flash-sinkhorn 0.3.2__tar.gz
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- flash_sinkhorn-0.3.2/LICENSE +21 -0
- flash_sinkhorn-0.3.2/PKG-INFO +315 -0
- flash_sinkhorn-0.3.2/README.md +283 -0
- flash_sinkhorn-0.3.2/pyproject.toml +57 -0
- flash_sinkhorn-0.3.2/setup.cfg +4 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/__init__.py +38 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/_autograd.py +519 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/bench/__init__.py +3 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/bench/bench_backward.py +1091 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/bench/bench_forward.py +1715 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/cg.py +369 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/hvp.py +835 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/implicit_grad.py +315 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/__init__.py +92 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/_common.py +231 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/_triton_helpers.py +174 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/apply_flash.py +951 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/apply_ott.py +566 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_flashstyle_sqeuclid.py +1373 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_apply_fused_sqeuclid.py +486 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_apply_sqeuclid.py +17 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_cg_dense.py +582 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_cg_python_batched.py +399 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_geomloss_sqeuclid.py +310 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_grad_sqeuclid.py +1207 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/kernels/sinkhorn_triton_ott_sqeuclid.py +750 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/samples_loss.py +597 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/sinkhorn_solvers.py +707 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/__init__.py +3 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/reference_hvp.py +356 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/reference_sinkhorn.py +233 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_apply_plan_flashstyle.py +585 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_flashstyle_parity.py +679 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_geomloss_sinkhorn_triton.py +411 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_geomloss_vs_triton.py +68 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_half_cost.py +143 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_hvp_parity.py +386 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_hvp_sqeuclid.py +332 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_ott_vs_triton.py +235 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_samples_loss_api.py +355 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_semi_unbalanced_forward.py +145 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_sinkhorn_triton.py +152 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn/testing/test_unbalanced_sinkhorn.py +564 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn.egg-info/PKG-INFO +315 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn.egg-info/SOURCES.txt +46 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn.egg-info/dependency_links.txt +1 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn.egg-info/requires.txt +11 -0
- flash_sinkhorn-0.3.2/src/flash_sinkhorn.egg-info/top_level.txt +1 -0
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MIT License
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Copyright (c) 2025 OT Triton Contributors
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Metadata-Version: 2.4
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Name: flash-sinkhorn
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Version: 0.3.2
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Summary: Sinkhorn optimal transport kernels in PyTorch + Triton (squared Euclidean, no cost matrix materialization).
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Author: OT Triton Contributors
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License-Expression: MIT
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Project-URL: Homepage, https://github.com/ot-triton-lab/flash-sinkhorn
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Project-URL: Repository, https://github.com/ot-triton-lab/flash-sinkhorn
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Keywords: optimal-transport,sinkhorn,triton,pytorch,gpu
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Classifier: Development Status :: 3 - Alpha
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Topic :: Scientific/Engineering
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Classifier: Environment :: GPU :: NVIDIA CUDA
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Requires-Python: >=3.9
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy
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Requires-Dist: torch>=2.5
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Requires-Dist: triton>=3.1
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Provides-Extra: dev
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Requires-Dist: pytest; extra == "dev"
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Requires-Dist: geomloss; extra == "dev"
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Requires-Dist: pykeops; extra == "dev"
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Requires-Dist: jax; extra == "dev"
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Requires-Dist: ott-jax; extra == "dev"
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Requires-Dist: matplotlib; extra == "dev"
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Dynamic: license-file
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<p align="center">
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<img src="FlashSinkhorn.png" alt="FlashSinkhorn" width="100%">
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</p>
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# FlashSinkhorn
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**Streaming Entropic Optimal Transport in PyTorch + Triton**
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FlashSinkhorn computes Sinkhorn OT using FlashAttention-style streaming—**never materializing the n×m cost matrix**—enabling **O(nd) memory** instead of O(n²).
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## Features
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- **FlashSinkhorn kernels** — shifted-potential formulation inspired by FlashAttention, 10-40% faster than previous Triton kernels at n >= 10k
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- **Fused Triton kernels** for forward, gradient, and HVP
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- **GeomLoss-compatible API** (`SamplesLoss`)
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- **Analytic gradients** (no backprop through Sinkhorn iterations)
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- **Hessian-vector products** via streaming CG solver
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- **Half-cost support** (`half_cost=True`) for exact GeomLoss parity
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- **Unbalanced/semi-unbalanced OT** via `reach` parameter
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- **Large-D support** (d > 1024) with tiled gradient kernel
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- **Early stopping** with convergence threshold
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## Install
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```bash
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pip install -e .
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pip install -e ".[dev]" # with dev dependencies
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```
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**Requirements:** PyTorch ≥2.5, Triton ≥3.1, CUDA 12.x
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## Quick Start
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### Basic Usage
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```python
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import torch
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from flash_sinkhorn import SamplesLoss
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x = torch.randn(4096, 64, device="cuda")
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y = torch.randn(4096, 64, device="cuda")
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# FlashSinkhorn is the default backend (use_flashstyle=True)
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loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True)
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cost = loss(x, y)
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```
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### Gradient Flow
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```python
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x = torch.randn(4096, 64, device="cuda", requires_grad=True)
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y = torch.randn(4096, 64, device="cuda")
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loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True)
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cost = loss(x, y)
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grad_x = torch.autograd.grad(cost, x)[0] # Analytic gradient
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```
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### GeomLoss Parity
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Use `half_cost=True` to match GeomLoss's cost convention:
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```python
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# FlashSinkhorn with half_cost matches GeomLoss exactly
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flash_loss = SamplesLoss(loss="sinkhorn", blur=0.1, half_cost=True, debias=True)
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# Equivalent GeomLoss call
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# geomloss_loss = geomloss.SamplesLoss(loss="sinkhorn", p=2, blur=0.1, debias="positive")
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```
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### Unbalanced OT
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For distributions with different total mass or outliers:
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```python
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loss = SamplesLoss(
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loss="sinkhorn",
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blur=0.1,
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debias=True,
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reach=1.0, # Unbalanced OT with KL penalty
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)
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```
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### Semi-Unbalanced OT
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Different constraints for source vs target:
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```python
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loss = SamplesLoss(
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loss="sinkhorn",
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blur=0.1,
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reach_x=1.0, # Relax source marginal
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reach_y=None, # Keep target marginal strict (balanced)
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)
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```
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### Early Stopping
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```python
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loss = SamplesLoss(
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loss="sinkhorn",
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blur=0.1,
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n_iters=100,
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threshold=1e-3, # Stop when potential change < threshold
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inner_iterations=10, # Check every N iterations
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)
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```
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### Hessian-Vector Product
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y = torch.randn(4096, 64, device="cuda")
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v = torch.randn_like(x)
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loss = SamplesLoss(loss="sinkhorn", blur=0.1)
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cost = loss(x, y)
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# First-order gradient
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grad_x = torch.autograd.grad(cost, x, create_graph=True)[0]
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# HVP via double backward (uses streaming CG solver)
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hvp = torch.autograd.grad((grad_x * v).sum(), x)[0]
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```
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## FlashSinkhorn (v0.3.0)
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FlashSinkhorn is a reformulated Sinkhorn kernel that uses **shifted potentials** inspired by FlashAttention. It reduces bias vector loads by 67% and elementwise operations by 78% per tile, yielding 10-40% speedups for n >= 10,000.
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### How It Works
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Standard Sinkhorn loads 3 bias vectors per tile (g, log_b, y²). FlashSinkhorn precomputes a single fused bias `u = (g_shifted + eps*log(b)) / eps` and uses raw coordinates with an inline scale factor, matching FlashAttention's score interface exactly.
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### Performance (d=64, A100-80GB, 100 iterations)
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**Symmetric solver (vs v0.2.0 GeomLoss-style kernel):**
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| n | v0.2.0 | v0.3.0 | Speedup |
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|---|--------|--------|---------|
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| 50,000 | 1730 ms | 1450 ms | **1.19x** |
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| 10,000 | 88 ms | 61 ms | **1.43x** |
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| 5,000 | 25 ms | 24 ms | 1.04x |
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**Alternating solver (vs v0.2.0 OTT-style kernel, 10 iterations):**
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| n | v0.2.0 | v0.3.0 | Speedup |
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|---|--------|--------|---------|
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| 50,000 | 137.9 ms | 102.6 ms | **1.34x** |
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| 20,000 | 25.7 ms | 21.7 ms | **1.19x** |
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| 10,000 | 8.9 ms | 8.3 ms | **1.07x** |
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### Usage
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FlashSinkhorn is enabled by default (`use_flashstyle=True`):
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```python
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# Default: uses FlashSinkhorn (fastest for n >= 5000)
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loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True)
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# Explicitly disable to use previous kernels
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loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True, use_flashstyle=False)
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```
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Low-level FlashSinkhorn API:
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```python
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from flash_sinkhorn.kernels import (
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sinkhorn_flashstyle_symmetric, # Full symmetric solver
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sinkhorn_flashstyle_alternating, # Full alternating solver
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flashsinkhorn_symmetric_step, # Single fused iteration
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apply_plan_vec_flashstyle, # Transport plan @ vector (shifted potentials)
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apply_plan_mat_flashstyle, # Transport plan @ matrix (shifted potentials)
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)
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```
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## API Reference
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### SamplesLoss
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```python
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SamplesLoss(
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loss="sinkhorn",
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p=2, # Only p=2 supported (squared Euclidean)
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blur=0.05, # Regularization: eps = blur^2
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debias=True, # Debiased Sinkhorn divergence
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half_cost=False, # Use ||x-y||²/2 to match GeomLoss
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reach=None, # Unbalanced OT (None = balanced)
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reach_x=None, # Semi-unbalanced: source marginal
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reach_y=None, # Semi-unbalanced: target marginal
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scaling=0.5, # Epsilon annealing factor
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n_iters=None, # Max iterations (None = use scaling)
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threshold=None, # Early stopping threshold
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inner_iterations=10, # Check convergence every N iters
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use_flashstyle=True, # Use FlashSinkhorn shifted-potential kernels
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)
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```
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### Low-Level API
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```python
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# FlashSinkhorn (recommended)
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from flash_sinkhorn.kernels import (
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sinkhorn_flashstyle_symmetric,
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sinkhorn_flashstyle_alternating,
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apply_plan_vec_flashstyle,
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apply_plan_mat_flashstyle,
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)
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# Legacy kernels (still available)
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from flash_sinkhorn.kernels.sinkhorn_triton_geomloss_sqeuclid import (
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sinkhorn_geomloss_online_potentials_sqeuclid,
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)
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from flash_sinkhorn.kernels.sinkhorn_triton_grad_sqeuclid import (
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sinkhorn_geomloss_online_grad_sqeuclid,
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)
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from flash_sinkhorn.hvp import hvp_x_sqeuclid_from_potentials
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```
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## Key Concepts
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### Cost Convention
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- **FlashSinkhorn default**: `C(x,y) = ||x-y||²`
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- **GeomLoss p=2 default**: `C(x,y) = ||x-y||²/2`
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- Use `half_cost=True` to match GeomLoss
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### Memory Efficiency
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FlashSinkhorn streams tiles of (x,y) and computes costs on-the-fly:
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- **Forward**: O(nd) memory (no n×m cost matrix)
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- **Gradient**: O(nd) memory (streaming accumulation)
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- **HVP**: O(nd) memory (CG solver with streaming matvec)
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### Numerical Stability
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- Uses `exp2/log2` for stable LSE computation
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- Safe log/division guards against underflow
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- TF32 enabled by default for ~2x speedup on A100/H100 (set `allow_tf32=False` for strict FP32)
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- HVP (double backward) uses strict FP32 internally for numerical stability
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## Benchmarks
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Compare FlashSinkhorn against GeomLoss (KeOps) and OTT-JAX.
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**Install benchmark dependencies:**
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```bash
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pip install geomloss pykeops ott-jax jax[cuda12]
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```
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**Run benchmarks:**
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```bash
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# Forward pass benchmark
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python -m flash_sinkhorn.bench.bench_forward --sizes 5000,10000,20000 --dims 64 --verify
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# Backward pass benchmark
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python -m flash_sinkhorn.bench.bench_backward --sizes 5000,10000,20000 --dims 64 --verify
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# Quick test (small size)
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python -m flash_sinkhorn.bench.bench_forward --sizes 5000 --dims 4 --verify
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# Run only FlashSinkhorn (skip GeomLoss/OTT-JAX)
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python -m flash_sinkhorn.bench.bench_forward --sizes 10000 --dims 64 --no-geomloss --no-ott
|
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+
```
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Results are saved to `output/paper_benchmarks/forward/` and `output/paper_benchmarks/backward/`.
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## Citation
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If you find FlashSinkhorn useful in your research, please cite our paper:
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|
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```bibtex
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+
@article{ye2026flashsinkhorn,
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+
title={FlashSinkhorn: IO-Aware Entropic Optimal Transport},
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author={Ye, Felix X.-F. and Li, Xingjie and Yu, An and Chang, Ming-Ching and Chu, Linsong and Wertheimer, Davis},
|
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journal={arXiv preprint arXiv:2602.03067},
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year={2026},
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url={https://arxiv.org/abs/2602.03067}
|
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}
|
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|
+
```
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## License
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MIT
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|
@@ -0,0 +1,283 @@
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<p align="center">
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<img src="FlashSinkhorn.png" alt="FlashSinkhorn" width="100%">
|
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</p>
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|
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# FlashSinkhorn
|
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7
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**Streaming Entropic Optimal Transport in PyTorch + Triton**
|
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|
+
|
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FlashSinkhorn computes Sinkhorn OT using FlashAttention-style streaming—**never materializing the n×m cost matrix**—enabling **O(nd) memory** instead of O(n²).
|
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+
|
|
11
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## Features
|
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|
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- **FlashSinkhorn kernels** — shifted-potential formulation inspired by FlashAttention, 10-40% faster than previous Triton kernels at n >= 10k
|
|
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|
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- **Fused Triton kernels** for forward, gradient, and HVP
|
|
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|
+
- **GeomLoss-compatible API** (`SamplesLoss`)
|
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+
- **Analytic gradients** (no backprop through Sinkhorn iterations)
|
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- **Hessian-vector products** via streaming CG solver
|
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- **Half-cost support** (`half_cost=True`) for exact GeomLoss parity
|
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|
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- **Unbalanced/semi-unbalanced OT** via `reach` parameter
|
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|
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- **Large-D support** (d > 1024) with tiled gradient kernel
|
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|
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- **Early stopping** with convergence threshold
|
|
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|
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|
+
## Install
|
|
24
|
+
|
|
25
|
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```bash
|
|
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|
+
pip install -e .
|
|
27
|
+
pip install -e ".[dev]" # with dev dependencies
|
|
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|
+
```
|
|
29
|
+
|
|
30
|
+
**Requirements:** PyTorch ≥2.5, Triton ≥3.1, CUDA 12.x
|
|
31
|
+
|
|
32
|
+
## Quick Start
|
|
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|
+
|
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34
|
+
### Basic Usage
|
|
35
|
+
|
|
36
|
+
```python
|
|
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|
+
import torch
|
|
38
|
+
from flash_sinkhorn import SamplesLoss
|
|
39
|
+
|
|
40
|
+
x = torch.randn(4096, 64, device="cuda")
|
|
41
|
+
y = torch.randn(4096, 64, device="cuda")
|
|
42
|
+
|
|
43
|
+
# FlashSinkhorn is the default backend (use_flashstyle=True)
|
|
44
|
+
loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True)
|
|
45
|
+
cost = loss(x, y)
|
|
46
|
+
```
|
|
47
|
+
|
|
48
|
+
### Gradient Flow
|
|
49
|
+
|
|
50
|
+
```python
|
|
51
|
+
x = torch.randn(4096, 64, device="cuda", requires_grad=True)
|
|
52
|
+
y = torch.randn(4096, 64, device="cuda")
|
|
53
|
+
|
|
54
|
+
loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True)
|
|
55
|
+
cost = loss(x, y)
|
|
56
|
+
grad_x = torch.autograd.grad(cost, x)[0] # Analytic gradient
|
|
57
|
+
```
|
|
58
|
+
|
|
59
|
+
### GeomLoss Parity
|
|
60
|
+
|
|
61
|
+
Use `half_cost=True` to match GeomLoss's cost convention:
|
|
62
|
+
|
|
63
|
+
```python
|
|
64
|
+
# FlashSinkhorn with half_cost matches GeomLoss exactly
|
|
65
|
+
flash_loss = SamplesLoss(loss="sinkhorn", blur=0.1, half_cost=True, debias=True)
|
|
66
|
+
|
|
67
|
+
# Equivalent GeomLoss call
|
|
68
|
+
# geomloss_loss = geomloss.SamplesLoss(loss="sinkhorn", p=2, blur=0.1, debias="positive")
|
|
69
|
+
```
|
|
70
|
+
|
|
71
|
+
### Unbalanced OT
|
|
72
|
+
|
|
73
|
+
For distributions with different total mass or outliers:
|
|
74
|
+
|
|
75
|
+
```python
|
|
76
|
+
loss = SamplesLoss(
|
|
77
|
+
loss="sinkhorn",
|
|
78
|
+
blur=0.1,
|
|
79
|
+
debias=True,
|
|
80
|
+
reach=1.0, # Unbalanced OT with KL penalty
|
|
81
|
+
)
|
|
82
|
+
```
|
|
83
|
+
|
|
84
|
+
### Semi-Unbalanced OT
|
|
85
|
+
|
|
86
|
+
Different constraints for source vs target:
|
|
87
|
+
|
|
88
|
+
```python
|
|
89
|
+
loss = SamplesLoss(
|
|
90
|
+
loss="sinkhorn",
|
|
91
|
+
blur=0.1,
|
|
92
|
+
reach_x=1.0, # Relax source marginal
|
|
93
|
+
reach_y=None, # Keep target marginal strict (balanced)
|
|
94
|
+
)
|
|
95
|
+
```
|
|
96
|
+
|
|
97
|
+
### Early Stopping
|
|
98
|
+
|
|
99
|
+
```python
|
|
100
|
+
loss = SamplesLoss(
|
|
101
|
+
loss="sinkhorn",
|
|
102
|
+
blur=0.1,
|
|
103
|
+
n_iters=100,
|
|
104
|
+
threshold=1e-3, # Stop when potential change < threshold
|
|
105
|
+
inner_iterations=10, # Check every N iterations
|
|
106
|
+
)
|
|
107
|
+
```
|
|
108
|
+
|
|
109
|
+
### Hessian-Vector Product
|
|
110
|
+
|
|
111
|
+
```python
|
|
112
|
+
x = torch.randn(4096, 64, device="cuda", requires_grad=True)
|
|
113
|
+
y = torch.randn(4096, 64, device="cuda")
|
|
114
|
+
v = torch.randn_like(x)
|
|
115
|
+
|
|
116
|
+
loss = SamplesLoss(loss="sinkhorn", blur=0.1)
|
|
117
|
+
cost = loss(x, y)
|
|
118
|
+
|
|
119
|
+
# First-order gradient
|
|
120
|
+
grad_x = torch.autograd.grad(cost, x, create_graph=True)[0]
|
|
121
|
+
|
|
122
|
+
# HVP via double backward (uses streaming CG solver)
|
|
123
|
+
hvp = torch.autograd.grad((grad_x * v).sum(), x)[0]
|
|
124
|
+
```
|
|
125
|
+
|
|
126
|
+
## FlashSinkhorn (v0.3.0)
|
|
127
|
+
|
|
128
|
+
FlashSinkhorn is a reformulated Sinkhorn kernel that uses **shifted potentials** inspired by FlashAttention. It reduces bias vector loads by 67% and elementwise operations by 78% per tile, yielding 10-40% speedups for n >= 10,000.
|
|
129
|
+
|
|
130
|
+
### How It Works
|
|
131
|
+
|
|
132
|
+
Standard Sinkhorn loads 3 bias vectors per tile (g, log_b, y²). FlashSinkhorn precomputes a single fused bias `u = (g_shifted + eps*log(b)) / eps` and uses raw coordinates with an inline scale factor, matching FlashAttention's score interface exactly.
|
|
133
|
+
|
|
134
|
+
### Performance (d=64, A100-80GB, 100 iterations)
|
|
135
|
+
|
|
136
|
+
**Symmetric solver (vs v0.2.0 GeomLoss-style kernel):**
|
|
137
|
+
|
|
138
|
+
| n | v0.2.0 | v0.3.0 | Speedup |
|
|
139
|
+
|---|--------|--------|---------|
|
|
140
|
+
| 50,000 | 1730 ms | 1450 ms | **1.19x** |
|
|
141
|
+
| 10,000 | 88 ms | 61 ms | **1.43x** |
|
|
142
|
+
| 5,000 | 25 ms | 24 ms | 1.04x |
|
|
143
|
+
|
|
144
|
+
**Alternating solver (vs v0.2.0 OTT-style kernel, 10 iterations):**
|
|
145
|
+
|
|
146
|
+
| n | v0.2.0 | v0.3.0 | Speedup |
|
|
147
|
+
|---|--------|--------|---------|
|
|
148
|
+
| 50,000 | 137.9 ms | 102.6 ms | **1.34x** |
|
|
149
|
+
| 20,000 | 25.7 ms | 21.7 ms | **1.19x** |
|
|
150
|
+
| 10,000 | 8.9 ms | 8.3 ms | **1.07x** |
|
|
151
|
+
|
|
152
|
+
### Usage
|
|
153
|
+
|
|
154
|
+
FlashSinkhorn is enabled by default (`use_flashstyle=True`):
|
|
155
|
+
|
|
156
|
+
```python
|
|
157
|
+
# Default: uses FlashSinkhorn (fastest for n >= 5000)
|
|
158
|
+
loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True)
|
|
159
|
+
|
|
160
|
+
# Explicitly disable to use previous kernels
|
|
161
|
+
loss = SamplesLoss(loss="sinkhorn", blur=0.1, debias=True, use_flashstyle=False)
|
|
162
|
+
```
|
|
163
|
+
|
|
164
|
+
Low-level FlashSinkhorn API:
|
|
165
|
+
|
|
166
|
+
```python
|
|
167
|
+
from flash_sinkhorn.kernels import (
|
|
168
|
+
sinkhorn_flashstyle_symmetric, # Full symmetric solver
|
|
169
|
+
sinkhorn_flashstyle_alternating, # Full alternating solver
|
|
170
|
+
flashsinkhorn_symmetric_step, # Single fused iteration
|
|
171
|
+
apply_plan_vec_flashstyle, # Transport plan @ vector (shifted potentials)
|
|
172
|
+
apply_plan_mat_flashstyle, # Transport plan @ matrix (shifted potentials)
|
|
173
|
+
)
|
|
174
|
+
```
|
|
175
|
+
|
|
176
|
+
## API Reference
|
|
177
|
+
|
|
178
|
+
### SamplesLoss
|
|
179
|
+
|
|
180
|
+
```python
|
|
181
|
+
SamplesLoss(
|
|
182
|
+
loss="sinkhorn",
|
|
183
|
+
p=2, # Only p=2 supported (squared Euclidean)
|
|
184
|
+
blur=0.05, # Regularization: eps = blur^2
|
|
185
|
+
debias=True, # Debiased Sinkhorn divergence
|
|
186
|
+
half_cost=False, # Use ||x-y||²/2 to match GeomLoss
|
|
187
|
+
reach=None, # Unbalanced OT (None = balanced)
|
|
188
|
+
reach_x=None, # Semi-unbalanced: source marginal
|
|
189
|
+
reach_y=None, # Semi-unbalanced: target marginal
|
|
190
|
+
scaling=0.5, # Epsilon annealing factor
|
|
191
|
+
n_iters=None, # Max iterations (None = use scaling)
|
|
192
|
+
threshold=None, # Early stopping threshold
|
|
193
|
+
inner_iterations=10, # Check convergence every N iters
|
|
194
|
+
use_flashstyle=True, # Use FlashSinkhorn shifted-potential kernels
|
|
195
|
+
)
|
|
196
|
+
```
|
|
197
|
+
|
|
198
|
+
### Low-Level API
|
|
199
|
+
|
|
200
|
+
```python
|
|
201
|
+
# FlashSinkhorn (recommended)
|
|
202
|
+
from flash_sinkhorn.kernels import (
|
|
203
|
+
sinkhorn_flashstyle_symmetric,
|
|
204
|
+
sinkhorn_flashstyle_alternating,
|
|
205
|
+
apply_plan_vec_flashstyle,
|
|
206
|
+
apply_plan_mat_flashstyle,
|
|
207
|
+
)
|
|
208
|
+
|
|
209
|
+
# Legacy kernels (still available)
|
|
210
|
+
from flash_sinkhorn.kernels.sinkhorn_triton_geomloss_sqeuclid import (
|
|
211
|
+
sinkhorn_geomloss_online_potentials_sqeuclid,
|
|
212
|
+
)
|
|
213
|
+
from flash_sinkhorn.kernels.sinkhorn_triton_grad_sqeuclid import (
|
|
214
|
+
sinkhorn_geomloss_online_grad_sqeuclid,
|
|
215
|
+
)
|
|
216
|
+
from flash_sinkhorn.hvp import hvp_x_sqeuclid_from_potentials
|
|
217
|
+
```
|
|
218
|
+
|
|
219
|
+
## Key Concepts
|
|
220
|
+
|
|
221
|
+
### Cost Convention
|
|
222
|
+
|
|
223
|
+
- **FlashSinkhorn default**: `C(x,y) = ||x-y||²`
|
|
224
|
+
- **GeomLoss p=2 default**: `C(x,y) = ||x-y||²/2`
|
|
225
|
+
- Use `half_cost=True` to match GeomLoss
|
|
226
|
+
|
|
227
|
+
### Memory Efficiency
|
|
228
|
+
|
|
229
|
+
FlashSinkhorn streams tiles of (x,y) and computes costs on-the-fly:
|
|
230
|
+
- **Forward**: O(nd) memory (no n×m cost matrix)
|
|
231
|
+
- **Gradient**: O(nd) memory (streaming accumulation)
|
|
232
|
+
- **HVP**: O(nd) memory (CG solver with streaming matvec)
|
|
233
|
+
|
|
234
|
+
### Numerical Stability
|
|
235
|
+
|
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236
|
+
- Uses `exp2/log2` for stable LSE computation
|
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237
|
+
- Safe log/division guards against underflow
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238
|
+
- TF32 enabled by default for ~2x speedup on A100/H100 (set `allow_tf32=False` for strict FP32)
|
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239
|
+
- HVP (double backward) uses strict FP32 internally for numerical stability
|
|
240
|
+
|
|
241
|
+
## Benchmarks
|
|
242
|
+
|
|
243
|
+
Compare FlashSinkhorn against GeomLoss (KeOps) and OTT-JAX.
|
|
244
|
+
|
|
245
|
+
**Install benchmark dependencies:**
|
|
246
|
+
```bash
|
|
247
|
+
pip install geomloss pykeops ott-jax jax[cuda12]
|
|
248
|
+
```
|
|
249
|
+
|
|
250
|
+
**Run benchmarks:**
|
|
251
|
+
```bash
|
|
252
|
+
# Forward pass benchmark
|
|
253
|
+
python -m flash_sinkhorn.bench.bench_forward --sizes 5000,10000,20000 --dims 64 --verify
|
|
254
|
+
|
|
255
|
+
# Backward pass benchmark
|
|
256
|
+
python -m flash_sinkhorn.bench.bench_backward --sizes 5000,10000,20000 --dims 64 --verify
|
|
257
|
+
|
|
258
|
+
# Quick test (small size)
|
|
259
|
+
python -m flash_sinkhorn.bench.bench_forward --sizes 5000 --dims 4 --verify
|
|
260
|
+
|
|
261
|
+
# Run only FlashSinkhorn (skip GeomLoss/OTT-JAX)
|
|
262
|
+
python -m flash_sinkhorn.bench.bench_forward --sizes 10000 --dims 64 --no-geomloss --no-ott
|
|
263
|
+
```
|
|
264
|
+
|
|
265
|
+
Results are saved to `output/paper_benchmarks/forward/` and `output/paper_benchmarks/backward/`.
|
|
266
|
+
|
|
267
|
+
## Citation
|
|
268
|
+
|
|
269
|
+
If you find FlashSinkhorn useful in your research, please cite our paper:
|
|
270
|
+
|
|
271
|
+
```bibtex
|
|
272
|
+
@article{ye2026flashsinkhorn,
|
|
273
|
+
title={FlashSinkhorn: IO-Aware Entropic Optimal Transport},
|
|
274
|
+
author={Ye, Felix X.-F. and Li, Xingjie and Yu, An and Chang, Ming-Ching and Chu, Linsong and Wertheimer, Davis},
|
|
275
|
+
journal={arXiv preprint arXiv:2602.03067},
|
|
276
|
+
year={2026},
|
|
277
|
+
url={https://arxiv.org/abs/2602.03067}
|
|
278
|
+
}
|
|
279
|
+
```
|
|
280
|
+
|
|
281
|
+
## License
|
|
282
|
+
|
|
283
|
+
MIT
|
|
@@ -0,0 +1,57 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["setuptools>=68", "wheel"]
|
|
3
|
+
build-backend = "setuptools.build_meta"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "flash-sinkhorn"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Sinkhorn optimal transport kernels in PyTorch + Triton (squared Euclidean, no cost matrix materialization)."
|
|
9
|
+
readme = "README.md"
|
|
10
|
+
license = "MIT"
|
|
11
|
+
requires-python = ">=3.9"
|
|
12
|
+
keywords = ["optimal-transport", "sinkhorn", "triton", "pytorch", "gpu"]
|
|
13
|
+
authors = [
|
|
14
|
+
{name = "OT Triton Contributors"}
|
|
15
|
+
]
|
|
16
|
+
classifiers = [
|
|
17
|
+
"Development Status :: 3 - Alpha",
|
|
18
|
+
"Programming Language :: Python :: 3",
|
|
19
|
+
"Programming Language :: Python :: 3.9",
|
|
20
|
+
"Programming Language :: Python :: 3.10",
|
|
21
|
+
"Programming Language :: Python :: 3.11",
|
|
22
|
+
"Programming Language :: Python :: 3.12",
|
|
23
|
+
"Topic :: Scientific/Engineering",
|
|
24
|
+
"Environment :: GPU :: NVIDIA CUDA",
|
|
25
|
+
]
|
|
26
|
+
dependencies = [
|
|
27
|
+
"numpy",
|
|
28
|
+
"torch>=2.5",
|
|
29
|
+
"triton>=3.1",
|
|
30
|
+
]
|
|
31
|
+
|
|
32
|
+
[project.urls]
|
|
33
|
+
Homepage = "https://github.com/ot-triton-lab/flash-sinkhorn"
|
|
34
|
+
Repository = "https://github.com/ot-triton-lab/flash-sinkhorn"
|
|
35
|
+
|
|
36
|
+
[project.optional-dependencies]
|
|
37
|
+
dev = [
|
|
38
|
+
"pytest",
|
|
39
|
+
"geomloss",
|
|
40
|
+
"pykeops",
|
|
41
|
+
"jax",
|
|
42
|
+
"ott-jax",
|
|
43
|
+
"matplotlib",
|
|
44
|
+
]
|
|
45
|
+
|
|
46
|
+
[tool.setuptools]
|
|
47
|
+
include-package-data = true
|
|
48
|
+
|
|
49
|
+
[tool.setuptools.packages.find]
|
|
50
|
+
where = ["src"]
|
|
51
|
+
|
|
52
|
+
[tool.setuptools.dynamic]
|
|
53
|
+
version = {attr = "flash_sinkhorn.__version__"}
|
|
54
|
+
|
|
55
|
+
[tool.pytest.ini_options]
|
|
56
|
+
addopts = "-ra"
|
|
57
|
+
testpaths = ["src/flash_sinkhorn/testing"]
|