Models
Please note that most functions are helper functions and are not meant to be used directly.
pyaging.models._models
-
class pyaging.models._models.ABEC[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.AltumAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Scales an array based on the median and standard deviation.
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class pyaging.models._models.BiTAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Binarizes an array based on the median of each row, excluding zeros.
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class pyaging.models._models.CamilloH3K27ac[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.CamilloH3K27me3[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.CamilloH3K36me3[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.CamilloH3K4me1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.CamilloH3K4me3[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.CamilloH3K9ac[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.CamilloH3K9me3[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.CamilloPanHistone[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.CpGPTGrimAge3[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Converts from a Cox parameter to age in units of years.
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preprocess(x)[source][source]
Scales an array based on the median and standard deviation.
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class pyaging.models._models.CpGPTPCGrimAge3[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Converts from a Cox parameter to age in units of years.
-
preprocess(x)[source][source]
Scales an array based on the mean and standard deviation.
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class pyaging.models._models.DNAmFitAge[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DNAmFitAgeGaitF[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.DNAmFitAgeGaitM[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.DNAmFitAgeGripF[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DNAmFitAgeGripM[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DNAmFitAgeVO2Max[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.DNAmIC[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DNAmPhenoAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DNAmTL[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DeconvoluteBloodEPIC[source][source]
Bases: DeconvolutionSingleCell
-
class pyaging.models._models.DeconvolutionSingleCell[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.DepressionBarbu[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.DunedinPACE[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Apply quantile normalization on x using gold standard means.
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class pyaging.models._models.ENCen100[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.ENCen40[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
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class pyaging.models._models.EnsembleAgeStatic[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.EnsembleAgeStaticTop[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Converts from a Cox parameter to age in units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Converts from a Cox parameter to age in units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2ADM[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2B2M[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2CystatinC[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2GDF15[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2Leptin[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2LogA1C[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2LogCRP[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2PAI1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2PackYrs[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.GrimAge2TIMP1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.HRSInCHPhenoAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Han[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Hannum[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Horvath2013[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.HypoClock[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Compute mean beta per sample, excluding missing (-1) values.
-
class pyaging.models._models.IntrinClock[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Knight[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.LeeControl[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.LeeRefinedRobust[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.LeeRobust[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Lin[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Mammalian1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic transformation with an offset of -2.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Mammalian2[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x, x_species)[source][source]
Converts output of relative age to age in units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Mammalian3[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x, x_species)[source][source]
Converts output of to units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.MammalianBlood2[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x, x_species)[source][source]
Converts output of relative age to age in units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.MammalianBlood3[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x, x_species)[source][source]
Converts output of to units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.MammalianFemale[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies a sigmoid transformation.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.MammalianLifespan[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-log transformation.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.MammalianSkin2[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x, x_species)[source][source]
Converts output of relative age to age in units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.MammalianSkin3[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x, x_species)[source][source]
Converts output of to units of years.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneyBMI[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneyBodyFat[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneyEducation[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneyHDLCholesterol[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneyLDLCholesterol[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneySmoking[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.McCartneyTotalCholesterol[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Meer[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Transforms age in days to age in months.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.OcampoATAC1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Normalize a PyTorch tensor of counts to TPM (Transcripts Per Million) then
transforms with log1p.
-
class pyaging.models._models.OcampoATAC2[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Normalize a PyTorch tensor of counts to TPM (Transcripts Per Million) then
transforms with log1p.
-
class pyaging.models._models.PCDNAmTL[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PCGrimAge[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PCHannum[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PCHorvath2013[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PCPhenoAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PCSkinAndBlood[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Pasta[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Apply linear scaling and shifting constants from the original Pasta definition.
-
preprocess(x)[source][source]
Fill missing values with the global median then rank-normalize per sample.
-
class pyaging.models._models.PastaMouse[source][source]
Bases: Pasta
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
set_mouse_features(full_features, full_reference_values=None, mouse_prefix='ENSMUSG')[source][source]
Configure the mouse-only interface while keeping the full feature space for the base model.
-
class pyaging.models._models.PedBE[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Petkovich[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies a convertion from the output of an ElasticNet to mouse age in months.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PhenoAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies a convertion from a CDF of the mortality score from a Gompertz
distribution to phenotypic age.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PipekElasticNet[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PipekFilteredH[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.PipekRetrainedH[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Reg[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Add the REG intercept term after linear prediction.
-
preprocess(x)[source][source]
Fill missing values with the global median then rank-normalize per sample.
-
class pyaging.models._models.RepliTali[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.RetroelementAgeV1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.RetroelementAgeV2[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.SexScoreBase[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.SkinAndBlood[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies an anti-logarithmic linear transformation to a PyTorch tensor.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.StocH[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.StocP[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.StocZ[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.Stubbs[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Applies a convertion from the output of an ElasticNet to mouse age in months.
-
preprocess(x)[source][source]
Apply quantile normalization on x using gold standard means
and then scale with the means and standard deviation.
-
class pyaging.models._models.SystemsAge[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeBase[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.SystemsAgeBlood[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeBrain[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeHeart[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeHormone[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeImmune[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeInflammation[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeKidney[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeLiver[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeLung[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeMetabolic[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.SystemsAgeMusculoSkeletal[source][source]
Bases: SystemsAgeBase
-
class pyaging.models._models.Thompson[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.TwelveCellDeconvoluteBloodEPIC[source][source]
Bases: DeconvolutionSingleCell
-
class pyaging.models._models.XChrom[source][source]
Bases: SexScoreBase
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
class pyaging.models._models.YChrom[source][source]
Bases: SexScoreBase
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
class pyaging.models._models.YingAdaptAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.YingCausAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.YingDamAge[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.ZhangBLUP[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Scales the input PyTorch tensor per row with mean 0 and std 1.
-
class pyaging.models._models.ZhangEN[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Scales the input PyTorch tensor per row with mean 0 and std 1.
-
class pyaging.models._models.ZhangMortality[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.cABEC[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.eABEC[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.epiTOC1[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
-
class pyaging.models._models.epiTOC2[source][source]
Bases: pyagingModel
-
forward(x)[source][source]
Define the computation performed at every call.
Should be overridden by all subclasses.
Note
Although the recipe for forward pass needs to be defined within
this function, one should call the Module instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Replace NaNs with zero; missing features should already be imputed via reference_values.
-
class pyaging.models._models.stemTOC[source][source]
Bases: pyagingModel
-
postprocess(x)[source][source]
Postprocess the model output. This method should be implemented by all subclasses.
-
preprocess(x)[source][source]
Preprocess the input data. This method should be implemented by all subclasses.
