Related papers: Bayesian Weighted Triplet and Quartet Methods for …
Large Language Models (LLMs) face significant inference latency challenges stemming from their autoregressive design and large size. To address this, speculative decoding emerges as a solution, enabling the simultaneous generation and…
We introduce inference trees (ITs), a new class of inference methods that build on ideas from Monte Carlo tree search to perform adaptive sampling in a manner that balances exploration with exploitation, ensures consistency, and alleviates…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
Trees corresponding to $\Lambda$- and $\Xi$-$n$-coalescents can be both quite similar and fundamentally different compared to bifurcating tree models based on Kingman's $n$-coalescent. This has consequences for inference of a well-fitting…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
Homogeneity across lineages is a common assumption in phylogenetics according to which nucleotide substitution rates remain constant in time and do not depend on lineages. This is a simplifying hypothesis which is often adopted to make the…
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
Long-tailed (LT) classification is an unavoidable and challenging problem in the real world. Most existing long-tailed classification methods focus only on solving the class-wise imbalance while ignoring the attribute-wise imbalance. The…
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 introduce a random recursive tree model with two communities, called balanced community modulated random recursive tree, or BCMRT in short. In this setting, pairs of nodes of different type appear sequentially. Each node of the pair…
In classical sparse representation based classification and weighted SRC algorithms, the test samples are sparely represented by all training samples. They emphasize the sparsity of the coding coefficients but without considering the local…
Feature level sets (FLS) have shown significant potential in the analysis of multi-field data by using traits defined in attribute space to specify features in the domain. In this work, we address key challenges in the practical use of FLS:…
We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model. In particular, every cycle of size at least 4 and every…
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets in many practical problems due to the…
Automatic plant classification is a challenging problem due to the wide biodiversity of the existing plant species in a fine-grained scenario. Powerful deep learning architectures have been used to improve the classification performance in…
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
In this paper, we propose the use of causal inference techniques for survival function estimation and prediction for subgroups of the data, upto individual units. Tree ensemble methods, specifically random forests were modified for this…