Related papers: A Simple Linear-Time Algorithm for the Common Refi…
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 consider the problem of learning underlying tree structure from noisy, mixed data obtained from a linear model. To achieve this, we use the expectation maximization algorithm combined with Chow-Liu minimum spanning tree algorithm. This…
We show how to solve a number of problems in numerical linear algebra, such as least squares regression, $\ell_p$-regression for any $p \geq 1$, low rank approximation, and kernel regression, in time $T(A) \poly(\log(nd))$, where for a…
A randomized algorithm for computing a data sparse representation of a given rank structured matrix $A$ (a.k.a. an $H$-matrix) is presented. The algorithm draws on the randomized singular value decomposition (RSVD), and operates under the…
Many common sequential data sources, such as source code and natural language, have a natural tree-structured representation. These trees can be generated by fitting a sequence to a grammar, yielding a hierarchical ordering of the tokens in…
We address here spanning tree problems on a graph with binary edge weights. For a general weighted graph the minimum spanning tree is solved in super-linear running time, even when the edges of the graph are pre-sorted. A related problem,…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…
Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Runtime repeated recursion unfolding was recently introduced as a just-in-time program transformation strategy that can achieve super-linear speedup. So far, the method was restricted to single linear direct recursive rules in the…
Linear tree constraints were introduced by Hofmann and Rodriguez in the context of amortized resource analysis for object oriented programs. More precisely, they gave a reduction from inference of resource types to constraint solving. Thus,…
Natural language text corpora are often available as sets of syntactically parsed trees. A wide range of expressive tree queries are possible over such parsed trees that open a new avenue in searching over natural language text. They not…
A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…
The evolving capabilities of large language models are accompanied by growing sizes and deployment costs, necessitating effective inference optimisation techniques. We propose a novel pruning method utilising centrality measures from graph…
Methods for forecasting time series adhering to linear constraints have seen notable development in recent years, especially with the advent of forecast reconciliation. This paper extends forecast reconciliation to the open question of…
Deliberative tree search is a cornerstone of modern Large Language Model (LLM) research, driving the pivot from brute-force scaling toward algorithmic efficiency. This single paradigm unifies two critical frontiers: \textbf{Test-Time…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…
The Classification Tree (CT) is one of the most common models in interpretable machine learning. Although such models are usually built with greedy strategies, in recent years, thanks to remarkable advances in Mixer-Integer Programming…