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mrpt

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Fast and lightweight header-only C++ library (with Python bindings) for approximate nearest neighbor search

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# MRPT - fast nearest neighbor search with random projection

![Fifty shades of green](https://raw.githubusercontent.com/vioshyvo/mrpt/master/docs/img/voting-candidates2.png)

[![Documentation](https://img.shields.io/badge/api-reference-green.svg)](http://vioshyvo.github.io/mrpt/html/index.html)
[![Paper](https://img.shields.io/badge/Paper-Big_Data%3A_MRPT-blue)](https://eliasjaasaari.com/pdf/bigdata2016.pdf)
[![PyPI](https://img.shields.io/pypi/v/mrpt?color=salmon)](https://pypi.org/project/mrpt)
[![GitHub stars](https://img.shields.io/github/stars/vioshyvo/mrpt)](https://github.com/vioshyvo/mrpt/stargazers)

MRPT is a lightweight and easy-to-use library for approximate nearest neighbor search. It is written in C++14 and has Python bindings. The index building has an integrated hyperparameter tuning algorithm, so the only hyperparameter required to construct the index is the target recall level!

According to [our experiments](https://github.com/ejaasaari/mrpt-comparison/) MRPT is one of the fastest libraries for approximate nearest neighbor search.

In the offline phase of the algorithm, MRPT indexes the data with a collection of *random projection trees*. In the online phase, the index structure allows us to answer queries rapidly. A detailed description of the algorithm with the time and space complexities, and the aforementioned comparisons can be found in [our article](https://www.cs.helsinki.fi/u/ttonteri/pub/bigdata2016.pdf) published at the IEEE International Conference on Big Data 2016.

The algorithm for automatic hyperparameter tuning is described in detail in our [article](https://arxiv.org/abs/1812.07484) presented at PAKDD 2019.

Currently the Euclidean distance is supported as a distance metric.

## Python installation

Install the module with `pip install mrpt`

On macOS, it is recommended to use the Homebrew version of Clang as the compiler:
```
brew install llvm libomp
CC=/opt/homebrew/opt/llvm/bin/clang CXX=/opt/homebrew/opt/llvm/bin/clang++ pip install mrpt
```

## Minimal examples

### Python

This example first generates a 200-dimensional data set of 10000 points, and 100 test query points. The `exact_search` function can be used to find the indices of the true 10 nearest neighbors of the first test query.

The `build_autotune_sample` function then builds an index for approximate k-nn search; it uses automatic parameter tuning, so only the target recall level (90% in this example) and the number of neighbors searched for have to be specified.

```python
import mrpt
import numpy as np

n, d, k = 10000, 200, 10
target_recall = 0.9

data = np.random.rand(n, d).astype(np.float32)
q = np.random.rand(d).astype(np.float32)

index = mrpt.MRPTIndex(data)
print(index.exact_search(q, k, return_distances=False))

index.build_autotune_sample(target_recall, k)
print(index.ann(q, return_distances=False))
```

The approximate nearest neighbors are then searched by the function `ann`; because the index was autotuned, no other arguments than the query point are required.

Here is a sample output:
```
[9738 5033 6520 2108 9216 9164  112 1442 1871 8020]
[9738 5033 6520 2108 9216 9164  112 1442 1871 6789]
```

### C++

MRPT is a header-only library, so no compilation is required: just include the header `cpp/Mrpt.h`. The only dependency is the Eigen linear algebra library (Eigen 3.3.5 is bundled in `cpp/lib`), so when using g++, the following minimal example can be compiled for example as:
```
g++ -std=c++14 -Ofast -march=native -Icpp -Icpp/lib ex1.cpp -o ex1 -fopenmp -lgomp
```

Let's first generate a 200-dimensional data set of 10000 points, and a query point (row = dimension, column = data point). Then `Mrpt::exact_knn` can be used to find the indices of the true 10 nearest neighbors of the test query.

The `grow_autotune` function builds an index for approximate k-nn search; it uses automatic parameter tuning, so only the target recall level (90% in this example), and the number of neighbors searched for have to be specified. This version automatically samples a test set of 100 query points from the data set to tune the parameters, so no separate test set is required.

```c++
#include <iostream>
#include "Eigen/Dense"
#include "Mrpt.h"

int main() {
  int n = 10000, d = 200, k = 10;
  double target_recall = 0.9;
  Eigen::MatrixXf X = Eigen::MatrixXf::Random(d, n);
  Eigen::MatrixXf q = Eigen::VectorXf::Random(d);

Eigen::VectorXi indices(k), indices_exact(k);

Mrpt::exact_knn(q, X, k, indices_exact.data());
  std::cout << indices_exact.transpose() << std::endl;

Mrpt mrpt(X);
  mrpt.grow_autotune(target_recall, k);

mrpt.query(q, indices.data());
  std::cout << indices.transpose() << std::endl;
}
```

The approximate nearest neighbors are then searched by the function `query`; because the index was autotuned, no other arguments than a query point and an output buffer for indices are required.

Here is a sample output:
```
8108 1465 6963 2165   83 5900  662 8112 3592 5505
8108 1465 6963 2165   83 5900 8112 3592 5505 7992
```
The approximate nearest neighbor search found 9 of 10 true nearest neighbors; so this time the observed recall happened to match the expected recall exactly (results vary between the runs because the algorithm is randomized).

## Citation
Automatic hyperparameter tuning:
~~~~
@inproceedings{Jaasaari2019,
  title={Efficient Autotuning of Hyperparameters in Approximate Nearest Neighbor Search},
  author={J{\"a}{\"a}saari, Elias and Hyv{\"o}nen, Ville and Roos, Teemu},
  booktitle={Pacific-Asia Conference on Knowledge Discovery and Data Mining},
  pages={In press},
  year={2019},
  organization={Springer}
}
~~~~

MRPT algorithm:
~~~~
@inproceedings{Hyvonen2016,
  title={Fast nearest neighbor search through sparse random projections and voting},
  author={Hyv{\"o}nen, Ville and Pitk{\"a}nen, Teemu and Tasoulis, Sotiris and J{\"a}{\"a}saari, Elias and Tuomainen, Risto and Wang, Liang and Corander, Jukka and Roos, Teemu},
  booktitle={Big Data (Big Data), 2016 IEEE International Conference on},
  pages={881--888},
  year={2016},
  organization={IEEE}
}
~~~~

## License

MRPT is available under the MIT License (see [LICENSE.txt](LICENSE.txt)). Note that third-party libraries in the cpp/lib folder may be distributed under other open source licenses. The Eigen library is licensed under the MPL2.