tetrad-port 0.1.0

C++ port of CMU's Tetrad causal discovery library with Python bindings

tetrad-port

C++ port of CMU's Tetrad causal inference library, with Python bindings via nanobind.

Algorithms

Algorithm	Type	Output	Latent Confounders
PC	Constraint-based (Fisher Z)	CPDAG	No
FGES	Score-based (BIC)	CPDAG	No
GFCI	Hybrid (FGES + FCI rules)	PAG	Yes

All algorithms support background knowledge: temporal tiers, forbidden edges, and required edges.

Quick Start

pip install -e ".[dev]"

import pandas as pd
from tetrad_port import TetradPort, Knowledge

tp = TetradPort()
df = pd.read_csv("data.csv")

# Run PC (constraint-based)
results, graph_info = tp.run_pc(df, alpha=0.05)

# Run FGES (score-based, faster for large graphs)
results, graph_info = tp.run_fges(df, penalty_discount=1.0)

# Run GFCI (handles latent confounders)
results, graph_info = tp.run_gfci(df, alpha=0.05)

# Add background knowledge
k = Knowledge()
k.set_tier(0, ["Age", "Genetics"])    # Cannot be caused by later variables
k.set_tier(1, ["Exercise", "Diet"])
k.set_forbidden("Exercise", "Cholesterol")
k.set_required("Smoking", "BP")
results, graph_info = tp.run_pc(df, alpha=0.05, knowledge=k)

Building from Source

C++ standalone

cmake -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build
./build/tetrad_tests        # Run all C++ tests
./build/run_pc              # Example CLI

Python package

pip install -e ".[dev]"
pytest tests/test_python_bindings.py -v

Documentation

• Python API Reference
• Examples
  • Causal Discovery Tutorial — PC, FGES, and GFCI comparison
  • Knowledge Tutorial — Temporal tiers, forbidden/required edges

Architecture

The C++ core lives in src/ under namespace tetrad:

• src/graph/ — Node, Edge, Graph (EdgeListGraph with TAIL/ARROW/CIRCLE endpoints)
• src/data/ — DataSet (Eigen matrix wrapper), Knowledge (tiers, forbidden/required edges)
• src/search/ — PC, FAS, MeekRules, FGES, FciOrient, GFCI, IndTestFisherZ, SemBicScore
• src/util/ — ChoiceGenerator, SublistGenerator

Python bindings (bindings/tetrad_bindings.cpp) expose algorithms via nanobind. The TetradPort facade class (python/tetrad_port/__init__.py) provides a pandas-friendly API with SEM fitting helpers.

Dependencies

C++ (auto-fetched via CMake FetchContent):

• Eigen 3.4.0 — linear algebra
• Catch2 v3.5.2 — testing
• nanobind 2.0+ — Python bindings

Python:

• numpy, pandas (required)
• semopy (optional, SEM fitting)

Reference

Ported from Tetrad 7.6.8 (Java). This version contains critical FciOrient correctness fixes reviewed by Peter Spirtes.