https://github.com/jpata/sparsedistance
Generate sparse distance matrices with gradients in tensorflow efficiently
https://github.com/jpata/sparsedistance
graph knn-graph-construction lsh machinelearning tensorflow
Last synced: about 1 month ago
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Generate sparse distance matrices with gradients in tensorflow efficiently
- Host: GitHub
- URL: https://github.com/jpata/sparsedistance
- Owner: jpata
- License: bsd-3-clause
- Created: 2020-10-21T11:59:14.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2020-10-22T17:28:48.000Z (almost 5 years ago)
- Last Synced: 2025-08-21T13:45:22.924Z (about 2 months ago)
- Topics: graph, knn-graph-construction, lsh, machinelearning, tensorflow
- Language: Python
- Homepage:
- Size: 8.92 MB
- Stars: 3
- Watchers: 3
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
SparseDistance
==============
[](https://zenodo.org/badge/latestdoi/306009785)
```bash
python3 -m pip install git+https://github.com/jpata/SparseDistance.git@v0.1
(or just copy the files from the repo to your project)
```
Efficiently generate sparse graph adjacency matrices using tensorflow, including gradient propagation and minibatches, for graph sizes up to 100k+ in subquadratic time.
On the following images, you see the input set on the left and the learned graph structure (edges) on the right for a toy clustering problem with approx. 5000 input elements per graph.
Here, we show the learned distance matrix on the left and the scaling of the training time on the right.
Here's how it works:
- *Input*: a set of elements with features, `shape=(N_batch, N_elem, N_feat)`, possibly in minibatches for efficient training (e.g. a minibatch may consist of several sets/graphs padded to the same size)
- *Output*: a sparse adjacency matrix for each input set `shape=(N_batch, N_elem, N_elem)`, the elements of which can be differentiated with respect to the input
- *Hyperparameters*: bin size M, number of neighbors K, LSH codebook size (maximum number of bins) L
The input data is divided into equal-sized bins with a locality sensitive hashing (LSH) which is based on random rotations. In each bin, we run a dense k-nearest-neighbors algo and update the final sparse adjacency matrix. The generated graph consists of `N_elem/bin_size` disjoint graphs.
The maximum input size is determined by the pre-generated LSH codebook size. Since the bin size is much smaller than the input size, the k-nearest-neighbors evaluation is efficient.
The input features to the hashing and knn can be learnable, so that the binning & knn graph construction can adapt to the problem based on gradient descent.
```python
import tensorflow as tf
import numpy as np
from sparsedistance.models import SparseHashedNNDistance
from sparsedistance.utils import sparse_dense_matmult_batch
num_batches = 10
num_points_per_batch = 1000
num_features = 32
X = np.array(np.random.randn(num_batches, num_points_per_batch, num_features), dtype=np.float32)
y = np.array(np.random.randn(num_batches, num_points_per_batch, ), dtype=np.float32)
#show that we can take a gradient of stuff with respect to the distance matrix values (but not indices!)
dense_transform = tf.keras.layers.Dense(128)
dm_layer = SparseHashedNNDistance(max_num_bins=200, bin_size=500, num_neighbors=5)
with tf.GradientTape(persistent=True) as g:
X_transformed = dense_transform(X)
dm = dm_layer(X_transformed)
ret = sparse_dense_matmult_batch(dm, X)
#reduce the output to a single scalar, just for demonstration purposes
ret = tf.reduce_sum(ret)
grad = g.gradient(ret, dense_transform.weights)
```
Features:
- [x] Works on a modest GPU (e.g. 2060S) or a CPU
- [x] Uses only native TF 2.x operations, no compilation needed
- [x] Fast evaluation and efficient memory use
- [x] TF graph mode for easy deployment
- [x] TF eager mode for debugging
Based on the Reformer [1] (LSH approach and description) and GravNet [2] (knn graph construction) papers.
- [1] https://arxiv.org/abs/2001.04451
- [2] https://arxiv.org/abs/1902.07987
If you use this code academically, please cite this repository as follows:
- Joosep Pata. (2020, October 22). jpata/SparseDistance v0.1 (Version v0.1). Zenodo. http://doi.org/10.5281/zenodo.4117570