Unsupervised word embeddings capture latent knowledge from materials science literature

Abstract

The overwhelming majority of scientific knowledge is published as text, which is difficult to analyse by either traditional statistical analysis or modern machine learning methods. By contrast, the main source of machine-interpretable data for the materials research community has come from structured property databases1,2, which encompass only a small fraction of the knowledge present in the research literature. Beyond property values, publications contain valuable knowledge regarding the connections and relationships between data items as interpreted by the authors. To improve the identification and use of this knowledge, several studies have focused on the retrieval of information from scientific literature using supervised natural language processing3,4,5,6,7,8,9,10, which requires large hand-labelled datasets for training. Here we show that materials science knowledge present in the published literature can be efficiently encoded as information-dense word embeddings11,12,13 (vector representations of words) without human labelling or supervision. Without any explicit insertion of chemical knowledge, these embeddings capture complex materials science concepts such as the underlying structure of the periodic table and structure–property relationships in materials. Furthermore, we demonstrate that an unsupervised method can recommend materials for functional applications several years before their discovery. This suggests that latent knowledge regarding future discoveries is to a large extent embedded in past publications. Our findings highlight the possibility of extracting knowledge and relationships from the massive body of scientific literature in a collective manner, and point towards a generalized approach to the mining of scientific literature.

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Fig. 1: Word2vec skip-gram and analogies.
Fig. 2: Prediction of new thermoelectric materials.
Fig. 3: Validation of the predictions.

Data availability

The scientific abstracts used in this study are available via Elsevier’s Scopus and Science Direct API’s (https://dev.elsevier.com/) and the Springer Nature API (https://dev.springernature.com/). The list of DOIs used in this study, the pre-trained word embeddings and the analogies used for validation of the embeddings are available at https://github.com/materialsintelligence/mat2vec. All other data generated and analysed during the current study are available from the corresponding authors on reasonable request.

Code availability

The code used for text preprocessing and Word2vec training are available at https://github.com/materialsintelligence/mat2vec.

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Acknowledgements

This work was supported by Toyota Research Institute through the Accelerated Materials Design and Discovery program. We thank T. Botari, M. Horton, D. Mrdjenovich, N. Mingione and A. Faghaninia for discussions.

Author information

All authors contributed to the conception and design of the study, as well as writing of the manuscript. V.T. developed the data processing pipeline, trained and optimized the Word2vec embeddings, trained the machine learning models for property predictions and generated the thermoelectric predictions. V.T., J.D. and L.W. analysed the results and developed the software infrastructure for the project. J.D. trained and optimized the GloVe embeddings and developed the data acquisition infrastructure. L.W. performed the abstract classification. A.D. performed the DFT calculation of thermoelectric power factors. Z.R. contributed to data acquisition. O.K. developed the code for normalization of material formulae. A.D., Z.R. and O.K. contributed to the analysis of the results. K.A.P., G.C. and A.J. supervised the work.

Correspondence to Vahe Tshitoyan or Gerbrand Ceder or Anubhav Jain.

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Competing interests

The authors declare no competing interests.

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Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Chemistry is captured by word embeddings.

a, Two-dimensional t-distributed stochastic neighbour embedding (t-SNE) projection of the word embeddings of 100 chemical element names (for example, ‘hydrogen’) labelled with the corresponding element symbols and grouped according to their classification. Chemically similar elements are seen to cluster together and the overall distribution exhibits a topology reminiscent of the periodic table itself (compare to b). Arranged from top left to bottom right are the alkali metals, alkaline earth metals, transition metals, and noble gases while the trend from top right to bottom left generally follows increasing atomic number (see Supplementary Information section S4 for a more detailed discussion). b, The periodic table coloured according to the classification shown in a. c, Predicted versus actual (DFT) values of formation energies of approximately 10,000 ABC2D6 elpasolite compounds40 using a simple neural network model with word embeddings of elements as features (see Supplementary Information section S6 for the details of the model). The data points in the plot use fivefold cross-validation. d, Error distribution for the 10% test set of elpasolite formation energies. With no extensive optimization, the word embeddings achieve a mean absolute error (MAE) of 0.056 eV per atom, which is substantially smaller than the 0.1 eV per atom error reported for the same task in the original study using hand-crafted features40 and the 0.15 eV per atom achieved in a recent study using element features automatically learned from crystal structures of more than 60,000 compounds41.

Extended Data Fig. 2 Historical validations of functional material predictions.

ac, Ferroelectric (a), photovoltaic (b) and topological insulator predictions (c) using word embeddings obtained from various historical datasets, similar to Fig. 3a. For ferroelectrics and photovoltaics, the range of prediction years is 2001–2018. The phrase ‘topological insulator’ obtained its own embedding in our corpus only in 2011 (owing to count and vocabulary size limits), so it is possible to analyse the results only over a shorter time period (2011–2018). Each grey line uses only abstracts published before a certain year to make predictions. The lines show the cumulative percentage of predicted materials studied in the years following their predictions; earlier predictions can be analysed over longer test periods. The results are averaged in red and compared to baseline percentages from all materials. d, The target word or phrase used to rank materials for each application (based on cosine similarity), and the corresponding words used as indicators for a potentially existing study.

Extended Data Table 1 Materials science analogies
Extended Data Table 2 Top 50 thermoelectric predictions
Extended Data Table 3 Top five functional material predictions and context words
Extended Data Table 4 Importance of the text corpus

Supplementary information

Supplementary Information

Supplementary Information, including Supplementary Figures 1–8, Supplementary Tables 1–3 and additional references.

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