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VEBER Philippe
codepi
Commits
4d54b9af
Commit
4d54b9af
authored
Mar 02, 2021
by
Philippe Veber
Browse files
app/Lmm_benchmark: cleanup
parent
63ab3739
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1
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app/lmm_benchmark.ml
app/lmm_benchmark.ml
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app/lmm_benchmark.ml
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4d54b9af
...
...
@@ -60,8 +60,8 @@ let meth ?(requires_rooted_tree = false) f label =
{
f
;
label
;
requires_rooted_tree
}
let
methods
=
Pipeline
.[
(*
meth tdg09 "tdg09" ;
meth pcoc "pcoc" ; *)
meth
tdg09
"tdg09"
;
(*
meth pcoc "pcoc" ; *)
(* meth pcoc_v2 ~col:3 "pcoc v2" ; *)
meth
(
gemma
~
lmm_test
:
`Score
~
relatedness_mode
:
`Standardized
)
"gemma"
;
meth
inhouse_lmm
"LMM"
;
...
...
@@ -74,7 +74,7 @@ let benchmark_rds ?(seed = 42) { tree = t ; rooted ; ne_s ; branch_scale ; _ } =
let
q
=
Pipeline
.
query
~
seed
~
tree
:
(
NHX
t
)
~
branch_scale
~
ne_s
~
profiles
:
"example/aa_fitness/263SelectedProfiles.tsv"
~
n_h0
:
900
~
n_ha
:
100
()
~
n_h0
:
900
0
~
n_ha
:
100
0
()
in
let
methods
=
List
.
filter_map
methods
~
f
:
(
fun
m
->
...
...
@@ -88,8 +88,7 @@ let benchmark_rds ?(seed = 42) { tree = t ; rooted ; ne_s ; branch_scale ; _ } =
let
()
=
let
open
Bistro_utils
.
Repo
in
(* let datasets = [ besnard2009 ; rubisco ; oneline_rodent ; orthomam_echolocation ] in *)
let
datasets
=
[
besnard2009
]
in
let
datasets
=
[
besnard2009
;
rubisco
;
oneline_rodent
;
orthomam_echolocation
]
in
let
repo
=
List
.
map
datasets
~
f
:
(
fun
d
->
item
[
d
.
label
^
".rds"
]
(
benchmark_rds
d
)
...
...
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