Note

Click here to download the full example code

# Linking KeOps with scipy.sparse.linalg¶

The scipy library provides a simple abstraction for implicit tensors: the LinearOperator class, which represents generic “Matrix-Vector” products and can be plugged seamlessly in a large collection of linear algebra routines.

Crucially, KeOps `pykeops.torch.LazyTensor`

are now **fully compatible**
with this interface.
As an example, let’s see how to combine KeOps with a
fast eigenproblem solver
to compute **spectral coordinates** on a large 2D or 3D point cloud.

Note

Ideally, we’d like to interface KeOps with some
methods of the scikit-learn library…
But this seems out of reach, as most of the sklearn codebase
relies internally on **explicit numpy arrays**. One day, maybe!

## Setup¶

Standard imports:

```
import matplotlib.pyplot as plt
import numpy as np
# noinspection PyUnresolvedReferences
from mpl_toolkits.mplot3d import Axes3D # noqa: F401 unused import
from pykeops.numpy import LazyTensor
from pykeops.numpy.utils import IsGpuAvailable
use_cuda = IsGpuAvailable()
dtype = "float32" # No need for double precision here!
```

Create a toy dataset, a spiral in 2D sampled with 10,000 points:

```
N = 10000 if use_cuda else 1000
t = np.linspace(0, 2 * np.pi, N + 1)[:-1]
x = np.stack((.4 + .4 * (t / 7) * np.cos(t), .5 + .3 * np.sin(t)), 1)
x = x + .01 * np.random.randn(*x.shape)
x = x.astype(dtype)
```

And display it:

```
plt.figure(figsize=(8, 8))
plt.scatter(x[:, 0], x[:, 1], s=5000 / len(x))
plt.axis("equal");
plt.axis([0, 1, 0, 1])
plt.tight_layout()
plt.show()
```

Out:

```
/home/bcharlier/tmp/libkeops/pykeops/tutorials/backends/plot_scipy.py:62: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
plt.show()
```

## Spectral coordinates¶

To showcase the potential of the KeOps-SciPy interface,
we now perform **spectral analysis** on the point cloud **x**.
As summarized by the Wikipedia page on spectral clustering,
spectral coordinates can be defined as the **eigenvectors** associated
to the smallest eigenvalues of a graph Laplacian.

When no explicit **adjacency matrix** is available,
a simple choice is to use a **soft kernel matrix** such as
the Gaussian RBF matrix:

which puts a smooth link between neighboring points at scale \(\sigma\).

```
sigma = .05
x_ = x / sigma
x_i, x_j = LazyTensor(x_[:, None, :]), LazyTensor(x_[None, :, :])
K_xx = (- ((x_i - x_j) ** 2).sum(2) / 2).exp() # Symbolic (N,N) Gaussian kernel matrix
print(K_xx)
```

Out:

```
KeOps LazyTensor
formula: Exp((Minus(Sum(Square((Var(0,2,0) - Var(1,2,1))))) / IntCst(2)))
shape: (10000, 10000)
```

### Linear operators¶

As far as **scipy** is concerned, a KeOps `pykeops.torch.LazyTensor`

such
as **K_xx** can be directly understood as a
LinearOperator:

```
from scipy.sparse.linalg import aslinearoperator
K = aslinearoperator(K_xx)
```

Just like regular numpy `arrays`

or KeOps `pykeops.torch.LazyTensor`

,
`LinearOperators`

fully support the “matrix” product operator `@`

.
For instance, to compute the mass coefficients

we can simply write:

```
D = K @ np.ones(N, dtype=dtype) # Sum along the lines of the adjacency matrix
```

Out:

```
Compiling libKeOpsnumpy80a3662533 in /home/bcharlier/tmp/libkeops/pykeops/common/../build//build-libKeOpsnumpy80a3662533:
formula: Sum_Reduction((Exp((Minus(Sum(Square((Var(0,2,0) - Var(1,2,1))))) / IntCst(2))) * Var(2,1,1)),0)
aliases: Var(0,2,0); Var(1,2,1); Var(2,1,1);
dtype : float32
... Done.
```

Going further, robust and efficient routines such as
eigsh
can be used to compute the largest (or smallest) eigenvalues of our kernel matrix **K**
at a reasonable computational cost:

```
from scipy.sparse.linalg import eigsh
eigenvalues, eigenvectors = eigsh(K, k=5) # Largest 5 eigenvalues/vectors
print("Largest eigenvalues:", eigenvalues)
print("Eigenvectors of shape:", eigenvectors.shape)
```

Out:

```
Largest eigenvalues: [ 626.59143 639.14667 663.38983 747.5554 1438.2162 ]
Eigenvectors of shape: (10000, 5)
```

### Graph Laplacian¶

Most importantly, `LinearOperators`

can be composed
or added with each other.
To define our implicit **graph Laplacian matrix**:

we can simply type:

```
from scipy.sparse import diags
L = aslinearoperator(diags(D)) - K
L.dtype = np.dtype(dtype) # Scipy Bugfix: by default, "-" removes the dtype information...
```

Alternatively, we can also use a **symmetric, normalized Laplacian matrix** defined through:

```
from scipy.sparse.linalg.interface import IdentityOperator
D_2 = aslinearoperator(diags(1 / np.sqrt(D)))
L_norm = IdentityOperator((N, N)) - D_2 @ K @ D_2
L_norm.dtype = np.dtype(dtype) # Scipy Bugfix: by default, "-" removes the dtype information...
```

Then, computing spectral coordinates on **x** is as simple
as typing:

```
from time import time
start = time()
# Compute the 7 smallest eigenvalues/vectors of our graph Laplacian
eigenvalues, coordinates = eigsh(L, k=7, which="SM")
print("Smallest eigenvalues of the graph Laplacian, computed in {:.3f}s:".format(time() - start))
print(eigenvalues)
```

Out:

```
Smallest eigenvalues of the graph Laplacian, computed in 0.146s:
[-1.7224378e-03 3.4779949e+00 1.4162757e+01 4.1543682e+01
6.6533485e+01 7.7429031e+01 1.1451020e+02]
```

**That’s it!**
As expected, our first eigenvalue is equal to 0,
up to the convergence of the Lanczos-like algorithm
used internally by **eigsh**.
The spectral coordinates, associated to the **smallest positive eigenvalues**
of our graph Laplacian, can then be displayed as signals on
the raw point cloud **x** and be used to perform
spectral clustering, shape matching or whatever’s relevant!

```
_, axarr = plt.subplots(nrows=2, ncols=3, figsize=(12, 8))
for i in range(2):
for j in range(3):
axarr[i][j].scatter(x[:, 0], x[:, 1],
c=coordinates[:, 3 * i + j],
cmap=plt.cm.Spectral,
s=9 * 500 / len(x))
axarr[i][j].set_title("Eigenvalue {} = {:.2f}".format(3 * i + j + 1, eigenvalues[3 * i + j]))
axarr[i][j].set_aspect("equal")
axarr[i][j].set_xlim(0, 1)
axarr[i][j].set_ylim(0, 1)
plt.tight_layout()
plt.show()
```

Out:

```
/home/bcharlier/tmp/libkeops/pykeops/tutorials/backends/plot_scipy.py:200: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
plt.show()
```

## Scaling up to large datasets with block-sparse matrices¶

Going further, `pykeops.torch.LazyTensor`

support
adaptive **block-sparsity patterns** (specified through an optional **.ranges** attribute)
which allow us to perform large matrix-vector products with **sub-quadratic** complexity.
To illustrate this advanced feature of KeOps,
let’s generate a large “noisy Swiss roll” with **1,000,000 points** in the unit cube:

```
N = 1000000 if use_cuda else 1000
t = np.linspace(0, 2 * np.pi, N + 1)[:-1]
x = np.stack((.4 + .4 * (t / 7) * np.cos(1.5 * t),
.1 + .8 * np.random.rand(N),
.5 + .3 * (t / 7) * np.sin(1.5 * t),), 1)
x = x + .01 * np.random.randn(*x.shape)
x = x.astype(dtype)
```

To **display** our toy dataset with the (not-so-efficient) PyPlot library,
we pick **10,000 points** at random:

```
N_display = 10000 if use_cuda else N
indices_display = np.random.randint(0, N, N_display)
_, ax = plt.subplots(nrows=1, ncols=1, figsize=(8, 8), subplot_kw=dict(projection='3d'))
x_ = x[indices_display, :]
ax.scatter3D(x_[:, 0], x_[:, 1], x_[:, 2],
c=t[indices_display],
cmap=plt.cm.Spectral)
ax.set_title("{:,} out of {:,} points in our source point cloud".format(N_display, N))
plt.show()
```

Out:

```
/home/bcharlier/tmp/libkeops/pykeops/tutorials/backends/plot_scipy.py:234: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
plt.show()
```

**Can we scale the spectral analysis presented above to this huge dataset?**

In practice, the radius \(\sigma\) of our
kernel “adjacency” function is often **much smaller than the diameter of the input point cloud**:
spectral methods rely on *small-range* neighborhoods to build
a *global* coordinate system.
Since \(k(x,y) \simeq 0\) above a threshold of, say, \(4\sigma\),
a simple way of accelerating
the kernel-vector product \(v\mapsto K_{xx}v\) in the (soft-)graph Laplacian is thus to
**skip computations** between pairs of points that are far away from each other.

As explained in the documentation,
fast GPU routines rely heavily on **memory contiguity**:
before going any further, we must
**sort our input dataset** to make sure that neighboring points are stored
next to each other on the device memory. As detailed in the
KeOps+NumPy tutorial on block-sparse reductions,
a simple way of doing so is to write:

```
# Import the KeOps helper routines for block-sparse reductions:
from pykeops.numpy.cluster import grid_cluster, cluster_ranges_centroids, sort_clusters, from_matrix
# Put our points in cubic bins of size eps, as we compute a vector of class labels:
eps = .05
x_labels = grid_cluster(x, eps)
# Compute the memory footprint and centroid of each of those non-empty "cubic" clusters:
x_ranges, x_centroids, _ = cluster_ranges_centroids(x, x_labels)
# Sort our dataset according to the vector of labels:
x, x_labels = sort_clusters(x, x_labels)
```

Note

In higher-dimensional settings, the simplistic
`grid_cluster`

scheme could be replaced by a more versatile routine such as
our KeOps+NumPy K-means implementation.

Points are now roughly sorted
according to their locations, with each cluster corresponding to
a contiguous slice of the (sorted) **x** array:

```
_, ax = plt.subplots(nrows=1, ncols=1, figsize=(8, 8), subplot_kw=dict(projection='3d'))
x_ = x[indices_display, :]
ax.scatter3D(x_[:, 0], x_[:, 1], x_[:, 2],
c=x_labels[indices_display],
cmap="prism")
ax.set_title("Cluster labels")
plt.show()
```

Out:

```
/home/bcharlier/tmp/libkeops/pykeops/tutorials/backends/plot_scipy.py:285: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
plt.show()
```

We can prune computations out of the \(v\mapsto K_{xx} v\)
matrix-vector product in a GPU-friendly way by **skipping whole blocks**
of cluster-cluster interactions.
A good rule of thumb is to **only consider pairs of points** belonging
to clusters \(X\) and \(Y\) whose centroids \(x_c\) and
\(y_c\) are such that:

Considering that our cubic bins of size \(\varepsilon\) all have a
diameter that is equal to \(\sqrt{3}\,\varepsilon\), this “block-sparsity”
pattern can be encoded in a small boolean matrix **keep** computed through:

```
sigma = .01 if use_cuda else .1 # Standard deviation of our Gaussian kernel
# Compute a coarse Boolean mask:
D = np.sum((x_centroids[:, None, :] - x_centroids[None, :, :]) ** 2, 2)
keep = D < (4 * sigma + np.sqrt(3) * eps) ** 2
```

which can then be converted to a GPU-friendly,
LIL-like sparsity pattern
with the `from_matrix`

helper:

```
ranges_ij = from_matrix(x_ranges, x_ranges, keep)
```

Now, leveraging this information with KeOps is as simple as typing:

```
x_ = x / sigma # N.B.: x is a **sorted** list of points
x_i, x_j = LazyTensor(x_[:, None, :]), LazyTensor(x_[None, :, :])
K_xx = (- ((x_i - x_j) ** 2).sum(2) / 2).exp() # Symbolic (N,N) Gaussian kernel matrix
K_xx.ranges = ranges_ij # block-sparsity pattern
print(K_xx)
```

Out:

```
KeOps LazyTensor
formula: Exp((Minus(Sum(Square((Var(0,3,0) - Var(1,3,1))))) / IntCst(2)))
shape: (1000000, 1000000)
```

A straightforward computation shows that our new
**block-sparse** operator may be **up to 20 times more efficient** than a
full KeOps `pykeops.torch.LazyTensor`

:

```
# Compute the area of each rectangle "cluster-cluster" tile in the full kernel matrix:
areas = (x_ranges[:, 1] - x_ranges[:, 0])[:, None] \
* (x_ranges[:, 1] - x_ranges[:, 0])[None, :]
total_area = np.sum(areas) # should be equal to N**2 = 1e12
sparse_area = np.sum(areas[keep])
print("We keep {:.2e}/{:.2e} = {:2d}% of the original kernel matrix.".format(
sparse_area, total_area, int(100 * sparse_area / total_area)))
```

Out:

```
We keep 5.19e+10/1.00e+12 = 5% of the original kernel matrix.
```

Good. Once we’re done with these pre-processing steps,
block-sparse `pykeops.torch.LazyTensor`

are just as easy to interface with **scipy** as
regular NumPy arrays:

```
K = aslinearoperator(K_xx)
```

The normalized graph Laplacian can be defined as usual:

```
D = K @ np.ones(N, dtype=dtype) # Sum along the lines of the adjacency matrix
D_2 = aslinearoperator(diags(1 / np.sqrt(D)))
L_norm = IdentityOperator((N, N)) - D_2 @ K @ D_2
L_norm.dtype = np.dtype(dtype) # Scipy Bugfix: by default, "-" removes the dtype information...
```

Out:

```
Compiling libKeOpsnumpy8dcd847cfd in /home/bcharlier/tmp/libkeops/pykeops/common/../build//build-libKeOpsnumpy8dcd847cfd:
formula: Sum_Reduction((Exp((Minus(Sum(Square((Var(0,3,0) - Var(1,3,1))))) / IntCst(2))) * Var(2,1,1)),0)
aliases: Var(0,3,0); Var(1,3,1); Var(2,1,1);
dtype : float32
... Done.
```

And our favourite solver will compute, as expected, the smallest eigenvalues of this custom operator:

```
from time import time
start = time()
# Compute the 7 smallest eigenvalues/vectors of our normalized graph Laplacian
eigenvalues, coordinates = eigsh(L_norm, k=7, which="SM")
print("Smallest eigenvalues of the normalized graph Laplacian, computed in {:.3f}s ".format(time() - start) \
+ "on a cloud of {:,} points in dimension {}:".format(x.shape[0], x.shape[1]))
print(eigenvalues)
```

Out:

```
Smallest eigenvalues of the normalized graph Laplacian, computed in 72.470s on a cloud of 1,000,000 points in dimension 3:
[-6.8904824e-06 1.5222424e-04 6.0631626e-04 7.8718102e-04
9.4820134e-04 1.4032408e-03 1.9742548e-03]
```

Note

On very large problems, a custom eigenproblem solver
implemented with the **PyTorch+KeOps** interface should be sensibly **faster**
than this SciPy wrapper: performing all computations on the GPU
would allow us to perform linear operations in parallel
and to **skip hundreds of unnecessary Host-Device memory transfers**.

Anyway. Displayed on a subsampled point cloud (for the sake of efficiency), our spectral coordinates look good!

```
x_ = x[indices_display, :]
# sphinx_gallery_thumbnail_number = 5
_, axarr = plt.subplots(nrows=2, ncols=3, figsize=(12, 8), subplot_kw=dict(projection='3d'))
for i in range(2):
for j in range(3):
axarr[i][j].scatter3D(x_[:, 0], x_[:, 1], x_[:, 2],
c=coordinates[indices_display, 3 * i + j],
cmap=plt.cm.Spectral)
axarr[i][j].set_title("Eigenvalue {} = {:.1e}".format(3 * i + j + 1, eigenvalues[3 * i + j]))
plt.tight_layout()
plt.show()
```

Out:

```
/home/bcharlier/tmp/libkeops/pykeops/tutorials/backends/plot_scipy.py:395: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
plt.show()
```

**Total running time of the script:** ( 1 minutes 45.696 seconds)