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

We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…

Climate-smart and biodiversity-preserving forestry demands precise information on forest resources, extending to the individual tree level. Multispectral airborne laser scanning (ALS) has shown promise in automated point cloud processing,…

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…

We consider the task of learning Ising models when the signs of different random variables are flipped independently with possibly unequal, unknown probabilities. In this paper, we focus on the problem of robust estimation of…

Close-range laser scanning provides detailed 3D captures of forest stands but requires efficient software for processing 3D point cloud data and extracting individual trees. Although recent studies have introduced deep learning methods for…

Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…

Bipartition cover probabilities quantify whether a collection of gene trees contains every bipartition of the underlying species tree, a condition that underlies finite-sample guarantees for summary methods such as ASTRAL. We study this…

A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…

Many applications in genetic analyses utilize sampling distributions, which describe the probability of observing a sample of DNA sequences randomly drawn from a population. In the one-locus case with special models of mutation such as the…

Spurred by advancements in scale, large language models (LLMs) have demonstrated strong few-shot learning ability via in-context learning (ICL). However, the performance of ICL has been shown to be highly sensitive to the selection of…

In-context learning (ICL) i.e. showing LLMs only a few task-specific demonstrations has led to downstream gains with no task-specific fine-tuning required. However, LLMs are sensitive to the choice of prompts, and therefore a crucial…

We study a model of a population with individuals sampled from different species. The Yule-$\Lambda$ nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a constant rate…

Recently, network lasso has drawn many attentions due to its remarkable performance on simultaneous clustering and optimization. However, it usually suffers from the imperfect data (noise, missing values etc), and yields sub-optimal…

The Colless index for bifurcating phylogenetic trees, introduced by Colless (1982), is defined as the sum, over all internal nodes $v$ of the tree, of the absolute value of the difference of the sizes of the clades defined by the children…

In this paper we address imbalanced binary classification (IBC) tasks. Applying resampling strategies to balance the class distribution of training instances is a common approach to tackle these problems. Many state-of-the-art methods find…

Self-consistency boosts inference-time performance by sampling multiple reasoning traces in parallel and voting. However, in constrained domains like math and code, this strategy is compute-inefficient because it samples with replacement,…

While many-shot ICL achieves remarkable performance, prior studies of its scaling behavior have mainly focused on non-reasoning tasks. In this work, we study many-shot ICL on reasoning tasks, with a particular focus on many-shot…

For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool…

A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…

A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…