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Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell)…
We study the distribution of the number of leaves of the subtree chosen uniformly at random among all the subtrees of the critical branching process tree at extinction.
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,…
Tree search algorithms, such as branch-and-bound, are the most widely used tools for solving combinatorial and nonconvex problems. For example, they are the foremost method for solving (mixed) integer programs and constraint satisfaction…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
In response to the lack of trust in Artificial Intelligence (AI) for sequential planning, we design a Computational Tree Logic-guided large language model (LLM)-based natural language explanation framework designed for the Monte Carlo Tree…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
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…
A merge tree is a topological descriptor of a real-valued function. Merge trees are used in visualization and topological data analysis, either directly or as a means to another end: computing a 0-dimensional persistence diagram,…
Large language models (LLMs) have achieved remarkable multi-step reasoning capabilities across various domains. However, LLMs still face distinct challenges in complex logical reasoning, as (1) proof-finding requires systematic exploration…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
It is a high-quality algorithm for hierarchical clustering of large software source code. This effectively allows to break the complexity of tens of millions lines of source code, so that a human software engineer can comprehend a software…
Monte Carlo tree search (MCTS) is one of the most capable online search algorithms for sequential planning tasks, with significant applications in areas such as resource allocation and transit planning. Despite its strong performance in…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable newick format. There are thus thousands of published trees in the scientific literature…
In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable…