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Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide…
Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the…
Few-shot anomaly generation is a key challenge in industrial quality control. Although diffusion models are promising, existing methods struggle: global prompt-guided approaches corrupt normal regions, and existing inpainting-based methods…
Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract this information (at least partially) but they require sophisticated statistical techniques that have been made…
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in…
We introduce a new algorithm called {\sc Rec-Gen} for reconstructing the genealogy or \textit{pedigree} of an extant population purely from its genetic data. We justify our approach by giving a mathematical proof of the effectiveness of…
There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…
Time series analysis has emerged as an important tool for improving patient diagnosis and management in healthcare applications. However, these applications commonly face two critical challenges: time misalignment and data sparsity.…
Multiple-merger coalescents, e.g. $\Lambda$-$n$-coalescents, have been proposed as models of the genealogy of $n$ sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's…
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics. Kingman's coalescent process enables inference of past population dynamics directly from…
The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…
The coalescent revolutionised theoretical population genetics, simplifying, or making possible for the first time, many analyses, proofs, and derivations, and offering crucial insights about the way in which the structure of data in samples…
Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard coalescent, is used to infer the sample's bifurcating…
Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
Kingman's coalescent is one of the most popular models in population genetics. It describes the genealogy of a population whose genetic composition evolves in time according to the Wright-Fisher model, or suitable approximations of it…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
There is a growing amount of clinical, anatomical and functional evidence for the heterogeneous presentation of neuropsychiatric and neurodegenerative diseases such as schizophrenia and Alzheimers Disease (AD). Elucidating distinct subtypes…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…