arXiv subjects

Supun Manathunga

Publications and source records attributed to Supun Manathunga.

4 recordsLinked to original sources

arXiv2026

When to repeat a biomarker test? Decomposing sources of variation from conditionally repeated measurements

Repeating an imperfect biomarker test based on an initial result can introduce bias and influence misclassification risk. For example, in some blood donation settings, blood donors' hemoglobin is remeasured when the initial measurement falls below a minimum threshold for donor eligibility. This paper explores methods that use data resulting from processes with conditionally repeated biomarker measurement to decompose the variation in observed measurements of a continuous biomarker into population variability and variability arising from the measurement procedure. We present two frequentist approaches with analytical solutions, but these approaches perform poorly in a dataset of conditionally repeated blood donor hemoglobin measurements where normality assumptions are not met. We then develop a Bayesian hierarchical framework that allows for different distributional assumptions, which we apply to the blood donor hemoglobin dataset. Using a Bayesian hierarchical model that assumes normally distributed population hemoglobin and heavy tailed $t$-distributed measurement variation, we found that the total measurement variation accounted for 22\% of the total variance among females and 25\% among males, with population standard deviations of $1.07\, \rm g/dL$ for female donors and $1.28\, \rm g/dL$ for male donors. Our Bayesian framework can use data resulting from any clinical process with conditionally repeated biomarker measurements to estimate individuals' misclassification risk after one or more noisy continuous measurements and inform evidence-based conditional retesting decision rules.

stat.AP↗

arXiv2025

PoPStat-COVID19: Leveraging Population Pyramids to Quantify Demographic Vulnerability to COVID-19

Understanding how population age structure shapes COVID-19 burden is crucial for pandemic preparedness, yet common summary measures such as median age ignore key distributional features like skewness, bimodality, and the proportional weight of high-risk cohorts. We extend the PoPStat framework, originally devised to link entire population pyramids with cause-specific mortality by applying it to COVID-19. Using 2019 United Nations World Population Prospects age-sex distributions together with cumulative cases and deaths per million recorded up to 5 May 2023 by Our World in Data, we calculate PoPDivergence (the Kullback-Leibler divergence from an optimised reference pyramid) for 180+ countries and derive PoPStat-COVID19 as the Pearson correlation between that divergence and log-transformed incidence or mortality. Optimisation selects Malta's old-skewed pyramid as the reference, yielding strong negative correlations for cases (r=-0.86, p<0.001, R^2=0.74) and deaths (r=-0.82, p<0.001, R^2=0.67). Sensitivity tests across twenty additional, similarly old-skewed references confirm that these associations are robust to reference choice. Benchmarking against eight standard indicators like gross domestic product per capita, Gini index, Human Development Index, life expectancy at birth, median age, population density, Socio-demographic Index, and Universal Health Coverage Index shows that PoPStat-COVID19 surpasses GDP per capita, median age, population density, and several other traditional measures, and outperforms every comparator for fatality burden. PoPStat-COVID19 therefore provides a concise, distribution-aware scalar for quantifying demographic vulnerability to COVID-19.

stat.AP↗

arXiv2025

Devising PoPStat: A Metric Bridging Population Pyramids with Global Disease Mortality

Understanding the relationship between population dynamics and disease-specific mortality is central to evidence-based health policy. This study introduces two novel metrics, PoPDivergence and PoPStat, one to quantify the difference between population pyramids and the other to assess the strength and nature of their association with the mortality of a given disease. PoPDivergence, based on Kullback-Leibler divergence, measures deviations between a countrys population pyramid and a reference pyramid. PoPStat is the correlation between these deviations and the log form of disease-specific mortality rates. The reference population is selected by a brute-force optimization that maximizes this correlation. Utilizing mortality data from the Global Burden of Disease 2021 and population statistics from the United Nations, we applied these metrics to 371 diseases across 204 countries. Results reveal that PoPStat outperforms traditional indicators such as median age, GDP per capita, and Human Development Index in explaining the mortality of most diseases. Noncommunicable diseases (NCDs) like neurological disorders and cancers, communicable diseases (CDs) like neglected tropical diseases, and maternal and neonatal diseases were tightly bound to the underlying demographic attributes whereas NCDs like diabetes, CDs like respiratory infections and injuries including self-harm and interpersonal violence were weakly associated with population pyramid shapes. Notably, except for diabetes, the NCD mortality burden was shared by constrictive population pyramids, while mortality of communicable diseases, maternal and neonatal causes and injuries were largely borne by expansive pyramids. Therefore, PoPStat provides insights into demographic determinants of health and empirical support for models on epidemiological transition. Code and scripts: https://github.com/Buddhi19/DevisingPoPStat.git

stat.AP↗

arXiv2023

Aligning Large Language Models for Clinical Tasks

Large Language Models (LLMs) have demonstrated remarkable adaptability, showcasing their capacity to excel in tasks for which they were not explicitly trained. However, despite their impressive natural language processing (NLP) capabilities, effective alignment of LLMs remains a crucial challenge when deploying them for specific clinical applications. The ability to generate responses with factually accurate content and to engage in non-trivial reasoning steps are crucial for the LLMs to be eligible for applications in clinical medicine. Employing a combination of techniques including instruction-tuning and in-prompt strategies like few-shot and chain-of-thought prompting has significantly enhanced the performance of LLMs. Our proposed alignment strategy for medical question-answering, known as 'expand-guess-refine', offers a parameter and data-efficient solution. A preliminary analysis of this method demonstrated outstanding performance, achieving a score of 70.63% on a subset of questions sourced from the USMLE dataset.

cs.CL↗