pyaging 0.5.1__tar.gz → 0.5.2__tar.gz

{pyaging-0.5.1 → pyaging-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: pyaging
-Version: 0.5.1
+Version: 0.5.2
 Summary: A Python-based compendium of GPU-optimized aging clocks.
 Project-URL: homepage, https://github.com/lucascamillomd/pyaging
 Project-URL: repository, https://github.com/lucascamillomd/pyaging

{pyaging-0.5.1 → pyaging-0.5.2}/src/pyaging/__init__.py

@@ -4,4 +4,4 @@ from . import data, logger, models, utils
 from . import predict as pred
 from . import preprocess as pp
 
-__version__ = "0.5.1"
+__version__ = "0.5.2"

{pyaging-0.5.1 → pyaging-0.5.2}/src/pyaging/models/__init__.py

@@ -34,10 +34,8 @@ from ._models import (
     DepressionBarbu,
     DNAmFILi,
     DNAmFitAge,
-    DNAmFitAgeGaitF,
-    DNAmFitAgeGaitM,
-    DNAmFitAgeGripF,
-    DNAmFitAgeGripM,
+    DNAmFitAgeGait,
+    DNAmFitAgeGrip,
     DNAmFitAgeVO2Max,
     DNAmIC,
     DNAmPhenoAge,
@@ -201,10 +199,8 @@ __all__ = [
     "CpGPTPCGrimAge3",
     "DNAmFILi",
     "DNAmFitAge",
-    "DNAmFitAgeGaitF",
-    "DNAmFitAgeGaitM",
-    "DNAmFitAgeGripF",
-    "DNAmFitAgeGripM",
+    "DNAmFitAgeGait",
+    "DNAmFitAgeGrip",
     "DNAmFitAgeVO2Max",
     "DNAmIC",
     "DNAmPhenoAge",

{pyaging-0.5.1 → pyaging-0.5.2}/src/pyaging/models/_base_models.py

@@ -41,6 +41,10 @@ class pyagingModel(nn.Module, ABC):
 
         self.features = None
         self.feature_units = None
+        # Optional internal range profile when the model consumes values that
+        # differ from the public assay modality (for example, cohort-centered
+        # transcriptomic values derived from raw RNA-seq counts).
+        self.feature_range_data_type = None
         self.base_model_features = self.features
 
         self.base_model = None

{pyaging-0.5.1 → pyaging-0.5.2}/src/pyaging/models/_models.py

@@ -2116,66 +2116,50 @@ class DNAmFitAge(pyagingModel):
     def __init__(self):
         super().__init__()
 
-        self.GaitF = None
-        self.GripF = None
-        self.GaitM = None
-        self.GripM = None
+        self.Gait = None
+        self.Grip = None
         self.VO2Max = None
+        self.GrimAge = None
 
-        self.features_GaitF = None
-        self.features_GripF = None
-        self.features_GaitM = None
-        self.features_GripM = None
+        self.features_Gait = None
+        self.features_Grip = None
         self.features_VO2Max = None
+        self.features_GrimAge = None
+        self.female_index = None
+        self.age_index = None
 
-    def forward(self, x):
-        Female = x[:, -3]  # .unsqueeze(1)
-        GrimAge = x[:, -1].unsqueeze(1)
-
-        is_female = Female == 1
-        is_male = Female == 0
-
-        x_f = x[is_female]
-        x_m = x[is_male]
+    def _component_input(self, x, indices, component):
+        values = x[:, indices]
+        return _fill_dnamfitage_references(values, component.reference_values)
 
-        GaitF = self.GaitF(x_f[:, self.features_GaitF])
-        GripF = self.GripF(x_f[:, self.features_GripF])
-        VO2MaxF = self.VO2Max(x_f[:, self.features_VO2Max])
-        GrimAgeF = GrimAge[is_female, :]
-
-        GaitM = self.GaitM(x_m[:, self.features_GaitM])
-        GripM = self.GripM(x_m[:, self.features_GripM])
-        VO2MaxM = self.VO2Max(x_m[:, self.features_VO2Max])
-        GrimAgeM = GrimAge[is_male, :]
+    def forward(self, x):
+        female = x[:, self.female_index].unsqueeze(1)
+        gait = self.Gait(self._component_input(x, self.features_Gait, self.Gait))
+        grip = self.Grip(self._component_input(x, self.features_Grip, self.Grip))
+        vo2max = self.VO2Max(self._component_input(x, self.features_VO2Max, self.VO2Max))
+        grimage = self.GrimAge(self._component_input(x, self.features_GrimAge, self.GrimAge))
 
-        x_f = torch.concat(
+        female_components = torch.concat(
             [
-                (VO2MaxF - 46.825091) / (-0.13620215),
-                (GripF - 39.857718) / (-0.22074456),
-                (GaitF - 2.508547) / (-0.01245682),
-                (GrimAgeF - 7.978487) / (0.80928530),
+                (vo2max - 46.825091) / -0.13620215,
+                (grip - 39.857718) / -0.22074456,
+                (gait - 2.508547) / -0.01245682,
+                (grimage - 7.978487) / 0.80928530,
             ],
             dim=1,
         )
-
-        x_m = torch.concat(
+        male_components = torch.concat(
             [
-                (VO2MaxM - 49.836389) / (-0.141862925),
-                (GripM - 57.514016) / (-0.253179827),
-                (GaitM - 2.349080) / (-0.009380061),
-                (GrimAgeM - 9.549733) / (0.835120557),
+                (vo2max - 49.836389) / -0.141862925,
+                (grip - 57.514016) / -0.253179827,
+                (gait - 2.349080) / -0.009380061,
+                (grimage - 9.549733) / 0.835120557,
             ],
             dim=1,
         )
-
-        y_f = self.base_model_f(x_f)
-        y_m = self.base_model_m(x_m)
-
-        y = torch.zeros((x.size(0), 1), dtype=x.dtype, device=x.device)
-        y[is_female] = y_f
-        y[is_male] = y_m
-
-        return y
+        female_prediction = self.base_model_f(female_components)
+        male_prediction = self.base_model_m(male_components)
+        return male_prediction + female * (female_prediction - male_prediction)
 
     def preprocess(self, x):
         if self.reference_values is None:
@@ -2190,6 +2174,45 @@ class DNAmFitAge(pyagingModel):
         return x
 
 
+def _fill_dnamfitage_references(x, reference_values):
+    reference = torch.as_tensor(reference_values, device=x.device, dtype=x.dtype)
+    return torch.where(torch.isnan(x), reference, x)
+
+
+class _DNAmFitAgeSexGated(pyagingModel):
+    def __init__(self):
+        super().__init__()
+        self.female_model = None
+        self.male_model = None
+        self.female_feature_indices = None
+        self.male_feature_indices = None
+        self.female_reference_values = None
+        self.male_reference_values = None
+        self.female_index = None
+
+    def forward(self, x):
+        female = x[:, self.female_index].unsqueeze(1)
+        female_x = _fill_dnamfitage_references(x[:, self.female_feature_indices], self.female_reference_values)
+        male_x = _fill_dnamfitage_references(x[:, self.male_feature_indices], self.male_reference_values)
+        female_prediction = self.female_model(female_x)
+        male_prediction = self.male_model(male_x)
+        return male_prediction + female * (female_prediction - male_prediction)
+
+    def preprocess(self, x):
+        return x
+
+    def postprocess(self, x):
+        return x
+
+
+class DNAmFitAgeGait(_DNAmFitAgeSexGated):
+    pass
+
+
+class DNAmFitAgeGrip(_DNAmFitAgeSexGated):
+    pass
+
+
 class StocH(pyagingModel):
     def __init__(self):
         super().__init__()
@@ -2680,74 +2703,6 @@ class GrimAge2LogCRP(pyagingModel):
         return x
 
 
-class DNAmFitAgeGaitF(pyagingModel):
-    def __init__(self):
-        super().__init__()
-
-    def preprocess(self, x):
-        if self.reference_values is None:
-            return x
-        if isinstance(self.reference_values, torch.Tensor):
-            reference = self.reference_values.to(device=x.device, dtype=x.dtype)
-        else:
-            reference = torch.tensor(self.reference_values, device=x.device, dtype=x.dtype)
-        return torch.where(torch.isnan(x), reference, x)
-
-    def postprocess(self, x):
-        return x
-
-
-class DNAmFitAgeGaitM(pyagingModel):
-    def __init__(self):
-        super().__init__()
-
-    def preprocess(self, x):
-        if self.reference_values is None:
-            return x
-        if isinstance(self.reference_values, torch.Tensor):
-            reference = self.reference_values.to(device=x.device, dtype=x.dtype)
-        else:
-            reference = torch.tensor(self.reference_values, device=x.device, dtype=x.dtype)
-        return torch.where(torch.isnan(x), reference, x)
-
-    def postprocess(self, x):
-        return x
-
-
-class DNAmFitAgeGripF(pyagingModel):
-    def __init__(self):
-        super().__init__()
-
-    def preprocess(self, x):
-        if self.reference_values is None:
-            return x
-        if isinstance(self.reference_values, torch.Tensor):
-            reference = self.reference_values.to(device=x.device, dtype=x.dtype)
-        else:
-            reference = torch.tensor(self.reference_values, device=x.device, dtype=x.dtype)
-        return torch.where(torch.isnan(x), reference, x)
-
-    def postprocess(self, x):
-        return x
-
-
-class DNAmFitAgeGripM(pyagingModel):
-    def __init__(self):
-        super().__init__()
-
-    def preprocess(self, x):
-        if self.reference_values is None:
-            return x
-        if isinstance(self.reference_values, torch.Tensor):
-            reference = self.reference_values.to(device=x.device, dtype=x.dtype)
-        else:
-            reference = torch.tensor(self.reference_values, device=x.device, dtype=x.dtype)
-        return torch.where(torch.isnan(x), reference, x)
-
-    def postprocess(self, x):
-        return x
-
-
 class DNAmFitAgeVO2Max(pyagingModel):
     def __init__(self):
         super().__init__()
@@ -3278,6 +3233,7 @@ class TAge(pyagingModel):
         # Cohort-relative clock: ``predict_age`` runs the tAge cohort
         # preprocessing on the raw counts before aligning these features.
         self.cohort_transform = "tage"
+        self.feature_range_data_type = "transcriptomics (relative)"
 
     def preprocess(self, x):
         """Substitute the fitted imputer statistics for genes absent from the sample.

{pyaging-0.5.1 → pyaging-0.5.2}/src/pyaging/predict/_pred_utils.py

@@ -122,8 +122,12 @@ def _load_clock_impl(clock_name: str, device: str, dir: str, logger, indent_leve
     try:
         weights_path = download_clock_weights(clock_name, dir, logger, indent_level=indent_level)
     except PyAgingResourceNotFoundError as exc:
+        from pyaging import __version__
+
         message = (
-            f"Clock {clock_name} is not available on pyaging. "
+            f"Clock {clock_name} is not available on pyaging {__version__}. "
+            "This clock may require a newer pyaging release; check PyPI and run "
+            "`pip install --upgrade pyaging` if a newer version is available. "
             "Please refer to the clock names in the clock glossary table "
             "in the package documentation page: pyaging.readthedocs.io"
         )
@@ -452,7 +456,7 @@ def check_feature_ranges(
     try:
         units, low, high = resolve_feature_bounds(
             model.features,
-            model.metadata.get("data_type"),
+            getattr(model, "feature_range_data_type", None) or model.metadata.get("data_type"),
             getattr(model, "feature_units", None),
         )
     except Exception as exc:

{pyaging-0.5.1 → pyaging-0.5.2}/src/pyaging/utils/_feature_ranges.py

@@ -159,7 +159,7 @@ def get_feature_ranges(clock_name: str):
         raise ValueError(f"clock {clock_name!r} has no feature list, so its feature ranges cannot be resolved")
     records = resolve_feature_ranges(
         model.features,
-        model.metadata.get("data_type"),
+        getattr(model, "feature_range_data_type", None) or model.metadata.get("data_type"),
         getattr(model, "feature_units", None),
     )
     return pd.DataFrame.from_records(records)