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feat: save stats of transfer learning to disk #338

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merged 1 commit into from
Sep 9, 2024
Merged

feat: save stats of transfer learning to disk #338

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29 changes: 24 additions & 5 deletions alphadia/outputtransform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,6 +302,7 @@ class SearchPlanOutput:
LIBRARY_OUTPUT = "speclib.mbr"
TRANSFER_OUTPUT = "speclib.transfer"
TRANSFER_MODEL = "peptdeep.transfer"
TRANSFER_STATS_OUTPUT = "stats.transfer"

def __init__(self, config: dict, output_folder: str):
"""Combine individual searches into and build combined outputs
Expand Down Expand Up @@ -377,9 +378,17 @@ def build(
_ = self.build_transfer_library(folder_list, save=True)

if self.config["transfer_learning"]["enabled"]:
_ = self.build_transfer_model()
_ = self.build_transfer_model(save=True)

def build_transfer_model(self):
def build_transfer_model(self, save=True):
"""
Finetune PeptDeep models using the transfer library

Parameters
----------
save : bool, optional
Whether to save the statistics of the transfer learning on disk, by default True
"""
logger.progress("Train PeptDeep Models")

transfer_lib_path = os.path.join(
Expand All @@ -400,14 +409,24 @@ def build_transfer_model(self):
tune_mgr = FinetuneManager(
device=device, settings=self.config["transfer_learning"]
)
tune_mgr.finetune_rt(transfer_lib.precursor_df)
tune_mgr.finetune_charge(transfer_lib.precursor_df)
tune_mgr.finetune_ms2(
rt_stats = tune_mgr.finetune_rt(transfer_lib.precursor_df)
charge_stats = tune_mgr.finetune_charge(transfer_lib.precursor_df)
ms2_stats = tune_mgr.finetune_ms2(
transfer_lib.precursor_df.copy(), transfer_lib.fragment_intensity_df.copy()
)

tune_mgr.save_models(os.path.join(self.output_folder, self.TRANSFER_MODEL))

combined_stats = pd.concat([rt_stats, charge_stats, ms2_stats])

if save:
logger.info("Writing transfer learning stats output to disk")
write_df(
combined_stats,
os.path.join(self.output_folder, self.TRANSFER_STATS_OUTPUT),
file_format="tsv",
)

def build_transfer_library(
self,
folder_list: list[str],
Expand Down
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