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Title: Towards algorithmic use of chemical data
Author: Jacob, Philipp-Maximilian
ISNI:       0000 0004 7229 6672
Awarding Body: University of Cambridge
Current Institution: University of Cambridge
Date of Award: 2018
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The growth of chemical knowledge available via online databases opens opportunities for new types of chemical research. In particular, by converting the data into a network, graph theoretical approaches can be used to study chemical reactions. In this thesis several research questions from the field of data science and graph theory are re-formulated for the chemistry-specific data. Firstly, the structure of chemical reactions data was studied using graph theory. It was found that the network of reactions obtained from the Reaxys data was scale-free, that on average any two species were separated by six reactions, and that evidence for a hierarchy of nodes existed, most clearly in that the hubs that combine a large share of connections onto them also facilitate a large proportion of routes across the network. The hierarchy was also evidenced in the clustering and degree correlations of nodes. Next, it was investigated whether Reaxys could be mined to construct a network of reactions and use it to plan and evaluate synthesis routes in two case studies. A number of heuristics were developed to find synthesis routes using the network taking chemical structures into account. These routes were fed into a multi-criteria decision making framework scoring the routes along environmental sustainability considerations. The approach was successful in discovering and scoring synthesis route candidates. It was found that Reaxys lacked process data in many instances. To address this a proposal for extension of the RInChI reaction data format was developed. The final question addressed was whether the network could be used to predict future reactions by using Stochastic Block Models. Block model-based link prediction performed impressively, being able to achieve a classification accuracy of close to 95% during time-split validation on historic data, differentiating future reaction discoveries from random data. Next, a set of transformation suggestions was thus evaluated and a framework for analysing these results was presented. Overall, the thesis was able to further the understanding of the network’s topology and to present a framework allowing the mining of Reaxys to plan synthesis routes and target R&D efforts in a specific area to discover new reactions.
Supervisor: Lapkin, Alexei Sponsor: Cambridge Trust ; Peterhouse
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
Keywords: networks ; network of organic chemistry ; chemoinformatics ; sustainability ; chemical engineering ; synthesis planning ; chemistry ; reaction prediction