From 4730aaa5d5ae509c3ca4bbeb3e4ba3536f8f8929 Mon Sep 17 00:00:00 2001 From: Chancen Law Date: Fri, 24 Jan 2025 19:10:19 -1000 Subject: [PATCH 1/3] Fix Yasamin's name in contributors --- doc/changes/names.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/changes/names.rst b/doc/changes/names.rst index b37e174..951becd 100644 --- a/doc/changes/names.rst +++ b/doc/changes/names.rst @@ -8,7 +8,7 @@ .. _Mehrnoosh Emamifar: https://www.linkedin.com/in/mehrnoosh-emamifar/ .. _Chancen Law: https://www.linkedin.com/in/chancenlaw/ .. _Nureldin Mohamed: https://www.linkedin.com/in/nureldin-m-19738625b/ -.. _Yasamin Joda: https://www.linkedin.com/in/yasamin-jodat/ +.. _Yasamin Jodat: https://www.linkedin.com/in/yasamin-jodat/ .. _Aneesh Mazumder: https://www.linkedin.com/in/aneesh-mazumder/ .. _AI4Life Institute: https://www.ai4lifeinstitute.com/ \ No newline at end of file From 12d77be52c61a3ae1dfc82406bb095a8e5a6e958 Mon Sep 17 00:00:00 2001 From: lex <125166100+alexiszxcv@users.noreply.github.com> Date: Mon, 17 Mar 2025 23:56:55 -0400 Subject: [PATCH 2/3] Update model.py with MiAge --- biolearn/model.py | 65 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/biolearn/model.py b/biolearn/model.py index 2a50b93..9683f0d 100644 --- a/biolearn/model.py +++ b/biolearn/model.py @@ -493,6 +493,18 @@ def anti_trafo(x, adult_age=20): "transform": lambda sum: sum + 55.808884324, }, }, + "MiAge" = { + "year": 2017, + "species": "Human", + "tissue": "Blood", + "source": "https://pubmed.ncbi.nlm.nih.gov/29160179/", + "output": "Mitotic Age (Years)", + "model": { + "type": "MiAgeNonlinearClock", + "file": "MiAge_coefficients.csv", + "parameter_file": "MiAge_parameters.csv", + }, + }, } @@ -910,6 +922,59 @@ def predict(self, geo_data): def __getattr__(self, name): return getattr(self.clock, name) +class MiAgeNonlinearClock: + def __init__(self, coefficient_file, parameter_file): + """ + Initializes the MiAge nonlinear methylation clock. + + :param coefficient_file: CSV file containing CpG site coefficients. + :param parameter_file: CSV file containing A, B, C nonlinear transformation parameters. + """ + self.coefficients = pd.read_csv(get_data_file(coefficient_file), index_col=0) + self.parameters = pd.read_csv(get_data_file(parameter_file), index_col=0) + + # Extract transformation parameters (A, B, C) + self.A = self.parameters.loc["A", "Coefficient"] + self.B = self.parameters.loc["B", "Coefficient"] + self.C = self.parameters.loc["C", "Coefficient"] + + @classmethod + def from_definition(cls, clock_definition): + """ + Instantiates the model from a dictionary definition. + """ + model_def = clock_definition["model"] + return cls(model_def["file"], model_def["parameter_file"]) + + def predict(self, geo_data): + """ + Predicts mitotic age (MiAge) using the nonlinear model. + """ + methylation_data = geo_data.dnam + + # Identify shared CpG sites between input data and model + shared_sites = methylation_data.index.intersection(self.coefficients.index) + if shared_sites.empty: + raise ValueError("No overlapping CpG sites found for MiAge clock.") + + # Extract methylation values and corresponding weights + X = methylation_data.loc[shared_sites] + beta_weights = self.coefficients.loc[shared_sites, "CoefficientTraining"] + + # Compute weighted sum of CpG values + weighted_sum = (X.T @ beta_weights).values + + # Apply the MiAge-specific nonlinear transformation + miage_pred = self.A * np.exp(self.B * weighted_sum) + self.C + + return pd.DataFrame(miage_pred, index=methylation_data.columns, columns=["Predicted MiAge"]) + + def methylation_sites(self): + """ + Returns the required CpG sites for MiAge calculation. + """ + return list(self.coefficients.index) + def single_sample_clock(clock_function, data): return clock_function(data).iloc[0, 0] From 712dc5eb2014cc720c771e03c3db9c794f5041d4 Mon Sep 17 00:00:00 2001 From: lex <125166100+alexiszxcv@users.noreply.github.com> Date: Mon, 17 Mar 2025 23:57:40 -0400 Subject: [PATCH 3/3] Add MiAge CSV files --- biolearn/data/MiAge_coefficients.csv | 269 +++++++++++++ biolearn/data/MiAge_parameters.csv | 544 +++++++++++++++++++++++++++ 2 files changed, 813 insertions(+) create mode 100644 biolearn/data/MiAge_coefficients.csv create mode 100644 biolearn/data/MiAge_parameters.csv diff --git a/biolearn/data/MiAge_coefficients.csv b/biolearn/data/MiAge_coefficients.csv new file mode 100644 index 0000000..1a932e8 --- /dev/null +++ b/biolearn/data/MiAge_coefficients.csv @@ -0,0 +1,269 @@ +"CpG_Site","Value1","Value2","Value3" +"CpG_1",0.997532178573722,0.521451605677157,-0.354770518960769 +"CpG_2",0.999515686071933,0.812465172078029,-0.63583405538151 +"CpG_3",0.999733159924055,0.435155243806152,-0.343761639293931 +"CpG_4",0.997810270123824,0.524318955013262,-0.328248646772022 +"CpG_5",0.998683802451356,0.850180749471286,-0.583592926503214 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