hyperbolics

Hyperbolic Embeddings

Setup

We use Docker to set up the environment for our code. See Docker/README.md for installation and launch instructions.

In this README, all instructions are assumed to be run inside the Docker container. All paths are relative to the /hyperbolics directory, and all commands are expected to be run from this directory.

Usage

The following programs and scripts expect the input graphs to exist in the /data/edges folder, e.g. /data/edges/phylo_tree.edges. All graphs that we report results on have been prepared and saved here.

Combinatorial construction

julia combinatorial/comb.jl --help to see options. Example usage (for better results on this dataset, raise the precision):

julia combinatorial/comb.jl -d data/edges/phylo_tree.edges -m phylo_tree.r10.emb -e 1.0 -p 64 -r 10 -a -s

Pytorch optimizer

pytorch pytorch/pytorch_hyperbolic.py learn --help to see options. Example usage:

python pytorch/pytorch_hyperbolic.py learn data/edges/phylo_tree.edges --batch-size 64 -r 10 -l 5.0 --epochs 100 --checkpoint-freq 10 -w phylo_tree.r10.emb

Experiment scripts

• scripts/run_exps.py runs a full set of experiments for a list of datasets. Example usage (note: the default run settings take a long time to finish):

  python scripts/run_exps.py phylo -d phylo_tree --epochs 20
  

  Currently, it executes the following experiments:

  1. The combinatorial construction with fixed precision in varying dimensions
  2. The combinatorial construction in dimension 2 (Sarkar's algorithm), with very high precision
  3. Pytorch optimizer in varying dimensions, random initialization
  4. Pytorch optimizer in varying dimensions, using the embedding produced by the combinatorial construction as initialization

• The combinatorial constructor combinatorial/comb.jl has an option for reporting the MAP and distortion statistics. However, this can be slow on larger datasets such as wordnet

  • scripts/comb_stats.py provides an alternate method for computing stats that can leverage multiprocessing Example usage: python scripts/comb_stats.py phylo_tree -e 1.0 -r 2 -p 1024 -q 4 to run on 4 cores