Installation and basic use of CrabNet

April 23, 2023 ยท View on GitHub

Use these steps to install and set up CrabNet and to reproduce the results presented in the publication:

A. Y.-T. Wang, S. K. Kauwe, R. J. Murdock, T. D. Sparks, Compositionally restricted attention-based network for materials property predictions, npj Comput. Mater., 2021, 7: 77. DOI: 10.1038/s41524-021-00545-1.

Table of Contents

  • Installation of CrabNet
  • Reproduction of publication results
  • Train or predict materials properties using CrabNet or DenseNet

Installation

This code uses PyTorch for creating the neural network models. For fast model training and inference, it is suggested you use an NVIDIA GPU with the most recent drivers.

Windows users should be able to install all required Python packages via Anaconda by following the steps below.

Linux users will additionally need to manually install CUDA and cuDNN.

Clone or download this GitHub repository

Do one of the following:

Install dependencies via Anaconda:

  1. Download and install Anaconda.
  2. Navigate to the project directory (from above).
  3. Open Anaconda prompt in this directory.
  4. Run the following command from Anaconda prompt to automatically create an environment from the conda-env.yml file:
    • conda env create --file conda-env.yml
    • conda env create --file conda-env-cpuonly.yml if you only have a CPU and no GPU in your system
  5. Run the following command from Anaconda prompt to activate the environment:
    • conda activate crabnet

For more information about creating, managing, and working with Conda environments, please consult the relevant help page.

Install dependencies via pip:

Open conda-env.yml and pip install all of the packages listed there. We recommend that you create a separate Python environment for this project.

Alternative installation

There is another version of CrabNet for which changes may be incorporated into (this) the parent repository at a future date. Similar to automatminer, this version facilitates passing of DataFrames for training and validation data, is conda and pip installable, and exposes many of the model hyperparameters at the top-level. Additional instructions can be found at the fork.

Reproduction of publication results

To reproduce the publication results, please follow the below steps. Results will slightly vary. It is a known phenomena that PyTorch model training may slightly vary on different computers and hardware.

Trained weights are provided at: http://doi.org/10.5281/zenodo.4633866.

As a reference, with a desktop computer with an IntelTM i9-9900K processor, 32GB of RAM, and two NVIDIA RTX 2080 Ti's, training our largest network (OQMD) takes roughly two hours.

Train CrabNet

  1. To train crabnet you need train.csv, val.csv, and optionally a test.csv files.
    • train.csv is used to find model weights.
    • val.csv ensures the model does not overfit.
    • test.csv will be run on the trained model for performance evaluation.
  2. Place the csv files in the data/materials_data directory.
    • The csv file must contain two columns, formula and target.
    • formula must be a string containing valid element symbols, numbers, and parentheses.
    • target is the target material property and should be provided as a number.
    • Additional csv files can be saved here. In the case of inference with no known targets, you may fill the target columns with 0's.
  3. Run train_crabnet.py to train CrabNet using default parameters.
    • If you desire to perform inference with additional csv files, you may add code to train_crabnet.py of the form
    _, mae_added_data = save_results(data_dir, mat_prop, classification,
                                 'my_added_data.csv', verbose=False)
  4. Note that your trained network will be associated with your given mat_prop folder. If you want to predict with this model, you must use the same mat_prop.

Plot results

  1. Inference outputs using the provided saved weights are in the predictions folder.
  2. Data are in the folder publication_predictions
  3. Run Paper_{FIG|TABLE}_{X}.py to produce the tables and figures shown in the manuscript.

IMPORTANT - if you want to reproduce the publication Figures 1 and 2:

The PyTorch-builtin function for outting the multi-headed attention operation defaults to averaging the attention matrix across all heads. Thus, in order to obtain the per-head attention information, we have to edit a bit of PyTorch's source code so that the individual attention matrices are returned.

To properly export the attention heads from the PyTorch nn.MultiheadAttention implementation within the transformer encoder layer, you will need to manually modify some of the source code of the PyTorch library. This applies to PyTorch v1.6.0, v1.7.0, and v1.7.1 (potentially to other untested versions as well).

For this, open the file: C:\Users\{USERNAME}\Anaconda3\envs\{ENVIRONMENT}\Lib\site-packages\torch\nn\functional.py (where USERNAME is your Windows user name and ENVIRONMENT is your conda environment name (if you followed the steps above, then it should be crabnet))

At the end of the function defition of multi_head_attention_forward (line numbers may differ slightly):

L4011 def multi_head_attention_forward(
# ...
# ... [some lines omitted]
# ...
L4291    if need_weights:
L4292        # average attention weights over heads
L4293        attn_output_weights = attn_output_weights.view(bsz, num_heads, tgt_len, src_len)
L4294        return attn_output, attn_output_weights.sum(dim=1) / num_heads
L4295    else:
L4296        return attn_output, None

Change the specific line

return attn_output, attn_output_weights.sum(dim=1) / num_heads

to:

return attn_output, attn_output_weights

This prevents the returning of the attention values as an average value over all heads, and instead returns each head's attention matrix individually. For more information see: