Related papers: Multi-SpaM: a Maximum-Likelihood approach to Phylo…
A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…
Language models generate reasoning sequentially, preventing them from decoupling irrelevant exploration paths during search. We introduce Tree-Structured Language Modeling (TSLM), which uses special tokens to encode branching structure,…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
The inherent probabilistic nature of Large Language Models (LLMs) introduces an element of unpredictability, raising concerns about potential discrepancies in their output. This paper introduces an innovative approach aims to generate…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…
In many applications of natural language processing (NLP) it is necessary to determine the likelihood of a given word combination. For example, a speech recognizer may need to determine which of the two word combinations ``eat a peach'' and…
Tokenising continuous speech into sequences of discrete tokens and modelling them with language models (LMs) has led to significant success in text-to-speech (TTS) synthesis. Although these models can generate speech with high quality and…
We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state…
This paper describes a new statistical parser which is based on probabilities of dependencies between head-words in the parse tree. Standard bigram probability estimation techniques are extended to calculate probabilities of dependencies…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
We address phylogenetic reconstruction when the data is generated from a mixture distribution. Such topics have gained considerable attention in the biological community with the clear evidence of heterogeneity of mutation rates. In our…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Recently multi-lingual pre-trained language models (PLM) such as mBERT and XLM-R have achieved impressive strides in cross-lingual dense retrieval. Despite its successes, they are general-purpose PLM while the multilingual PLM tailored for…