bayes_nets

A lightweight, standalone Python library for learning, sampling, and visualizing discrete Bayesian networks (BNs).

Designed as a drop-in replacement for pgmpy within estimation-of-distribution algorithm (EDA) workflows, while remaining fully usable as a general-purpose BN toolkit.

Goals

• Discrete representation – all variables take a finite number of states; each variable's cardinality is specified at construction time.
• Multiple structure-learning algorithms – BIC, AIC, and K2 scoring with greedy hill-climbing or the K2 algorithm.
• Probabilistic logic sampling – forward (ancestral) sampling from a learned BN.
• EDA integration – the library is designed to work seamlessly with the eda_code learning and sampling modules as a replacement for pgmpy.
• Visualization – plot BN structures and marginal/conditional probability distributions.

Installation

# Clone the repository and install the package
git clone https://github.com/rsantana-isg/edas_bayes_nets.git
cd edas_bayes_nets
pip install -e .

Core dependencies

Optional dependencies (needed for visualization)

Quick start

import numpy as np
from bayes_nets import BayesianNetwork

# ── 1. Create a BN for 5 binary variables ──────────────────────────────
bn = BayesianNetwork(n_vars=5, cardinality=np.array([2, 2, 2, 2, 2]))

# ── 2. Simulate some data ──────────────────────────────────────────────
rng = np.random.default_rng(42)
data = rng.integers(0, 2, size=(500, 5))

# ── 3. Learn structure and parameters with BIC ──────────────────────────
bn.fit(data, method="bic", max_parents=2)

# ── 4. Inspect the learned structure ───────────────────────────────────
print(bn)
# BayesianNetwork(n_vars=5, cardinality=[2, 2, 2, 2, 2], n_edges=3)

print("Parents of X3:", bn.get_parents(3))

# ── 5. Draw samples from the BN ────────────────────────────────────────
samples = bn.sample(n_samples=200)
print(samples.shape)   # (200, 5)

# ── 6. Visualise ───────────────────────────────────────────────────────
fig = bn.plot(title="Learned BN (BIC)")
fig.savefig("bn_structure.png")

Scoring metrics

BIC (Bayesian Information Criterion)

Balances goodness-of-fit against model complexity:

BIC = log P(D | θ_ML, G)  −  (k / 2) · log(n)

where k is the number of free parameters and n is the sample size. The penalty term grows with n, making BIC more conservative for large datasets.

AIC (Akaike Information Criterion)

Uses a lighter penalty:

AIC = log P(D | θ_ML, G)  −  k

K2

Bayesian scoring metric based on the Dirichlet-multinomial marginal likelihood:

K2(X_i, Pa_i) = Σ_j [  Γ(α)  /  Γ(N_ij + α)
                       ·  Π_k  Γ(N_ijk + α/r_i) / Γ(α/r_i)  ]

where α is the equivalent sample size of the Dirichlet prior, r_i is the cardinality of X_i, N_ij is the count of samples matching parent configuration j, and N_ijk is the joint count for X_i = k and parent config j.

Structure learning algorithms

K2StructureLearner

Uses the K2 algorithm (Cooper & Herskovits, 1992). A variable ordering must be provided; each variable may only have parents that appear earlier in the ordering, which guarantees acyclicity.

from bayes_nets import BayesianNetwork
import numpy as np

bn = BayesianNetwork(n_vars=4, cardinality=np.full(4, 3))
bn.learn_structure(data, method="k2", ordering=np.array([0, 2, 1, 3]))

GreedyHillClimbLearner

Unconstrained greedy hill-climbing with BIC or AIC scoring. No ordering needed; cycle detection is performed explicitly.

bn.learn_structure(data, method="bic", max_parents=3)

Polytree (singly connected) learners

A polytree is a DAG whose skeleton has no undirected cycle, so at most one path connects any two variables. Polytrees admit exact linear-time inference and need far fewer samples than general BNs, which is why they are the model class of the Polytree Approximation Distribution Algorithm (PADA / FDA-SC). These learners live in bayes_nets/polytree_learning.py and were implemented from the papers in docs/PADA/:

# LPA, the learner used inside PADA / FDA-SC
bn.learn_structure(data, method="lpa", alpha=0.05)

# quadratic variant: rank by marginal dependency only
bn.learn_structure(data, method="lpa_marginal")

All four guarantee a singly connected result. alpha sets the significance level of the independence tests; the LPA thresholds e0/e1 are derived from it and scale as 1/N, reproducing the population-size dependence the PADA paper requires. "chow_liu" restricts every node to a single parent (a branching); the other three can represent head-to-head patterns.

Note that a pure XOR-style collider is invisible to any of these learners: each parent is then marginally independent of the child, so no pairwise dependency measure can place the edge (Dasgupta 1999, Example 2).

Advanced learners from the recent literature

These learners were implemented from the papers surveyed in Other_BN_Papers_Ranked.md (sources in docs/Other_BN_Structure_Learning_Methods/). Each is available both as a class and through learn_structure(method=...):

# order-free Markov-blanket learner
bn.learn_structure(data, method="dmbbn", max_parents=3)

# iterative decomposition learner for large networks
bn.learn_structure(data, method="iterdsla", max_parents=3)

# exact optimum for small problems (n_vars <= ~18)
bn.learn_structure(data, method="levelwise")

# prune a fully-connected DAG given a topological order
bn.learn_structure(data, method="sartre", permutation=order)

# differentiable learner for binary data
bn.learn_structure(binary_data, method="binotears")

Parameter learning

Conditional probability distributions (CPDs) are estimated by maximum-likelihood with optional Dirichlet smoothing (alpha parameter):

bn.learn_parameters(data, alpha=1.0)   # Laplace smoothing

For a root variable the CPD is a 1-D probability vector. For a variable with parents it is a 2-D array of shape (n_parent_configs, cardinality[var]).

LogisticRegressionParameterLearner

An alternative CPD estimator that fits each node with an L1-regularised multinomial logistic regression over parent-derived features (dummy encodings plus optional pairwise XOR interactions), following Moral et al. (2026). The number of effective parameters grows linearly with the number of parents instead of exponentially, which helps in dense networks; it is a drop-in replacement for the MLE learner:

from bayes_nets import LogisticRegressionParameterLearner

bn.learn_parameters(data, parameter_learner=LogisticRegressionParameterLearner(C=5.0))

Sampling

Probabilistic logic sampling (forward/ancestral sampling):

samples = bn.sample(n_samples=1000, rng=np.random.default_rng(0))

Variables are sampled in topological order; each variable is drawn from its CPD conditioned on the already-sampled parent values.

EDA integration

The library is designed to work alongside the eda_code modules. The learned BN is represented with a plain numpy adjacency matrix and a Python dict of CPDs – the same data structures used by eda_code/learning/ and eda_code/sampling/.

Example in an EDA learning step:

from bayes_nets import BayesianNetwork
import numpy as np

def learn_bn_model(data: np.ndarray, cardinality: np.ndarray, **kwargs):
    bn = BayesianNetwork(n_vars=data.shape[1], cardinality=cardinality)
    bn.fit(data, method="bic", **kwargs)
    return bn

API reference

BayesianNetwork

References

• Cooper, G. F., & Herskovits, E. (1992). A Bayesian method for the induction of probabilistic networks from data. Machine Learning, 9(4), 309–347.
• Etxeberria, R., & Larrañaga, P. (1999). Global optimization using Bayesian networks. CIMAF-99, pp. 332–339.
• Pelikan, M., Goldberg, D. E., & Cantú-Paz, E. (1999). BOA: The Bayesian Optimization Algorithm. GECCO 1999, pp. 525–532.
• Schwarz, G. (1978). Estimating the dimension of a model. Annals of Statistics, 6(2), 461–464.
• Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716–723.

Recent structure- and parameter-learning methods

• Carvalho Dâmaso, A., et al. (2026). Learning Bayesian Network Structures Without Variable Ordering Influence: A Markov Blanket-Based Approach. Computational Intelligence. — DMBBNStructureLearner
• Jia, X., & Li, Z. (2026). An iterative structure decomposition learning method for complex Bayesian networks. Complex & Intelligent Systems, 12:164. — IterDSLALearner
• Moral, S., Moral-García, S., Cano, A., et al. (2026). Computing conditional probabilities in Bayesian networks using logistic regression. Applied Soft Computing, 198, 115284. — LogisticRegressionParameterLearner
• Kanamori, T., Takagi, S., & Kobayashi, K. (2026). Sparse Additive Model Pruning for Order-Based Causal Structure Learning. AAAI 2026. — SARTREPruner
• Huang, Z., & Suzuki, J. (2026). Memory-efficient exact Bayesian network structure learning: a single-pass level-wise dynamic program. Behaviormetrika. — LevelWiseDPLearner
• Deng, C., & Aragam, B. (2025). Differentiable Structure Learning and Causal Discovery for General Binary Data. NeurIPS 2025. — BinaryNotearsLearner
• Silander, T., & Myllymäki, P. (2012). A simple approach for finding the globally optimal Bayesian network structure. UAI 2006. (basis for the level-wise DP)
• Zheng, X., Aragam, B., Ravikumar, P., & Xing, E. P. (2018). DAGs with NO TEARS: Continuous Optimization for Structure Learning. NeurIPS 2018. (basis for BINOTEARS)