Pymc Fundamentals

PyMC Fundamentals

When to Use This Skill

• Writing new PyMC models in Python
• Understanding PyMC syntax and API
• Converting models from Stan/JAGS to PyMC
• Diagnosing sampling issues with ArviZ

Model Structure

import pymc as pm
import numpy as np
import arviz as az

with pm.Model() as model:
    # 1. Priors
    mu = pm.Normal("mu", mu=0, sigma=10)
    sigma = pm.HalfNormal("sigma", sigma=1)

    # 2. Likelihood
    y_obs = pm.Normal("y_obs", mu=mu, sigma=sigma, observed=y_data)

    # 3. Sample
    trace = pm.sample(1000, tune=1000, return_inferencedata=True)

# 4. Diagnostics
az.summary(trace)

CRITICAL: SD Parameterization

PyMC uses SD (like Stan), NOT precision (like BUGS):

# PyMC (SD)
pm.Normal("x", mu=0, sigma=1)      # sigma is SD

# BUGS equivalent would be tau = 1/sigma² = 1

Distribution Quick Reference

Continuous

pm.Normal("x", mu=0, sigma=1)           # Normal
pm.HalfNormal("x", sigma=1)             # Half-normal (>0)
pm.HalfCauchy("x", beta=2.5)            # Half-Cauchy (>0)
pm.Exponential("x", lam=1)              # Exponential
pm.Uniform("x", lower=0, upper=1)       # Uniform
pm.Beta("x", alpha=1, beta=1)           # Beta
pm.Gamma("x", alpha=2, beta=1)          # Gamma
pm.StudentT("x", nu=3, mu=0, sigma=1)   # Student-t
pm.LogNormal("x", mu=0, sigma=1)        # Log-normal
pm.TruncatedNormal("x", mu=0, sigma=1, lower=0)  # Truncated

Discrete

pm.Bernoulli("x", p=0.5)                # Bernoulli
pm.Binomial("x", n=10, p=0.5)           # Binomial
pm.Poisson("x", mu=5)                   # Poisson
pm.NegativeBinomial("x", mu=5, alpha=1) # Negative binomial
pm.Categorical("x", p=[0.3, 0.5, 0.2])  # Categorical

Multivariate

pm.MvNormal("x", mu=np.zeros(K), cov=np.eye(K))
pm.Dirichlet("x", a=np.ones(K))
pm.LKJCholeskyCov("chol", n=K, eta=2, sd_dist=pm.Exponential.dist(1))

Sampling

# Standard NUTS
trace = pm.sample(
    draws=1000,          # Samples per chain
    tune=1000,           # Warmup
    chains=4,
    cores=4,
    target_accept=0.8,   # Increase for divergences
    random_seed=42,
    return_inferencedata=True
)

# Variational inference (fast)
approx = pm.fit(n=30000, method="advi")
trace = approx.sample(1000)

# Predictive sampling
prior_pred = pm.sample_prior_predictive(500)
post_pred = pm.sample_posterior_predictive(trace)

Bayesian Workflow (Statistical Rethinking)

1. Prior Predictive Check

with model:
    prior_pred = pm.sample_prior_predictive(500, random_seed=42)
az.plot_ppc(prior_pred, group="prior")

2. Fit Model

with model:
    trace = pm.sample(1000, tune=1000, target_accept=0.9,
                      return_inferencedata=True)

3. Diagnostics

az.summary(trace, hdi_prob=0.89)
az.plot_trace(trace)
az.plot_rank_hist(trace)  # Ranked histograms (preferred)

4. Posterior Predictive Check

with model:
    post_pred = pm.sample_posterior_predictive(trace)
az.plot_ppc(post_pred, num_pp_samples=100)

5. Model Comparison

loo1 = az.loo(trace1)
loo2 = az.loo(trace2)
az.compare({"m1": trace1, "m2": trace2})
az.plot_khat(loo1)  # k > 0.7 is problematic

pm.Deterministic for Tracking

Always track mu for plotting:

# Inside model
mu = pm.Deterministic("mu", alpha + pm.math.dot(X, beta))

# Access later
trace.posterior["mu"]  # All samples of mu

Data Extraction Patterns

# Extract to DataFrame
trace_df = az.extract_dataset(trace).to_dataframe()

# Access specific parameters
post = az.extract_dataset(trace["posterior"])
mu_samples = post["mu"].values

# Get numpy arrays
alpha_values = trace.posterior["alpha"].values  # (chains, draws)

HDI Visualization

# Compute mu at new x values
x_seq = np.linspace(x.min(), x.max(), 100)
mu_pred = post["alpha"] + post["beta"] * x_seq[:, None]

# Plot HDI bands
az.plot_hdi(x_seq, mu_pred.T, hdi_prob=0.89)
plt.scatter(x, y)

ArviZ Diagnostics

import arviz as az

# Configure defaults
az.rcParams["stats.hdi_prob"] = 0.89

# Summary table
summary = az.summary(trace, hdi_prob=0.89)

# Key metrics
max_rhat = summary["r_hat"].max()       # Should be  400

# Plots
az.plot_trace(trace)                    # Trace plots
az.plot_rank_hist(trace)                # Ranked histograms (preferred!)
az.plot_posterior(trace)                # Posteriors
az.plot_forest(trace)                   # Forest plot
az.plot_pair(trace)                     # Pairs plot

# Model comparison
az.loo(trace)                           # LOO-CV
az.waic(trace)                          # WAIC
az.compare({"m1": trace1, "m2": trace2})

Diagnostic Checklist

• [ ] Rhat 400
• [ ] ESS_tail > 400
• [ ] Prior predictive produces sensible values
• [ ] Posterior predictive matches data pattern
• [ ] Pareto k < 0.7 for LOO

Non-Centered Parameterization

For hierarchical models:

# Centered (may have divergences)
theta = pm.Normal("theta", mu=mu, sigma=tau, shape=J)

# Non-centered (recommended)
theta_raw = pm.Normal("theta_raw", mu=0, sigma=1, shape=J)
theta = pm.Deterministic("theta", mu + tau * theta_raw)

PyTensor Math Operations

Inside with pm.Model(), use pm.math not np:

# Correct
mu = pm.math.dot(X, beta)
p = pm.math.sigmoid(eta)
log_x = pm.math.log(x)

# Wrong (will fail)
mu = np.dot(X, beta)  # Don't use numpy inside model

Common Priors

# Intercept
alpha = pm.Normal("alpha", mu=0, sigma=10)

# Coefficients
beta = pm.Normal("beta", mu=0, sigma=2.5, shape=K)

# Scale (SD)
sigma = pm.HalfNormal("sigma", sigma=1)
sigma = pm.HalfCauchy("sigma", beta=2.5)
sigma = pm.Exponential("sigma", lam=1)

# Hierarchical SD
tau = pm.HalfCauchy("tau", beta=2.5)

# Correlation matrix
chol, corr, stds = pm.LKJCholeskyCov("chol", n=K, eta=2,
                                      sd_dist=pm.Exponential.dist(1))

Key Differences from Stan

| Feature | PyMC | Stan | |---------|------|------| | Syntax | Python | DSL | | Arrays | shape=K | array[K] | | Math | pm.math.dot() | * operator | | Blocks | Single context | 7 blocks | | Output | InferenceData | CmdStanMCMC |

Troubleshooting

| Issue | Solution | |-------|----------| | Divergences | Increase target_accept to 0.9-0.99 | | Low ESS | Run longer chains, reparameterize | | Shape errors | Check shape= parameter | | Slow | Use ADVI for quick approximation | | Memory | Reduce chains or use mini-batch |

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: choxos
• Source: choxos/BiostatAgent
• License: MIT

Install and usage instructions live in the source repository linked above.