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The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
In this paper we propose a novel approach to identify dynamical systems. The method estimates the model structure and the parameters of the model simultaneously, automating the critical decisions involved in identification such as model…
This book objective is to develop an algebraization of graph grammars. Equivalently, we study graph dynamics. From the point of view of a computer scientist, graph grammars are a natural generalization of Chomsky grammars for which a purely…
Graph clustering aims at discovering a natural grouping of the nodes such that similar nodes are assigned to a common cluster. Many different algorithms have been proposed in the literature: for simple graphs, for graphs with attributes…
Chemical theory can be made more rigorous using the Lean theorem prover, an interactive theorem prover for complex mathematics. We formalize the Langmuir and BET theories of adsorption, making each scientific premise clear and every step of…
A GraphMaps is a system that visualizes a graph using zoom levels, which is similar to a geographic map visualization. GraphMaps reveals the structural properties of the graph and enables users to explore the graph in a natural way by using…
Formal proofs are challenging to write even for experienced experts. Recent progress in Neural Theorem Proving (NTP) shows promise in expediting this process. However, the formal corpora available on the Internet are limited compared to the…
Most chemical processes, such as distillation, absorption, extraction, and catalytic reactions, are extremely complex processes that are affected by multiple factors. The relationships between their input variables and output variables are…
Applications of machine learning in chemistry are often limited by the scarcity and expense of labeled data, restricting traditional supervised methods. In this work, we introduce a framework for molecular reasoning using general-purpose…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
Procedural material graphs are a compact, parameteric, and resolution-independent representation that are a popular choice for material authoring. However, designing procedural materials requires significant expertise and publicly…
Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to…
In this note, we introduce the notion of support graph to define explanations for any model of a logic program. An explanation is an acyclic support graph that, for each true atom in the model, induces a proof in terms of program rules…
Mass spectrometry-based metabolomics generates complex, high-dimensional data that holds vast potential for biological discovery but remains difficult to integrate and interpret. Knowledge graphs (KGs) unify this heterogeneous information…
A new graph-based order parameter is introduced for the characterization of atomistic structures. The order parameter is universal to any material/chemical system, and is transferable to all structural geometries. Three sets of data are…
This paper presents a large language model (LLM) agent named AgentCAT, which extracts and analyzes catalytic reaction data from chemical engineering papers, %and supports natural language based interactive analysis of the extracted data.…
Synthetic polymers are versatile and widely used materials. Similar to small organic molecules, a large chemical space of such materials is hypothetically accessible. Computational property prediction and virtual screening can accelerate…
Chemical disorder, originating from the mixed occupation of crystallographic sites by multiple elements, is widespread in alloys, ceramics, and compositionally complex materials, where short- and long-range orderings can strongly influence…
Large-scale electrification is vital to addressing the climate crisis, but several scientific and technological challenges remain to fully electrify both the chemical industry and transportation. In both of these areas, new electrochemical…
We introduce and investigate the concept of Stratified Algebra, a new algebraic framework equipped with a layer-based structure on a vector space. We formalize a set of axioms governing intra-layer and inter-layer interactions, study their…