Most of the members of this group are from the Statistics Section and Biomaths research group of the Department of Mathematics. Below you can find a list of research areas that members of this group are currently working on and/or would like to work on by applying their developed mathematical and statistical methods.
Research areas
Research areas
- Systems Biology
- Statistical genomics and Epidemiology
- Medical Imaging
- Precision and Stratified Medicine
- Analysis of clinical trials, observational and longitudinal studies
- Infectious Disease Epidemiology
Publications
Results
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Journal articleKaveh F, Green A, Jones N, 2026,
The Joint Spectrum over Trees under the Kingman coalescent with varying population.
, Theor Popul Biol, Vol: 171, Pages: 59-78The Kingman coalescent process models the genealogy of a sample taken from a large population of individuals who reproduce and die according to models such as the Moran or Wright-Fisher processes. The occurrence and spread of neutral mutations in the sample can be modelled by a Poisson process over sample phylogenies from the Kingman coalescent. We study the joint probability distribution of frequencies for multiple mutations occurring on the same tree. We call this the Joint Spectrum over Trees (JST). We derive a closed-form solution for this joint distribution in the case of two mutations with varying population size. We specialise the result for specific population histories, including constant population size. In the process, we highlight how different averaging procedures can lead to different distributions for the frequency of mutations, even when considering only the frequency of a single mutation. We provide a systematic approximation scheme for the Joint Spectrum over Trees under constant population when the number of samples is large. The exact form of the Joint Spectrum over Trees has implications for genealogical inference with the Kingman coalescent, specifically for the characterisation of tree structure near the root and in parameter inference when the underlying tree structures are unknown. To this end, we also comment on the validity of the independence approximation to the true joint distribution under different population histories.
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Journal articleChertock A, Degond P, Sagiv A, et al., 2026,
The Evolution of Pointwise Statistics in Hyperbolic Equations with Random Data
, SIAM/ASA Journal on Uncertainty Quantification, Vol: 14, Pages: 1045-1079<jats:p>Abstract.</jats:p> <jats:p>We consider one-dimensional hyperbolic PDEs, linear and nonlinear, with random initial data. Our focus is the pointwise statistics, i.e., the probability measure of the solution at any fixed point in space and time. For linear hyperbolic equations, the probability density function (PDF) of these statistics satisfies the same linear PDE. For nonlinear hyperbolic PDEs, we derive a linear transport equation for the cumulative distribution function (CDF) and a nonlocal linear PDE for the PDF. Both results are valid only as long as no shocks have formed, a limitation which is inherent to the problem, as demonstrated by a counterexample. For systems of linear hyperbolic equations, we introduce the multi-point statistics and derive their evolution equations. In all of the settings we consider, the resulting PDEs for the statistics are of practical significance: they enable efficient evaluation of the random dynamics, without requiring an ensemble of solutions of the underlying PDE, and their cost is not affected by the dimension of the random parameter space. Additionally, the evolution equations for the statistics lead to a priori statistical error bounds for Monte Carlo methods (in particular, kernel density estimators) when applied to hyperbolic PDEs with random data.</jats:p>
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Journal articleHalder A, Peiris HV, Thorp S, et al., 2026,
<tt>pop-cosmos</tt> : redshifts and physical properties of KiDS-1000 galaxies
, Monthly Notices of the Royal Astronomical Society, Vol: 551, ISSN: 0035-8711<jats:title>ABSTRACT</jats:title> <jats:p>Principled Bayesian inference of galaxy properties has not previously been performed for wide-area weak-lensing surveys with millions of sources. We address this gap by applying the pop-cosmos generative model to perform spectral energy distribution (SED) fitting for 4 million KiDS (Kilo-Degree Survey)-1000 galaxies. Calibrated on deep COSMOS2020 photometric data, pop-cosmos specifies a physically motivated prior over the galaxy population up to $z \simeq 6$ in stellar population synthesis (SPS) parameter space. Using the Speculator SPS emulator with GPU (graphics processing unit)-accelerated Markov Chain Monte Carlo sampling, we perform full posterior inference at 8.2 GPU seconds per galaxy, obtaining joint constraints on galaxy redshifts and physical properties. We validate photometric redshifts against $\sim \!185\,\!000$ KiDS galaxies cross-matched to Dark Energy Spectroscopic Instrument Data Release 1 spectroscopic samples, achieving low bias ($2\times 10^{-3}$), scatter ($\sigma _{\mathrm{MAD}}=0.03$), and outlier fraction (3.2 per cent) for the Bright Galaxy Survey, with comparable performance (bias $3\times 10^{-2}$, $\sigma _{\mathrm{MAD}}=0.05$, 1.0 per cent outliers) for luminous red galaxies (LRGs). Within the LRG sample, we identify massive, dusty, star-forming contaminants at $z \simeq 0.4$ satisfying standard colour selections for quenched populations. We infer trends in stellar mass, star formation, metallicity, and dust across five tomographic redshift bins consistent with established scaling relations. Using specific star formation rate constraints, we identify $\sim$7 per cent of KiDS-1000 galaxies as quenched, versus 37 per cent implied by conservative colour cuts. This enables the construction of weak-lensing samples defined by physical properties while mitigating intrinsic alignment systematics and preserving statist
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Journal articleGartside J, 2026,
Few-shot neuromorphic vision in a nonlinear photonic network laser
, Science Advances, ISSN: 2375-2548With the growing prevalence of AI, demand increases for hardware that mimics the brain’s ability to extract structure from limited data. In the retina, ganglion cells detect features from sparse inputs via lateral inhibition, where neurons antagonistically suppress activity of neighbouring cells. Biological neurons exhibit diverse heterogeneous nonlinear responses, linked to robustlearning and strong performance in low-data regimes.Here, we introduce a retinally-inspired photonic computing system where spatially-competing lasing modes in a random network laser act as heterogeneous, inhibitively-coupled neurons- enabling feature detection, few-shot classification, and segmentation. This silicon-compatible scheme harnesses heterogeneous excitatory and inhibitory nonlinear physical dynamics which give rise to emergent photonic computing behaviour, including parallel feature detection and strong performance when training data is scarce. We report 98.05% and 87.85% accuracy on MNIST and Fashion-MNIST, and 90.12% on BreaKHis cancer diagnosis- outperforming software CNNs including EfficientNetV2 and the vision transformer ViT in few-shot and class-imbalanced regimes with training sets of up to several hundred images. We demonstrate combined segmentation and classification on the HAM10k skin lesion dataset, achieving DICE and Jaccard scores of 84.49% and 74.80%. These results demonstratethe potential of random lasing networks as nonlinear photonic learning systems, and highlight the ability of heterogeneous nonlinear dynamics to support strong learning in challenging low-data scenarios.
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Journal articleTucker S, Baldonado N, Ruina OH, et al., 2026,
Effectiveness of the hope groups intervention on mental health, parenting practices, and violence against children among Ukrainian parents and caregivers affected by war and displacement: a cluster randomised controlled trial
, The Lancet Regional Health - Europe, ISSN: 2666-7762BackgroundAlmost two-thirds of the world’s children live in conflict-affected countries, including Ukraine, where two-thirds of children were displaced after Russia’s 2022 invasion. To address the urgent need for effective approaches to support parents and protect children in war, we designed Hope Groups—a group-based mental health, parenting, and violence prevention intervention—and used a cluster randomised controlled trial (cRCT) to evaluate its effectiveness.MethodsWe conducted a two-arm, parallel cRCT comprising K = 90 clusters and N = 510 parents/caregivers, who were internally displaced, externally displaced, or at home in war-affected Ukraine. Primary outcomes, assessed at baseline and after completing the 12-session intervention (endline), included caregiver mental health, parenting practices, and violence against children. Clusters were randomly assigned to immediate Hope Groups intervention (K = 45; N = 255) or waitlist control (K = 45; N = 255). Interim analyses were conducted after the first 20 clusters reached trial endline. The trial was prospectively registered with Open Science Framework (https://osf.io/uvj67) and subsequently registered on ClinicalTrials.gov to align with ICMJE guidance (NCT07470333).FindingsAfter completion of the 12-session intervention, the Hope Groups intervention demonstrated medium-to-large effects across all measured primary outcomes compared with the control arm. Caregivers in the intervention arm reported 57.4% lower levels of parental depression and anxiety (β = −2.85; 95% CI = −3.49, −2.22; d = −0.86); 52.7% lower levels of violence against children (β = −0.5; 95% CI = −0.64, −0.36; d = −0.43); 33% higher parenting practices (β = 1.32, 95% CI = 0.92, 1.71, d = 0.57), compared to the control arm. Response rate was high: 98.6%. There were no adverse events or harms.InterpretationThe results demonstrate that the Hope Groups intervention i
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Journal articleGeorgiev D, Xie R, Reumann D, et al., 2026,
Label-free biochemical imaging and timepoint analysis of neural organoids via deep learning-enhanced Raman microspectroscopy
, Science Advances, ISSN: 2375-2548Three-dimensional organoids have emerged as powerful models for studying human development, disease and drug response in vitro. Yet, their analysis remains constrained by standard imaging and characterisation techniques, which are invasive, require exogenous labelling and offer limited multiplexing. Here, we present a non-invasive, label-free imaging platform that integrates Raman microspectroscopy with deep learning-based hyperspectral unmixing for unsupervised, spatiallyresolved biochemical analysis of neural organoids. Our approach enables 2D and 3D mapping of cellular and subcellular structures in both cryosectioned and intact organoids, achieving improved imaging accuracy and robustness compared to conventional methods for hyperspectral analysis. Using our platform, we demonstrate volumetric imaging of a neural rosettewithin a neural organoid, and interrogate changes in biochemical composition during early developmental stages in intact neural organoids, revealing spatiotemporal variations in lipids, proteins and nucleic acids. This work establishes a versatile framework for high-content, label-free (bio)chemical phenotyping with broad applications in organoid research and beyond.
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Journal articleKim S, Blenkinsop A, Martin MA, et al., 2026,
Molecular Epidemiology of HIV in an African Epidemic with Declining HIV incidence but High Prevalence: A Longitudinal, Population-based Study in Uganda.
, medRxivBACKGROUND: As HIV incidence declines in African settings with high treatment coverage, it remains unclear how transmission is structured within populations and whether new infections arise from external introductions or local transmission. We characterized the molecular epidemiology of ongoing transmission in a mature multi-subtype epidemic in Uganda. METHODS: We analyzed HIV genome sequences and survey data from the Rakai Community Cohort Study collected between 1994 and 2019. We identified phylogenetic clusters at 5·3% and 2·5% genetic distance thresholds and inferred long-horizon transmission chains with phylogeographic models. Newly diagnosed infections identified between 2016 and 2019 were mapped onto subtype- specific phylogenies to assess their origins and transmission context. A Bayesian negative binomial branching process model estimated undersampled chain sizes and case reproduction numbers. FINDINGS: Among 4215 participants living with HIV between December 2016 and May 2019, 474 were newly diagnosed, of whom 269 had at least one pure-subtype sequence available. We identified 649 phylogenetic clusters at 5·3% genetic distance and 673 phylogeographic chains including ≥2 individuals. Most clusters and chains were small (median sizes 2 [IQR 2-3] and 3 [2-4], respectively), with new diagnoses rarely clustered together. Only 46/269 (17·1%) new diagnoses had phylogeographic external origins, while the remaining 82·9% were partially or fully linked to local chains. Mixed-subtypes/recombinant chains were larger and had higher case reproduction numbers (A1/D: 0.84 [95% CrI: 0.79-0.93]; mixed: 0.84 [0.73-0.97]) than single- subtype chains (A1: 0.56 [0.51-0.60]; D: 0.63 [0.59-0.66]; C: 0.55 [0.41-0.71]), yet all estimates were less than one. INTERPRETATION: HIV transmission was fragmented across numerous, slowly propagating lineages, maintained by local clusters with occasional introduction. Continued transmission across many ch
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Journal articleHartley J, Kelly S, Team VS, et al., 2026,
Moderately age-disparate relationships dominate phylogenetically linked pairs involving young women with HIV in KwaZulu-Natal, South Africa
, International Journal of Infectious Diseases, Vol: 169, ISSN: 1201-9712ObjectivesYoung women aged 15-24 years bear a disproportionate burden of new human immunodeficiency virus (HIV) infections in sub-Saharan Africa. Age-disparate relationships with older men have been proposed as a major contributor to this pattern.MethodsWe conducted whole-genome sequencing of HIV in large cohort of individuals in KwaZulu-Natal, South Africa (the Vukuzazi cohort). Samples with viral loads >50 copies/mL were sequenced. Genomes passing quality control were grouped into clusters using maximum likelihood phylogenetic analysis. Potential transmission pairs were analyzed alongside participant age and sex data. A Bayesian random-effects model estimated transmission rates between demographic groups while accounting for population age-sex structure.ResultsAmong 18,025 participants enrolled in 2018-2020, 6096 were HIV-positive. Sequencing yielded 1097 genomes, identifying 89 clusters containing 205 individuals and 73 likely male-female linked phylogenetic pairs. Across pairs, men were a median of 5 years older than women (interquartile range −1 to 12). Women aged <30 years paired with men aged a median of 7 years older, whereas among women aged ≥30 years men were typically younger. After accounting for population structure, the strongest signal for transmission was between women aged 25-29 years and men up to 4 years older.ConclusionRelative transmission rates were greatest with moderate age differences. Large intergenerational age gaps were not dominant.
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Journal articleLeung HH, Wild V, Papathomas M, et al., 2026,
Spatially resolved star formation histories of local post-starburst galaxies: starburst and quenching spatial patterns consistent with recent mergers
, Monthly Notices of the Royal Astronomical Society, Vol: 550, ISSN: 0035-8711Post-starburst (PSB) galaxies, having recently experienced a starburst followed by rapid quenching, are excellent laboratories to probe physical mechanisms that drive starbursts and shutting down of star formation. Integral-field spectroscopy reveals the galaxies’ spatially resolved properties, where observed directional patterns can be linked to the galaxies’ past evolution. We measure the resolved star formation histories, stellar metallicity evolution, and dust properties of three local PSBs from the MaNGA survey, down to 0.5 arcsec resolution ((Formula presented) kpc) using a hierarchical Bayesian model. Local parameters were constrained simultaneously with parameters describing spatial trends. We found that all three galaxies first experienced an outer, weaker, and slower quenching starburst, followed by a central, stronger and faster quenching starburst that peaked (Formula presented) Gyr after the first. The central starbursts induced a significantly stronger rise in stellar metallicity compared to the outer starbursts. These results are consistent with the effects of a recent gas-rich (wet) merger, where the first pericentre passage triggered starbursts in the outer regions, while the later coalescence triggers a stronger centralized starburst. We find non-axisymmetric features in the maps of burst mass fraction and dust attenuation in all galaxies, which could be caused by tidal effects during the recent merger. Comparisons with literature binary merger simulations suggest that the galaxies’ rapid quenching was driven by gas consumption and the stabilization against gas gravitational collapse by a growing spheroid, while AGN feedback was not necessarily a primary cause.
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Journal articleBattey H, Rasines DG, Tang Y, 2026,
Post-reduction inference for confidence sets of models
, Biometrika, ISSN: 0006-3444Sparsity in a regression context makes the model itself an object of interest, pointing to a confidence set of models as the appropriate presentation of evidence. A difficulty in areas such as genomics, where the number of candidate variables is vast, arises from the need for preliminary reduction prior to the assessment of models. The present paper considers a resolution usinginferential separations fundamental to the Fisherian approach to conditional inference, namely, the sufficiency/co-sufficiency separation, and the ancillary/co-ancillary separation. Tests of model adequacy based on such separations do not involve specifying a direction for departure from any postulated model, avoiding issues of calibration that would arise in directed tests from using the same data for reduction and for model assessment. In idealised cases with no nuisance parameters, the separations extract the relevant information without loss or redundancy. The extent to which estimation of nuisance parameters affects this idealisation is illustrated in detail for the normal theory linear regression model, extending immediately to a log-normal accelerated-life model for time-to-event outcomes. As part of the analysis, we introduce a modified version of the refitted cross-validation estimator of Fan et al. (2012), whose distribution theory is tractable in the appropriate conditional sense. The paper concludes, among other things, that in settings where reduction on a reduced sample is unproblematic, sample splitting has high efficiency relative to our conditional analysis, echoing Cox (1975); otherwise it gives miscalibrated confidence sets.
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Contact us
If you are interested in meeting with members of the group please contact Marina Evangelou