Related papers: Forward-backward algorithms with a biallelic mutat…
Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the…
Study sample sizes in human genetics are growing rapidly, and in due course it will become routine to analyze samples with hundreds of thousands if not millions of individuals. In addition to posing computational challenges, such large…
We propose a data-driven, coarse-graining formulation in the context of equilibrium statistical mechanics. In contrast to existing techniques which are based on a fine-to-coarse map, we adopt the opposite strategy by prescribing a…
The Backpropagation algorithm has often been criticised for its lack of biological realism. In an attempt to find a more biologically plausible alternative, the recently introduced Forward-Forward algorithm replaces the forward and backward…
Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no…
Computation of the marginal likelihood from a simulated posterior distribution is central to Bayesian model selection but is computationally difficult. I argue that the marginal likelihood can be reliably computed from a posterior sample by…
We study a model of selection acting on a diploid population (one in which each individual carries two copies of each gene) living in one spatial dimension. We suppose a particular gene appears in two forms (alleles) $A$ and $a$, and that…
In this work we describe a new model for the evolution of a diploid structured population backwards in time that allows for large migrations and uneven offspring distributions. The model generalizes both the mean-field model of Birkner et…
We provide a comprehensive study of the convergence of the forward-backward algorithm under suitable geometric conditions, such as conditioning or {\L}ojasiewicz properties. These geometrical notions are usually local by nature, and may…
Counterfactual learning has become promising for understanding and modeling causality in complex and dynamic systems. This paper presents a novel method for counterfactual learning in the context of multivariate time series analysis and…
The Backpropagation algorithm relies on the abstraction of using a neural model that gets rid of the notion of time, since the input is mapped instantaneously to the output. In this paper, we claim that this abstraction of ignoring time,…
Sex difference in allele frequency is an emerging topic that is critical to our understanding of ascertainment bias, as well as data quality particularly of the largely overlooked X chromosome. To detect sex difference in allele frequency…
Forward-backward methods are a very useful tool for the minimization of a functional given by the sum of a differentiable term and a nondifferentiable one and their investigation has experienced several efforts from many researchers in the…
For a genetic locus carrying a strongly beneficial allele which has just fixed in a large population, we study the ancestry at a linked neutral locus. During this ``selective sweep'' the linkage between the two loci is broken up by…
In real applications, the construction of prior and acceleration of sampling for posterior are usually two key points of Bayesian inversion algorithm for engineers. In this paper, q-analogy of Gaussian distribution, q-Gaussian distribution,…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
This paper examines the use of a hierarchical coevolutionary genetic algorithm under different partnering strategies. Cascading clusters of sub-populations are built from the bottom up, with higher-level sub-populations optimising larger…
The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al. allows the computation of…
Generative models which use explicit density modeling (e.g., variational autoencoders, flow-based generative models) involve finding a mapping from a known distribution, e.g. Gaussian, to the unknown input distribution. This often requires…
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…