SENSE CDT (University of Leeds) triplet-trainer course

This repository contains material to work with the neural network model used in L Denby (2020) and was created for SENSE CDT training at University of Leeds on 6th March 2024 (material from previous years: 2021, 2022 and 2023)

Exercises are stored as jupyter notebooks in notebooks/

Getting started

To work through the exercises you will need two things:

1. A copy of the exercises (the repository you're looking at right now!)

2. A copy of the convml-tt python module installed into a conda environment

If you are on Windows and are having trouble some more detailed notes are given here.

1. Downloading the exercises

Choose a suitable parent directory (for example your desktop, ~/Desktop) and clone this repository so that you have a local copy of the exercises

git clone https://github.com/leifdenby/SENSE_convml_tt
cd SENSE_convml_tt

In the execises you will work with a dataset and trained model that comes bundled with convml-tt and instructions for how to download these is contained within the exercises.

2. Install convml-tt and its dependencies with conda

Instructions on how to create a conda environment and install convml-tt into it are here). But it essentially boils down to three steps: 1) install conda, 2) install pytorch using conda for GPU or CPU use (depending on whether you have a GPU) and 3) install convml-tt with pip.

Exercises

Once convml-tt is installed you can activate the convml-tt conda environment:

conda activate convml-tt

Move to the path where you checked out the exercises (e.g. ~/Desktop/SENSE_convml_tt)

And start up a jupyter session and get going with the exercises:

jupyter notebook

The exercises are broken down as follows:

1130 - 1230:

1. Dimensionality reduction: Examine how the neural network has used the embedding space; are all 100 dimensions necessary? Can we identify what features the neural network has learnt by comparing tiles in different parts of the embedding space? notebook: 1a_Use_PCA_analysis_to_study_tile_embeddings.ipynb

2. High-dimensional clustering: use different clustering methods to study the extent to which the neural network has formed distinct clusters in the embedding space. notebook: 1b_Exploring_embedding_space_with_clustering_methods.ipynb

1330 - 1500:

3. Using your own input data: either by generating synthetic input tiles or using your own data source you will work with the pre-trained model to study whether the trained neural network groups them together in the embedding space. notebook: 2_Working_with_your_own_data.ipynb