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Topological Uncertainty

This repository provides code related to the paper Topological Uncertainty: Monitoring Trained Neural Networks through Persistence of Activation Graphs. It aims at being integrated to the Gudhi library in the future.

Note: this repository is still in a preliminary state. Do not hesitate to report any issue you come accross or suggest options you may like to see in the future.

Summary

In a nutshell, the idea is to extract topological information from a sample of weighted graphs (with fixed combinatorics) and then aggregate this topological information through a Fréchet mean (a.k.a barycenter). Given a new observation (graph), we can compute its (topological) distance to this mean and use this quantity, called Topological Uncertainty, as a way to detect unusual weight distributions.

In the aforementioned paper, we used this technique in the context of monitoring neural networks (as a way to detect Out-of-Distribution samples and similar anomalies), but this code can be used in a more general setting.

Note: in the context of neural networks, current implementation only handles tensorflow 2 sequential networks and fully-connected layers (seen as bipartite graphs): your (sequential) network can contain convolutional layers etc., but topological information is only extracted from the fully-connected layers for now. Further implementations (in particular compatible with Torch) will come in the future.

Get started

Dependencies

This code was developed and tested with Ubuntu 20.04 (it is likely that other versions/OS work as well) and Python 3.8 # (note: it seems tensorflow 2.4 is not compatible Python 3.9), using the following python packages (stared packages are required, others are optional):

  • numpy 1.20 *
  • gudhi 3.3.0 * (used to store activation graphs and compute MST/diagrams on top of them)
  • tensorflow 2.4.1
  • matplotlib.pyplot 1.19.2

Note that tensorflow is only needed if you want to manipulate fully connected neural networks. In the notebook, it is only used in Section 2 (you should be able to run Section 1 without it.)

Play with the tutorial

We provide a tutorial to play quickly with these notions and see how you can use them for your own purpose. It shows how you can get TU

  • directly from a set of graphs saved as numpy adjacency matrices. Extension to handle networkx.graphs, scipy.sparse adjacency matrices , will come in the future.
  • From a trained (tensorflow, sequential) neural network.

Finally, an experiment (reproducing a result in the reference paper) using a network trained on the MUTAG and COX2 datasets is also provided at the end of the notebook. For the sake of simplicity, these datasets are provided in the ./datesets/ folder, along with the features we used to incorporate graphs in neural networks.

Notebook additional dependencies:

Along with the aforementioned dependencies, the notebook makes use of the following packages:

  • pandas 1.1.3 (used to store features computed from MUTAG and COX2; section 2.2 only)

Use this code / Run the notebook:

We suggest to use a fresh conda env. For this, you can start by typing in a terminal

conda create -n test-TU python=3.8 jupyterlab
conda activate test-TU

You can then install the dependecies, for instance using

conda install pandas tensorflow
conda install -c conda-forge gudhi matplotlib