{"action":"created","issue":{"url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/issues/116","repository_url":"https://api.github.com/repos/debbiemarkslab/EVcouplings","labels_url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/issues/116/labels{/name}","comments_url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/issues/116/comments","events_url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/issues/116/events","html_url":"https://github.com/debbiemarkslab/EVcouplings/issues/116","id":291956983,"number":116,"title":"Improve mean-field integration","user":{"login":"thomashopf","id":7434098,"avatar_url":"https://avatars0.githubusercontent.com/u/7434098?v=4","gravatar_id":"","url":"https://api.github.com/users/thomashopf","html_url":"https://github.com/thomashopf","followers_url":"https://api.github.com/users/thomashopf/followers","following_url":"https://api.github.com/users/thomashopf/following{/other_user}","gists_url":"https://api.github.com/users/thomashopf/gists{/gist_id}","starred_url":"https://api.github.com/users/thomashopf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thomashopf/subscriptions","organizations_url":"https://api.github.com/users/thomashopf/orgs","repos_url":"https://api.github.com/users/thomashopf/repos","events_url":"https://api.github.com/users/thomashopf/events{/privacy}","received_events_url":"https://api.github.com/users/thomashopf/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"b-schubert","id":6513079,"avatar_url":"https://avatars1.githubusercontent.com/u/6513079?v=4","gravatar_id":"","url":"https://api.github.com/users/b-schubert","html_url":"https://github.com/b-schubert","followers_url":"https://api.github.com/users/b-schubert/followers","following_url":"https://api.github.com/users/b-schubert/following{/other_user}","gists_url":"https://api.github.com/users/b-schubert/gists{/gist_id}","starred_url":"https://api.github.com/users/b-schubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/b-schubert/subscriptions","organizations_url":"https://api.github.com/users/b-schubert/orgs","repos_url":"https://api.github.com/users/b-schubert/repos","events_url":"https://api.github.com/users/b-schubert/events{/privacy}","received_events_url":"https://api.github.com/users/b-schubert/received_events","type":"User","site_admin":false},"assignees":[{"login":"b-schubert","id":6513079,"avatar_url":"https://avatars1.githubusercontent.com/u/6513079?v=4","gravatar_id":"","url":"https://api.github.com/users/b-schubert","html_url":"https://github.com/b-schubert","followers_url":"https://api.github.com/users/b-schubert/followers","following_url":"https://api.github.com/users/b-schubert/following{/other_user}","gists_url":"https://api.github.com/users/b-schubert/gists{/gist_id}","starred_url":"https://api.github.com/users/b-schubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/b-schubert/subscriptions","organizations_url":"https://api.github.com/users/b-schubert/orgs","repos_url":"https://api.github.com/users/b-schubert/repos","events_url":"https://api.github.com/users/b-schubert/events{/privacy}","received_events_url":"https://api.github.com/users/b-schubert/received_events","type":"User","site_admin":false},{"login":"thomashopf","id":7434098,"avatar_url":"https://avatars0.githubusercontent.com/u/7434098?v=4","gravatar_id":"","url":"https://api.github.com/users/thomashopf","html_url":"https://github.com/thomashopf","followers_url":"https://api.github.com/users/thomashopf/followers","following_url":"https://api.github.com/users/thomashopf/following{/other_user}","gists_url":"https://api.github.com/users/thomashopf/gists{/gist_id}","starred_url":"https://api.github.com/users/thomashopf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thomashopf/subscriptions","organizations_url":"https://api.github.com/users/thomashopf/orgs","repos_url":"https://api.github.com/users/thomashopf/repos","events_url":"https://api.github.com/users/thomashopf/events{/privacy}","received_events_url":"https://api.github.com/users/thomashopf/received_events","type":"User","site_admin":false},{"login":"sophiamersmann","id":12461810,"avatar_url":"https://avatars2.githubusercontent.com/u/12461810?v=4","gravatar_id":"","url":"https://api.github.com/users/sophiamersmann","html_url":"https://github.com/sophiamersmann","followers_url":"https://api.github.com/users/sophiamersmann/followers","following_url":"https://api.github.com/users/sophiamersmann/following{/other_user}","gists_url":"https://api.github.com/users/sophiamersmann/gists{/gist_id}","starred_url":"https://api.github.com/users/sophiamersmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sophiamersmann/subscriptions","organizations_url":"https://api.github.com/users/sophiamersmann/orgs","repos_url":"https://api.github.com/users/sophiamersmann/repos","events_url":"https://api.github.com/users/sophiamersmann/events{/privacy}","received_events_url":"https://api.github.com/users/sophiamersmann/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/milestones/3","html_url":"https://github.com/debbiemarkslab/EVcouplings/milestone/3","labels_url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/milestones/3/labels","id":3248060,"number":3,"title":"Release 0.0.5","description":"","creator":{"login":"sacdallago","id":6240943,"avatar_url":"https://avatars0.githubusercontent.com/u/6240943?v=4","gravatar_id":"","url":"https://api.github.com/users/sacdallago","html_url":"https://github.com/sacdallago","followers_url":"https://api.github.com/users/sacdallago/followers","following_url":"https://api.github.com/users/sacdallago/following{/other_user}","gists_url":"https://api.github.com/users/sacdallago/gists{/gist_id}","starred_url":"https://api.github.com/users/sacdallago/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sacdallago/subscriptions","organizations_url":"https://api.github.com/users/sacdallago/orgs","repos_url":"https://api.github.com/users/sacdallago/repos","events_url":"https://api.github.com/users/sacdallago/events{/privacy}","received_events_url":"https://api.github.com/users/sacdallago/received_events","type":"User","site_admin":false},"open_issues":3,"closed_issues":0,"state":"open","created_at":"2018-04-06T14:51:24Z","updated_at":"2018-04-06T14:58:57Z","due_on":null,"closed_at":null},"comments":4,"created_at":"2018-01-26T16:29:54Z","updated_at":"2018-04-10T09:17:56Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"While investigating #104 I found a couple of issues with the mean-field protocol and couplings objects that would be great to address:\r\n\r\n1) The mean_field couplings protocol should allow to specify the pseudocount weight as a parameter (given the inference method itself has the option already)\r\n\r\n2) It looks like there may be some sign problem with the mutation effects computed using mean-field couplings models (damaging > 0 instead of < 0)\r\n\r\n3) Inference of the independent model shoul be based on pseudocounted f_i matrix (this is the way I originally implemented it, before we moved over to the l2-based inference that is currently present in the CouplingsModel object. Ideally, this would be based on detecting the model is from mean-field upon loading, and returning a MeanFieldCouplingsObject that has the appropriate behavior. For now, the fix from #104 is to specify a default lambda_h of 0.01 and apply l2-regularized inference instead.\r\n\r\n@sophiamersmann if you have any time to look into this would be greatly appreciated!\r\n"},"comment":{"url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/issues/comments/380031985","html_url":"https://github.com/debbiemarkslab/EVcouplings/issues/116#issuecomment-380031985","issue_url":"https://api.github.com/repos/debbiemarkslab/EVcouplings/issues/116","id":380031985,"user":{"login":"sophiamersmann","id":12461810,"avatar_url":"https://avatars2.githubusercontent.com/u/12461810?v=4","gravatar_id":"","url":"https://api.github.com/users/sophiamersmann","html_url":"https://github.com/sophiamersmann","followers_url":"https://api.github.com/users/sophiamersmann/followers","following_url":"https://api.github.com/users/sophiamersmann/following{/other_user}","gists_url":"https://api.github.com/users/sophiamersmann/gists{/gist_id}","starred_url":"https://api.github.com/users/sophiamersmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sophiamersmann/subscriptions","organizations_url":"https://api.github.com/users/sophiamersmann/orgs","repos_url":"https://api.github.com/users/sophiamersmann/repos","events_url":"https://api.github.com/users/sophiamersmann/events{/privacy}","received_events_url":"https://api.github.com/users/sophiamersmann/received_events","type":"User","site_admin":false},"created_at":"2018-04-10T09:17:56Z","updated_at":"2018-04-10T09:17:56Z","author_association":"CONTRIBUTOR","body":"Sure! Do you want me to use any specific dataset?"}}
{"actor":{"display_login":"sophiamersmann"}}