vpet-abc 0.1.5

Fast likelihood-free PET kinetic modelling in JAX

vPET-ABC

Fast, likelihood‑free PET kinetic modelling implemented in JAX

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1 · What is this repository?

vpetabc is a pure‑Python re‑implementation of the vPET‑ABC framework [(Grazian et al., 2021)](https://ieeexplore.ieee.org/document/9875446/, peer-reviewed paper coming soon) for large‑scale dynamic PET kinetic modelling, written from the ground up in JAX.

Compared with the earlier CuPy version, the JAX rewrite

• removes CUDA‑specific boiler‑plate – the same code runs on CPU, multi‑GPU, or TPU via XLA;
• exposes a clean, PyTorch‑like API centred on an abstract KineticModel;
• relies on vectorised primitives (vmap, lax.scan) so that even > 40 M‑voxel datasets fit into a single JIT‑compiled graph;
• delivers further speed‑ups;
• depends only on jax, pandas, and tqdm – no CuPy, no manual builds.

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2 · Repository layout

.
├── data/
│   ├── sample_2TCM.csv
│   └── sample_lpntPET.csv
├── dist/                     # wheels/sdists created by `python -m build`
├── example_usage.ipynb
├── pyproject.toml
├── README.md
└── src/
    └── vpetabc/
        ├── __init__.py       # package namespace
        ├── engine.py         # ABC engine + helpers
        ├── models.py         # TwoTissueModel, lpntPETModel, …
        ├── priors.py         # prior samplers
        └── utilities.py      # I/O + posterior utilities

Module	Description
engine.py	ABCRejection, the fully vectorised, JIT‑compiled rejection‑ABC driver
models.py	KineticModel base‑class + TwoTissueModel, lpntPETModel, OneTissueModel, SRTMModel, AATHModel implementations
priors.py	Uniform × Bernoulli prior samplers (TwoTissuePrior, lpntPETPrior), or Uniform prior samplers with a single model (OneTissuePrior, SRTMPrior, AATHPrior)
utilities.py	preprocess_table, get_conditional_posterior_mean, get_posterior_mean misc. helpers

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3 · Installation

TL;DR pip install vpet-abc[cuda]

3.1  Stable release from PyPI

# create & activate a virtual environment
python -m venv .venv && source .venv/bin/activate

# CPU‑only:
pip install vpet-abc

# NVIDIA GPUs
pip install vpet-abc[cuda]

jax[cuda] wheels already bundle matching CUDA/cuDNN libraries; you only need a driver on Linux / Windows WSL. For TPU, Metal (macOS), or ROCm see the official
JAX installation guide.

3.2  Tested environments

OS	Python	jax / jaxlib	Accelerator
macOS 15.5 (arm64)	3.11.12	0.6.1 [CPU]	Apple M2
Rocky Linux 8.10	3.9.2	0.4.30 [cuda]	NVIDIA V100

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4 · Quick start

See example_usage.ipynb for an executable walkthrough, or run:

import jax
import jax.numpy as jnp
import jax.random as jr
import pandas as pd
from vpetabc import *

df = pd.read_csv("data/sample_2TCM.csv", index_col=0)
Cp_fine, A, TACs, _ = preprocess_table(df)

lower_bounds = jnp.array([0, 0, 0, 0, 0])
upper_bounds = jnp.array([1, 1, 1, 1, 1])

engine = ABCRejection(
    TwoTissueModel(),
    prior_sampler = TwoTissuePrior,
    lower_bounds  = lower_bounds,
    upper_bounds  = upper_bounds,
    num_sims      = 200_000,
    accept_frac   = 0.005,
)

post = engine.run(jr.PRNGKey(0), TACs, Cp_fine, A, batch_size=50_000)
means, chosen = get_conditional_posterior_mean(post)

To run preprocess_table() your CSV must be organised by rows as follows:

Row (0-based)	Purpose	Shape
0	Mid-frame time of each dynamic frame	(F,)
1	Frame length	(F,)
2	Input function ($C_p$) / reference TAC ($C_r$)	(F,)
3 to 3 + V−1	One row per voxel TAC	(V, F)

F – number of frames, V – number of voxels

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5 · Extending the framework

1. Define your kinetic model

class MyModel(KineticModel):
    @partial(jax.jit, static_argnums=(0,))
    def simulate(self, θ, Cp, dt):
        # return Ct(t) as a (T_fine,) array
        ...

2. Write a prior

def MyPrior(key, n, lows, highs):
    return jr.uniform(key, (n, P), lows, highs)

3. Pass MyModel and MyPrior to ABCRejection.
   Batching, GPU kernels, and distance evaluation are handled automatically.

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6 · Evaluations & Citation

See arXiv.

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7 · Known Issues

• Stale GPU allocations after an interrupted run: If a notebook-cell or script is killed part-way through execution, the CUDA context can remain resident, leaving most of the GPU memory “in use”. Subsequent calls will then fail with “CUDA out of memory” even though no computation is running. Work-around: restart the Python/Jupyter kernel (or the entire Python process). This releases the orphaned context and frees the GPU memory. A full system reboot is not required. This is a limitation of JAX + XLA.
• Doesn't Support JAX-Metal yet.

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9 · Licence

vpetabc is released under the MIT Licence (see LICENCE).
The sample dataset is provided for non‑commercial research use only.