lmm_benchmark.ml 924 Bytes
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open Codepi

let benchmark d =
  let open Simulation_dataset in
  Utils.recall_precision_curve
    ~oracle:(oracle d)
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    ~labels:[| "topological"; "multinomial";"gemma_score";"inhouse"; "pcoc"; (* "pcocv2" ; *)"tdg09" |]
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    ~results:[
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      topological d, 1 ;
      multinomial_asymptotic_lrt d, 1 ;
      gemma ~lmm_test:`Score ~relatedness_mode:`Standardized d, 1 ;
      inhouse_lmm d, 1 ;
      pcoc d, 3 ;
      (* pcoc_v2 d ; *)
      tdg09 d, 1 ;
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    ]

let () =
  let sim =
    let open Simulation_dataset in
    convdet_simulation
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      ~tree:(NHX "data/besnard2009/besnard2009.nhx")
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      ~profiles:"example/aa_fitness/263SelectedProfiles.tsv"
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      ~n_h0:900 ~n_ha:100 ~branch_scale:3. ~ne_s:(2., 2.) ()
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  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