Abstract Natural language processing (NLP) techniques can enhance our ability to interpret plant science literature. Many state-of-the-art algorithms for NLP tasks require high-quality labelled data in the target domain, in which entities like genes and proteins, as well as the relationships between entities, are labelled according to a set of annotation guidelines. While there exist such datasets for other domains, these resources need development in the plant sciences. Here, we present the Plant ScIenCe KnowLedgE Graph (PICKLE) corpus, a collection of 250 plant science abstracts annotated with entities and relations, along with its annotation guidelines. The annotation guidelines were refined by iterative rounds of overlapping annotations, in which inter-annotator agreement was leveraged to improve the guidelines. To demonstrate PICKLE’s utility, we evaluated the performance of pretrained models from other domains and trained a new, PICKLE-based model for entity and relation extraction (RE). The PICKLE-trained models exhibit the second-highest in-domain entity performance of all models evaluated, as well as a RE performance that is on par with other models. Additionally, we found that computer science-domain models outperformed models trained on a biomedical corpus (GENIA) in entity extraction, which was unexpected given the intuition that biomedical literature is more similar to PICKLE than computer science. Upon further exploration, we established that the inclusion of new types on which the models were not trained substantially impacts performance. The PICKLE corpus is, therefore, an important contribution to training resources for entity and RE in the plant sciences.
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Tackling Structured Knowledge Extraction from Polymer Nanocomposite Literature as an NER/RE Task with seq2seq
There is an urgent need for ready access to published data for advances in materials design, and natural language processing (NLP) techniques offer a promising solution for extracting relevant information from scientific publications. In this paper, we present a domain-specific approach utilizing a Transformer-based model, T5, to automate the generation of sample lists in the field of polymer nanocomposites (PNCs). Leveraging large-scale corpora, we employ advanced NLP techniques including named entity recognition and relation extraction to accurately extract sample codes, compositions, group references, and properties from PNC papers. The T5 model demonstrates competitive performance in relation extraction using a TANL framework and an EM-style input sequence. Furthermore, we explore multi-task learning and joint-entity-relation extraction to enhance efficiency and address deployment concerns. Our proposed methodology, from corpora generation to model training, showcases the potential of structured knowledge extraction from publications in PNC research and beyond.
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- PAR ID:
- 10539882
- Publisher / Repository:
- Springer
- Date Published:
- Journal Name:
- Integrating Materials and Manufacturing Innovation
- Volume:
- 13
- Issue:
- 3
- ISSN:
- 2193-9764
- Page Range / eLocation ID:
- 656 to 668
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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