Merge branch 'main' into ciguaran_pretuning_adaptive_test

blackjax/__init__.py

@@ -13,6 +13,7 @@
 from .diagnostics import effective_sample_size as ess
 from .diagnostics import potential_scale_reduction as rhat
 from .mcmc import adjusted_mclmc as _adjusted_mclmc
+from .mcmc import adjusted_mclmc_dynamic as _adjusted_mclmc_dynamic
 from .mcmc import barker
 from .mcmc import dynamic_hmc as _dynamic_hmc
 from .mcmc import elliptical_slice as _elliptical_slice
@@ -113,6 +114,7 @@ def generate_top_level_api_from(module):
 additive_step_random_walk.register_factory("normal_random_walk", normal_random_walk)
 
 mclmc = generate_top_level_api_from(_mclmc)
+adjusted_mclmc_dynamic = generate_top_level_api_from(_adjusted_mclmc_dynamic)
 adjusted_mclmc = generate_top_level_api_from(_adjusted_mclmc)
 elliptical_slice = generate_top_level_api_from(_elliptical_slice)
 ghmc = generate_top_level_api_from(_ghmc)

blackjax/adaptation/adjusted_mclmc_adaptation.py

@@ -74,14 +74,20 @@ def adjusted_mclmc_find_L_and_step_size(
     dim = pytree_size(state.position)
     if params is None:
         params = MCLMCAdaptationState(
-            jnp.sqrt(dim), jnp.sqrt(dim) * 0.2, sqrt_diag_cov=jnp.ones((dim,))
+            jnp.sqrt(dim), jnp.sqrt(dim) * 0.2, inverse_mass_matrix=jnp.ones((dim,))
         )
 
     part1_key, part2_key = jax.random.split(rng_key, 2)
 
+    total_num_tuning_integrator_steps = 0
     for i in range(num_windows):
         window_key = jax.random.fold_in(part1_key, i)
-        (state, params, eigenvector) = adjusted_mclmc_make_L_step_size_adaptation(
+        (
+            state,
+            params,
+            eigenvector,
+            num_tuning_integrator_steps,
+        ) = adjusted_mclmc_make_L_step_size_adaptation(
             kernel=mclmc_kernel,
             dim=dim,
             frac_tune1=frac_tune1,
@@ -90,22 +96,38 @@ def adjusted_mclmc_find_L_and_step_size(
             diagonal_preconditioning=diagonal_preconditioning,
             max=max,
             tuning_factor=tuning_factor,
-        )(state, params, num_steps, window_key)
+        )(
+            state, params, num_steps, window_key
+        )
+        total_num_tuning_integrator_steps += num_tuning_integrator_steps
 
     if frac_tune3 != 0:
         for i in range(num_windows):
             part2_key = jax.random.fold_in(part2_key, i)
             part2_key1, part2_key2 = jax.random.split(part2_key, 2)
 
-            state, params = adjusted_mclmc_make_adaptation_L(
+            (
+                state,
+                params,
+                num_tuning_integrator_steps,
+            ) = adjusted_mclmc_make_adaptation_L(
                 mclmc_kernel,
                 frac=frac_tune3,
                 Lfactor=0.5,
                 max=max,
                 eigenvector=eigenvector,
-            )(state, params, num_steps, part2_key1)
+            )(
+                state, params, num_steps, part2_key1
+            )
+
+            total_num_tuning_integrator_steps += num_tuning_integrator_steps
 
-            (state, params, _) = adjusted_mclmc_make_L_step_size_adaptation(
+            (
+                state,
+                params,
+                _,
+                num_tuning_integrator_steps,
+            ) = adjusted_mclmc_make_L_step_size_adaptation(
                 kernel=mclmc_kernel,
                 dim=dim,
                 frac_tune1=frac_tune1,
@@ -115,9 +137,13 @@ def adjusted_mclmc_find_L_and_step_size(
                 diagonal_preconditioning=diagonal_preconditioning,
                 max=max,
                 tuning_factor=tuning_factor,
-            )(state, params, num_steps, part2_key2)
+            )(
+                state, params, num_steps, part2_key2
+            )
+
+            total_num_tuning_integrator_steps += num_tuning_integrator_steps
 
-    return state, params
+    return state, params, total_num_tuning_integrator_steps
 
 
 def adjusted_mclmc_make_L_step_size_adaptation(
@@ -152,7 +178,7 @@ def step(iteration_state, weight_and_key):
                 state=previous_state,
                 avg_num_integration_steps=avg_num_integration_steps,
                 step_size=params.step_size,
-                sqrt_diag_cov=params.sqrt_diag_cov,
+                inverse_mass_matrix=params.inverse_mass_matrix,
             )
 
             # step updating
@@ -256,6 +282,7 @@ def L_step_size_adaptation(state, params, num_steps, rng_key):
             update_da=update_da,
         )
 
+        num_tuning_integrator_steps = info.num_integration_steps.sum()
         final_stepsize = final_da(dual_avg_state)
         params = params._replace(step_size=final_stepsize)
 
@@ -283,9 +310,7 @@ def L_step_size_adaptation(state, params, num_steps, rng_key):
                 L=params.L * change, step_size=params.step_size * change
             )
             if diagonal_preconditioning:
-                params = params._replace(
-                    sqrt_diag_cov=jnp.sqrt(variances), L=jnp.sqrt(dim)
-                )
+                params = params._replace(inverse_mass_matrix=variances, L=jnp.sqrt(dim))
 
             initial_da, update_da, final_da = dual_averaging_adaptation(target=target)
             (
@@ -301,9 +326,11 @@ def L_step_size_adaptation(state, params, num_steps, rng_key):
                 initial_da=initial_da,
             )
 
+            num_tuning_integrator_steps += info.num_integration_steps.sum()
+
             params = params._replace(step_size=final_da(dual_avg_state))
 
-        return state, params, eigenvector
+        return state, params, eigenvector, num_tuning_integrator_steps
 
     return L_step_size_adaptation
 
@@ -318,16 +345,16 @@ def adaptation_L(state, params, num_steps, key):
         adaptation_L_keys = jax.random.split(key, num_steps)
 
         def step(state, key):
-            next_state, _ = kernel(
+            next_state, info = kernel(
                 rng_key=key,
                 state=state,
                 step_size=params.step_size,
                 avg_num_integration_steps=params.L / params.step_size,
-                sqrt_diag_cov=params.sqrt_diag_cov,
+                inverse_mass_matrix=params.inverse_mass_matrix,
             )
-            return next_state, next_state.position
+            return next_state, (next_state.position, info)
 
-        state, samples = jax.lax.scan(
+        state, (samples, info) = jax.lax.scan(
             f=step,
             init=state,
             xs=adaptation_L_keys,
@@ -348,10 +375,14 @@ def step(state, key):
         # number of effective samples per 1 actual sample
         ess = contract(effective_sample_size(flat_samples[None, ...])) / num_steps
 
-        return state, params._replace(
-            L=jnp.clip(
-                Lfactor * params.L / jnp.mean(ess), max=params.L * Lratio_upperbound
-            )
+        return (
+            state,
+            params._replace(
+                L=jnp.clip(
+                    Lfactor * params.L / jnp.mean(ess), max=params.L * Lratio_upperbound
+                )
+            ),
+            info.num_integration_steps.sum(),
         )
 
     return adaptation_L

blackjax/adaptation/mclmc_adaptation.py

@@ -30,13 +30,13 @@ class MCLMCAdaptationState(NamedTuple):
         The momentum decoherent rate for the MCLMC algorithm.
     step_size
         The step size used for the MCLMC algorithm.
-    sqrt_diag_cov
+    inverse_mass_matrix
         A matrix used for preconditioning.
     """
 
     L: float
     step_size: float
-    sqrt_diag_cov: float
+    inverse_mass_matrix: float
 
 
 def mclmc_find_L_and_step_size(
@@ -87,10 +87,10 @@ def mclmc_find_L_and_step_size(
     Example
     -------
     .. code::
-        kernel = lambda sqrt_diag_cov : blackjax.mcmc.mclmc.build_kernel(
+        kernel = lambda inverse_mass_matrix : blackjax.mcmc.mclmc.build_kernel(
         logdensity_fn=logdensity_fn,
         integrator=integrator,
-        sqrt_diag_cov=sqrt_diag_cov,
+        inverse_mass_matrix=inverse_mass_matrix,
         )
 
         (
@@ -106,7 +106,7 @@ def mclmc_find_L_and_step_size(
     """
     dim = pytree_size(state.position)
     params = MCLMCAdaptationState(
-        jnp.sqrt(dim), jnp.sqrt(dim) * 0.25, sqrt_diag_cov=jnp.ones((dim,))
+        jnp.sqrt(dim), jnp.sqrt(dim) * 0.25, inverse_mass_matrix=jnp.ones((dim,))
     )
     part1_key, part2_key = jax.random.split(rng_key, 2)
 
@@ -123,10 +123,10 @@ def mclmc_find_L_and_step_size(
 
     if frac_tune3 != 0:
         state, params = make_adaptation_L(
-            mclmc_kernel(params.sqrt_diag_cov), frac=frac_tune3, Lfactor=0.4
+            mclmc_kernel(params.inverse_mass_matrix), frac=frac_tune3, Lfactor=0.4
         )(state, params, num_steps, part2_key)
 
-    return state, params
+    return state, params, num_steps * (frac_tune1 + frac_tune2 + frac_tune3)
 
 
 def make_L_step_size_adaptation(
@@ -152,7 +152,7 @@ def predictor(previous_state, params, adaptive_state, rng_key):
         rng_key, nan_key = jax.random.split(rng_key)
 
         # dynamics
-        next_state, info = kernel(params.sqrt_diag_cov)(
+        next_state, info = kernel(params.inverse_mass_matrix)(
             rng_key=rng_key,
             state=previous_state,
             L=params.L,
@@ -247,15 +247,15 @@ def L_step_size_adaptation(state, params, num_steps, rng_key):
 
         L = params.L
         # determine L
-        sqrt_diag_cov = params.sqrt_diag_cov
+        inverse_mass_matrix = params.inverse_mass_matrix
         if num_steps2 > 1:
             x_average, x_squared_average = average[0], average[1]
             variances = x_squared_average - jnp.square(x_average)
             L = jnp.sqrt(jnp.sum(variances))
 
             if diagonal_preconditioning:
-                sqrt_diag_cov = jnp.sqrt(variances)
-                params = params._replace(sqrt_diag_cov=sqrt_diag_cov)
+                inverse_mass_matrix = variances
+                params = params._replace(inverse_mass_matrix=inverse_mass_matrix)
                 L = jnp.sqrt(dim)
 
                 # readjust the stepsize
@@ -265,7 +265,7 @@ def L_step_size_adaptation(state, params, num_steps, rng_key):
                     xs=(jnp.ones(steps), keys), state=state, params=params
                 )
 
-        return state, MCLMCAdaptationState(L, params.step_size, sqrt_diag_cov)
+        return state, MCLMCAdaptationState(L, params.step_size, inverse_mass_matrix)
 
     return L_step_size_adaptation
 
@@ -274,8 +274,8 @@ def make_adaptation_L(kernel, frac, Lfactor):
     """determine L by the autocorrelations (around 10 effective samples are needed for this to be accurate)"""
 
     def adaptation_L(state, params, num_steps, key):
-        num_steps = int(num_steps * frac)
-        adaptation_L_keys = jax.random.split(key, num_steps)
+        num_steps_3 = int(num_steps * frac)
+        adaptation_L_keys = jax.random.split(key, num_steps_3)
 
         def step(state, key):
             next_state, _ = kernel(
@@ -297,7 +297,7 @@ def step(state, key):
         ess = effective_sample_size(flat_samples[None, ...])
 
         return state, params._replace(
-            L=Lfactor * params.step_size * jnp.mean(num_steps / ess)
+            L=Lfactor * params.step_size * jnp.mean(num_steps_3 / ess)
         )
 
     return adaptation_L

blackjax/mcmc/__init__.py

@@ -1,5 +1,6 @@
 from . import (
     adjusted_mclmc,
+    adjusted_mclmc_dynamic,
     barker,
     elliptical_slice,
     ghmc,
@@ -25,5 +26,6 @@
     "marginal_latent_gaussian",
     "random_walk",
     "mclmc",
+    "adjusted_mclmc_dynamic",
     "adjusted_mclmc",
 ]