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We provide an overview of the emergence of large language models for scientific computing applications. We highlight use cases that involve natural language processing of scientific documents and specialized languages designed to describe…
The well-known Unified Modeling Language (UML) describes software entities, such as interfaces, classes, operations and attributes, as well as relationships among them, e.g. inheritance, containment and dependency. The power of UML lies in…
Different from general documents, it is recognised that the ease with which people can understand a biomedical text is eminently varied, owing to the highly technical nature of biomedical documents and the variance of readers' domain…
Text embeddings have become an essential part of a variety of language applications. However, methods for interpreting, exploring and reversing embedding spaces are limited, reducing transparency and precluding potentially valuable…
We develop a system that formally represents spatial semantics concepts within natural language descriptions of spatial arrangements. The system builds on a model of spatial semantics representation according to which words in a sentence…
Any file is fundamentally a binary data stream. A practical solution was achieved to interpret binary data stream. A new scripting language named Data Format Scripting Language (DFSL) was developed to describe the physical layout of the…
Antimony is a high-level, human-readable text-based language designed for defining and sharing models in the systems biology community. It enables scientists to describe biochemical networks and systems using a simple and intuitive syntax.…
This paper presents boldsea, Boldachev's semantic-event approach -- an architecture for modeling complex dynamic systems using executable ontologies -- semantic models that act as dynamic structures, directly controlling process execution.…
Deep learning has significantly accelerated drug discovery, with 'chemical language' processing (CLP) emerging as a prominent approach. CLP learns from molecular string representations (e.g., Simplified Molecular Input Line Entry Systems…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
User-schedulable languages (USLs) help programmers productively optimize programs by providing safe means of transforming them. Current USLs are designed to give programmers exactly the control they want, while automating all other…
Biological nervous systems exhibit astonishing complexity .Neuroscientists aim to capture this com- plexity by modeling and simulation of biological processes. Often very comple xm odels are nec- essary to depict the processes, which makes…
In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for…
Building software-driven systems that are easily understood becomes a challenge, with their ever-increasing complexity and autonomy. Accordingly, recent research efforts strive to aid in designing explainable systems. Nevertheless, a common…
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…
Large language models (LLMs) are deployed in a wide variety of user-facing applications. Typically, these deployments have some specific purpose, like answering questions grounded on documentation or acting as coding assistants, but they…
Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and…
The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an…
Chemical compound space (CCS), the set of all theoretically conceivable combinations of chemical elements and (meta-)stable geometries that make up matter, is colossal. The first principles based virtual sampling of this space, for example…
Lexical simplification has attracted much attention in many languages, which is the process of replacing complex words in a given sentence with simpler alternatives of equivalent meaning. Although the richness of vocabulary in Chinese makes…