{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/126","labels_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/126/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/126/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/126/events","html_url":"https://github.com/broadinstitute/hellbender-protected/issues/126","id":109834153,"number":126,"title":"Possible enhancements to MCMC.","user":{"login":"samuelklee","id":11076296,"avatar_url":"https://avatars.githubusercontent.com/u/11076296?v=3","gravatar_id":"","url":"https://api.github.com/users/samuelklee","html_url":"https://github.com/samuelklee","followers_url":"https://api.github.com/users/samuelklee/followers","following_url":"https://api.github.com/users/samuelklee/following{/other_user}","gists_url":"https://api.github.com/users/samuelklee/gists{/gist_id}","starred_url":"https://api.github.com/users/samuelklee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samuelklee/subscriptions","organizations_url":"https://api.github.com/users/samuelklee/orgs","repos_url":"https://api.github.com/users/samuelklee/repos","events_url":"https://api.github.com/users/samuelklee/events{/privacy}","received_events_url":"https://api.github.com/users/samuelklee/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-05T16:16:18Z","updated_at":"2015-11-03T19:46:48Z","closed_at":null,"body":"Some possible enhancements/improvements, in no particular order and of varying scope:\r\n\r\n-Change SliceSampler to be able to handle multimodal univariate distributions. Should just be a matter of implementing the pseudocode in Neal 2003 http://projecteuclid.org/download/pdf_1/euclid.aos/1056562461\r\n\r\n-Add Metropolis-Hastings univariate sampler as alternative to SliceSampler.\r\n\r\n-Add Metropolis-Hastings/nested/etc. multivariate samplers as alternatives to GibbsSampler.  This should only be tackled if a model/dataset necessitates it.\r\n\r\n-Implement hierarchical/multilevel models in an OOP way.  Currently, the samplers operate on lists of global parameters and lists of lists of \"local\" parameters (i.e., segment-level or site-level parameters), which is a bit clunky.\r\n\r\n-Add convergence diagnostics (e.g., autocorrelation time).\r\n\r\n-Add ability to make trace plots and corner plots.\r\n\r\n-Implement more flexible discarding of burn-in.  Currently, samples from all iterations are aggregated in memory.  Depending on the maximum number of iterations we want to allow, it might be better to write samples to disk, only store samples in memory after burn-in, etc. so we don't run into memory issues.\r\n\r\n-Parallelization (again, only if a model/dataset necessitates it)."},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/comments/153466956","html_url":"https://github.com/broadinstitute/hellbender-protected/issues/126#issuecomment-153466956","issue_url":"https://api.github.com/repos/broadinstitute/hellbender-protected/issues/126","id":153466956,"user":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"created_at":"2015-11-03T19:46:47Z","updated_at":"2015-11-03T19:46:47Z","body":"@samuelklee Do we need this for the beta release?"}}