相关论文: A phylogenetic approach disentangles interlocus ge…
Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the "Parent-Daughter" relationship among…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
The transfer of genetic materials across species (lateral genetic transfer, LGT) contributes to genomic and physiological innovation in prokaryotes. The extent of LGT in prokaryotes has been examined in a number of studies, but the unit of…
In-context learning (ICL) enables large language models (LLMs) to acquire new behaviors from the input sequence alone without any parameter updates. Recent studies have shown that ICL can surpass the original meaning learned in pretraining…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Timing features such as the silence gaps between vocal units -- inter-call intervals (ICIs) -- often correlate with biological information such as context or genetic information. Such correlates between the ICIs and biological information…
In many species, females are hypothesised to obtain 'good genes' for their offspring by mating with males in good condition. However, female preferences might deplete genetic variance and make choice redundant. Additionally, high-condition…
In this paper, we study the composition of two independent GCPs which we call the iterated generalized counting process (IGCP). Its distributional properties such as the transition probabilities, probability generating function, state…
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
Background: Intra-tumour heterogeneity (ITH) is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance and if so would have…
In-context learning (ICL) derives its power from enabling Large Language Models to adapt to new tasks via prompt-based reasoning alone, entirely bypassing the need for parameter updates. Existing theories primarily study ICL in single-task…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
This paper explores the trade-off relation between the rate and the strong converse exponent for asymptotic LOCC transformations between pure multipartite states. Any single-copy probabilistic transformation between a pair of states implies…
Large Language models (LLMs) possess the capability to engage In-context Learning (ICL) by leveraging a few demonstrations pertaining to a new downstream task as conditions. However, this particular learning paradigm suffers from high…
We study the iterated Galton-Watson process (IGW), possibly with thinning, introduced by Gawe{\l}and Kimmel to model the number of repeats of DNA triplets during some genetic disorders. If the process involves some thinning, then extinction…
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed to lateral genetic transfer (LGT) between different strains or species. However, there has been very little study of the extent…