uot-bench 0.1.6

Utilities for optimal transport algorithms and benchmarking

uot-bench

uot-bench is a Python toolkit for optimal transport solvers and benchmarking. It provides JAX-first implementations of common OT methods, utilities for generating problems and measures, and a configurable benchmarking pipeline for running experiments at scale.

• Documentation index: docs/index.md
• Problems module: docs/problems.md
• Problem generators: docs/generators.md
• SLURM guide: docs/slurm.md
• Color transfer experiment: docs/color_transfer.md
• MNIST classification experiment: docs/mnist.md

Install

Core install:

pip install uot-bench

Extras (optional):

pip install "uot-bench[viz,image-analysis,color-transfer,gurobi]"

CUDA (optional, JAX):

pip install "uot-bench[cuda12]"

Quickstart (Python API)

A minimal two-marginal Sinkhorn example:

import numpy as np

from uot.data.measure import PointCloudMeasure
from uot.problems.two_marginal import TwoMarginalProblem
from uot.solvers.sinkhorn import SinkhornTwoMarginalSolver
from uot.utils.costs import cost_euclid_squared

# Create two 1D point-cloud measures
x = np.linspace(0.0, 1.0, 64).reshape(-1, 1)
y = np.linspace(0.0, 1.0, 64).reshape(-1, 1)

a = np.exp(-((x - 0.3) ** 2) / 0.01).reshape(-1)
a = a / a.sum()
b = np.exp(-((y - 0.7) ** 2) / 0.02).reshape(-1)
b = b / b.sum()

mu = PointCloudMeasure(x, a, name="mu")
nu = PointCloudMeasure(y, b, name="nu")

problem = TwoMarginalProblem("toy", mu, nu, cost_euclid_squared)
solver = SinkhornTwoMarginalSolver()
inputs = problem.solver_inputs()

result = solver.solve(
    marginals=inputs.marginals,
    costs=inputs.costs,
    reg=1e-2,
)

print("cost:", float(result["cost"]))

Benchmarking CLI tools (Pixi)

This project uses Pixi to manage benchmarking dependencies and tasks.

Installing Pixi

• Linux
• macOS
• Windows

After installation run pixi install to set up the environment. Available commands can be invoked with pixi run <task>.

Common commands

• pixi run serialize --config <config.yaml> --export-dir <directory>
• pixi run benchmark --config <config.yaml> --folds <n> --export <file>
• pixi run lint or ruff check .

Slurm

On Compute Canada clusters

The generic script for both SLURM and local runs is scripts/run_benchmark.sh. Example:

sbatch scripts/run_benchmark.sh configs/generators/gaussians.yaml configs/runners/gaussians.yaml

Monitor GPU usage with:

srun --jobid 123456 --pty watch -n 30 nvidia-smi

Synthetic datasets

Create a generator config like:

generators:
  1D-gaussians-64:
    generator: uot.problems.generators.GaussianMixtureGenerator
    dim: 1
    num_components: 1
    n_points: 64
    num_datasets: 30
    borders: (-6, 6)
    cost_fn: uot.utils.costs.cost_euclid_squared
    use_jax: true
    seed: 42

Then serialize:

pixi run serialize --config configs/generators/gaussians.yaml --export-dir datasets/synthetic

Running experiments

Example config:

param-grids:
  regularizations:
    - reg: 1
    - reg: 0.001

solvers:
  sinkhorn:
    solver: uot.solvers.sinkhorn.SinkhornTwoMarginalSolver
    jit: true
    param-grid: regularizations

problems:
  dir: datasets/synthetic
  names:
    - 1D-gaussians-64
  
experiment: 
  name: Measure on Gaussians
  function: uot.experiments.measurement.measure_time

Run the benchmark:

pixi run benchmark --config configs/runners/gaussians.yaml --folds 1 --export results/raw/gaussians.csv

Color Transfer

Example config:

param-grids:
  epsilons:
    - reg: 1
    - reg: 0.01

solvers:
  sinkhorn:
    solver: uot.solvers.sinkhorn.SinkhornTwoMarginalSolver
    param-grid: epsilons
    jit: true

bin-number:
  - 16
  - 32
soft-extension:
  - no
  - yes
displacement-interpolation:
  - 0.0
  - 1.0
color-space: rgb
# active-channels: [r, g]
batch-size: 100000
pair-number: 3
images-dir: ./datasets/images
rng-seed: 42

drop-columns:
  - transport_plan
  - monge_map
  - u_final
  - v_final

experiment: 
  name: Time and test
  output-dir: ./outputs/color_transfer

For detailed explanation of parameters, see docs/color_transfer.md. Notably, soft-extension and displacement-interpolation can be single values or lists, and the pipeline will run once per option.

Example: Lab space with selected channels.

color-space: lab
active-channels: [l, a]

Run the experiment:

pixi run color-transfer --config ./configs/color_transfer/example.yaml

Dashboard visualization:

pixi run color-transfer-visualization --origin_folder <path_to_input_images> --results_folder <path_to_resulting_images>

MNIST Classification

The MNIST experiment is performed in two steps:

• Distance matrix calculation
• Classification

See docs/mnist.md for configs.

Step 1:

pixi run mnist_distances --config ./configs/mnist_dist_example.yaml

Step 2:

pixi run mnist_classification --config ./configs/mnist_classification_example.yaml

Linting

Run pixi run lint or ruff check ..