Related papers: An Ant-Based Model for Multiple Sequence Alignment
We propose an active walker model for the motion of individual ants communicating via chemical signals. It is assumed that communication takes the form of a time-dependent pheromone field that feedbacks into the motion ants through…
In this paper we propose a new language model called AGENT, which stands for Adversarial Generation and Encoding of Nested Texts. AGENT is designed for encoding, generating and refining documents that consist of a long and coherent text,…
Entity alignment (EA) aims to identify entities across different knowledge graphs (KGs) that refer to the same real-world object and plays a critical role in knowledge fusion and integration. Traditional EA methods mainly rely on knowledge…
Here we propose a novel model family with the objective of learning to disentangle the factors of variation in data. Our approach is based on the spike-and-slab restricted Boltzmann machine which we generalize to include higher-order…
Agents based on Large Language Models (LLMs) are increasingly permeating various domains of human production and life, highlighting the importance of aligning them with human values. The current alignment of AI systems primarily focuses on…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Factor analysis is a classical data reduction technique that seeks a potentially lower number of unobserved variables that can account for the correlations among the observed variables. This paper presents an extension of the factor…
Neural machine translation (NMT) usually works in a seq2seq learning way by viewing either source or target sentence as a linear sequence of words, which can be regarded as a special case of graph, taking words in the sequence as nodes and…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Multinomial processing tree (MPT) models are tools for disentangling the contributions of latent cognitive processes in a given experimental paradigm. The present note analyzes MPT models subject to order constraints on subsets of its…
We introduce a taxonomy of interaction types and show that graphs are focal hypergraphs: every graph is canonically a focal hypergraph via its closed neighbourhood structure, and every graph dynamical model is a special case of the general…
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…
The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading…
Accurate biodiversity monitoring is essential for effective environmental policy, yet current practices often rely on arbitrarily defined ecosystems, communities, and ad-hoc indicator species, limiting cost-efficiency and reproducibility.…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Gradual pattern extraction is a field in (KDD) Knowledge Discovery in Databases that maps correlations between attributes of a data set as gradual dependencies. A gradual dependency may take a form of "the more Attribute K , the less…
Aiming to generate easy-to-handle assembly sequences for robotic assembly, this study tackles assembly sequence generation by considering two tradeoff objectives: (1) insertion conditions and (2) degrees of constraints among assembled…
An emerging way of tackling the dimensionality issues arising in the modeling of a multivariate process is to assume that the inherent data structure can be captured by a graph. Nevertheless, though state-of-the-art graph-based methods have…
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the…