Sparse Storage

Sparse storage support is an important element to numeric computing systems as it allows desktop machines to processing and work with data of very high element counts. This data comes in problems of loosely coupled systems and is common in NLP algorithms. We present a simplified but but fully functional sparse storage system built upon the concepts of the previous documents. For a sparse item, we assume on of the values is far, far more prevalent than other values. The number of non-sparse elements we will call NS.

Objectives

Key objects of sparse storage are as follows:

1. Unary operations are constant time.
2. Binary operations are linear with respect to the union of non-sparse-indexes.
3. Storage is space is linear with respect to the non-sparse-indexes.
4. Assignment is linear with respect to the union of non-sparse-indexes.
5. Conversion to CSR and CSC formats is efficient, 0(NS) in the worst case.

For more background on CSR and CSC formats, see wikipedia.

One way the sparse storage in tech.datatype differs from the wikipedia article is that we allow any value to be considered the sparse value. This allows unary operations to be constant time and ensures the result of a binary operation will have the same sparse properties as the initial 2 buffers assuming both inputs are themselves sparse buffers. It also allows the concept of sparse to extend into arbitrary spaces where the sparse value can be an arbitrary object.

Sparse Readers And Buffers

A sparse reader is a reader but it implements a new protocol, tech.datatype.sparse.PSparse:

(defprotocol PSparse
  (index-seq [item]
    "Return a sequence of records of
:global-index
:data-index")
  (sparse-value [item])
  (sparse-ecount [item]
    "Number of sparse elements in this datastructure.  Constant time query.")

  (readers [item]
    "Return a map containing
{
 :indexes - int32 reader of indexes in global space.
 :data - (optional) reader of data values.
}")
  (iterables [item]
    "Return a map containing:
{
 :indexes int32 iterable of indexes in global space.
 :data iterable of values in global space.
}"))

It has optimized methods for read-indexes and unary, binary operations are implemented in terms of sparse readers when the underlying buffer type is advertised as sparse. Copying a sparse buffer to either a dense or sparse buffer is an optimized operation. The system has multimethods defined for the operations so it will automatically detect the buffer type and switch to the appropriate optimized implemention so aside from allocating the sparse buffer you may not need to know at any point that it is sparse.

The sparse reader namespace has a function for definition of a const sparse reader which is an important optimization as, for instance, multiplying sparse constant by another sparse bufffer results in something that is O(NS) of the first buffer.

Sparse Buffers

Allocating a sparse buffer via (make-container :sparse & rest) allocates a sparse buffer that will set the sparse value to a datatype-dependent sparse value:

• 0 for numbers
• false for booleans
• nil for objects

To set a specific sparse value, use the full version of the make container protocol:

user> (require '[tech.datatype :as dtype])
:tech.resource.gc Reference thread starting
nil
user> (dtype/make-container :sparse :int32 [1 0 1 0 1 0 1])
{:b-offset 0,
 :b-elem-count 7,
 :sparse-value 0,
 :indexes [0 2 4 6],
 :data [1 1 1 1],
 :buffer-datatype :int32}
user> (dtype/make-container :sparse :int32 [1 0 1 0 1 0 1] {:sparse-value 1})
{:b-offset 0,
 :b-elem-count 7,
 :sparse-value 1,
 :indexes [1 3 5],
 :data [0 0 0],
 :buffer-datatype :int32}

Outside of very special cases we don't recommend setting the sparse value. It will most likely achieve only confusion.

The sparse buffer implements an optimized version of write-indexes! that will sort the incoming indexes unless :indexes-in-order? is specified. This forms the core implementation of an optimized copy operation. In addition, set-constant! to the sparse value is a fairly simple operation of removing that range from the index mutable and data mutable.

All datatypes are supported for sparse readers and sparse buffers.

Notes

Union

There are, unfortunately, 2 union operations. One for assignment and one for binary operations:

1. For assignment, if we find matching indexes we want to take the right data value. Else, we want to take the data value from the lower of the two indexes.
2. For binary operations, if the indexes match the result is a binary operation of both of the values. Else the result is a binary operation of the lower value and the other reader's sparse value.

Alternative Implementations

We have reason to believe there is an alternative implementation that would offer superior performance for some subset of operations using the bifurcan library. The argument against this is the 2 union operations above and the ability to share data as a sparse vector with java matrix libraries such as ejml.