See full documentation for detailed info.
OTT is a JAX toolbox that bundles a few utilities to solve optimal transport problems. These tools can help you compare and match two weighted point clouds (or histograms, measures, etc.), given a cost (e.g. a distance) between single points.
Most of OTT is, for now, supported by a sturdy, versatile and efficient implementation of the Sinkhorn algorithm that takes advantage of JAX features, such as JIT, auto-vectorization and implicit differentiation.
A typical OT problem has two ingredients: a pair of weight vectors
b (one for each measure), with a ground cost matrix that is either directly given, or derived as the pairwise evaluation of a cost function on pairs of points taken from two measures. The main design choice in OTT comes from encapsulating the cost in a
Geometry object, and bundle it with a few useful operations (notably kernel applications). The most common geometry is that of two clouds of vectors compared with the squared Euclidean distance, as illustrated in the example below:
import jax import jax.numpy as jnp from ott.tools import transport # Samples two point clouds and their weights. rngs = jax.random.split(jax.random.PRNGKey(0),4) n, m, d = 12, 14, 2 x = jax.random.normal(rngs, (n,d)) + 1 y = jax.random.uniform(rngs, (m,d)) a = jax.random.uniform(rngs, (n,)) b = jax.random.uniform(rngs, (m,)) a, b = a / jnp.sum(a), b / jnp.sum(b) # Computes the couplings via Sinkhorn algorithm. ot = transport.Transport(x, y, a=a, b=b) P = ot.matrix
The call to
sinkhorn above works out the optimal transport solution by storing its output. The transport matrix can be instantiated using those optimal solutions and the
Geometry again. That transoprt matrix links each point from the first point cloud to one or more points from the second, as illustrated below.
To be more precise, the
sinkhorn algorithm operates on the
taking into account weights
b, to solve the OT problem, produce a named tuple that contains two optimal dual potentials
g (vectors of the same size as
b), the objective
reg_ot_cost and a log of the
errors of the algorithm as it converges, and a
Currently implements the following classes and functions:
In the geometry folder,
CostFn class in costs.py and its descendants define cost functions between points. Two simple costs are currently provided,
Euclidean between vectors, and
Bures, between a pair of mean vector and covariance (p.d.) matrix.
Geometry class in geometry.py and its descendants describe a cost structure between two measures. That cost structure is accessed through various member functions, either used when running the Sinkhorn algorithm (typically kernel multiplications, or log-sum-exp row/column-wise application) or after (to apply the OT matrix to a vector).
In its generic
Geometry implementation, as in geometry.py, an object can be initialized with either a
cost_matrix along with an
epsilon regularization parameter (or scheduler), or with a
If one wishes to compute OT between two weighted point clouds
and endowed with a
given cost function (e.g. Euclidean) , the
class in pointcloud.py can be used to define the corresponding kernel
. When the number of these points grows very large, this geometry can be instantiated with an
online=True parameter, to avoid storing the kernel matrix and choose instead to recompute the matrix on the fly at each application.
Simlarly, if all measures to be considered are supported on a
separable grid (e.g. ), and the cost is separable
along all axis, i.e. the cost between two points on that
grid is equal to the sum of (possibly different) cost
functions evaluated on each of the pairs of coordinates, then
the application of the kernel is much simplified, both in log space
or on the histograms themselves. This particular case is exploited in the
Grid geometry in grid.py which can be instantiated as a hypercube using a
grid_size parameter, or directly through grid locations in
In the core folder,
sinkhorn function in sinkhorn.py runs the Sinkhorn algorithm, with the aim of solving approximately one or various optimal transport problems in parallel. An OT problem is defined by a
Geometry object, and a pair (or batch thereof) of histograms. The function's outputs are stored in a
SinkhornOutput named t-uple, containing potentials, regularized OT cost, sequence of errors and a convergence flag. Such outputs (with the exception of errors and convergence flag) can be differentiated w.r.t. any of the three inputs
(Geometry, a, b) either through backprop or implicit differentiation of the optimality conditions of the optimal potentials
In discrete_barycenter.py: implementation of discrete Wasserstein barycenters : given histograms all supported on the same
Geometry, compute a barycenter of theses measures, using an algorithm by Janati et al. (2020)
In gromov_wasserstein.py: implementation of the Gromov-Wasserstein metric between measured-metric spaces, here encoded as a pair of
Geometry objects along with weights
In the tools folder,
sinkhorn_divergence function in sinkhorn_divergence.py, implements the unbalanced formulation of the Sinkhorn divergence, a variant of the Wasserstein distance that uses regularization and is computed by centering the output of
sinkhorn when comparing two measures.
Transport class in sinkhorn_divergence.py, provides a simple wrapper to the
sinkhorn function defined above when the user is primarily interested in computing and storing an OT matrix.
Disclaimer: this is not an official Google product.