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Action models are semantic structures similar to Kripke models that represent a change in knowledge in an epistemic setting. Whereas the language of action model logic embeds the semantic structure of an action model directly within the…
We present SynRXN, a unified benchmarking framework and open-data resource for computer-aided synthesis planning (CASP). SynRXN decomposes end-to-end synthesis planning into five task families, covering reaction rebalancing, atom-to-atom…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…
We provide a simple semi-classical formalism to describe the coupling between one or several quantum emitters and a structured environment. Describing the emitter by an electric polarizability, and the surrounding medium by a Green…
Understanding the evolution of electrified solid-liquid interfaces during electrochemical reactions is crucial. However, capturing the dynamic behavior of the interfaces with high temporal resolution and accuracy over long timescales…
In this paper an ontological representation and reasoning paradigm has been proposed for interpretation of time-series signals. The signals come from sensors observing a smart environment. The signal chosen for the annotation process is a…
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…
In recent years, there has been an increased need for the use of active systems - systems required to act automatically based on events, or changes in the environment. Such systems span many areas, from active databases to applications that…
A new lattice Boltzmann model for reactive ideal gas mixtures is presented. The model is an extension to reactive flows of the recently proposed multi-component lattice Boltzmann model for compressible ideal gas mixtures with Stefan-Maxwell…
It is standard in chemistry to represent a sequence of reactions by a single overall reaction, often called a complex reaction in contrast to an elementary reaction. Photosynthesis $6 \text{CO}_2+6 \text{H}_2\text{O} \to \…
Taking inspiration from the hypothesis of muscle synergies, we propose a method to generate open loop controllers for an agent solving point-to-point reaching tasks. The controller output is defined as a linear combination of a small set of…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
Patterns in reaction-diffusion systems near primary bifurcations can be studied locally and classified by means of amplitude equations. This is not possible for excitable reaction-diffusion systems. In this Letter we propose a global…
In nonmonotonic reasoning from conditional belief bases, an inference operator satisfying syntax splitting postulates allows for taking only the relevant parts of a belief base into account, provided that the belief base splits into…
The concept of reaction extent (the progress of a reaction, advancement of the reaction, conversion, etc.) was introduced around 100 years ago. Most of the literature provides a definition for the exceptional case of a single reaction step…
Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping…
Syntax is a latent hierarchical structure which underpins the robust and compositional nature of human language. In this work, we explore the hypothesis that syntactic dependencies can be represented in language model attention…
The distributed representations currently used are dense and uninterpretable, leading to interpretations that themselves are relative, overcomplete, and hard to interpret. We propose a method that transforms these word vectors into reduced…
We present a multimodal search tool that facilitates retrieval of chemical reactions, molecular structures, and associated text from scientific literature. Queries may combine molecular diagrams, textual descriptions, and reaction data,…
Circuit representations are becoming the lingua franca to express and reason about tractable generative and discriminative models. In this paper, we show how complex inference scenarios for these models that commonly arise in machine…