Related papers: Using RuleBuilder to graphically define and visual…
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…
In recent years, research on transforming natural language into graph query language (NL2GQL) has been increasing. Most existing methods focus on single-turn transformation from NL to GQL. In practical applications, user interactions with…
Dominant sequence models like the Transformer represent structure implicitly through dense attention weights, incurring quadratic complexity. We propose RewriteNets, a novel neural architecture built on an alternative paradigm: explicit,…
Machine learning models, and in particular language models, are being applied to various tasks that require reasoning. While such models are good at capturing patterns their ability to reason in a trustable and controlled manner is…
This paper introduces NLDS-QL, a translator of data science questions expressed in natural language (NL) into data science queries on graph databases. Our translator is based on a simplified NL described by a grammar that specifies…
The ever higher complexity of manufacturing systems, continually shortening life cycles of products and their increasing variety, as well as the unstable market situation of the recent years require introducing grater flexibility and…
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…
Existing paper review methods often rely on superficial manuscript features or directly on large language models (LLMs), which are prone to hallucinations, biased scoring, and limited reasoning capabilities. Moreover, these methods often…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…
Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications…
Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…
While Vision Language Models (VLMs) have demonstrated remarkable capabilities in general visual understanding, their application in the chemical domain has been limited, with previous works predominantly focusing on text and thus…
By combining voice and touch interactions, multimodal interfaces can surpass the efficiency of either modality alone. Traditional multimodal frameworks require laborious developer work to support rich multimodal commands where the user's…
Published biomedical information has and continues to rapidly increase. The recent advancements in Natural Language Processing (NLP), have generated considerable interest in automating the extraction, normalization, and representation of…
Software documentation frequently becomes outdated or fails to exist entirely, yet developers need focused views of their codebase to understand complex systems. While automated reverse engineering tools can generate UML diagrams from code,…
Model repair is an essential topic in model-driven engineering. Since models are suitably formalized as graph-like structures, we consider the problem of rule-based graph repair: Given a rule set and a graph constraint, try to construct a…
Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…