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4985c6709..54b5a20ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,8 @@ scikit-learn = "^1.3.2" pandas = { extras = ["gcp", "parquet"], version = "^2.2.2" } skops = ">=0.9,<0.11" google-cloud-secret-manager = "^2.20.0" +shap = "^0.46.0" +matplotlib = "3.7.3" [tool.poetry.dev-dependencies] pre-commit = "^4.0.0" diff --git a/src/gentropy/method/l2g/model.py b/src/gentropy/method/l2g/model.py index 45d90f90d..e35e255a2 100644 --- a/src/gentropy/method/l2g/model.py +++ b/src/gentropy/method/l2g/model.py @@ -2,10 +2,12 @@ from __future__ import annotations +import json from dataclasses import dataclass, field from pathlib import Path from typing import TYPE_CHECKING, Any, Type +import pandas as pd import skops.io as sio from pandas import DataFrame as pd_dataframe from pandas import to_numeric as pd_to_numeric @@ -148,6 +150,23 @@ def save(self: LocusToGeneModel, path: str) -> None: else: sio.dump(self.model, path) + @staticmethod + def load_feature_matrix_from_wandb(wandb_run_name: str) -> pd.DataFrame: + """Loads dataset of feature matrix used during a wandb run. + + Args: + wandb_run_name (str): Name of the wandb run to load the feature matrix from + + Returns: + pd.DataFrame: Feature matrix used during the wandb run + """ + with open(wandb_run_name) as f: + raw_data = json.load(f) + + data = raw_data["data"] + columns = raw_data["columns"] + return pd.DataFrame(data, columns=columns) + def _create_hugging_face_model_card( self: LocusToGeneModel, local_repo: str, diff --git a/src/gentropy/method/l2g/trainer.py b/src/gentropy/method/l2g/trainer.py index 1c4088462..fe56b3f42 100644 --- a/src/gentropy/method/l2g/trainer.py +++ b/src/gentropy/method/l2g/trainer.py @@ -2,11 +2,14 @@ from __future__ import annotations +import os from dataclasses import dataclass from functools import partial -from typing import Any +from typing import TYPE_CHECKING, Any +import matplotlib.pyplot as plt import pandas as pd +import shap from sklearn.metrics import ( accuracy_score, f1_score, @@ -15,7 +18,8 @@ roc_auc_score, ) from sklearn.model_selection import train_test_split -from wandb.data_types import Table +from wandb.data_types import Image, Table +from wandb.errors.term import termlog as wandb_termlog from wandb.sdk.wandb_init import init as wandb_init from wandb.sdk.wandb_sweep import sweep as wandb_sweep from wandb.sklearn import plot_classifier @@ -24,6 +28,11 @@ from gentropy.dataset.l2g_feature_matrix import L2GFeatureMatrix from gentropy.method.l2g.model import LocusToGeneModel +if TYPE_CHECKING: + from matplotlib.axes._axes import Axes + from shap._explanation import Explanation + from wandb.sdk.wandb_run import Run + @dataclass class LocusToGeneTrainer: @@ -34,13 +43,22 @@ class LocusToGeneTrainer: # Initialise vars features_list: list[str] | None = None - target_labels: list[str] | None = None + label_col: str = "goldStandardSet" x_train: pd.DataFrame | None = None y_train: pd.Series | None = None x_test: pd.DataFrame | None = None y_test: pd.Series | None = None + run: Run | None = None wandb_l2g_project_name: str = "gentropy-locus-to-gene" + def __post_init__(self) -> None: + """Set default features_list to feature_matrix's features_list if not provided.""" + self.features_list = ( + self.feature_matrix.features_list + if self.features_list is None + else self.features_list + ) + def fit( self: LocusToGeneTrainer, ) -> LocusToGeneModel: @@ -65,6 +83,54 @@ def fit( return self.model raise ValueError("Train data not set, nothing to fit.") + def _get_shap_explanation( + self: LocusToGeneTrainer, + model: LocusToGeneModel, + ) -> Explanation: + """Get the SHAP values for the given model and data. We pass the full X matrix (without the labels) to interpret their shap values. + + Args: + model (LocusToGeneModel): Model to explain. + + Returns: + Explanation: SHAP values for the given model and data. + + Raises: + ValueError: Train data not set, cannot get SHAP values. + """ + if self.x_train is not None and self.x_test is not None: + training_data = pd.concat([self.x_train, self.x_test], ignore_index=True) + explainer = shap.TreeExplainer( + model.model, + data=training_data, + feature_perturbation="interventional", + ) + return explainer(training_data) + raise ValueError("Train data not set.") + + def log_plot_image_to_wandb( + self: LocusToGeneTrainer, title: str, plot: Axes + ) -> None: + """Accepts a plot object, and saves the fig to PNG to then log it in W&B. + + Args: + title (str): Title of the plot. + plot (Axes): Shap plot to log. + + Raises: + ValueError: Run not set, cannot log to W&B. + """ + if self.run is None: + raise ValueError("Run not set, cannot log to W&B.") + if not plot: + # Scatter plot returns none, so we need to handle this case + plt.savefig("tmp.png", bbox_inches="tight") + else: + plot.figure.savefig("tmp.png", bbox_inches="tight") + self.run.log({title: Image("tmp.png")}) + plt.close() + os.remove("tmp.png") + def log_to_wandb( self: LocusToGeneTrainer, wandb_run_name: str, @@ -76,12 +142,16 @@ def log_to_wandb( Args: wandb_run_name (str): Name of the W&B run + + Raises: + ValueError: If dependencies are not available. """ if ( self.x_train is not None and self.x_test is not None and self.y_train is not None and self.y_test is not None + and self.features_list is not None ): assert ( not self.x_train.empty and not self.y_train.empty @@ -89,7 +159,7 @@ def log_to_wandb( fitted_classifier = self.model.model y_predicted = fitted_classifier.predict(self.x_test.values) y_probas = fitted_classifier.predict_proba(self.x_test.values) - run = wandb_init( + self.run = wandb_init( project=self.wandb_l2g_project_name, name=wandb_run_name, config=fitted_classifier.get_params(), @@ -109,39 +179,66 @@ def log_to_wandb( is_binary=True, ) # Track evaluation metrics - run.log( + self.run.log( { "areaUnderROC": roc_auc_score( self.y_test, y_probas[:, 1], average="weighted" ) } ) - run.log({"accuracy": accuracy_score(self.y_test, y_predicted)}) - run.log( + self.run.log({"accuracy": accuracy_score(self.y_test, y_predicted)}) + self.run.log( { "weightedPrecision": precision_score( self.y_test, y_predicted, average="weighted" ) } ) - run.log( + self.run.log( { "weightedRecall": recall_score( self.y_test, y_predicted, average="weighted" ) } ) - run.log({"f1": f1_score(self.y_test, y_predicted, average="weighted")}) + self.run.log({"f1": f1_score(self.y_test, y_predicted, average="weighted")}) # Track gold standards and their features - run.log( + self.run.log( {"featureMatrix": Table(dataframe=self.feature_matrix._df.toPandas())} ) # Log feature missingness - run.log( + self.run.log( { "missingnessRates": self.feature_matrix.calculate_feature_missingness_rate() } ) + # Plot marginal contribution of each feature + explanation = self._get_shap_explanation(self.model) + self.log_plot_image_to_wandb( + "Feature Contribution", + shap.plots.bar( + explanation, max_display=len(self.x_train.columns), show=False + ), + ) + self.log_plot_image_to_wandb( + "Beeswarm Plot", + shap.plots.beeswarm( + explanation, max_display=len(self.x_train.columns), show=False + ), + ) + # Plot correlation between feature values and their importance + for feature in self.features_list: + self.log_plot_image_to_wandb( + f"Effect of {feature} on the predictions", + shap.plots.scatter( + explanation[:, feature], + show=False, + ), + ) + wandb_termlog("Logged Shapley contributions.") + self.run.finish() + else: + raise ValueError("Something went wrong, couldn't log to W&B.") def train( self: LocusToGeneTrainer, @@ -158,20 +255,12 @@ def train( data_df = self.feature_matrix._df.drop("geneId", "studyLocusId").toPandas() # Encode labels in `goldStandardSet` to a numeric value - data_df["goldStandardSet"] = data_df["goldStandardSet"].map( - self.model.label_encoder - ) + data_df[self.label_col] = data_df[self.label_col].map(self.model.label_encoder) # Ensure all columns are numeric and split data_df = data_df.apply(pd.to_numeric) - self.feature_cols = [ - col - for col in data_df.columns - if col not in ["studyLocusId", "goldStandardSet"] - ] - label_col = "goldStandardSet" - X = data_df[self.feature_cols].copy() - y = data_df[label_col].copy() + X = data_df[self.features_list].copy() + y = data_df[self.label_col].copy() self.x_train, self.x_test, self.y_train, self.y_test = train_test_split( X, y, test_size=0.2, random_state=42 ) diff --git a/utils/install_dependencies_on_cluster.sh b/utils/install_dependencies_on_cluster.sh index b0a165c04..849dee0c3 100644 --- a/utils/install_dependencies_on_cluster.sh +++ b/utils/install_dependencies_on_cluster.sh @@ -62,7 +62,7 @@ function main() { echo "Install package..." # NOTE: ensure the gentropy is reinstalled each time without version cache # see https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-force-reinstall - run_with_retry pip install --force-reinstall ${PACKAGENAME} + run_with_retry pip install --force-reinstall --ignore-installed ${PACKAGENAME} }