Pipelines for Procedural Information Extraction from Scientific Literature: Towards Recipes using Machine Learning and Data Science

Huichen Yang; Carlos A. Aguirre; Maria F. De La Torre; Derek Christensen; Luis Bobadilla; Emily Davich; Jordan Roth; Lei Luo; Yihong Theis; Alice Lam; T. Yong-Jin Han; David Buttler; William H. Hsu

doi:10.1109/icdarw.2019.10037

arXiv · 1912.07747

Pipelines for Procedural Information Extraction from Scientific Literature: Towards Recipes using Machine Learning and Data Science

Huichen Yang·Carlos A. Aguirre·Maria F. De La Torre·Derek Christensen·Luis Bobadilla·Emily Davich·Jordan Roth·Lei Luo·Yihong Theis·Alice Lam·T. Yong-Jin Han·David Buttler·William H. Hsu

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Abstract

This paper describes a machine learning and data science pipeline for structured information extraction from documents, implemented as a suite of open-source tools and extensions to existing tools. It centers around a methodology for extracting procedural information in the form of recipes, stepwise procedures for creating an artifact (in this case synthesizing a nanomaterial), from published scientific literature. From our overall goal of producing recipes from free text, we derive the technical objectives of a system consisting of pipeline stages: document acquisition and filtering, payload extraction, recipe step extraction as a relationship extraction task, recipe assembly, and presentation through an information retrieval interface with question answering (QA) functionality. This system meets computational information and knowledge management (CIKM) requirements of metadata-driven payload extraction, named entity extraction, and relationship extraction from text. Functional contributions described in this paper include semi-supervised machine learning methods for PDF filtering and payload extraction tasks, followed by structured extraction and data transformation tasks beginning with section extraction, recipe steps as information tuples, and finally assembled recipes. Measurable objective criteria for extraction quality include precision and recall of recipe steps, ordering constraints, and QA accuracy, precision, and recall. Results, key novel contributions, and significant open problems derived from this work center around the attribution of these holistic quality measures to specific machine learning and inference stages of the pipeline, each with their performance measures. The desired recipes contain identified preconditions, material inputs, and operations, and constitute the overall output generated by our computational information and knowledge management (CIKM) system.

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Huichen Yang, Carlos A. Aguirre, Maria F. De La Torre, Derek Christensen, Luis Bobadilla, Emily Davich, Jordan Roth, Lei Luo, Yihong Theis, Alice Lam, T. Yong-Jin Han, David Buttler, William H. Hsu. 2019-12-16. Pipelines for Procedural Information Extraction from Scientific Literature: Towards Recipes using Machine Learning and Data Science. https://doi.org/10.1109/icdarw.2019.10037

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