相关论文: A phylogenetic approach disentangles interlocus ge…

Using Monte Carlo methods, we simulated the effects of bias in generation and elimination of paralogs on the size distribution of paralog groups. It was found that the function describing the decay of the number of paralog groups with their…

In this paper, we study the problem of designing efficient convolutional neural network architectures with the interest in eliminating the redundancy in convolution kernels. In addition to structured sparse kernels, low-rank kernels and the…

This paper investigates context stickiness in in-context learning (ICL), a phenomenon where earlier examples in a prompt interfere with a transformer's ability to adapt to later tasks. Using synthetic regression tasks over linear and…

Let ${\cal G}$ be the incipient infinite cluster (IIC) for percolation on a homogeneous tree of degree $n_0+1$. We obtain estimates for the transition density of the continuous time simple random walk $Y$ on ${\cal G}$; the process…

Intermediate token generation (ITG), where a model produces output before the solution, has been proposed as a method to improve the performance of language models on reasoning tasks. While these reasoning traces or Chain of Thoughts (CoTs)…

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. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…

In population genetics, mutation rate is often treated as a homogeneous parameter across the genome. Empirical evidence, however, shows systematic variation across genomic contexts associated with chromatin organization and epigenomic…

Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect…

The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…

The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…

The isolation-with-migration (IM) model is a common tool to make inferences about the presence of gene flow during speciation, using polymorphism data. However, Becquet and Przeworski (2009) report that the parameter estimates obtained by…

In this paper, we present a simple and modularized neural network architecture, named interleaved group convolutional neural networks (IGCNets). The main point lies in a novel building block, a pair of two successive interleaved group…

In phylogenomics, species-tree methods must contend with two major sources of noise; stochastic gene-tree variation under the multispecies coalescent model (MSC) and finite-sequence substitutional noise. Fast agglomerative methods such as…

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…

Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence remains very challenging. Both evolutionary coupling (EC) analysis and supervised machine learning methods are…

Colocalization analyses assess whether two traits are affected by the same or distinct causal genetic variants in a single gene region. A class of Bayesian colocalization tests are now routinely used in practice; for example, for genetic…

The emergence of In-Context Learning (ICL) in LLMs remains a remarkable phenomenon that is partially understood. To explain ICL, recent studies have created theoretical connections to Gradient Descent (GD). We ask, do such connections hold…