arXiv subjects

Benjamin Partridge

Publications and source records attributed to Benjamin Partridge.

3 recordsLinked to original sources

arXiv2024

Llettuce: An Open Source Natural Language Processing Tool for the Translation of Medical Terms into Uniform Clinical Encoding

This paper introduces Llettuce, an open-source tool designed to address the complexities of converting medical terms into OMOP standard concepts. Unlike existing solutions such as the Athena database search and Usagi, which struggle with semantic nuances and require substantial manual input, Llettuce leverages advanced natural language processing, including large language models and fuzzy matching, to automate and enhance the mapping process. Developed with a focus on GDPR compliance, Llettuce can be deployed locally, ensuring data protection while maintaining high performance in converting informal medical terms to standardised concepts.

cs.CL↗

arXiv2023

Modeling growing confluent tissues using a lattice Boltzmann method: interface stability and fluctuations

Tissue growth underpins a wide array of biological and developmental processes, and numerical modeling of growing systems has been shown to be a useful tool for understanding these processes. However, the phenomena that can be captured are often limited by the size of systems that can be modeled. Here, we address this limitation by introducing a Lattice-Boltzmann method (LBM) for a growing system that is able to efficiently model hydrodynamic length-scales. The model incorporates a novel approach to describing the growing front of a tissue, which we use to investigate the dynamics of the interface of growing model tissues. We find that the interface grows with scaling in agreement with the Kardar-Parisi-Zhang (KPZ) universality class when growth in the system is bulk driven. Interestingly, we also find the emergence of a previously unreported hydrodynamic instability when proliferation is restricted to the tissue edge. We then develop an analytical theory to show that the instability arises due to a coupling between the number of cells actively proliferating and the position of the interface.

cond-mat.soft↗

arXiv2018

Critical motility-induced phase separation belongs to the Ising universality class

A collection of self-propelled particles with volume exclusion interactions can exhibit the phenomenology of gas-liquid phase separation, known as motility-induced phase separation (MIPS). The non-equilibrium nature of the system is fundamental to the phase transition, however, it is unclear whether MIPS at criticality contributes a novel universality class to non-equilibrium physics. We demonstrate here that this is not the case by showing that a generic critical MIPS belongs to the Ising universality class with conservative dynamics.

cond-mat.soft↗