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We design two classes of ultra-fast meta-solvers for linear systems arising after discretizing PDEs by combining neural operators with either simple iterative solvers, e.g., Jacobi and Gauss-Seidel, or with Krylov methods, e.g., GMRES and…
A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
The maximum-likelihood decoding problem is known to be NP-hard for general linear and Reed-Solomon codes. In this paper, we introduce the notion of A-covered codes, that is, codes that can be decoded through a polynomial time algorithm A…
The proposed approach is to formalise the probabilistic puzzle in equational FOL. Two formalisations are needed: one theory for all models of the given puzzle, and a second theory for the favorable models. Then Mace4 - that computes all the…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
The graph isomorphism problem has a long history in mathematics and computer science, with applications in computational chemistry and biology, and it is believed to be neither solvable in polynomial time nor NP-complete. E. Luks proposed…
We consider the problems of finding a maximum clique in a graph and finding a maximum-edge biclique in a bipartite graph. Both problems are NP-hard. We write both problems as matrix-rank minimization and then relax them using the nuclear…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
Symbolic indefinite integration in Computer Algebra Systems such as Maple involves selecting the most effective algorithm from multiple available methods. Not all methods will succeed for a given problem, and when several do, the results,…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
We propose a novel molecular computing scheme for statistical inference. We focus on the much-studied statistical inference problem of computing maximum likelihood estimators for log-linear models. Our scheme takes log-linear models to…
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…
In this paper we consider the classical maximum set packing problem where set cardinality is upper bounded by $k$. We show how to design a variant of a polynomial-time local search algorithm with performance guarantee $(k+2)/3$. This local…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
The controlled branching process is a generalization of the classical Bienaym\'e-Galton-Watson branching process. It is a useful model for describing the evolution of populations in which the population size at each generation needs to be…
We consider the problem of computing optimal search trees on trees (STTs). STTs generalize binary search trees (BSTs) in which we search nodes in a path (linear order) to search trees that facilitate search over general tree topologies.…
Classification trees continue to be widely adopted in machine learning applications due to their inherently interpretable nature and scalability. We propose a rolling subtree lookahead algorithm that combines the relative scalability of the…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…