bella-companion 0.0.48__tar.gz → 0.1.1__tar.gz

{bella_companion-0.0.48 → bella_companion-0.1.1}/PKG-INFO

@@ -1,12 +1,15 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.3
 Name: bella-companion
-Version: 0.0.48
+Version: 0.1.1
 Summary: Bayesian Evolutionary Layered Learning Architectures (BELLA) companion
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
+Author: gabriele-marino
+Author-email: gabriele-marino <gabmarino.8601@gmail.com>
 Requires-Dist: arviz>=0.22.0
-Requires-Dist: bella-lumiere>=0.0.19
+Requires-Dist: bella-lumiere>=0.1.0
 Requires-Dist: dotenv>=0.9.9
 Requires-Dist: phylogenie>=3.1.4
 Requires-Dist: poetry>=2.2.1
 Requires-Dist: seaborn>=0.13.2
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+

{bella_companion-0.0.48 → bella_companion-0.1.1}/pyproject.toml

@@ -1,18 +1,28 @@
 [project]
 name = "bella-companion"
-version = "0.0.48"
+version = "0.1.1"
 description = "Bayesian Evolutionary Layered Learning Architectures (BELLA) companion"
 readme = "README.md"
+authors = [
+    { name = "gabriele-marino", email = "gabmarino.8601@gmail.com" }
+]
 requires-python = ">=3.10"
 dependencies = [
     "arviz>=0.22.0",
-    "bella-lumiere>=0.0.19",
+    "bella-lumiere>=0.1.0",
     "dotenv>=0.9.9",
     "phylogenie>=3.1.4",
     "poetry>=2.2.1",
     "seaborn>=0.13.2",
 ]
 
+[project.scripts]
+bella = "bella_companion.cli:main"
+
+[build-system]
+requires = ["uv_build>=0.9.5,<0.10.0"]
+build-backend = "uv_build"
+
 [dependency-groups]
 dev = [
     "joblib-stubs>=1.5.2.0.20250831",
@@ -22,13 +32,3 @@ dev = [
 [tool.pyright]
 typeCheckingMode = "strict"
 
-[project.scripts]
-bella = "bella_companion.cli:main"
-
-[build-system]
-requires = ["setuptools>=42"]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools]
-packages = ["bella_companion"]
-

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/eucovid/beast_configs/GLM.xml

@@ -48,7 +48,7 @@
                 <populationModel spec="ConstantPopulation" popSize="0.1"/>
             </stateNode>
             <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
-            <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
+            <stateNode id="samplingProportion" spec="RealParameter" value="1.1E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4 1.11E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4 0.0 0.0 0.0 0.0 0.0"/>
             <stateNode id="migrationRateW" spec="RealParameter" value="0"/>
             <stateNode id="migrationRateScaler" spec="RealParameter" value="0.1"/>
             <stateNode id="processLength" spec="RealParameter" value="10.0"/>
@@ -76,9 +76,7 @@
                         <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
                         <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
                             <skylineValues spec="glmprior.util.GLMLogLinear" coefficients="@migrationRateW" scaleFactor="@migrationRateScaler" transform="false">
-                                <plate var="predictorFile" range="$(predictorFiles)">
-                                    <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
-                                </plate>
+                                <predictor spec="RealParameterFromXSV" fileName="$(flightsPredictorFile)"/>
                                 <indicators spec="BooleanParameter" value="1"/>
                             </skylineValues>
                             <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
@@ -94,26 +92,37 @@
                 <distribution spec="SmartZeroExcludingPrior" x="@Re">
                     <LogNormal name="distr" M="0.8" S="0.5"/>
                 </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.15"/>
+
+                <!-- Sampling proportion in China -->
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4">
+                    <Uniform name="distr" upper="0.024714828897338403"/> 
+                </distribution>
+                <!-- Sampling proportion in China -->
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.11E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4">
+                    <Uniform name="distr" upper="$1.8682742128337982e-4"/>
                 </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.093"/>
+                 <!-- Sampling proportion in France -->
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.3E-4 1.4E-4 1.5E-4">
+                    <Uniform name="distr" upper="0.09217877094972067"/>
                 </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.10"/>
+                <!-- Sampling proportion in Germany -->
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.4E-4 1.5E-4">
+                    <Uniform name="distr" upper="0.01770956316410862"/>
                 </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
-                    <Uniform name="distr" lower="0" upper="0.005"/>
+                <!-- Sampling proportion in Germany -->
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.3E-4 1.5E-4">
+                    <Uniform name="distr" upper="0.002209756926738059"/>
                 </distribution>
-                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
-                    <Uniform name="distr" lower="0" upper="0.057"/>
+                <!-- Sampling proportion in EU -->
+                <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.3E-4 1.4E-4">
+                    <Uniform name="distr" lower="0" upper="0.012770137524557957"/>
                 </distribution>
+
                 <prior name="distribution" x="@migrationRateW">
                     <Normal name="distr" mean="0.0" sigma="1.0"/>
                 </prior>
                 <prior name="distribution" x="@migrationRateScaler">
-                    <LogNormal name="distr" M="0.0" S="0.8"/>
+                    <LogNormal name="distr" M="0.0" S="1"/>
                 </prior>
                 <prior name="distribution" x="@gammaShape">
                     <Exponential name="distr" mean="0.5"/>
@@ -136,8 +145,9 @@
         <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
         <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
         <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
-        <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
-        <operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1"> 
+        <operator spec="BactrianScaleOperator" parameter="@migrationRateScaler" scaleFactor="0.25" weight="3.0"/>
+        <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" scaleFactor="0.1" weight="5.0"/>
+        <operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" scaleFactor="0.5" coefficient="1.0" beta="0.05" initial="800" burnin="400" every="1"> 
             <transformations spec="Transform$NoTransform" f="@migrationRateW"/>
         </operator>
         <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/eucovid/beast_configs/MLP.xml

@@ -77,12 +77,11 @@
                         <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
                         <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
                             <skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
-                                <plate var="predictorFile" range="$(predictorFiles)">
-                                    <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
-                                </plate>
+                                <predictor spec="RealParameterFromXSV" fileName="$(flightsPredictorFile)"/>
                                 <plate var="n" range="$(layersRange)">
                                     <weights idref="migrationRateW$(n)"/>
                                 </plate>
+                                <activationFunctionsOutput spec="bella.SoftPlus"/>
                             </skylineValues>
                             <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
                         </migrationRate> 

bella_companion-0.1.1/src/bella_companion/eucovid/run_beast.py

@@ -0,0 +1,36 @@
+import os
+from itertools import product
+from pathlib import Path
+
+from bella_companion.utils import submit_job
+
+
+def run_beast():
+    base_output_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"])
+    output_dir = base_output_dir / "eucovid"
+    os.makedirs(output_dir, exist_ok=True)
+
+    base_log_dir = Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "eucovid"
+    data_dir = Path(__file__).parent / "data"
+    beast_configs_dir = Path(__file__).parent / "beast_configs"
+
+    for seed, model in product(range(3), ["GLM", "MLP"]):
+        extra_data = '-D layersRange="0,1,2",nodes="16 8"' if model == "MLP" else ""
+        os.makedirs(output_dir / model, exist_ok=True)
+        submit_job(
+            " ".join(
+                [
+                    *os.environ["BELLA_RUN_BEAST_CMD"],
+                    f"-seed {seed}",
+                    f"-D msa_file={data_dir / 'msa.fasta'}",
+                    f"-D changeTimesFile={data_dir / 'changetimes.csv'}",
+                    f"-D flightsPredictorFile={data_dir / 'flights.csv'}",
+                    extra_data,
+                    f"-prefix {output_dir / model}{os.sep}{seed}-",
+                    str(beast_configs_dir / f"{model}.xml"),
+                ]
+            ),
+            base_log_dir / model / str(seed),
+            cpus=128,
+            mem_per_cpu=12000,
+        )

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/simulations/figures/epi_multitype.py

@@ -6,7 +6,7 @@ import joblib
 import matplotlib.pyplot as plt
 import numpy as np
 import polars as pl
-from lumiere.backend import relu, sigmoid
+from bella_lumiere.backend import relu, sigmoid
 
 from bella_companion.simulations.scenarios.epi_multitype import (
     MIGRATION_PREDICTOR,

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/simulations/figures/fbd_2traits.py

@@ -6,7 +6,7 @@ import joblib
 import matplotlib.pyplot as plt
 import numpy as np
 import polars as pl
-from lumiere.backend import relu, sigmoid
+from bella_lumiere.backend import relu, sigmoid
 
 from bella_companion.simulations.figures.utils import step
 from bella_companion.simulations.scenarios.fbd_2traits import (

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/utils/beast.py

@@ -7,9 +7,9 @@ from typing import Any
 import arviz as az
 import numpy as np
 import polars as pl
+from bella_lumiere import read_log_file, read_weights
+from bella_lumiere.typing import Weights
 from joblib import Parallel, delayed
-from lumiere import read_log_file, read_weights
-from lumiere.typing import Weights
 from tqdm import tqdm
 
 from bella_companion.utils.slurm import get_job_metadata

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/utils/explain/pdp.py

@@ -1,13 +1,15 @@
 import os
 from functools import partial
+from itertools import product
 from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numpy as np
 import seaborn as sns
+from bella_lumiere import get_partial_dependence_values
+from bella_lumiere.typing import ActivationFunction, Weights
 from joblib import Parallel, delayed
-from lumiere import get_partial_dependence_values
-from lumiere.typing import ActivationFunction, ArrayLike, Weights
+from numpy.typing import ArrayLike
 from tqdm import tqdm
 
 import bella_companion.utils.explain.typeguards as tg
@@ -24,6 +26,7 @@ def _get_median_partial_dependence_values(
     pdvalues = [
         get_partial_dependence_values(
             weights=w,
+            inputs=inputs,
             features_grid=features_grid,
             hidden_activation=hidden_activation,
             output_activation=output_activation,
@@ -42,6 +45,7 @@ def plot_partial_dependencies(
     output_dir: str | Path,
     hidden_activation: ActivationFunction,
     output_activation: ActivationFunction,
+    inputs: ArrayLike | None = None,
 ):
     output_dir = Path(output_dir)
     os.makedirs(output_dir, exist_ok=True)
@@ -51,6 +55,8 @@ def plot_partial_dependencies(
         [0, 1] if feature.is_binary else continuous_grid
         for feature in features.values()
     ]
+    if inputs is None:
+        inputs = list(product(*features_grid))
 
     if tg.is_weights_list(weights):
         func = get_partial_dependence_values
@@ -65,6 +71,7 @@ def plot_partial_dependencies(
         delayed(
             partial(
                 func,
+                inputs=inputs,
                 features_grid=features_grid,
                 hidden_activation=hidden_activation,
                 output_activation=output_activation,
@@ -99,11 +106,11 @@ def plot_partial_dependencies(
                 plt.plot(  # pyright: ignore
                     continuous_grid, median, color=feature.color, label=label
                 )
-        plt.xlabel("Feature value")  # pyright: ignore
-        plt.ylabel("MLP Output")  # pyright: ignore
-        plt.legend()  # pyright: ignore
-        plt.savefig(output_dir / "PDPs-continuous.svg")  # pyright: ignore
-        plt.close()
+                plt.xlabel("Feature value")  # pyright: ignore
+                plt.ylabel("MLP Output")  # pyright: ignore
+                plt.legend()  # pyright: ignore
+                plt.savefig(output_dir / f"PDPs-continuous-{label}.svg")  # pyright: ignore
+                plt.close()
 
     if any(f.is_binary for f in features.values()):
         data: list[float] = []

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/utils/explain/shap.py

@@ -6,9 +6,9 @@ from typing import Callable
 import matplotlib.pyplot as plt
 import numpy as np
 import seaborn as sns
+from bella_lumiere import get_shap_features_importance
+from bella_lumiere.typing import ActivationFunction, Array, Weights
 from joblib import Parallel, delayed
-from lumiere import get_shap_features_importance
-from lumiere.typing import ActivationFunction, Array, Weights
 from numpy.typing import ArrayLike
 from tqdm import tqdm
 
@@ -68,13 +68,15 @@ def plot_shap_features_importance(
     output_file: str | Path,
     hidden_activation: ActivationFunction,
     output_activation: ActivationFunction,
+    inputs: ArrayLike | None = None,
 ):
-    continuous_grid: list[float] = np.linspace(0, 1, 10).tolist()
-    features_grid: list[list[float]] = [
-        [0, 1] if feature.is_binary else continuous_grid
-        for feature in features.values()
-    ]
-    inputs = list(product(*features_grid))
+    if inputs is None:
+        continuous_grid: list[float] = np.linspace(0, 1, 10).tolist()
+        features_grid: list[list[float]] = [
+            [0, 1] if feature.is_binary else continuous_grid
+            for feature in features.values()
+        ]
+        inputs = list(product(*features_grid))
 
     if tg.is_weights_list(weights):
         func = get_shap_features_importance

{bella_companion-0.0.48 → bella_companion-0.1.1/src}/bella_companion/utils/explain/typeguards.py

@@ -1,7 +1,7 @@
 from typing import Any, TypeGuard
 
 import numpy as np
-from lumiere.typing import Weights
+from bella_lumiere.typing import Weights
 
 
 def is_list(obj: Any) -> TypeGuard[list[Any]]: