John Dagdelen

John Dagdelen

Computational Materials and Machine Learning

Publications

Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature

Published in Journal of Chemical Information and Modeling, 2019

The number of published materials science articles has increased manyfold over the past few decades. Now, a major bottleneck in the materials discovery pipeline arises in connecting new results with the previously established literature. A potential solution to this problem is to map the unstructured raw text of published articles onto structured database entries that allow for programmatic querying. To this end, we apply text mining with named entity recognition (NER) for large-scale information extraction from the published materials science literature. The NER model is trained to extract summary-level information from materials science documents, including inorganic material mentions, sample descriptors, phase labels, material properties and applications, as well as any synthesis and characterization methods used. Our classifier achieves an accuracy (f1) of 87%, and is applied to information extraction from 3.27 …

Recommended citation: Weston, L., Tshitoyan, V., Dagdelen, J., Kononova, O., Trewartha, A., Persson, K. A., … Jain, A. (2019). Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature. Journal of Chemical Information and Modeling, 59(9), 3692–3702. https://doi.org/10.1021/acs.jcim.9b00470 https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00470

Unsupervised word embeddings capture latent knowledge from materials science literature

Published in Nature, 2019

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 databases, 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 processing, 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 embeddings (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.

Recommended citation: Tshitoyan, V., Dagdelen, J., Weston, L., Dunn, A., Rong, Z., Kononova, O., … Jain, A. (2019). Unsupervised word embeddings capture latent knowledge from materials science literature. Nature, 571(7763), 95–98. https://doi.org/10.1038/s41586-019-1335-8 https://www.nature.com/articles/s41586-019-1335-8

Atomate: A high-level interface to generate, execute, and analyze computational materials science workflows

Published in Computational Materials Science, 2017

We introduce atomate, an open-source Python framework for computational materials science simulation, analysis, and design with an emphasis on automation and extensibility. Built on top of open source Python packages already in use by the materials community such as pymatgen, FireWorks, and custodian, atomate provides well-tested workflow templates to compute various materials properties such as electronic bandstructure, elastic properties, and piezoelectric, dielectric, and ferroelectric properties. Atomate also enables the computational characterization of materials by providing workflows that calculate X-ray absorption (XAS), Electron energy loss (EELS) and Raman spectra. One of the major features of atomate is that it provides both fully functional workflows as well as reusable components that enable one to compose complex materials science workflows that use a diverse set of computational tools…

Recommended citation: K Mathew, JH Montoya, A Faghaninia, S Dwarakanath, M Aykol, H Tang, ... Computational Materials Science 139, 140-152 https://www.sciencedirect.com/science/article/pii/S0927025617303919

Computational prediction of new auxetic materials

Published in Nature Communications, 2017

Auxetics comprise a rare family of materials that manifest negative Poisson’s ratio, which causes an expansion instead of contraction under tension. Most known homogeneously auxetic materials are porous foams or artificial macrostructures and there are few examples of inorganic materials that exhibit this behavior as polycrystalline solids. It is now possible to accelerate the discovery of materials with target properties, such as auxetics, using high-throughput computations, open databases, and efficient search algorithms. Candidates exhibiting features correlating with auxetic behavior were chosen from the set of more than 67 000 materials in the Materials Project database. Poisson’s ratios were derived from the calculated elastic tensor of each material in this reduced set of compounds. We report that this strategy results in the prediction of three previously unidentified homogeneously auxetic materials as well as…

Recommended citation: Dagdelen, J., Montoya, J., de Jong, M., & Persson, K. (2017). Computational prediction of new auxetic materials. Nature Communications, 8(323). https://doi.org/10.1038/s41467-017-00399-6 https://www.nature.com/articles/s41467-017-00399-6