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_sources/algorithms/mclmc.md

@@ -44,7 +44,7 @@ MCLMC in Blackjax comes with a tuning algorithm which attempts to find optimal v
 
 An example is given below, of tuning and running a chain for a 1000 dimensional Gaussian target (of which a 2 dimensional marginal is plotted):
 
-```{code-cell} ipython3
+```{code-cell}
 :tags: [hide-cell]
 
 import matplotlib.pyplot as plt
@@ -66,7 +66,7 @@ from numpyro.infer.util import initialize_model
 rng_key = jax.random.key(int(date.today().strftime("%Y%m%d")))
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 def run_mclmc(logdensity_fn, num_steps, initial_position, key, transform, desired_energy_variance= 5e-4):
     init_key, tune_key, run_key = jax.random.split(key, 3)
 
@@ -115,7 +115,7 @@ def run_mclmc(logdensity_fn, num_steps, initial_position, key, transform, desire
     return samples, blackjax_state_after_tuning, blackjax_mclmc_sampler_params, run_key
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 # run the algorithm on a high dimensional gaussian, and show two of the dimensions
 
 logdensity_fn = lambda x: -0.5 * jnp.sum(jnp.square(x))
@@ -134,13 +134,13 @@ samples, initial_state, params, chain_key = run_mclmc(
 samples.mean()
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 plt.scatter(x=samples[:, 0], y=samples[:, 1], alpha=0.1)
 plt.axis("equal")
 plt.title("Scatter Plot of Samples")
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 def visualize_results_gauss(samples, label, color):
   x1 = samples[:, 0]
   plt.hist(x1, bins= 30, density= True, histtype= 'step', lw= 4, color= color, label= label)
@@ -165,12 +165,12 @@ ground_truth_gauss()
 
 A natural sanity check is to see if reducing $\epsilon$ changes the inferred distribution to an extent you care about. For example, we can inspect the 1D marginal with a stepsize $\epsilon$ as above, and compare it to a stepsize $\epsilon/2$ (and double the number of steps). We show this comparison below:
 
-```{code-cell} ipython3
+```{code-cell}
 new_params = params._replace(step_size= params.step_size / 2)
 new_num_steps = num_steps * 2
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 sampling_alg = blackjax.mclmc(
     logdensity_fn,
     L=new_params.L,
@@ -211,7 +211,7 @@ Our task is to find the posterior of the parameters $\{R_n\}_{n =1}^N$, $\sigma$
 
 First, we get the data, define a model using NumPyro, and draw samples:
 
-```{code-cell} ipython3
+```{code-cell}
 import matplotlib.dates as mdates
 from numpyro.examples.datasets import SP500, load_dataset
 from numpyro.distributions import StudentT
@@ -243,7 +243,7 @@ def setup():
 setup()
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 def from_numpyro(model, rng_key, model_args):
   init_params, potential_fn_gen, *_ = initialize_model(
       rng_key,
@@ -272,13 +272,13 @@ rng_key = jax.random.key(42)
 logp_sv, x_init = from_numpyro(stochastic_volatility, rng_key, model_args)
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 num_steps = 20000
 
 samples, initial_state, params, chain_key = run_mclmc(logdensity_fn= logp_sv, num_steps= num_steps, initial_position= x_init, key= sample_key, transform=lambda state, info: state.position)
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 def visualize_results_sv(samples, color, label):
 
   R = np.exp(np.array(samples['s'])) # take an exponent to get R
@@ -297,7 +297,7 @@ plt.legend()
 plt.show()
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 new_params = params._replace(step_size = params.step_size/2)
 new_num_steps = num_steps * 2
 
@@ -318,10 +318,9 @@ _, new_samples = blackjax.util.run_inference_algorithm(
     transform=lambda state, info : state.position,
     progress_bar=True,
 )
-
 ```
 
-```{code-cell} ipython3
+```{code-cell}
 setup()
 visualize_results_sv(new_samples,'red', 'MCLMC', )
 visualize_results_sv(samples,'teal', 'MCLMC (stepsize/2)', )
@@ -332,7 +331,7 @@ plt.show()
 
 Here, we have again inspected the effect of halving $\epsilon$. This looks OK, but suppose we are interested in the hierarchial parameters in particular, which tend to be harder to infer. We now inspect the marginal of a hierarchical parameter:
 
-```{code-cell} ipython3
+```{code-cell}
 def visualize_results_sv_marginal(samples, color, label):
     # plt.subplot(1, 2, 1)
     # plt.hist(samples['nu'], bins = 20, histtype= 'step', lw= 4, density= True, color= color, label= label)
@@ -354,9 +353,131 @@ If we care about this parameter in particular, we should reduce step size furthe
 
 +++
 
+## Adjusted MCLMC
+
+Blackjax also provides an adjusted version of the algorithm. This also has two hyperparameters, `step_size` and `L`. `L` is related to the `L` parameter of the unadjusted version, but not identical. The tuning algorithm is also similar, but uses a dual averaging scheme to tune the step size. We find in practice that a target MH acceptance rate of 0.9 is a good choice.
+
+```{code-cell}
+from blackjax.mcmc.adjusted_mclmc import rescale
+from blackjax.util import run_inference_algorithm
+
+def run_adjusted_mclmc(
+    logdensity_fn,
+    num_steps,
+    initial_position,
+    key,
+    transform=lambda state, _ : state.position,
+    diagonal_preconditioning=False,
+    random_trajectory_length=True,
+    L_proposal_factor=jnp.inf
+):
+
+    init_key, tune_key, run_key = jax.random.split(key, 3)
+
+    initial_state = blackjax.mcmc.adjusted_mclmc.init(
+        position=initial_position,
+        logdensity_fn=logdensity_fn,
+        random_generator_arg=init_key,
+    )
+
+    if random_trajectory_length:
+        integration_steps_fn = lambda avg_num_integration_steps: lambda k: jnp.ceil(
+            jax.random.uniform(k) * rescale(avg_num_integration_steps))
+    else:
+        integration_steps_fn = lambda avg_num_integration_steps: lambda _: jnp.ceil(avg_num_integration_steps)
+
+    kernel = lambda rng_key, state, avg_num_integration_steps, step_size, sqrt_diag_cov: blackjax.mcmc.adjusted_mclmc.build_kernel(
+        integration_steps_fn=integration_steps_fn(avg_num_integration_steps),
+        sqrt_diag_cov=sqrt_diag_cov,
+    )(
+        rng_key=rng_key,
+        state=state,
+        step_size=step_size,
+        logdensity_fn=logdensity_fn,
+        L_proposal_factor=L_proposal_factor,
+    )
+
+    target_acc_rate = 0.9 # our recommendation
+
+    (
+        blackjax_state_after_tuning,
+        blackjax_mclmc_sampler_params,
+    ) = blackjax.adjusted_mclmc_find_L_and_step_size(
+        mclmc_kernel=kernel,
+        num_steps=num_steps,
+        state=initial_state,
+        rng_key=tune_key,
+        target=target_acc_rate,
+        frac_tune1=0.1,
+        frac_tune2=0.1,
+        frac_tune3=0.0, # our recommendation
+        diagonal_preconditioning=diagonal_preconditioning,
+    )
+
+    step_size = blackjax_mclmc_sampler_params.step_size
+    L = blackjax_mclmc_sampler_params.L
+
+    alg = blackjax.adjusted_mclmc(
+        logdensity_fn=logdensity_fn,
+        step_size=step_size,
+        integration_steps_fn=lambda key: jnp.ceil(
+            jax.random.uniform(key) * rescale(L / step_size)
+        ),
+        sqrt_diag_cov=blackjax_mclmc_sampler_params.sqrt_diag_cov,
+        L_proposal_factor=L_proposal_factor,
+    )
+
+    _, out = run_inference_algorithm(
+        rng_key=run_key,
+        initial_state=blackjax_state_after_tuning,
+        inference_algorithm=alg,
+        num_steps=num_steps,
+        transform=transform,
+        progress_bar=False,
+    )
+
+    return out
+```
+
+```{code-cell}
+# run the algorithm on a high dimensional gaussian, and show two of the dimensions
+
+sample_key, rng_key = jax.random.split(rng_key)
+samples = run_adjusted_mclmc(
+    logdensity_fn=lambda x: -0.5 * jnp.sum(jnp.square(x)),
+    num_steps=1000,
+    initial_position=jnp.ones((1000,)),
+    key=sample_key,
+)
+plt.scatter(x=samples[:, 0], y=samples[:, 1], alpha=0.1)
+plt.axis("equal")
+plt.title("Scatter Plot of Samples")
+```
+
+```{code-cell}
+# run the algorithm on a high dimensional gaussian, and show two of the dimensions
+
+sample_key, rng_key = jax.random.split(rng_key)
+samples = run_adjusted_mclmc(
+    logdensity_fn=lambda x: -0.5 * jnp.sum(jnp.square(x)),
+    num_steps=1000,
+    initial_position=jnp.ones((1000,)),
+    key=sample_key,
+    random_trajectory_length=False,
+    L_proposal_factor=1.25,
+)
+plt.scatter(x=samples[:, 0], y=samples[:, 1], alpha=0.1)
+plt.axis("equal")
+plt.title("Scatter Plot of Samples")
+```
+
 ```{bibliography}
 :filter: docname in docnames
 ```
 
 
+```
+
+```{code-cell}
+
 ```