The aim of PyData/Sparse is to create sparse containers that implement the ndarray interface. Traditionally in the PyData ecosystem, sparse arrays have been provided by the scipy.sparse submodule. All containers there depend on and emulate the numpy.matrix interface. This means that they are limited to two dimensions and also don’t work well in places where numpy.ndarray would work.
PyData/Sparse is well on its way to replacing
scipy.sparse as the de-facto sparse array
implementation in the PyData ecosystem.
- More storage formats (the most important being CSF, a generalisation of CSR/CSC).
- Better performance/algorithms
- Covering more of the NumPy API
- SciPy Integration
- Dask integration for high scalability
- CuPy integration for GPU-acceleration
- Maintenance and General Improvements
More Storage Formats¶
In the sparse domain, you have to make a choice of format when representing your array in memory, and different formats have different trade-offs. For example:
- CSR/CSC are usually expected by external libraries, and have good space characteristics for most arrays
- DOK allows in-place modification and writes
- LIL has faster writes if written to in-order.
- BSR allows block-writes and reads
The most important formats are, of course, CSR and CSC, because they allow zero-copy interaction
with a number of libraries including MKL, LAPACK and others. This will allow PyData/Sparse to
quickly reach the functionality of
scipy.sparse, accelerating the path to its replacement.
There are a few places in scipy.sparse where algorithms are sub-optimal, sometimes due to reliance on NumPy which doesn’t have these algorithms. We intend to both improve the algorithms in NumPy, giving the broader community a chance to use them; as well as in PyData/Sparse, to reach optimal efficiency in the broadest use-cases.
Covering More of the NumPy API¶
Our eventual aim is to cover all areas of NumPy where algorithms exist that give sparse arrays an edge over dense arrays. Currently, PyData/Sparse supports reductions, element-wise functions and other common functions such as stacking, concatenating and tensor products. Common uses of sparse arrays include linear algebra and graph theoretic subroutines, so we plan on covering those first.
PyData/Sparse aims to build containers and elementary operations on them, such as element-wise operations,
reductions and so on. We plan on modifying the current graph theoretic subroutines in
to support PyData/Sparse arrays. The same applies for linear algebra and
Dask Integration for High Scalability¶
Dask is a project that takes ndarray style containers and then allows them to scale across multiple cores or clusters. We plan on tighter integration and cooperation with the Dask team to ensure the highest amount of Dask functionality works with sparse arrays.
CuPy integration for GPU-acceleration¶
CuPy is a project that implements a large portion of NumPy’s ndarray interface on GPUs. We plan to integrate with CuPy so that it’s possible to accelerate sparse arrays on GPUs.