相关论文: An analytical comparison of coalescent-based multi…

Multimodal in-context learning (ICL) has emerged as a key mechanism for harnessing the capabilities of large vision-language models (LVLMs). However, its effectiveness remains highly sensitive to the quality of input ICL sequences,…

This article considers a model of genealogy corresponding to a regular exchangeable coalescent (also known as Xi-coalescent) started from a large finite configuration, and undergoing neutral mutations. Asymptotic expressions for the number…

The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However even with modern sequencing technologies the distances on the individuals required for the construction of such a…

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…

In-context learning (ICL) of large language models (LLMs) has attracted increasing attention in the community where LLMs make predictions only based on instructions augmented with a few examples. Existing example selection methods for ICL…

Oblique decision trees have attracted attention due to their potential for improved classification performance over traditional axis-aligned decision trees. However, methods that rely on exhaustive search to find oblique splits face…

Large language models have achieved high performance on various question answering (QA) benchmarks, but the explainability of their output remains elusive. Structured explanations, called entailment trees, were recently suggested as a way…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…

When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…

Recent work on large language models (LLMs) has emphasized the importance of scaling inference compute. From this perspective, the state-of-the-art method Scattered Forest Search (SFS) has been proposed, employing Monte Carlo Tree Search…

Counterfactual explanations are usually generated through heuristics that are sensitive to the search's initial conditions. The absence of guarantees of performance and robustness hinders trustworthiness. In this paper, we take a…

Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…

An involutive Stone algebra (IS-algebra) is a structure that is simultaneously a De Morgan algebra and a Stone algebra (i.e. a pseudo-complemented distributive lattice satisfying the well-known Stone identity ~xv~~x=1). IS-algebras have…

Terraces are potentially large sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The set of trees on a terrace can be…

We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of species post speciation but also allows for species to converge, i.e. become more…