Knowledge engineering in chemistry: from expert systems to agents of creation

ConspectusPassing knowledge from human to human is a natural process that has continued since the beginning of humankind. Over the past few decades, we have witnessed that knowledge is no longer passed only between humans but also from humans to machines. The latter form of knowledge transfer repres...

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Main Authors: Kondinski, Aleksandar, Bai, Jiaru, Mosbach, Sebastian, Akroyd, Jethro, Kraft, Markus
Other Authors: School of Chemical and Biomedical Engineering
Format: Article
Language:English
Published: 2023
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Online Access:https://hdl.handle.net/10356/164481
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Institution: Nanyang Technological University
Language: English
id sg-ntu-dr.10356-164481
record_format dspace
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering::Chemical engineering
Ontology
Oxidation
spellingShingle Engineering::Chemical engineering
Ontology
Oxidation
Kondinski, Aleksandar
Bai, Jiaru
Mosbach, Sebastian
Akroyd, Jethro
Kraft, Markus
Knowledge engineering in chemistry: from expert systems to agents of creation
description ConspectusPassing knowledge from human to human is a natural process that has continued since the beginning of humankind. Over the past few decades, we have witnessed that knowledge is no longer passed only between humans but also from humans to machines. The latter form of knowledge transfer represents a cornerstone in artificial intelligence (AI) and lays the foundation for knowledge engineering (KE). In order to pass knowledge to machines, humans need to structure, formalize, and make knowledge machine-readable. Subsequently, humans also need to develop software that emulates their decision-making process. In order to engineer chemical knowledge, chemists are often required to challenge their understanding of chemistry and thinking processes, which may help improve the structure of chemical knowledge.Knowledge engineering in chemistry dates from the development of expert systems that emulated the thinking process of analytical and organic chemists. Since then, many different expert systems employing rather limited knowledge bases have been developed, solving problems in retrosynthesis, analytical chemistry, chemical risk assessment, etc. However, toward the end of the 20th century, the AI winters slowed down the development of expert systems for chemistry. At the same time, the increasing complexity of chemical research, alongside the limitations of the available computing tools, made it difficult for many chemistry expert systems to keep pace.In the past two decades, the semantic web, the popularization of object-oriented programming, and the increase in computational power have revitalized knowledge engineering. Knowledge formalization through ontologies has become commonplace, triggering the subsequent development of knowledge graphs and cognitive software agents. These tools enable the possibility of interoperability, enabling the representation of more complex systems, inference capabilities, and the synthesis of new knowledge.This Account introduces the history, the core principles of KE, and its applications within the broad realm of chemical research and engineering. In this regard, we first discuss how chemical knowledge is formalized and how a chemist's cognition can be emulated with the help of reasoning algorithms. Following this, we discuss various applications of knowledge graph and agent technology used to solve problems in chemistry related to molecular engineering, chemical mechanisms, multiscale modeling, automation of calculations and experiments, and chemist-machine interactions. These developments are discussed in the context of a universal and dynamic knowledge ecosystem, referred to as The World Avatar (TWA).
author2 School of Chemical and Biomedical Engineering
author_facet School of Chemical and Biomedical Engineering
Kondinski, Aleksandar
Bai, Jiaru
Mosbach, Sebastian
Akroyd, Jethro
Kraft, Markus
format Article
author Kondinski, Aleksandar
Bai, Jiaru
Mosbach, Sebastian
Akroyd, Jethro
Kraft, Markus
author_sort Kondinski, Aleksandar
title Knowledge engineering in chemistry: from expert systems to agents of creation
title_short Knowledge engineering in chemistry: from expert systems to agents of creation
title_full Knowledge engineering in chemistry: from expert systems to agents of creation
title_fullStr Knowledge engineering in chemistry: from expert systems to agents of creation
title_full_unstemmed Knowledge engineering in chemistry: from expert systems to agents of creation
title_sort knowledge engineering in chemistry: from expert systems to agents of creation
publishDate 2023
url https://hdl.handle.net/10356/164481
_version_ 1787136614446661632
spelling sg-ntu-dr.10356-1644812023-12-29T06:49:17Z Knowledge engineering in chemistry: from expert systems to agents of creation Kondinski, Aleksandar Bai, Jiaru Mosbach, Sebastian Akroyd, Jethro Kraft, Markus School of Chemical and Biomedical Engineering Cambridge Centre for Advanced Research and Education in Singapore Engineering::Chemical engineering Ontology Oxidation ConspectusPassing knowledge from human to human is a natural process that has continued since the beginning of humankind. Over the past few decades, we have witnessed that knowledge is no longer passed only between humans but also from humans to machines. The latter form of knowledge transfer represents a cornerstone in artificial intelligence (AI) and lays the foundation for knowledge engineering (KE). In order to pass knowledge to machines, humans need to structure, formalize, and make knowledge machine-readable. Subsequently, humans also need to develop software that emulates their decision-making process. In order to engineer chemical knowledge, chemists are often required to challenge their understanding of chemistry and thinking processes, which may help improve the structure of chemical knowledge.Knowledge engineering in chemistry dates from the development of expert systems that emulated the thinking process of analytical and organic chemists. Since then, many different expert systems employing rather limited knowledge bases have been developed, solving problems in retrosynthesis, analytical chemistry, chemical risk assessment, etc. However, toward the end of the 20th century, the AI winters slowed down the development of expert systems for chemistry. At the same time, the increasing complexity of chemical research, alongside the limitations of the available computing tools, made it difficult for many chemistry expert systems to keep pace.In the past two decades, the semantic web, the popularization of object-oriented programming, and the increase in computational power have revitalized knowledge engineering. Knowledge formalization through ontologies has become commonplace, triggering the subsequent development of knowledge graphs and cognitive software agents. These tools enable the possibility of interoperability, enabling the representation of more complex systems, inference capabilities, and the synthesis of new knowledge.This Account introduces the history, the core principles of KE, and its applications within the broad realm of chemical research and engineering. In this regard, we first discuss how chemical knowledge is formalized and how a chemist's cognition can be emulated with the help of reasoning algorithms. Following this, we discuss various applications of knowledge graph and agent technology used to solve problems in chemistry related to molecular engineering, chemical mechanisms, multiscale modeling, automation of calculations and experiments, and chemist-machine interactions. These developments are discussed in the context of a universal and dynamic knowledge ecosystem, referred to as The World Avatar (TWA). National Research Foundation (NRF) Published version This research was supported by the National Research Foundation, Prime Ministers Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) programme. A.K. and M.K. thank the Humboldt Foundation (Berlin, Germany) and the Isaac Newton Trust (Cambridge, UK) for a Feodor Lynen Fellowship. J.B. acknowledges financial support provided by CSC Cambridge International Scholarship from Cambridge Trust and China Scholarship Council. 2023-01-30T01:32:13Z 2023-01-30T01:32:13Z 2023 Journal Article Kondinski, A., Bai, J., Mosbach, S., Akroyd, J. & Kraft, M. (2023). Knowledge engineering in chemistry: from expert systems to agents of creation. Accounts of Chemical Research, 56(2), 128-139. https://dx.doi.org/10.1021/acs.accounts.2c00617 0001-4842 https://hdl.handle.net/10356/164481 10.1021/acs.accounts.2c00617 36516456 2-s2.0-85144176349 2 56 128 139 en Accounts of Chemical Research © 2022 The Authors. Published by American Chemical Society. This is an open-access article distributed under the terms of the Creative Commons Attribution License. application/pdf