luyang-ai4med / mat2vec

Supplementary Materials for Tshitoyan et al. "Unsupervised word embeddings capture latent knowledge from materials science literature", Nature (2019).

Supplementary Materials for "Unsupervised word embeddings capture latent knowledge from materials science literature", Nature 571, 95–98 (2019).

Tshitoyan, V., Dagdelen, J., Weston, L., Dunn, A., Rong, Z., Kononova, O., Persson, K. A., Ceder, G. and Jain, A.

doi: 10.1038/s41586-019-1335-8

A view-only (no download) link to the paper: https://rdcu.be/bItqk

For those interested in the ab initio thermoelectric data, see below

Set up

1. Make sure you have python3.6 and the pip module installed. We recommend using conda environments.
2. Navigate to the root folder of this repository (the same folder that contains this README file) and run pip install --ignore-installed -r requirements.txt. Note: If you are using a conda env and any packages fail to compile during this step, you may need to first install those packages separately with conda install package_name.
3. Wait for all the requirements to be downloaded and installed.
4. Run python setup.py install to install this module. This will also download the Word2vec model files. If the download fails, manually download the model, word embeddings and output embeddings and put them in mat2vec/training/models.
5. Finalize your chemdataextractor installation by executing cde data download (You may need to restart your virtual environment for the cde command line interface to be found).
6. You are ready to go!

Processing

Example python usage:

from mat2vec.processing import MaterialsTextProcessor
text_processor = MaterialsTextProcessor()
text_processor.process("LiCoO2 is a battery cathode material.")

(['CoLiO2', 'is', 'a', 'battery', 'cathode', 'material', '.'], [('LiCoO2', 'CoLiO2')])

For the various methods and options see the docstrings in the code.

Pretrained Embeddings

Load and query for similar words and phrases:

from gensim.models import Word2Vec
w2v_model = Word2Vec.load("mat2vec/training/models/pretrained_embeddings")
w2v_model.wv.most_similar("thermoelectric")

[('thermoelectrics', 0.8435688018798828), ('thermoelectric_properties', 0.8339033126831055), ('thermoelectric_power_generation', 0.7931368350982666), ('thermoelectric_figure_of_merit', 0.7916493415832 52), ('seebeck_coefficient', 0.7753845453262329), ('thermoelectric_generators', 0.7641351819038391), ('figure_of_merit_ZT', 0.7587921023368835), ('thermoelectricity', 0.7515754699707031), ('Bi2Te3', 0 .7480161190032959), ('thermoelectric_modules', 0.7434879541397095)]

Phrases can be queried with underscores:

w2v_model.wv.most_similar("band_gap", topn=5)

[('bandgap', 0.934801459312439), ('band_-_gap', 0.933477520942688), ('band_gaps', 0.8606899380683899), ('direct_band_gap', 0.8511275053024292), ('bandgaps', 0.818678617477417)]

Analogies:

# helium is to He as ___ is to Fe? 
w2v_model.wv.most_similar(
    positive=["helium", "Fe"], 
    negative=["He"], topn=1)

[('iron', 0.7700884938240051)]

Material formulae need to be normalized before analogies:

# "GaAs" is not normalized
w2v_model.wv.most_similar(
    positive=["cubic", "CdSe"], 
    negative=["GaAs"], topn=1)

KeyError: "word 'GaAs' not in vocabulary"

from mat2vec.processing import MaterialsTextProcessor
text_processor = MaterialsTextProcessor()
w2v_model.wv.most_similar(
    positive=["cubic", text_processor.normalized_formula("CdSe")], 
    negative=[text_processor.normalized_formula("GaAs")], topn=1)

[('hexagonal', 0.6162797212600708)]

Keep in mind that words should also be processed before queries. Most of the time this is as simple as lowercasing, however, it is the safest to use the process() method of mat2vec.processing.MaterialsTextProcessor.

Training

To run an example training, navigate to mat2vec/training/ and run

python phrase2vec.py --corpus=data/corpus_example --model_name=model_example

from the terminal. It should run an example training and save the files in models and tmp folders. It should take a few seconds since the example corpus has only 5 abstracts.

For more options, run

python phrase2vec.py --help

Thermoelectric Datasets

You can find the condensed thermoelectric CRTA data in the thermoelectric_data directory.

Related Work

• Weston, L., Tshitoyan, V., Dagdelen, J., Kononova, O., Persson, K. A., Ceder, G. and Jain, A. Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature, ChemRxiv. Preprint. (2019).

Issues?

You can either report an issue on github or contact one of us directly. Try [email protected], [email protected], [email protected] or [email protected].