Automated Discovery of Chemical Reaction Networks using Program Synthesis
R.A. Wijers (TU Delft - Electrical Engineering, Mathematics and Computer Science)
Sebastijan Dumančić – Mentor (TU Delft - Algorithmics)
R.J. Gardos Reid – Mentor (TU Delft - Algorithmics)
Jana M. Weber – Mentor (TU Delft - Pattern Recognition and Bioinformatics)
N. Yorke-Smith – Graduation committee member (TU Delft - Algorithmics)
J.A. Baaijens – Graduation committee member (TU Delft - Pattern Recognition and Bioinformatics)
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Abstract
This thesis explores the automated construction of Chemical Reaction Networks (CRNs) from incomplete experimental data, a task traditionally dependent on expert knowledge and manual effort. CRNs model the interactions between chemical species through a network of reactions and are essential in fields such as medicine and chemistry. However, many real-world systems include unobserved or unmeasurable species, making CRN construction challenging. To address this, this thesis frames CRN discovery as a program synthesis problem, using grammars and constraints to define the space of possible CRNs. A modular synthesis pipeline is developed that incrementally builds candidate molecules, reactions, and networks given a problem definition. Experimental results demonstrate that constraints effectively reduce the search space and that the solver is capable of identifying the correct reaction networks. Moreover, a scoring mechanism ranks the expected CRN highly among generated candidates.