Distance Matrices
Fast Numba-enabled CPU and GPU computations of 1D Earth Mover's (scipy.stats.wasserstein_distance) and Euclidean distances. 10000 x 10000 weighted Wasserstein distance matrix in ~15 s on an NVIDIA GeForce RTX 2060 GPU. GPU tends to be ~2x faster than parallelized CPU on Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz (6 physical cores).
Installation
| conda | pip |
|---|---|
conda install -c sgbaird dist_matrix |
pip install dist_matrix |
To best reflect the development workflow, you can clone the repository and install via flit:
git clone https://github.com/sparks-baird/dist-matrix.git
cd dist-matrix
conda install flit # alternatively, `pip install -e .`
flit install --pth-file # --pth-file flag is a Windows-compatible local installation; you can edit the source without reinstallingUsage
You can compute distance matrices (more efficient per distance calculation) or access the lower-level single distance calculation.
Distance Matrices
There is a GPU version (dist_matrix.cuda_dist_matrix_full) as well as a CPU version (dist_matrix.njit_dist_matrix_full).
import numpy as np
from dist_matrix.cuda_dist_matrix_full import dist_matrix as gpu_dist_matrix
# from dist_matrix.njit_dist_matrix_full import dist_matrix as cpu_dist_matrix
n_features = 10
n_rows = 100
U, V, U_weights, V_weights = np.random.rand(4, n_rows, n_features)
distances = gpu_dist_matrix(
U,
V=V,
U_weights=U_weights, # optional
V_weights=V_weights, # optional
metric="wasserstein", # "euclidean"
)Single Distance Calculations
See metrics.py. Note that these lower-level functions are not GPU-accelerated.
import numpy as np
from dist_matrix.utils.metrics import wasserstein_distance, euclidean_distance
n_features = 10
u, v, u_weights, v_weights = np.random.rand(4, n_features)
presorted, cumweighted, prepended = [False, False, False]
em_dist = wasserstein_distance(u, v, u_weights, v_weights, presorted, cumweighted, prepended)
eucl_dist = euclidean_distance(u, v)See Also
Element Mover's Distances via chem_wasserstein (based on ElM2D)
