move example simulators to own submodule

Author: daniel-habermann

bayesflow/experimental/graphical_simulator/__init__.py

@@ -1 +1,2 @@
 from .graphical_simulator import GraphicalSimulator
+from . import example_simulators

bayesflow/experimental/graphical_simulator/example_simulators.py

@@ -0,0 +1,4 @@
+from .single_level import single_level
+from .two_level import two_level
+from .two_level_repeated_roots import two_level_repeated_roots
+from .irt import irt

bayesflow/experimental/graphical_simulator/example_simulators/__init__.py

@@ -0,0 +1,87 @@
+import numpy as np
+
+from ..graphical_simulator import GraphicalSimulator
+
+
+def irt():
+    r"""
+    Item Response Theory (IRT) model implemented as a graphical simultor.
+
+      schools
+       /     \
+    exams  students
+      |       |
+    questions |
+       \     /
+     observations
+    """
+
+    # schools have different exam difficulties
+    def sample_school():
+        mu_exam_mean = np.random.normal(loc=1.1, scale=0.2)
+        sigma_exam_mean = abs(np.random.normal(loc=0, scale=1))
+
+        # hierarchical mu/sigma for the exam difficulty standard deviation (logscale)
+        mu_exam_std = np.random.normal(loc=0.5, scale=0.3)
+        sigma_exam_std = abs(np.random.normal(loc=0, scale=0.5))
+
+        return dict(
+            mu_exam_mean=mu_exam_mean,
+            sigma_exam_mean=sigma_exam_mean,
+            mu_exam_std=mu_exam_std,
+            sigma_exam_std=sigma_exam_std,
+        )
+
+    # exams have different question difficulties
+    def sample_exam(mu_exam_mean, sigma_exam_mean, mu_exam_std, sigma_exam_std):
+        # mean question difficulty for an exam
+        exam_mean = np.random.normal(loc=mu_exam_mean, scale=sigma_exam_mean)
+
+        # standard deviation of question difficulty
+        log_exam_std = np.random.normal(loc=mu_exam_std, scale=sigma_exam_std)
+        exam_std = float(np.exp(log_exam_std))
+
+        return dict(exam_mean=exam_mean, exam_std=exam_std)
+
+    # realizations of individual question difficulties
+    def sample_question(exam_mean, exam_std):
+        question_difficulty = np.random.normal(loc=exam_mean, scale=exam_std)
+
+        return dict(question_difficulty=question_difficulty)
+
+    # realizations of individual student abilities
+    def sample_student():
+        student_ability = np.random.normal(loc=0, scale=1)
+
+        return dict(student_ability=student_ability)
+
+    # realizations of individual observations
+    def sample_observation(question_difficulty, student_ability):
+        theta = np.exp(question_difficulty + student_ability) / (1 + np.exp(question_difficulty + student_ability))
+
+        obs = np.random.binomial(n=1, p=theta)
+
+        return dict(obs=obs)
+
+    def meta_fn():
+        return {
+            "num_exams": np.random.randint(2, 4),
+            "num_questions": np.random.randint(10, 21),
+            "num_students": np.random.randint(100, 201),
+        }
+
+    simulator = GraphicalSimulator(meta_fn=meta_fn)
+
+    simulator.add_node("schools", sample_fn=sample_school)
+    simulator.add_node("exams", sample_fn=sample_exam, reps="num_exams")
+    simulator.add_node("questions", sample_fn=sample_question, reps="num_questions")
+    simulator.add_node("students", sample_fn=sample_student, reps="num_students")
+    simulator.add_node("observations", sample_fn=sample_observation)
+
+    simulator.add_edge("schools", "exams")
+    simulator.add_edge("schools", "students")
+    simulator.add_edge("exams", "questions")
+    simulator.add_edge("questions", "observations")
+    simulator.add_edge("students", "observations")
+
+    return simulator

bayesflow/experimental/graphical_simulator/example_simulators/irt.py

@@ -0,0 +1,36 @@
+import numpy as np
+
+from ..graphical_simulator import GraphicalSimulator
+
+
+def single_level():
+    """
+    Simple single-level simulator that implements the same model as in
+    https://bayesflow.org/main/_examples/Linear_Regression_Starter.html
+    """
+
+    def prior():
+        beta = np.random.normal([2, 0], [3, 1])
+        sigma = np.random.gamma(1, 1)
+
+        return {"beta": beta, "sigma": sigma}
+
+    def likelihood(beta, sigma, N):
+        x = np.random.normal(0, 1, size=N)
+        y = np.random.normal(beta[0] + beta[1] * x, sigma, size=N)
+
+        return {"x": x, "y": y}
+
+    def meta():
+        N = np.random.randint(5, 15)
+
+        return {"N": N}
+
+    simulator = GraphicalSimulator(meta_fn=meta)
+
+    simulator.add_node("prior", sample_fn=prior)
+    simulator.add_node("likelihood", sample_fn=likelihood)
+
+    simulator.add_edge("prior", "likelihood")
+
+    return simulator

bayesflow/experimental/graphical_simulator/example_simulators/single_level.py

@@ -0,0 +1,57 @@
+import numpy as np
+
+from ..graphical_simulator import GraphicalSimulator
+
+
+def two_level():
+    r"""
+    Simple hierarchical model with two levels of parameters: hyperparameters
+    and local parameters, along with a shared parameter:
+
+    hypers
+       |
+    locals  shared
+        \    /
+         \  /
+          y
+
+    """
+
+    def sample_hypers():
+        hyper_mean = np.random.normal()
+        hyper_std = np.abs(np.random.normal())
+
+        return {"hyper_mean": hyper_mean, "hyper_std": hyper_std}
+
+    def sample_locals(hyper_mean, hyper_std):
+        local_mean = np.random.normal(hyper_mean, hyper_std)
+
+        return {"local_mean": local_mean}
+
+    def sample_shared():
+        shared_std = np.abs(np.random.normal())
+
+        return {"shared_std": shared_std}
+
+    def sample_y(local_mean, shared_std):
+        y = np.random.normal(local_mean, shared_std)
+
+        return {"y": y}
+
+    simulator = GraphicalSimulator()
+    simulator.add_node("hypers", sample_fn=sample_hypers)
+
+    simulator.add_node(
+        "locals",
+        sample_fn=sample_locals,
+        reps=6,
+    )
+
+    simulator.add_node("shared", sample_fn=sample_shared)
+    simulator.add_node("y", sample_fn=sample_y, reps=10)
+
+    simulator.add_edge("hypers", "locals")
+    simulator.add_edge("locals", "y")
+    simulator.add_edge("shared", "y")
+
+    return simulator