2023 Conference

On 8th-9th June 2023, we held the 2nd Bioinference conference at the Pitt Rivers Museum at the University of Oxford. This year’s conference was organised by: Ioana Bouros (Oxford); Fergus Cooper (Oxford); Richard Creswell (Oxford); Aden Forrow (Maine); David Gavaghan (Oxford); Ben Lambert (Exeter); Chon Lok Lei (Macau); Massimiliano Tamborrino (Warwick); Tom Thorne (Surrey).

The conference was generously sponsored by:

• The Doctoral Training Centre, University of Oxford
• The Department of Computer Science, University of Oxford
• The European Society for Mathematical and Theoretical Biology

Posters #

• Enrico Bibbona, Politecnico di Torino, Estimating the ratio between the contagiousness of two viral strains

  

• Julia Brettschneider, University of Warwick, Microscopic images and infections counts from a point process perspective

  

• Austin Brown, University of Warwick, Geometric ergodicity of Gibbs samplers for Bayesian error-in-variable regression

  

• Alexander Browning, University of Oxford, Modelling heterogenity with random parameters

  

• Raiha Browning, University of Warwick, AMISforInfectiousDiseases: an R package to fit a transmission model to a prevalence map

  

• Viktoria Brunner, University of Oxford, Large-scale Identification of Compensatory Mutations in the RNA Polymerase of Mycobacterium tuberculosis

  

• Lloyd Chapman, Lancaster University, Bayesian inference for spatiotemporal individual-level epidemic models

  

• Molly Cui, Kings College London, Bayesian modelling and sequential learning of latent epidemic dynamics

  

• Alicia Gill, University of Warwick, Bayesian inference of reproduction number from genomic and epidemic data using particle MCMC

  

• Adam Howes, Imperial College London, Fast approximate Bayesian inference for small-area estimation of HIV indicators using the Naomi model

  

• Owen Jones, Cardiff University, Estimating the virulence of managed parasite populations

  

• Lutecia Servius, King’s College London, “Comparing classification methods and their generalisability on antibody repertoire”

• Maria Veretennikova, University of Oxford, Circadian clock analysis for precision medicine

  

• Hiu Ching Yip, Politecnico di Torino, Modelling lemurs’ calls with nearest neighbour Gaussian process

  

• Reza Taheri, University of Turin, Using Generalized Lagrange Chebyshev collocation method in order to solve the shortest path problems

  

Thursday 8th June #

• Ben Lambert, Exeter (now Oxford), Welcome

• Darren Wilkinson, Durham, Statistical emulation for individual-based models of microbial community dynamics

• Sandor Beregi, Imperial College London, Can we control an epidemic in real-time with noisy data?

• Joseph Shuttleworth, Nottingham, Training models with an ensemble of experimental designs to account for model discrepancy: quantifying uncertainty for predictive models of ion channel currents

• Jonas Arruda, Bonn, An amortized approach to non-linear mixed-effects modeling based on neural density posterior estimation

• Marina Evangelou, Imperial College London, Unsupervised Learning approaches for Multi-OMICS data

• Thijs van der Plas, Oxford, Neural assemblies uncovered by generative modeling explain whole-brain activity statistics and reflect structural connectivity

• Robin Thompson, Warwick, Inference of pathogen transmissibility during infectious disease outbreaks

• Ruihua Zhang, Oxford, Simulating weak attacks in a new duplication-divergence model with gene loss

Friday 9th June #

• Richard Everitt, Warwick, Rare event ABC-SMC^2

• Elena Sabbioni, Turin, A Bayesian approach for estimating RNA velocity

• Juliette Unwin, Imperial College London, The development journey of a spatio-temporal infectious disease transmission model

• Constandina Koki, Warwick, Bayesian computational analysis of cell division dynamics

• Andrew Glover, Imperial College London, Parametrically Smoothened Likelihood Inference (PARSLI)

• Jaromir Sant, Oxford, Inferring natural selection and allele age from allele frequency time series data via exact simulation

• Arnau Quera-Bofarull, Oxford, Bayesian calibration of differentiable simulators

• Ritabrata Dutta, Warwick, Inference of selection coefficients in multivariate Wright-Fisher: Generalized Bayesian Inference with Signature Kernel Score

• Ben Lambert, Exeter (now Oxford), Best ECR talk and poster prize presentation and summing up

Prize giving #

• Best ECR poster: Alicia Gill (Warwick), Bayesian inference of reproduction number from genomic and epidemic data using particle MCMC
• Best ECR talk: Jonas Arruda (Bonn), An amortized approach to non-linear mixed-effects modeling based on neural density posterior estimation
• ECR reproducibility prizes: shared between Adam Howes (Imperial; repo) and Thijs van der Plas (Oxford; repo)