Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Open sidebar
VEBER Philippe
codepi
Commits
75d45de4
Commit
75d45de4
authored
Nov 03, 2020
by
Philippe Veber
Browse files
app: added a validation benchmark for lmm
parent
df7bfedf
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
26 additions
and
0 deletions
+26
-0
app/lmm_benchmark.ml
app/lmm_benchmark.ml
+26
-0
No files found.
app/lmm_benchmark.ml
0 → 100644
View file @
75d45de4
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
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment