{"shas":[["deac525a84bc0c216f6299761d19a9ecd98a97da","6fea36cbb95d0d9800fb9224813d5738559b1144@systemsbiology.org","Relatively major improvements, primarily to annealing schedule and motif finding:\n\n* Motif finding starts later, and increases in frequency near end.\n* Motif finding is skipped for a given cluster if it has not chanced since last motif finding.\n* \"Fuzzy-index\" doesn't get as close to zero - keeps improving near end of run\n* \"consensus\" seeding to Meme is turned off by default (seemed to be to constraining)\n* parameter to recalc bg seq frequency for each bicluster individually (turned off by default because it's slow)\n\nOther changes:\n\n* added parallelized kmeans seeding via \"bigkmeans\" in package \"biganalytics\"\n* bug fix to clusters.w.func(), clusters.w.genes(), cluster.summary()","David Reiss"],["b75ed7e56bae30b6ce190aad1b1040e321c202da","6fea36cbb95d0d9800fb9224813d5738559b1144@systemsbiology.org","minor fixes to updated annealing schedules, other small tweaks","David Reiss"],["5e4f2866c44cd0cb6e2e1d55747fa9bd1cbcd154","6fea36cbb95d0d9800fb9224813d5738559b1144@systemsbiology.org","minor bugfixes wrt. new schedule; make it work with no.genome.info=TRUE","David Reiss"],["83d3db665489b7cbb7d4abade90309b8cdff74a7","6fea36cbb95d0d9800fb9224813d5738559b1144@systemsbiology.org","Updated to version 4.8.3\n* modified motif annealing schedule to start motifing later and increase frequency towards end\n* no motifing of biclusters that havent changed since last motifing\n* improvements to write.bicluster.network() including node images for cytoscape\n* other relatively minor changes and improvements and bug fixes","David Reiss"]],"repo":"dreiss-isb/cmonkey","actor":"dreiss-isb","ref":"refs/heads/master","size":4,"head":"83d3db665489b7cbb7d4abade90309b8cdff74a7","actor_gravatar":"53949fa7e9d7c39f470e849cc94dd1e5","push_id":27557208}