Related papers: An Ant-Based Model for Multiple Sequence Alignment

Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on…

Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…

Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…

The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…

We tackle the problem of multi-class relational sequence learning using relevant patterns discovered from a set of labelled sequences. To deal with this problem, firstly each relational sequence is mapped into a feature vector using the…

Factor analysis provides linear factors that describe relationships between individual variables of a data set. We extend this classical formulation into linear factors that describe relationships between groups of variables, where each…

In this paper we address the problem of modeling relational data, which appear in many applications such as social network analysis, recommender systems and bioinformatics. Previous studies either consider latent feature based models but…

Entity alignment is to find identical entities in different knowledge graphs. Although embedding-based entity alignment has recently achieved remarkable progress, training data insufficiency remains a critical challenge. Conventional…

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…

It is well-known in biology that ants are able to find shortest paths between their nest and the food by successive random explorations, without any mean of communication other than the pheromones they leave behind them. This striking…

Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

For graph classification tasks, many traditional kernel methods focus on measuring the similarity between graphs. These methods have achieved great success on resolving graph isomorphism problems. However, in some classification problems,…

Formal modelling of Multi-Agent Systems (MAS) is a challenging task due to high complexity, interaction, parallelism and continuous change of roles and organisation between agents. In this paper we record our research experience on formal…

Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…

Most of the grand challenges of humanity today involve complex agent-based systems, such as epidemiology, economics or ecology. However, remains as a pending task the challenge of identifying the general principles underlying their…

Using a simple model for the trail formation of ants, the relation between i)the schedule of feeding which represents the unsteady natural environment, ii)emerging patterns of trails connecting a nest with food resources, and iii)the…

Multi-label classification is an important yet challenging task in natural language processing. It is more complex than single-label classification in that the labels tend to be correlated. Existing methods tend to ignore the correlations…

Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…