Related papers: A Software Package for Chemically Inspired Graph T…

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these…

Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited…

The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…

We study binomiality of the steady state ideals of chemical reaction networks. Considering rate constants as indeterminates, the concept of unconditional binomiality has been introduced and an algorithm based on linear algebra has been…

Rapid discovery of new reactions and molecules in recent years has been facilitated by the advancements in high throughput screening, accessibility to a much more complex chemical design space, and the development of accurate molecular…

We target the problem of provably computing the equivalence between two complex expression trees. To this end, we formalize the problem of equivalence between two such programs as finding a set of semantics-preserving rewrite rules from one…

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph…

This work is about diagrammatic languages, how they can be represented, and what they in turn can be used to represent. More specifically, it focuses on representations and applications of string diagrams. String diagrams are used to…

This paper investigates the use of graph rewriting systems as a modelling tool, and advocates the embedding of such systems in an interactive environment. One important application domain is the modelling of biochemical systems, where…

We introduce a new class of graph transformation systems in which rewrite rules can be guarded by universally quantified conditions on the neighbourhood of nodes. These conditions are defined via special graph patterns which may be…

The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional…

Chemputation reframes synthesis as the programmable execution of reaction code on a universally re-configurable hardware graph. Here we prove that a chemputer equipped with a finite, but extensible, set of reagents, catalysts and process…

In the last decade, temporal networks and static and temporal hypergraphs have enabled modelling connectivity and spreading processes in a wide array of real-world complex systems such as economic transactions, information spreading, brain…

Double-pushout rewriting is an established categorical approach to the rule-based transformation of graphs and graph-like objects. One of its standard results is the construction of concurrent rules and the Concurrency Theorem pertaining to…

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of…

In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…

Here I report about the modifications of and relations between graphic lambda calculus, various formalisms which appeared under the name chemlambda and a version of directed interaction combinators. This is part of the study and experiments…

ReacProc is a program written in C/C++ programming language which can be used (1) to check out of reactions describing particles interactions against conservation laws and (2) to reduce input reaction into some canonical form. A table with…

In this work we target the problem of provably computing the equivalence between two programs represented as dataflow graphs. To this end, we formalize the problem of equivalence between two programs as finding a set of semantics-preserving…

Graph translation is very promising research direction and has a wide range of potential real-world applications. Graph is a natural structure for representing relationship and interactions, and its translation can encode the intrinsic…