vernal: Fuzzy Recurrent Subgraph Mining

This is a reference implementation of veRNAl, an algorithm for identifying fuzzy recurrent subgraphs in RNA 3D networks.

Please cite:

@article{vernal,
    author = {Oliver, Carlos and Mallet, Vincent and Philippopoulos, Pericles and Hamilton, William L and Waldispühl, Jérôme},
    title = "{VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA}",
    journal = {Bioinformatics},
    year = {2021},
    month = {11},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btab768},
    url = {https://doi.org/10.1093/bioinformatics/btab768},
    note = {btab768},
    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab768/41153095/btab768.pdf},
}

See full paper for complete description of the algorithm.

You can browse the results from an already trained model here.

This repository has three main components:

• Preparing Data /prepare_data
• Subgraph Embeddings /train_embeddings
• Motif Building /build_motifs

Each subdirectory contrains a main.py file which controls the behaviour of that stage.
For full usage, run python <dir>/main.py -h

0. Install Dependencies

The command below will install the full list of dependencies.

The main packages we use are:

• multiset
• NetworkX
• BioPython
• Pytorch
• DGL (Deep Graph Library)
• Scikit-learn

conda env create -f environment.yml
conda activate vernal

1. Data Preparation

This step loads the whole PDBs, creates uniformly-sized chunks (chopper.py) and builds
newtorkx graphs for each chunk.

We build a rooted subgraph and graphlet hashtable for each node in annotate.py to
speed up the similarity function computations at training time.

Create two directories where the data will be kept:

mkdir data/graphs
mkdir data/annotated

Data building and loading will take some time (~1 hr), you can skip all the data preparation if you want to use a pre-built dataset, just download and move to the data/annotated/ folder and move to step 2.

Download RNA networks:

• whole crystal structures (non-redundant)
• whole graphs (non-redundant)

Save the crystal structures (first link) to the data/ folder.

Save the whole graphs (second link) to the data/graphs folder.

Bulid the dataset. This will take some time as it involves loading many large PDB files.

python prepare_data/main.py -n <data-id>

2. Subgraph Embeddings

Once the training data is built, we train the RGCN.

python train_embedding/main.py train -n my_model

3. Motif Building

Finally, the trained RGCN and the whole graphs are used to build motifs.

Here, you have three options:

1. Build/load a new meta graph
2. Use a meta graph to build motifs
3. Use a meta graph to search for matches to a graph query

To build a new meta graph:

If this is the first time you build a meta-graph, create the following folder:

mkdir results/mggs

python build_motifs/main.py -r my_model --mgg_name my_metagraph

The new meta-graph will be built and dumped in the folder results/mggs/my_metagraph.p