arXiv subjects

Liam Wright

Publications and source records attributed to Liam Wright.

4 recordsLinked to original sources

arXiv2026

Agentic coding without the cloud: evaluating open-weight large language models on longitudinal data preparation tasks

Large language models (LLMs) and agents are now widely used tools in code development, with data typically sent to third-party cloud-based models. Their adoption in research using personal data is constrained by governance requirements that typically prohibit data transmission to external services. Locally deployable open-weight models offer an alternative since sensitive data never leave the local environment. We introduce an open-source framework for evaluating the efficacy of AI agents powered by open-weight LLMs on one of the most persistent bottlenecks in research on longitudinal population studies: data preparation. The framework comprises: a curated ground-truth dataset (cleaning scripts preparing six sweeps of data from a British cohort study), task definitions encompassing tasks such as category harmonization and multi-wave merging, and automated routines for evaluating the LLM-produced R code and outputted data. We benchmark LLMs across the (consumer grade) deployment spectrum to assess their efficacy in 20 data preparation tasks (creation of 102 variables). Current state-of-the-art, 31-35B parameter models almost saturated our benchmark ('average task completion' up to 87.9%). The performance of open-weight LLMs running on consumer-grade hardware shows promise of a viable path toward AI-assisted data preparation in governance-restricted research settings. Our framework is publicly available at: https://github.com/UCL-ARC/RRBench.

cs.AI↗

arXiv2026

TrueEBSD in MTEX: automatic image matching for correlative microscopy applications

TrueEBSD is an open-source MATLAB program for image alignment and spatial distortion correction of images and electron backscatter diffraction (EBSD) maps. We have re-implemented TrueEBSD as an add-on to MTEX, an established toolbox for EBSD data analysis. Spatial alignment enables correlative analysis methods, such as augmenting EBSD orientation maps with data from other imaging modes. The augmented EBSD maps can then be analysed further using MTEX. We demonstrate TrueEBSD on two example case studies: one for measuring Co phase fraction and WC contiguity in a WC-Co composite, and another for determining the relative susceptibility of grain boundaries to void formation in a copper polycrystal. In both examples, the EBSD map was augmented with scanning electron microscopy (SEM) image data. This enabled quantitative crystallographic measurements which would not be possible from analysing the EBSD maps and images separately.

cond-mat.mtrl-sci↗

arXiv2025

How can the use of different modes of survey data collection introduce bias? A simple introduction to mode effects using directed acyclic graphs (DAGs)

Survey data are self-reported data collected directly from respondents by a questionnaire or an interview and are commonly used in epidemiology. Such data are traditionally collected via a single mode (e.g. face-to-face interview alone), but use of mixed-mode designs (e.g. offering face-to-face interview or online survey) has become more common. This introduces two key challenges. First, individuals may respond differently to the same question depending on the mode; these differences due to measurement are known as 'mode effects'. Second, different individuals may participate via different modes; these differences in sample composition between modes are known as 'mode selection'. Where recognised, mode effects are often handled by straightforward approaches such as conditioning on survey mode. However, while reducing mode effects, this and other equivalent approaches may introduce collider bias in the presence of mode selection. The existence of mode effects and the consequences of na\"ive conditioning may be underappreciated in epidemiology. This paper offers a simple introduction to these challenges using directed acyclic graphs by exploring a range of possible data structures. We discuss the potential implications of using conditioning- or imputation-based approaches and outline the advantages of quantitative bias analyses for dealing with mode effects.

stat.ME↗

arXiv2025

Why can't Epidemiology be automated (yet)?

Recent advances in artificial intelligence (AI) - particularly generative AI - present new opportunities to accelerate, or even automate, epidemiological research. Unlike disciplines based on physical experimentation, a sizable fraction of Epidemiology relies on secondary data analysis and thus is well-suited for such augmentation. Yet, it remains unclear which specific tasks can benefit from AI interventions or where roadblocks exist. Awareness of current AI capabilities is also mixed. Here, we map the landscape of epidemiological tasks using existing datasets - from literature review to data access, analysis, writing up, and dissemination - and identify where existing AI tools offer efficiency gains. While AI can increase productivity in some areas such as coding and administrative tasks, its utility is constrained by limitations of existing AI models (e.g. hallucinations in literature reviews) and human systems (e.g. barriers to accessing datasets). Through examples of AI-generated epidemiological outputs, including fully AI-generated papers, we demonstrate that recently developed agentic systems can now design and execute epidemiological analysis, albeit to varied quality (see https://github.com/edlowther/automated-epidemiology). Epidemiologists have new opportunities to empirically test and benchmark AI systems; realising the potential of AI will require two-way engagement between epidemiologists and engineers.

cs.CY↗