Skip to content

Add preselection cut off to settings #226

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
niekdejonge wants to merge 5 commits into
base: main
Choose a base branch
from
Draft

Add preselection cut off to settings #226

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
3039ee6
Add add compound classes to settings
niekdejonge Nov 23, 2023
66f0edc
Move the init of SettingsTrainingModels and set k_fold_cross_validati…
niekdejonge Nov 23, 2023
0d1a143
Also don't use add_compound_classes for test_train_models.py
niekdejonge Nov 23, 2023
c1017d3
and set to False...
niekdejonge Nov 23, 2023
c481474
Added preselection cut_off to SettingsTrain
niekdejonge Nov 23, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions ms2query/benchmarking/k_fold_cross_validation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
clean_normalize_and_split_annotated_spectra
from ms2query.create_new_library.split_data_for_training import (
select_spectra_per_unique_inchikey, split_spectra_in_random_inchikey_sets)
from ms2query.create_new_library.train_models import train_all_models
from ms2query.create_new_library.train_models import train_all_models, SettingsTrainingModels
from ms2query.ms2library import create_library_object_from_one_dir
from ms2query.utils import (load_matchms_spectrum_objects_from_file,
save_pickled_file)
Expand Down Expand Up @@ -102,7 +102,8 @@ def train_models_and_test_result_from_k_fold_folder(k_fold_split_folder:str,
# Train all models
train_all_models(annotated_training_spectra,
unannotated_training_spectra,
models_folder)
models_folder,
SettingsTrainingModels({"add_compound_classes": False}))

# Generate test results
ms2library = create_library_object_from_one_dir(models_folder)
Expand Down
32 changes: 25 additions & 7 deletions ms2query/create_new_library/train_models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,20 @@

class SettingsTrainingModels:
def __init__(self,
settings):
settings: dict = None):
"""

:param settings:
preselection_cut_off:
This determines the number of highest scoring matches of MS2Deepscore that are used during training of MS2Query.
For these top library matches all scores are calculated
"""
default_settings = {"ms2ds_fraction_validation_spectra": 30,
"ms2ds_epochs": 150,
"spec2vec_iterations": 30,
"ms2query_fraction_for_making_pairs": 40}
"ms2query_fraction_for_making_pairs": 40,
"add_compound_classes": True,
"preselection_cut_off": 2000}
if settings:
for setting in settings:
assert setting in default_settings, \
Expand All @@ -32,15 +41,16 @@ def __init__(self,
self.ms2ds_epochs: int = default_settings["ms2ds_epochs"]
self.ms2query_fraction_for_making_pairs: int = default_settings["ms2query_fraction_for_making_pairs"]
self.spec2vec_iterations = default_settings["spec2vec_iterations"]
self.add_compound_classes = default_settings["add_compound_classes"]
self.preselection_cut_off = default_settings["preselection_cut_off"]


def train_all_models(annotated_training_spectra,
unannotated_training_spectra,
output_folder,
other_settings: dict = None):
settings: SettingsTrainingModels):
if not os.path.isdir(output_folder):
os.mkdir(output_folder)
settings = SettingsTrainingModels(other_settings)
# set file names of new generated files
ms2deepscore_model_file_name = os.path.join(output_folder, "ms2deepscore_model.hdf5")
spec2vec_model_file_name = os.path.join(output_folder, "spec2vec_model.model")
Expand Down Expand Up @@ -69,14 +79,15 @@ def train_all_models(annotated_training_spectra,
os.path.join(output_folder, "library_for_training_ms2query"),
ms2deepscore_model_file_name,
spec2vec_model_file_name,
fraction_for_training=settings.ms2query_fraction_for_making_pairs)
settings)
convert_to_onnx_model(ms2query_model, ms2query_model_file_name)

# Create library with all training spectra
library_files_creator = LibraryFilesCreator(annotated_training_spectra,
output_folder,
spec2vec_model_file_name,
ms2deepscore_model_file_name)
ms2deepscore_model_file_name,
add_compound_classes=settings.add_compound_classes)
library_files_creator.create_all_library_files()


Expand All @@ -92,17 +103,24 @@ def clean_and_train_models(spectrum_file: str,
The ion mode of the spectra you want to use for training the models, choose from "positive" or "negative"
:param output_folder:
The folder in which the models and library files are stored.
:param model_train_settings:
The settings used for training the models, options can be found in SettingsTrainingModels. If None is given
all the default settings are used. The options and default settings are:
{"ms2ds_fraction_validation_spectra": 30, "ms2ds_epochs": 150, "spec2vec_iterations": 30,
"ms2query_fraction_for_making_pairs": 40, "add_compound_classes": False}
"""
if not os.path.exists(output_folder):
os.mkdir(output_folder)
assert os.path.isdir(output_folder), "The specified folder is not a folder"
assert ion_mode in {"positive", "negative"}, "ion_mode should be set to 'positive' or 'negative'"

settings = SettingsTrainingModels(model_train_settings)

spectra = load_matchms_spectrum_objects_from_file(spectrum_file)
annotated_spectra, unnnotated_spectra = clean_normalize_and_split_annotated_spectra(spectra,
ion_mode,
do_pubchem_lookup=True)
train_all_models(annotated_spectra,
unnnotated_spectra,
output_folder,
model_train_settings)
settings)
16 changes: 9 additions & 7 deletions ms2query/create_new_library/train_ms2query_model.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
split_spectra_on_inchikeys, split_training_and_validation_spectra)
from ms2query.query_from_sqlite_database import SqliteLibrary
from ms2query.utils import return_non_existing_file_name, save_pickled_file

from ms2query.create_new_library.train_models import SettingsTrainingModels

class DataCollectorForTraining():
"""Class to collect data needed to train a ms2query random forest"""
Expand Down Expand Up @@ -115,13 +115,15 @@ def train_ms2query_model(training_spectra,
library_files_folder,
ms2ds_model_file_name,
s2v_model_file_name,
fraction_for_training):
settings: SettingsTrainingModels):
# Select spectra belonging to a single InChIKey
library_spectra, unique_inchikey_query_spectra = split_spectra_on_inchikeys(training_spectra,
fraction_for_training)
library_spectra, unique_inchikey_query_spectra = split_spectra_on_inchikeys(
training_spectra,
settings.ms2query_fraction_for_making_pairs)
# Select random spectra from the library
library_spectra, single_spectra_query_spectra = split_training_and_validation_spectra(library_spectra,
fraction_for_training)
library_spectra, single_spectra_query_spectra = split_training_and_validation_spectra(
library_spectra,
settings.ms2query_fraction_for_making_pairs)
query_spectra_for_training = unique_inchikey_query_spectra + single_spectra_query_spectra

# Create library files for training ms2query
Expand All @@ -138,7 +140,7 @@ def train_ms2query_model(training_spectra,
pickled_ms2ds_embeddings_file_name=library_creator_for_training.ms2ds_embeddings_file_name,
ms2query_model_file_name=None)
# Create training data MS2Query model
collector = DataCollectorForTraining(ms2library_for_training)
collector = DataCollectorForTraining(ms2library_for_training, preselection_cut_off=settings.preselection_cut_off)
training_scores, training_labels = collector.get_matches_info_and_tanimoto(query_spectra_for_training)

save_pickled_file(training_scores, os.path.join(library_files_folder, "training_scores_ms2query"))
Expand Down
3 changes: 2 additions & 1 deletion tests/test_train_models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@ def test_train_all_models(path_to_general_test_files, tmp_path):
{"ms2ds_fraction_validation_spectra": 2,
"ms2ds_epochs": 2,
"spec2vec_iterations": 2,
"ms2query_fraction_for_making_pairs": 400}
"ms2query_fraction_for_making_pairs": 400,
"add_compound_classes": False}
)
ms2library = create_library_object_from_one_dir(models_folder)
assert isinstance(ms2library, MS2Library)
7 changes: 5 additions & 2 deletions tests/test_train_ms2query_model.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,14 @@
import pandas as pd
import pytest
from onnxruntime import InferenceSession
from ms2query.create_new_library.train_models import SettingsTrainingModels
from ms2query.create_new_library.train_ms2query_model import (
DataCollectorForTraining, calculate_tanimoto_scores_with_library,
convert_to_onnx_model, train_ms2query_model, train_random_forest)
from ms2query.ms2library import MS2Library
from ms2query.utils import predict_onnx_model
from matchms import Spectrum


if sys.version_info < (3, 8):
pass
else:
Expand Down Expand Up @@ -78,5 +79,7 @@ def test_train_ms2query_model(path_to_general_test_files, tmp_path, hundred_test
"ms2ds_siamese_210301_5000_500_400.hdf5"),
s2v_model_file_name=os.path.join(path_to_general_test_files,
"100_test_spectra_s2v_model.model"),
fraction_for_training=10
settings=SettingsTrainingModels({"ms2query_fraction_for_making_pairs": 10,
"add_compound_classes": False,
"preselection_cut_off": 10})
)