diff --git a/scripts/run_lda.R b/scripts/run_lda.R index bdf1fe3..154412f 100755 --- a/scripts/run_lda.R +++ b/scripts/run_lda.R @@ -11,10 +11,8 @@ # ./run_lda.R --counts test.RData --init test.rds # -# countsfile <- "../data/nips.RData" # countsfile <- "../data/droplet.RData" # countsfile <- "../data/pbmc_68k.RData" -# initfile <- "../output/nips/rds/fit-nips-scd-ex-k=10.rds" # initfile <- "../output/droplet/rds/fit-droplet-scd-ex-k=10.rds" # initfile <- "../output/pbmc68k/rds/fit-pbmc68k-scd-ex-k=10.rds" @@ -59,12 +57,6 @@ k <- ncol(fit0$F) # ------- # Now we are ready to perform variational inference for the LDA model. # -# For the nips data with k = 10, this step took roughly 40 s per -# iteration. -# -# For the newsgroups data with k = 10, this step took roughly 70 s per -# iteration. -# # For the droplet data with k = 10, this step took roughly 6 min per # iteration. # diff --git a/scripts/run_lda_all.sh b/scripts/run_lda_all.sh index a2c3905..fd611a3 100644 --- a/scripts/run_lda_all.sh +++ b/scripts/run_lda_all.sh @@ -101,7 +101,53 @@ sbatch ${MAIN_SCRIPT} nips nips/rds/fit-nips-scd-ex-k=11 sbatch ${MAIN_SCRIPT} nips nips/rds/fit-nips-scd-ex-k=12 # Run LDA on the droplet data. -# TO DO. +# +# data initfile +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=2 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=2 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=3 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=4 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=5 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=6 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=7 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=8 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=9 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=10 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=11 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-k=12 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=2 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=3 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=4 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=5 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=6 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=7 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=8 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=9 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=10 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=11 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-em-ex-k=12 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=2 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=3 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=4 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=5 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=6 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=7 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=8 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=9 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=10 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=11 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-k=12 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=2 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=3 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=4 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=5 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=6 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=7 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=8 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=9 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=10 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=11 +sbatch ${MAIN_SCRIPT} droplet droplet/rds/fit-droplet-scd-ex-k=12 # Run LDA on the 68k pbmc data. # TO DO.