相关论文: Efficient Quartet Representations of Trees and App…

It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…

Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet most reconstruction methods like ML do not explicitly maximize this accuracy. To address this problem, we propose a…

State-of-the-art machine learning solutions mainly focus on creating highly accurate models without constraints on hardware resources. Stream mining algorithms are designed to run on resource-constrained devices, thus a focus on low power…

Decision trees are widely adopted machine learning models due to their simplicity and explainability. However, as training data size grows, standard methods become increasingly slow, scaling polynomially with the number of training…

We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…

Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…

The clever hybridization of quantum computing concepts and evolutionary algorithms (EAs) resulted in a new field called quantum-inspired evolutionary algorithms (QIEAs). Unlike traditional EAs, QIEAs employ quantum bits to adopt a…

Most biological data are multidimensional, posing a major challenge to human comprehension and computational analysis. Principal component analysis is the most popular approach to rendering two- or three-dimensional representations of the…

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC)…

Fault tree analysis is a technique widely used in risk and reliability analysis of complex engineering systems given its deductive nature and relatively simple interpretation. In a fault tree, events are usually represented by a binary…

Recently, deep neural networks have expanded the state-of-art in various scientific fields and provided solutions to long standing problems across multiple application domains. Nevertheless, they also suffer from weaknesses since their…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…

This paper introduces a novel quantum embedding search algorithm (QES, pronounced as "quest"), enabling search for optimal quantum embedding design for a specific dataset of interest. First, we establish the connection between the…

Learning a Bayesian networks with bounded treewidth is important for reducing the complexity of the inferences. We present a novel anytime algorithm (k-MAX) method for this task, which scales up to thousands of variables. Through extensive…

Counterfactual explanations are usually generated through heuristics that are sensitive to the search's initial conditions. The absence of guarantees of performance and robustness hinders trustworthiness. In this paper, we take a…

We derive ensembles of decision trees through a nonparametric Bayesian model, allowing us to view random forests as samples from a posterior distribution. This insight provides large gains in interpretability, and motivates a class of…

We study the complexity and expressive power of conjunctive queries over unranked labeled trees represented using a variety of structure relations such as ``child'', ``descendant'', and ``following'' as well as unary relations for node…

We propose a scheme to simulate the exciton energy transfer (EET) of photosynthetic complexes in a quantum superconducting circuit system. Our system is composed of two pairs of superconducting charge qubits coupled to two separated high-Q…

Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…