相关论文: A format for phylogenetic placements

Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

Ecological studies have now gone beyond measures of species turnover towards measures of phylogenetic and functional dissimilarity with a main objective: disentangling the processes that drive species distributions from local to broad…

We propose Partition Tree, a novel tree-based framework for conditional density estimation over general outcome spaces that supports both continuous and categorical variables within a unified formulation. Our approach models conditional…

Narrow bit-width data formats are key to reducing the computational and storage costs of modern deep learning applications. This paper evaluates Microscaling (MX) data formats that combine a per-block scaling factor with narrow…

The introduction of large language models and other influential developments in AI-based language processing have led to an evolution in the methods available to quantitatively analyse language data. With the resultant growth of attention…

Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…

Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the…

Learning permutations is fundamental to sorting, ranking, and matching, but existing differentiable methods based on entropy-regularized Sinkhorn produce a single softened solution and collapse under ambiguity. We present PermFlow, a…

Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a…

Most phylogenetic analyses result in a sample of trees, but summarizing and visualizing these samples can be challenging. Consensus trees often provide limited information about a sample, and so methods such as consensus networks,…

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…

Optimization algorithms are widely employed to tackle complex problems, but designing them manually is often labor-intensive and requires significant expertise. Global placement is a fundamental step in electronic design automation (EDA).…

Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…

With the ubiquity of computer vision in industry, the importance of image provenance is becoming more apparent. Provenance provides information about the origin and derivation of some resource, e.g., an image dataset, enabling users to…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…

Decision trees and random forest remain highly competitive for classification on medium-sized, standard datasets due to their robustness, minimal preprocessing requirements, and interpretability. However, a single tree suffers from high…

We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…