Related papers: Convex characters, algorithms and matchings
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
We describe several algorithms for matrix completion and matrix approximation when only some of its entries are known. The approximation constraint can be any whose approximated solution is known for the full matrix. For low rank…
Accurately dating historical texts is essential for organizing and interpreting cultural heritage collections. This article addresses temporal text classification using interpretable, feature-engineered tree-based machine learning models.…
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
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…
In sparse coding, we attempt to extract features of input vectors, assuming that the data is inherently structured as a sparse superposition of basic building blocks. Similarly, neural networks perform a given task by learning features of…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
The dynamic trees problem is to maintain a forest subject to edge insertions and deletions while facilitating queries such as connectivity, path weights, and subtree weights. Dynamic trees are a fundamental building block of a large number…
We study adaptive approximation algorithms for general multivariate linear problems where the sets of input functions are non-convex cones. While it is known that adaptive algorithms perform essentially no better than non-adaptive…
Fast exact algorithms are known for Hamiltonian paths in undirected and directed bipartite graphs through elegant though involved algorithms that are quite different from each other. We devise algorithms that are simple and similar to each…
Subgraph counting aims to count occurrences of a template T in a given network G(V, E). It is a powerful graph analysis tool and has found real-world applications in diverse domains. Scaling subgraph counting problems is known to be memory…
We study a class of projective transformations of spectraplexes associated with self-dual cones and, on this basis, propose a polynomial-time algorithm for convex feasibility problems with positive definite constraints. At each iteration of…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Variable selection for high-dimensional linear models has received a lot of attention lately, mostly in the context of l1-regularization. Part of the attraction is the variable selection effect: parsimonious models are obtained, which are…
Dynamic tree data structures maintain a forest while supporting insertion and deletion of edges and a broad set of queries in $O(\log n)$ time per operation. Such data structures are at the core of many modern algorithms. Recent work has…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
This paper introduces a novel hypergraph classification algorithm. The use of hypergraphs in this framework has been widely studied. In previous work, hypergraph models are typically constructed using distance or attribute based methods.…