github.com/birdwatcheryt/learning-interpretable-metric-between-graphs

Learning Interpretable Metric between Graphs

Source code for KDD2019 accepted paper "Learning Interpretable Metric between Graphs: Convex Formulation and Computation with Graph Mining".

arXiv version is "Distance Metric Learning for Graph Structured Data".

Abstract

Graph is a standard approach to modeling structured data. Although many machine learning methods depend on the metric of the input objects, defining an appropriate distance function on graph is still a controversial issue. We propose a novel supervised metric learning method for a subgraph-based distance, called interpretable graph metric learning (IGML). IGML optimizes the distance function in such a way that a small number of important subgraphs can be adaptively selected. This optimization is computationally intractable with naive application of existing optimization algorithms. We construct a graph mining based efficient algorithm to deal with this computational difficulty. Important advantages of our method are 1) guarantee of the optimality from the convex formulation, and 2) high interpretability of results. To our knowledge, none of the existing studies provide an interpretable subgraph-based metric in a supervised manner. In our experiments, we empirically verify superior or comparable prediction performance of IGML to other existing graph classification methods which do not have clear interpretability. Further, we demonstrate usefulness of IGML through some illustrative examples of extracted subgraphs and an example of data analysis on the learned metric space.

Programs

There are eleven programs as follows:

• SS&SP: Performs safe screening (SS) and safe pruning (SP).
• RSS&RSP: Performs range-based SS (RSS) and SP (RSP).
• WS&WP: Performs working-set selection (WS) and pruning (WP).
• RSS&RSP+WS&WP: Performs both RSS&RSP and WS&WP.
• RSS&RSP+WS&WP+FullMetric: Contains post-processing, in which learns Maharanobis distance.
• Extension: Contains six programs:
  • Triplet: Uses a triplet loss formulation.
  • LogApproxFrequency: Uses g(x)=log(1+x) as a graph feature instead of indicator function g(x)=I(x>0), where x is approximate frequency without overlap.
  • ASIF: Uses approximate subgraph isomorphism feature (ASIF) as a graph feature.
  • sim-ASIF: Uses sim-ASIF, which considers a vertex-label similarity, as a graph feature.
  • Itemset: For item-set data.
  • Sequence: For sequence data.

Each directory has Makefile. Type make, and compile will begin.

RSS&RSP+WS&WP+FullMetric-, Itemset-, and Sequence-program require C++ Eigen library. You must change INCLUDE variable in Makefile as follows:

INCLUDE  =  -I[your Eigen library path]

Containing tree.hh was obtained from http://tree.phi-sci.com/.

A part of source code in graph mining is based on gBoost.

Usage

./run srand filename maxpat

• srand: Seed of random.
• filename: Dataset name.
• maxpat: Max pattern size.

Example

./run 1 AIDS 15

Comment

Because the kernel matrix has a large capacity, the neighborhood of the sample is chosen at random unlike the paper.