MatText: A framework for text-based materials modeling

MatText is a framework for text-based materials modeling. It supports

conversion of crystal structures in to text representations
transformations of crystal structures for sensitivity analyses
decoding of text representations to crystal structures
tokenization of text-representation of crystal structures
pre-training, finetuning and testing of language models on text-representations of crystal structures
analysis of language models trained on text-representations of crystal structures

Local Installation

We recommend that you create a virtual conda environment on your computer in which you install the dependencies for this package. To do so head over to Miniconda and follow the installation instructions there.

Install development version

Clone this repository (you need git for this, if you get a missing command error for git you can install it with sudo apt-get install git)

git clone https://github.com/lamalab-org/mattext.git
cd mattext

pip install -e .

If you want to use the Local Env representation, you will also need to install OpenBabel, e.g. using

conda install openbabel -c conda-forge

Getting started

Converting crystals into text

from mattext.representations import TextRep
from pymatgen.core import Structure

# Load structure from a CIF file
from_file = "InCuS2_p1.cif"
structure = Structure.from_file(from_file, "cif")

# Initialize TextRep Class
text_rep = TextRep.from_input(structure)

requested_reps = [
    "cif_p1",
    "slices",
    "atom_sequences",
    "atom_sequences_plusplus",
    "crystal_text_llm",
    "zmatrix"
]

# Get the requested text representations
requested_text_reps = text_rep.get_requested_text_reps(requested_reps)

Pretrain

python main.py -cn=pretrain model=pretrain_example +model.representation=composition +model.dataset_type=pretrain30k +model.context_length=32

Running a benchmark

python main.py -cn=benchmark model=benchmark_example +model.dataset_type=filtered +model.representation=composition +model.dataset=perovskites +model.checkpoint=path/to/checkpoint

The + symbol before a configuration key indicates that you are adding a new key-value pair to the configuration. This is useful when you want to specify parameters that are not part of the default configuration.

To override the existing default configuration, use ++, for e.g., ++model.pretrain.training_arguments.per_device_train_batch_size=32. Refer to the docs for more examples and advanced ways to use the configs with config groups.

Using data

The MatText datasets can be easily obtained from HuggingFace, for example

from datasets import load_dataset

dataset = load_dataset("n0w0f/MatText", "pretrain300k")

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

Citation

If you use MatText in your work, please cite

@misc{alampara2024mattextlanguagemodelsneed,
      title={MatText: Do Language Models Need More than Text & Scale for Materials Modeling?}, 
      author={Nawaf Alampara and Santiago Miret and Kevin Maik Jablonka},
      year={2024},
      eprint={2406.17295},
      archivePrefix={arXiv},
      primaryClass={cond-mat.mtrl-sci}
      url={https://arxiv.org/abs/2406.17295}, 
}

⚖️ License

The code in this package is licensed under the MIT License.

💰 Funding

This project has been supported by the Carl Zeiss Foundation as well as Intel and Merck.

lamalab-org / MatText

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