Modify linear regressions to parameters in R

examples/Introduction.md

@@ -29,16 +29,17 @@ import blackjax
 
 ## The Problem
 
-We'll generate observations from a normal distribution of known `loc` and `scale` to see if we can recover the parameters in sampling. Let's take a decent-size dataset with 1,000 points:
+We'll generate observations from a normal distribution of known `loc` and `scale` to see if we can recover the parameters in sampling. **MCMC algorithms usually assume samples are being drawn from an unconstrained Euclidean space.** Hence why we'll log transform the scale parameter, so that sampling is done on the real line. Samples can be transformed back to their original space in post-processing. Let's take a decent-size dataset with 1,000 points:
 
 ```{code-cell} ipython3
 loc, scale = 10, 20
 observed = np.random.normal(loc, scale, size=1_000)
 ```
 
 ```{code-cell} ipython3
-def logprob_fn(loc, scale, observed=observed):
+def logprob_fn(loc, log_scale, observed=observed):
     """Univariate Normal"""
+    scale = jnp.exp(log_scale)
     logpdf = stats.norm.logpdf(observed, loc, scale)
     return jnp.sum(logpdf)
 
@@ -51,7 +52,7 @@ logprob = lambda x: logprob_fn(**x)
 ### Sampler Parameters
 
 ```{code-cell} ipython3
-inv_mass_matrix = np.array([0.5, 0.5])
+inv_mass_matrix = np.array([0.5, 0.01])
 num_integration_steps = 60
 step_size = 1e-3
 
@@ -63,7 +64,7 @@ hmc = blackjax.hmc(logprob, step_size, inv_mass_matrix, num_integration_steps)
 The initial state of the HMC algorithm requires not only an initial position, but also the potential energy and gradient of the potential energy at this position. BlackJAX provides a `new_state` function to initialize the state from an initial position.
 
 ```{code-cell} ipython3
-initial_position = {"loc": 1.0, "scale": 2.0}
+initial_position = {"loc": 1.0, "log_scale": 1.0}
 initial_state = hmc.init(initial_position)
 initial_state
 ```
@@ -100,7 +101,7 @@ rng_key = jax.random.PRNGKey(0)
 states = inference_loop(rng_key, hmc_kernel, initial_state, 10_000)
 
 loc_samples = states.position["loc"].block_until_ready()
-scale_samples = states.position["scale"]
+scale_samples = jnp.exp(states.position["log_scale"])
 ```
 
 ```{code-cell} ipython3
@@ -121,14 +122,14 @@ ax1.set_ylabel("scale")
 NUTS is a *dynamic* algorithm: the number of integration steps is determined at runtime. We still need to specify a step size and a mass matrix:
 
 ```{code-cell} ipython3
-inv_mass_matrix = np.array([0.5, 0.5])
+inv_mass_matrix = np.array([0.5, 0.01])
 step_size = 1e-3
 
 nuts = blackjax.nuts(logprob, step_size, inv_mass_matrix)
 ```
 
 ```{code-cell} ipython3
-initial_position = {"loc": 1.0, "scale": 2.0}
+initial_position = {"loc": 1.0, "log_scale": 1.0}
 initial_state = nuts.init(initial_position)
 initial_state
 ```
@@ -139,7 +140,7 @@ rng_key = jax.random.PRNGKey(0)
 states = inference_loop(rng_key, nuts.step, initial_state, 4_000)
 
 loc_samples = states.position["loc"].block_until_ready()
-scale_samples = states.position["scale"]
+scale_samples = jnp.exp(states.position["log_scale"])
 ```
 
 ```{code-cell} ipython3
@@ -176,7 +177,7 @@ We can use the obtained parameters to define a new kernel. Note that we do not h
 states = inference_loop(rng_key, kernel, state, 1_000)
 
 loc_samples = states.position["loc"].block_until_ready()
-scale_samples = states.position["scale"]
+scale_samples = jnp.exp(states.position["log_scale"])
 ```
 
 ```{code-cell} ipython3

examples/RegimeSwitchingModel.md

@@ -171,7 +171,6 @@ dist = RegimeSwitchHMM(T, y)
 ```
 
 ```{code-cell} ipython3
-batch_fn = jax.vmap
 [n_chain, n_warm, n_iter] = [128, 5000, 200]
 ksam, kinit = jrnd.split(jrnd.PRNGKey(0), 2)
 dist.initialize_model(kinit, n_chain)
@@ -181,7 +180,7 @@ dist.initialize_model(kinit, n_chain)
 print("Running MEADS...")
 tic1 = pd.Timestamp.now()
 k_warm, k_sample = jrnd.split(ksam)
-warmup = blackjax.meads(dist.logprob_fn, n_chain, batch_fn=batch_fn)
+warmup = blackjax.meads(dist.logprob_fn, n_chain)
 init_state, kernel, _ = warmup.run(k_warm, dist.init_params, n_warm)
 
 def one_chain(k_sam, init_state):

examples/SparseLogisticRegression.md

@@ -101,14 +101,13 @@ N_OBS, N_REG = X.shape
 N_PARAM = N_REG * 2 + 1
 dist = HorseshoeLogisticReg(X, y)
 
-batch_fn = jax.vmap
 [n_chain, n_warm, n_iter] = [128, 20000, 10000]
 ksam, kinit = jrnd.split(jrnd.PRNGKey(0), 2)
 dist.initialize_model(kinit, n_chain)
 
 tic1 = pd.Timestamp.now()
 k_warm, k_sample = jrnd.split(ksam)
-warmup = blackjax.meads(dist.logprob_fn, n_chain, batch_fn=batch_fn)
+warmup = blackjax.meads(dist.logprob_fn, n_chain)
 adaptation_results = warmup.run(k_warm, dist.init_params, n_warm)
 init_state = adaptation_results.state
 kernel = adaptation_results.kernel

examples/howto_sample_multiple_chains.md

@@ -54,8 +54,9 @@ loc, scale = 10, 20
 observed = np.random.normal(loc, scale, size=1_000)
 
 
-def logprob_fn(loc, scale, observed=observed):
+def logprob_fn(loc, log_scale, observed=observed):
     """Univariate Normal"""
+    scale = jnp.exp(log_scale)
     logpdf = stats.norm.logpdf(observed, loc, scale)
     return jnp.sum(logpdf)
 
@@ -83,7 +84,7 @@ To make our demonstration more dramatic we will used a NUTS sampler with poorly
 import blackjax
 
 
-inv_mass_matrix = np.array([0.5, 0.5])
+inv_mass_matrix = np.array([0.5, 0.01])
 step_size = 1e-3
 
 nuts = blackjax.nuts(logprob, step_size, inv_mass_matrix)
@@ -125,7 +126,7 @@ def inference_loop_multiple_chains(
 We now prepare the initial states using `jax.vmap` again, to vectorize the `init` function:
 
 ```{code-cell} ipython3
-initial_positions = {"loc": np.ones(num_chains), "scale": 2.0 * np.ones(num_chains)}
+initial_positions = {"loc": np.ones(num_chains), "log_scale": np.ones(num_chains)}
 initial_states = jax.vmap(nuts.init, in_axes=(0))(initial_positions)
 ```
 

setup.py

@@ -25,7 +25,7 @@
         "fastprogress>=0.2.0",
         "jax>=0.3.13",
         "jaxlib>=0.3.10",
-        "jaxopt>=0.4.2",
+        "jaxopt>=0.5.5",
     ],
     long_description_content_type="text/markdown",
     keywords="probabilistic machine learning bayesian statistics sampling algorithms",

tests/test_benchmarks.py

@@ -15,9 +15,10 @@
 import blackjax
 
 
-def regression_logprob(scale, coefs, preds, x):
+def regression_logprob(log_scale, coefs, preds, x):
     """Linear regression"""
-    scale_prior = stats.expon.logpdf(scale, 1, 1)
+    scale = jnp.exp(log_scale)
+    scale_prior = stats.expon.logpdf(scale, 0, 1) + log_scale
     coefs_prior = stats.norm.logpdf(coefs, 0, 5)
     y = jnp.dot(x, coefs)
     logpdf = stats.norm.logpdf(preds, y, scale)
@@ -53,7 +54,7 @@ def run_regression(algorithm, **parameters):
         is_mass_matrix_diagonal=False,
         **parameters,
     )
-    state, kernel, _ = warmup.run(warmup_key, {"scale": 1.0, "coefs": 2.0}, 1000)
+    state, kernel, _ = warmup.run(warmup_key, {"log_scale": 0.0, "coefs": 2.0}, 1000)
 
     states = inference_loop(kernel, 10_000, inference_key, state)
 

tests/test_optimizers.py

@@ -58,9 +58,10 @@ def test_minimize_lbfgs(self, maxiter, maxcor):
         the same between two loop recursion algorthm of LBFGS and formulas of the
         pathfinder paper"""
 
-        def regression_logprob(scale, coefs, preds, x):
+        def regression_logprob(log_scale, coefs, preds, x):
             """Linear regression"""
-            scale_prior = stats.expon.logpdf(scale, 1, 1)
+            scale = jnp.exp(log_scale)
+            scale_prior = stats.expon.logpdf(scale, 0, 1) + log_scale
             coefs_prior = stats.norm.logpdf(coefs, 0, 5)
             y = jnp.dot(x, coefs)
             logpdf = stats.norm.logpdf(preds, y, scale)
@@ -79,7 +80,7 @@ def regression_model(key):
             return logposterior_fn
 
         fn = regression_model(self.key)
-        b0 = {"scale": 1.0, "coefs": 2.0}
+        b0 = {"log_scale": 0.0, "coefs": 2.0}
         b0_flatten, unravel_fn = ravel_pytree(b0)
         objective_fn = lambda x: -fn(unravel_fn(x))
         (_, status), history = self.variant(

tests/test_sampling.py

@@ -46,14 +46,14 @@ def irmh_proposal_distribution(rng_key):
 regression_test_cases = [
     {
         "algorithm": blackjax.hmc,
-        "initial_position": {"scale": 1.0, "coefs": 2.0},
+        "initial_position": {"log_scale": 0.0, "coefs": 4.0},
         "parameters": {"num_integration_steps": 90},
         "num_warmup_steps": 1_000,
         "num_sampling_steps": 3_000,
     },
     {
         "algorithm": blackjax.nuts,
-        "initial_position": {"scale": 1.0, "coefs": 2.0},
+        "initial_position": {"log_scale": 0.0, "coefs": 4.0},
         "parameters": {},
         "num_warmup_steps": 1_000,
         "num_sampling_steps": 1_000,
@@ -68,9 +68,10 @@ def setUp(self):
         super().setUp()
         self.key = jax.random.PRNGKey(19)
 
-    def regression_logprob(self, scale, coefs, preds, x):
+    def regression_logprob(self, log_scale, coefs, preds, x):
         """Linear regression"""
-        scale_prior = stats.expon.logpdf(scale, 1, 1)
+        scale = jnp.exp(log_scale)
+        scale_prior = stats.expon.logpdf(scale, 0, 1) + log_scale
         coefs_prior = stats.norm.logpdf(coefs, 0, 5)
         y = jnp.dot(x, coefs)
         logpdf = stats.norm.logpdf(preds, y, scale)
@@ -109,7 +110,7 @@ def test_window_adaptation(self, case, is_mass_matrix_diagonal):
         )
 
         coefs_samples = states.position["coefs"]
-        scale_samples = states.position["scale"]
+        scale_samples = np.exp(states.position["log_scale"])
 
         np.testing.assert_allclose(np.mean(scale_samples), 1.0, atol=1e-1)
         np.testing.assert_allclose(np.mean(coefs_samples), 3.0, atol=1e-1)
@@ -128,11 +129,11 @@ def test_mala(self):
         warmup_key, inference_key = jax.random.split(rng_key, 2)
 
         mala = blackjax.mala(logposterior_fn, 1e-5)
-        state = mala.init({"coefs": 1.0, "scale": 2.0})
+        state = mala.init({"coefs": 1.0, "log_scale": 1.0})
         states = inference_loop(mala.step, 10_000, inference_key, state)
 
         coefs_samples = states.position["coefs"][3000:]
-        scale_samples = states.position["scale"][3000:]
+        scale_samples = np.exp(states.position["log_scale"][3000:])
 
         np.testing.assert_allclose(np.mean(scale_samples), 1.0, atol=1e-1)
         np.testing.assert_allclose(np.mean(coefs_samples), 3.0, atol=1e-1)
@@ -172,7 +173,7 @@ def test_pathfinder_adaptation(
         states = inference_loop(kernel, num_sampling_steps, inference_key, state)
 
         coefs_samples = states.position["coefs"]
-        scale_samples = states.position["scale"]
+        scale_samples = np.exp(states.position["log_scale"])
 
         np.testing.assert_allclose(np.mean(scale_samples), 1.0, atol=1e-1)
         np.testing.assert_allclose(np.mean(coefs_samples), 3.0, atol=1e-1)
@@ -190,26 +191,28 @@ def test_meads(self):
 
         init_key, warmup_key, inference_key = jax.random.split(rng_key, 3)
 
+        num_chains = 128
         warmup = blackjax.meads(
             logposterior_fn,
-            num_chains=128,
+            num_chains=num_chains,
         )
         scale_key, coefs_key = jax.random.split(init_key, 2)
-        scales = 1.0 + jax.random.normal(scale_key, (128,))
-        coefs = 3.0 + jax.random.normal(coefs_key, (128,))
-        initial_positions = {"scale": scales, "coefs": coefs}
+        log_scales = 1.0 + jax.random.normal(scale_key, (num_chains,))
+        coefs = 4.0 + jax.random.normal(coefs_key, (num_chains,))
+        initial_positions = {"log_scale": log_scales, "coefs": coefs}
         last_states, kernel, _ = warmup.run(
             warmup_key,
             initial_positions,
-            num_steps=100,
+            num_steps=1000,
         )
 
-        states = jax.vmap(
-            lambda state: inference_loop(kernel, 100, inference_key, state)
-        )(last_states)
+        chain_keys = jax.random.split(inference_key, num_chains)
+        states = jax.vmap(lambda key, state: inference_loop(kernel, 100, key, state))(
+            chain_keys, last_states
+        )
 
         coefs_samples = states.position["coefs"]
-        scale_samples = states.position["scale"]
+        scale_samples = np.exp(states.position["log_scale"])
 
         np.testing.assert_allclose(np.mean(scale_samples), 1.0, atol=1e-1)
         np.testing.assert_allclose(np.mean(coefs_samples), 3.0, atol=1e-1)

tests/test_tempered_smc.py

@@ -42,8 +42,9 @@ def setUp(self):
         super().setUp()
         self.key = jax.random.PRNGKey(42)
 
-    def logprob_fn(self, scale, coefs, preds, x):
+    def logprob_fn(self, log_scale, coefs, preds, x):
         """Linear regression"""
+        scale = jnp.exp(log_scale)
         y = jnp.dot(x, coefs)
         logpdf = stats.norm.logpdf(preds, y, scale)
         return jnp.sum(logpdf)
@@ -55,12 +56,16 @@ def test_adaptive_tempered_smc(self, N, use_log):
         y_data = 3 * x_data + np.random.normal(size=x_data.shape)
         observations = {"x": x_data, "preds": y_data}
 
-        prior = lambda x: stats.expon.logpdf(x[0], 1, 1) + stats.norm.logpdf(x[1])
+        def prior(x):
+            return (
+                stats.expon.logpdf(jnp.exp(x[0]), 0, 1) + x[0] + stats.norm.logpdf(x[1])
+            )
+
         conditioned_logprob = lambda x: self.logprob_fn(*x, **observations)
 
-        scale_init = 1 + np.random.exponential(1, N)
+        log_scale_init = np.log(np.random.exponential(1, N))
         coeffs_init = 3 + 2 * np.random.randn(N)
-        smc_state_init = [scale_init, coeffs_init]
+        smc_state_init = [log_scale_init, coeffs_init]
 
         iterates = []
         results = []  # type: List[TemperedSMCState]
@@ -91,7 +96,9 @@ def test_adaptive_tempered_smc(self, N, use_log):
             iterates.append(n_iter)
             results.append(result)
 
-            np.testing.assert_allclose(np.mean(result.particles[0]), 1.0, rtol=1e-1)
+            np.testing.assert_allclose(
+                np.mean(np.exp(result.particles[0])), 1.0, rtol=1e-1
+            )
             np.testing.assert_allclose(np.mean(result.particles[1]), 3.0, rtol=1e-1)
 
         assert iterates[1] >= iterates[0]
@@ -103,12 +110,12 @@ def test_fixed_schedule_tempered_smc(self, N, n_schedule):
         y_data = 3 * x_data + np.random.normal(size=x_data.shape)
         observations = {"x": x_data, "preds": y_data}
 
-        prior = lambda x: stats.norm.logpdf(jnp.log(x[0])) + stats.norm.logpdf(x[1])
+        prior = lambda x: stats.norm.logpdf(x[0]) + stats.norm.logpdf(x[1])
         conditionned_logprob = lambda x: self.logprob_fn(*x, **observations)
 
-        scale_init = np.exp(np.random.randn(N))
+        log_scale_init = np.random.randn(N)
         coeffs_init = np.random.randn(N)
-        smc_state_init = [scale_init, coeffs_init]
+        smc_state_init = [log_scale_init, coeffs_init]
 
         lambda_schedule = np.logspace(-5, 0, n_schedule)
         hmc_parameters = {
@@ -136,7 +143,7 @@ def body_fn(carry, lmbda):
             return (rng_key, new_state), (new_state, info)
 
         (_, result), _ = jax.lax.scan(body_fn, (self.key, init_state), lambda_schedule)
-        np.testing.assert_allclose(np.mean(result.particles[0]), 1.0, rtol=1e-1)
+        np.testing.assert_allclose(np.mean(np.exp(result.particles[0])), 1.0, rtol=1e-1)
         np.testing.assert_allclose(np.mean(result.particles[1]), 3.0, rtol=1e-1)