Grounding Large Language Models (LLMs) in chemical knowledge graphs (KGs) offers a promising way to support synthesis planning, but reliably retrieving information from these complex structures remains a challenge. Therefore, this work addresses that gap by constructing a bipartite KG and evaluating Text2Cypher query generation across both single- and multi-step retrieval tasks. Different prompting strategies were tested, including zero-shot, one-shot with static, random, or embedding-based example selection, and a checklist-driven self-correction pipeline. Results indicate that one-shot prompting is most effective when the exemplar aligns with the query both structurally and logically. When such an exemplar is provided as context to the Cypher generation prompt, self-correction does not yield significant performance gains. Overall, this study introduces a reproducible setup for Text2Cypher experimentation and evaluation. ... Read more

Motivation: Metabolic kinetic models are widely used to model biological systems. Despite their widespread use, it remains challenging to parameterize these Ordinary Differential Equations (ODE) for large scale kinetic models. Recent work on neural ODEs has shown the potential for modeling time-series data using neural networks, and many methodological developments in this field can similarly be applied to kinetic models. Results: We have implemented a simulation and training framework for Systems Biology Markup Language (SBML) models using JAX/Diffrax, which we named jaxkineticmodel. JAX allows for automatic differentiation and just-in-time compilation capabilities to speed up the parameterization of kinetic models, while also allowing for hybridizing kinetic models with neural networks. We show the robust capabilities of training kinetic models using this framework on a large collection of SBML models with different degrees of prior information on parameter initialization. We furthermore showcase the training framework implementation on a complex model of glycolysis. Finally, we show an example of hybridizing kinetic model with a neural network if a reaction mechanism is unknown. These results show that our framework can be used to fit large metabolic kinetic models efficiently and provides a strong platform for modeling biological systems. Implementation: Implementation of jaxkineticmodel is available as a Python package at https://github.com/AbeelLab/jaxkineticmodel. ... Read more