相关论文: A phylogenetic approach disentangles interlocus ge…

Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…

Variation in the evolutionary process across the sites of nucleotide sequence alignments is well established, and is an increasingly pervasive feature of datasets composed of gene regions sampled from multiple loci and/or different genomes.…

This thesis investigates two key phenomena in large language models (LLMs): in-context learning (ICL) and model collapse. We study ICL in a linear transformer with tied weights trained on linear regression tasks, and show that minimising…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…

A first step when fitting multilevel models to continuous responses is to explore the degree of clustering in the data. Researchers fit variance-component models and then report the proportion of variation in the response that is due to…

Pre-trained language models (LMs) are capable of in-context learning (ICL): they can adapt to a task with only a few examples given in the prompt without any parameter update. However, it is unclear where this capability comes from as there…

Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding…

We are concerned about the main encoding granule cells (GCs) in the hippocampal dentate gyrus (DG). Young immature GCs (imGCs) appear through adult neurogenesis. In comparison to the mature GCs (mGCs) (born during development), the imGCs…

We consider the stepping stone model on the torus of side $L$ in $\mathbb{Z}^2$ in the limit $L\to\infty$, and study the time it takes two lineages tracing backward in time to coalesce. Our work fills a gap between the finite range…

Interrelated Two-way Clustering (ITC) is an unsupervised clustering method developed to divide samples into two groups in gene expression data obtained through microarrays, selecting important genes simultaneously in the process. This has…

B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation, and therefore…

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…

So far mutations analysis was performed in terms of transitions and trasversions, so on the basis of the molecule, or in terms of GC-content and isochors, through the quantification of GC->AT mutations over AT->GC mutations. We tried a…

Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…

We consider a population subdivided into two demes connected by migration in which selection acts in opposite direction. We explore the effects of recombination and migration on the maintenance of multilocus polymorphism, on local…

Although transformers have demonstrated impressive capabilities for in-context learning (ICL) in practice, theoretical understanding of the underlying mechanism that allows transformers to perform ICL is still in its infancy. This work aims…

In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…

When organisms adapt to spatially heterogeneous environments, selection may drive divergence at multiple genes. If populations under divergent selection also exchange migrants, we expect genetic differentiation to be high at selected loci,…

We introduce a strategy for specifying informative inverse-gamma (IG) priors for variance components in Bayesian multilevel models (MLMs), derived via transformations from chi-square to gamma to inverse-gamma distributions. A Monte Carlo…