Related papers: Inferring Heterogeneous Evolutionary Processes Thr…
Phylodynamics focuses on the problem of reconstructing past population size dynamics from current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology, but is particularly…
Traditionally, Hawkes processes are used to model time--continuous point processes with history dependence. Here we propose an extended model where the self--effects are of both excitatory and inhibitory type and follow a Gaussian Process.…
Traditional disease transmission models assume that the infectious period is exponentially distributed with a recovery rate fixed in time and across individuals. This assumption provides analytical and computational advantages, however it…
Accurate and reliable forecasting of epidemic incidences is critical for public health preparedness, yet it remains a challenging task due to complex nonlinear temporal dependencies and heterogeneous spatial interactions. Often, point…
The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…
Recent work has developed Bayesian methods for the automatic statistical analysis and description of single time series as well as of homogeneous sets of time series data. We extend prior work to create an interpretable kernel embedding for…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Generative modeling offers a promising solution to data scarcity and privacy challenges in time series analysis. However, the structural complexity of time series, characterized by multi-scale temporal patterns and heterogeneous components,…
This work develops a rigorous framework for analysing ergodicity and mixing in time-inhomogeneous quantum dynamics. It considers quantum evolutions generated by sequences of quantum channels and examines in detail the relationship between…
Recent studies have actively employed persistent homology (PH), a topological data analysis technique, to analyze the topological information in time series data. Many successful studies have utilized graph representations of time series…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…
In this study, we propose a general model capable of addressing heterogeneity in higher-order moments while preserving mean and variance, including the t, Laplace, and skew-normal distributions as special cases. Our model flexibly…
Regression models are used in a wide range of applications providing a powerful scientific tool for researchers from different fields. Linear, or simple parametric, models are often not sufficient to describe complex relationships between…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Despite recent molecular technique improvements, biological knowledge remains incomplete. Reasoning on living systems hence implies to integrate heterogeneous and partial informations. Although current investigations successfully focus on…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
In many clustering scenes, data samples' attribute values change over time. For such data, we are often interested in obtaining a partition for each time step and tracking the dynamic change of partitions. Normally, a smooth change is…