Commit 75d45de4 authored by Philippe Veber's avatar Philippe Veber
Browse files

app: added a validation benchmark for lmm

parent df7bfedf
open Codepi
let benchmark d =
let open Simulation_dataset in
Utils.recall_precision_curve
~oracle:(oracle d)
~labels:[|"topological";"multinomial";"gemma_score";"tdg09"|]
~results:[
topological d ;
multinomial_asymptotic_lrt d ;
gemma ~lmm_test:`Score ~relatedness_mode:`Standardized d ;
tdg09 d ;
]
let () =
let sim =
let open Simulation_dataset in
convdet_simulation
~tree:(NHX "example/trees4analyses_db/cyp_coding.Chrysithr_root.nhx")
~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
~n_h0:100 ~n_ha:100 ~ne_s:(2., 2.) ()
in
let w = benchmark sim in
let loggers = [ Bistro_utils.Console_logger.create () ] in
Bistro_engine.Scheduler.simple_eval_exn ~loggers ~np:4 ~mem:(`GB 4) (Bistro.Workflow.path w)
|> print_endline
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