jact 0.1.2

JAX-based transition probability computation for multi-state models

jact

JAX-based transition probability computation for multi-state models with duration-dependent transition intensities.

What is jact?

jact computes transition probabilities in semi-Markov multi-state models. It takes fitted intensity models — parametric functions, GLMs, neural networks, or any JIT-compatible callable — and produces transition probabilities for thousands of individuals in a single vectorized pass on GPU. Computations are optimized for JIT-compiled GPU execution.

Quick example

import jax.numpy as jnp
import jact

# Define the state space
state_space = jact.StateSpace(
    states=["healthy", "disabled", "dead"],
    transitions=[
        ("healthy", "disabled"),
        ("healthy", "dead"),
        ("disabled", "dead"),
    ],
)

# Build a model with intensity functions
model = state_space.build(
    transitions={
        ("healthy", "disabled"): onset_fn,
        ("healthy", "dead"): mortality_fn,
        ("disabled", "dead"): disabled_mort_fn,
    }
)

# Compute transition probabilities for 1000 individuals
ages = jnp.linspace(30, 80, 1_000)
result = model.solve(initial="healthy", horizon=30, steps_per_unit=12, age=ages)

Key features

• Plug in any model: Gompertz, GLM, neural network — anything that's JIT-compatible.
• Swap and compare: Same StateSpace, different intensity models. Experiment easily.
• Compute only what's needed: The solver reduces to states reachable from the initial state.
• Exact seeded starts: Initial point masses preserve per-individual starting duration d_0 exactly.
• Batch-first: Designed for 100K+ individuals in a single pass.

Documentation

See the documentation index for the public documentation set. For the full API contract, use the API specification. For a runnable walkthrough of the main workflow, see the example notebook.

Namespace

The recommended user API is the top-level jact namespace: jact.StateSpace, jact.InitialDistribution, jact.solve, and the cashflow declarations such as jact.StateRate and jact.Total. Advanced callback state objects remain available from submodules, for example jact.callbacks.PointMass and jact.model.ReducedModel.

Installation

pip install jax jaxlib
pip install jact

For local development from this repository:

pip install -e '.[dev]'
pytest

The package uses a src/ layout, so editable install is the intended local workflow.

To run the example notebook with plotting support from a local checkout:

pip install -e '.[dev,notebook]'

Release checks

Before cutting a PyPI release:

rm -rf build dist src/*.egg-info
python -m build --no-isolation
python -m twine check dist/*
pytest -q

The tag-driven publish flow is documented in RELEASING.md.

Requirements

• Python >= 3.10
• JAX >= 0.4

License

Apache-2.0