Related papers: MetaChem: An Algebraic Framework for Artificial Ch…
Graph analysis is fundamental in real-world applications. Traditional approaches rely on SPARQL-like languages or clicking-and-dragging interfaces to interact with graph data. However, these methods either require users to possess high…
Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Large language models (LLMs) are beginning to reshape how chemists plan and run reactions in organic synthesis. Trained on millions of reported transformations, these text-based models can propose synthetic routes, forecast reaction…
We introduce Metatheory.jl: a lightweight and performant general purpose symbolics and metaprogramming framework meant to simplify the act of writing complex Julia metaprograms and to significantly enhance Julia with a native term rewriting…
Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction…
Metadata vocabularies are used in various domains of study. It provides an in-depth description of the resources. In this work, we develop Algorithm Metadata Vocabulary (AMV), a vocabulary for capturing and storing the metadata about the…
The new approach to representation of syntax of formal languages-- a formalism of syntax diagrams is offered. Syntax diagrams look a convenient language for the description of syntactic relations in the languages having nonlinear…
We present an oriented numerical summarizer algorithm, applied to producing automatic summaries of scientific documents in Organic Chemistry. We present its implementation named Yachs (Yet Another Chemistry Summarizer) that combines a…
For the calculation of complex neutral/ionized gas phase chemical equilibria, we present a semi-analytical versatile and efficient computer program, called FastChem. The applied method is based on the solution of a system of coupled…
Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized…
Large Language Models (LLMs) face significant limitations when applied to large-scale graphs, struggling with context constraints and inflexible reasoning. We present GraphChain, a framework that enables LLMs to analyze complex graphs…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
The applications of machine learning techniques to chemistry and materials science become more numerous by the day. The main challenge is to devise representations of atomic systems that are at the same time complete and concise, so as to…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
Natural language processing models have emerged that can generate usable software and automate a number of programming tasks with high fidelity. These tools have yet to have an impact on the chemistry community. Yet, our initial testing…
We explore the effectiveness and reliability of an artificial intelligence (AI)-based grading system for a handwritten general chemistry exam, comparing AI-assigned scores to human grading across various types of questions. Exam pages and…
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
In this paper we present Ethane, a parallel search algorithm specifically designed for its execution on heterogeneous hardware environments. With Ethane we propose an algorithm inspired in the structure of the chemical compound of the same…