t-viSNE/README.md

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This software package contains a Barnes-Hut implementation of the t-SNE algorithm. The implementation is described in [this paper](http://lvdmaaten.github.io/publications/papers/JMLR_2014.pdf).

**Note:** This repository is a version of t-SNE modified to support ongoing research. It may be slightly slower than the original. If you're just trying to run t-SNE, check the original repository that we forked from.

# Installation #

On Linux or OS X, compile the source using the following command:

```
g++ sptree.cpp tsne.cpp tsne_main.cpp -o bh_tsne -O2
```

The executable will be called `bh_tsne`.

On Windows using Visual C++, do the following in your command line:

- Find the `vcvars64.bat` file in your Visual C++ installation directory. This file may be named `vcvars64.bat` or something similar. For example:

```
  // Visual Studio 12
  "C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\amd64\vcvars64.bat"

  // Visual Studio 2013 Express:
  C:\VisualStudioExp2013\VC\bin\x86_amd64\vcvarsx86_amd64.bat
```

- From `cmd.exe`, go to the directory containing that .bat file and run it.

- Go to `bhtsne` directory and run:

```
  nmake -f Makefile.win all
```

The executable will be called `windows\bh_tsne.exe`.

# Usage #

The code comes with wrappers for Matlab and Python. These wrappers write your data to a file called `data.dat`, run the `bh_tsne` binary, and read the result file `result.dat` that the binary produces. There are also external wrappers available for [Torch](https://github.com/clementfarabet/manifold), [R](https://github.com/jkrijthe/Rtsne), and [Julia](https://github.com/zhmz90/BHTsne.jl). Writing your own wrapper should be straightforward; please refer to one of the existing wrappers for the format of the data and result files.

Demonstration of usage in Matlab:

```matlab
filename = websave('mnist_train.mat', 'https://github.com/awni/cs224n-pa4/blob/master/Simple_tSNE/mnist_train.mat?raw=true');
load(filename);
numDims = 2; pcaDims = 50; perplexity = 50; theta = .5; alg = 'svd';
map = fast_tsne(digits', numDims, pcaDims, perplexity, theta, alg);
gscatter(map(:,1), map(:,2), labels');
```

Demonstration of usage in Python:

```python
import numpy as np
import bhtsne

data = np.loadtxt("mnist2500_X.txt", skiprows=1)

embedding_array = bhtsne.run_bh_tsne(data, initial_dims=data.shape[1])
```

### Python Wrapper

Usage:

```bash
python bhtsne.py [-h] [-d NO_DIMS] [-p PERPLEXITY] [-t THETA]
                  [-r RANDSEED] [-n INITIAL_DIMS] [-v] [-i INPUT]
                  [-o OUTPUT] [--use_pca] [--no_pca] [-m MAX_ITER]
```

Below are the various options the wrapper program `bhtsne.py` expects:

- `-h, --help`                      show this help message and exit
- `-d NO_DIMS, --no_dims`           NO_DIMS
- `-p PERPLEXITY, --perplexity`     PERPLEXITY
- `-t THETA, --theta`               THETA
- `-r RANDSEED, --randseed`         RANDSEED
- `-n INITIAL_DIMS, --initial_dims` INITIAL_DIMS
- `-v, --verbose`
- `-i INPUT, --input`               INPUT: the input file, expects a TSV with the first row as the header.
- `-o OUTPUT, --output`             OUTPUT: A TSV file having each row as the `d` dimensional embedding.
- `--use_pca`
- `--no_pca`
- `-m MAX_ITER, --max_iter`         MAX_ITER