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VEBER Philippe
codepi
Commits
ba9835df
Commit
ba9835df
authored
Nov 17, 2020
by
Philippe Veber
Browse files
removed app/diffseldsparse_benchmark
parent
e4fd8e26
Changes
3
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-84
app/diffseldsparse_benchmark.ml
app/diffseldsparse_benchmark.ml
+0
-31
app/dune
app/dune
+0
-8
app/lmm_benchmark.ml
app/lmm_benchmark.ml
+10
-45
No files found.
app/diffseldsparse_benchmark.ml
deleted
100644 → 0
View file @
e4fd8e26
open
Core
open
Codepi
let
main
~
n_h0
~
n_ha
~
seed
:
i
()
=
let
open
Simulation_dataset
in
let
sim
=
bppseqgen_mixed
~
tree
:
(
NHX
(
Bistro
.
Workflow
.
input
"example/trees_analyses/cyp_coding.Chrysithr_root.nhx"
))
~
profiles
:
"example/aa_fitness/263SelectedProfiles.tsv"
~
n_h0
~
n_ha
~
ne_s
:
4
.
~
seed
:
i
()
in
let
w
=
benchmark
sim
in
Bistro_engine
.
Scheduler
.
simple_eval_exn
~
np
:
4
~
mem
:
(
`GB
4
)
(
Bistro
.
Workflow
.
path
w
)
|>
print_endline
let
command
=
let
open
Command
.
Let_syntax
in
Command
.
basic
~
summary
:
"Run diffseldsparse bench"
[
%
map_open
let
n_ha
=
flag
"--n-ha"
(
required
int
)
~
doc
:
"INT Number of Ha sites"
and
n_h0
=
flag
"--n-h0"
(
required
int
)
~
doc
:
"INT Number of H0 sites"
and
seed
=
flag
"--seed"
(
required
int
)
~
doc
:
"INT Global seed"
in
main
~
n_ha
~
n_h0
~
seed
]
let
()
=
Command
.
run
command
app/dune
View file @
ba9835df
...
...
@@ -6,14 +6,6 @@
(preprocess
(pps ppx_jane)))
(executable
(name diffseldsparse_benchmark)
(public_name diffseldsparse_benchmark)
(modules diffseldsparse_benchmark)
(libraries codepi)
(preprocess
(pps ppx_jane)))
(executable
(name orthomam_app)
(public_name orthomam_convergence)
...
...
app/lmm_benchmark.ml
View file @
ba9835df
...
...
@@ -3,6 +3,8 @@ open Bistro
open
Codepi
open
Codepi
.
File_formats
module
Pipeline
=
Simulation_pipeline
.
Mutsel
type
dataset
=
{
label
:
string
;
tree
:
nhx
file
;
...
...
@@ -49,7 +51,7 @@ let orthomam_echolocation = {
}
type
detection_method
=
{
result
:
Simulation_dataset
.
t
->
text
file
;
result
:
Pipeline
.
query
->
text
file
;
col
:
int
;
label
:
string
;
requires_rooted_tree
:
bool
;
...
...
@@ -58,7 +60,7 @@ type detection_method = {
let
meth
?
(
col
=
1
)
?
(
requires_rooted_tree
=
false
)
result
label
=
{
result
;
col
;
label
;
requires_rooted_tree
}
let
methods
=
Simulation_dataset
.[
let
methods
=
Pipeline
.[
meth
tdg09
"tdg09"
;
meth
pcoc
~
col
:
3
"pcoc"
;
(* meth pcoc_v2 ~col:3 "pcoc v2" ; *)
...
...
@@ -68,65 +70,28 @@ let methods = Simulation_dataset.[
meth
topological
"topological"
~
requires_rooted_tree
:
true
;
]
let
benchmark
{
tree
=
t
;
rooted
;
ne_s
;
branch_scale
;
_
}
=
let
open
Simulation_dataset
in
let
sim
=
convdet_simulation
~
seed
:
42
~
tree
:
(
NHX
t
)
~
branch_scale
~
ne_s
~
profiles
:
"example/aa_fitness/263SelectedProfiles.tsv"
~
n_h0
:
900
~
n_ha
:
100
()
in
let
results
,
labels
=
List
.
filter_map
methods
~
f
:
(
fun
m
->
if
not
m
.
requires_rooted_tree
||
rooted
then
Some
((
m
.
result
sim
,
m
.
col
)
,
m
.
label
)
else
None
)
|>
List
.
unzip
in
Utils
.
average_precision_plot
~
oracle
:
(
oracle
sim
)
~
labels
~
results
let
benchmark_rds
?
(
seed
=
42
)
{
tree
=
t
;
rooted
;
ne_s
;
branch_scale
;
_
}
=
let
open
Simulation_dataset
in
let
param
=
Convdet_simulation_param
.
make
~
seed
~
tree
:
(
NHX
t
)
~
branch_scale
~
ne_s
let
q
=
Pipeline
.
query
~
seed
~
tree
:
(
NHX
t
)
~
branch_scale
~
ne_s
~
profiles
:
"example/aa_fitness/263SelectedProfiles.tsv"
~
n_h0
:
900
~
n_ha
:
100
()
in
let
sim
=
convdet_simulation_of_param
param
in
let
simulation
=
Convdet_simulation_param
.
simulation
param
in
let
simulation
=
Pipeline
.
simulation
q
in
let
results
,
labels
=
List
.
filter_map
methods
~
f
:
(
fun
m
->
if
not
m
.
requires_rooted_tree
||
rooted
then
Some
((
m
.
result
sim
,
m
.
col
)
,
m
.
label
)
Some
((
m
.
result
q
,
m
.
col
)
,
m
.
label
)
else
None
)
|>
List
.
unzip
in
benchmark_statistics
simulation
~
labels
~
results
let
report
=
let
module
H
=
Bistro_utils
.
Html_report
in
H
.
make
~
title
:
"Codepi benchmark"
[
H
.
section
"Besnard 2009 dataset"
;
H
.
pdf
(
benchmark
besnard2009
)
;
H
.
section
"Rubisco dataset"
;
H
.
pdf
(
benchmark
rubisco
)
;
H
.
section
"Rodent dataset"
;
H
.
pdf
(
benchmark
oneline_rodent
)
;
H
.
section
"Orthomam/echolocation dataset"
;
H
.
pdf
(
benchmark
orthomam_echolocation
)
;
]
|>
H
.
render
Pipeline
.
benchmark_statistics
simulation
~
labels
~
results
let
()
=
let
open
Bistro_utils
.
Repo
in
let
datasets
=
[
besnard2009
;
rubisco
;
oneline_rodent
;
orthomam_echolocation
]
in
let
repo
=
item
[
"report.html"
]
report
::
List
.
map
datasets
~
f
:
(
fun
d
->
List
.
map
datasets
~
f
:
(
fun
d
->
item
[
d
.
label
^
".rds"
]
(
benchmark_rds
d
)
)
in
...
...
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