA gives different results","user":{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars.githubusercontent.com/u/7935362?v=3","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-22T08:44:33Z","updated_at":"2016-09-22T09:15:19Z","closed_at":null,"body":"This is the data after projecting with TICA. First using `pyemma.coordinates.tica` with all the data and second using `pyemma.coordinates.transform.tica.TICA` and `partial_fit`\r\n```python\r\nIn [6]: datatica.dat[0][:,-2:]  # All data fit at once\r\nOut[6]: \r\narray([[-0.4935593605041504, -1.3321048021316528],\r\n       [-0.6039726138114929, -0.8984045386314392],\r\n       [-0.882770836353302, -0.6442685127258301],\r\n       ..., \r\n       [1.1503621339797974, -0.2566051483154297],\r\n       [1.11582612991333, -0.15375858545303345],\r\n       [0.6859675645828247, -0.40854212641716003]], dtype=object)\r\n\r\nIn [7]: datatica2.dat[0][:,-2:]  # Partial fitting\r\nOut[7]: \r\narray([[-0.4906449 ,  1.43816116],\r\n       [-0.59790296,  1.11159589],\r\n       [-0.8722117 ,  0.93744147],\r\n       ..., \r\n       [ 1.16218741,  0.28601332],\r\n       [ 1.13041911,  0.15576127],\r\n       [ 0.6934242 ,  0.38047258]])\r\n```\r\n\r\nSigns are flipped sometimes and some values diverge a bit. Is that to be expected?"},"comment":{"url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/comments/248850663","html_url":"https://github.com/markovmodel/PyEMMA/issues/939#issuecomment-248850663","issue_url":"https://api.github.com/repos/markovmodel/PyEMMA/issues/939","id":248850663,"user":{"login":"stefdoerr","id":7935362,"avatar_url":"https://avatars.githubusercontent.com/u/7935362?v=3","gravatar_id":"","url":"https://api.github.com/users/stefdoerr","html_url":"https://github.com/stefdoerr","followers_url":"https://api.github.com/users/stefdoerr/followers","following_url":"https://api.github.com/users/stefdoerr/following{/other_user}","gists_url":"https://api.github.com/users/stefdoerr/gists{/gist_id}","starred_url":"https://api.github.com/users/stefdoerr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stefdoerr/subscriptions","organizations_url":"https://api.github.com/users/stefdoerr/orgs","repos_url":"https://api.github.com/users/stefdoerr/repos","events_url":"https://api.github.com/users/stefdoerr/events{/privacy}","received_events_url":"https://api.github.com/users/stefdoerr/received_events","type":"User","site_admin":false},"created_at":"2016-09-22T09:15:19Z","updated_at":"2016-09-22T09:15:19Z","body":"And lastly also maybe try to get rid of this warning:\r\n`/shared/sdoerr/Software/anaconda3/lib/python3.5/site-packages/pyEMMA-2.2.1-py3.5-linux-x86_64.egg/pyemma/coordinates/transform/tica.py:282: VisibleDeprecationWarning: converting an array with ndim > 0 to an index will result in an error in the future\r\n  self._used_data += len(it)`"}}
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