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Spatial Information in Dimensionality Reduction (Spidr)

A more up-to-date version of this library can be found at the fork https://github.com/biovault/Spidr .

Introduces spatial neighborhood information in dimensionality reduction for high-dimensional images. Extends t-SNE such that similarities are based on a point's spatial neighborhood instead of only the high-dimensional point itself.

To clone the repo and its external submodules (hnswlib, glfw, spdlog):

git clone --recurse-submodule https://github.com/alxvth/Spidr/

Currently, tested on Windows with Visual Studio 2017. Use cmake for setting up the project:

mkdir build
cd build
cmake .. -G "Visual Studio 15 2017 Win64"

The standard cpp implementation uses the A-tSNE implementation from the HDILib and Hnswlib for approximated nearest neighbor search. Other DR techniques might also be used, as shown in the python example below.

Usage

See example/SpidrExample.cpp for a example on how to use the library in cpp.

See python_wrapper for install intructions and a usage example on how to use the library in python. The example showcases spatially informed t-SNE, UMAP and MDS embeddings.

Dependencies

Not all dependencies are included in this repo (see submodules in external/), some need to be downloaded/installed by yourself. Make sure to adjust your system variables respectively:

  • HDILibSlim (build and install the library and define the system variable HDILIBSLIM_ROOT pointing to the install DIR for cmake to automatically find the library.)
  • OpenMP