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Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

Phylogenetic analysis, which allow to understand the evolution of bacterial and viral epidemics, requires large quantities of data to be analysed and processed for knowledge extraction. One of the major challenges consists on the…

Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…

The increasing risk of epidemics and a fast-growing world population has contributed to a great investment in phylogenetic analysis, in order to track numerous diseases and conceive effective medication and treatments. Phylogenetic analysis…

Knowledge workers frequently encounter repetitive web data entry tasks, like updating records or placing orders. Web automation increases productivity, but translating tasks to web actions accurately and extending to new specifications is…

Optimizing scientific computing algorithms for modern GPUs is a labor-intensive and iterative process involving repeated code modification, benchmarking, and tuning across complex hardware and software stacks. Recent work has explored large…

The evolution analysis on Web service ecosystems has become a critical problem as the frequency of service changes on the Internet increases rapidly. Developers need to understand these evolution patterns to assist in their decision-making…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

This work examines the interconnections between logic, epistemology, and sciences within the Naturalist tradition. It presents a scheme that connects logic, mathematics, physics, chemistry, biology, and cognition, emphasizing…

Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities…

The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…

Checklists have been widely recognized as effective tools for completing complex tasks in a systematic manner. Although originally intended for use in procedural tasks, their interpretability and ease of use have led to their adoption for…

We formulate the search for phenomenological models of synaptic plasticity as an optimization problem. We employ Cartesian genetic programming to evolve biologically plausible human-interpretable plasticity rules that allow a given network…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which…

Evolutionary algorithms are wildly used in unmanned aerial vehicle path planning for their flexibility and effectiveness. Nevertheless, they are so sensitive to the change of environment that can't adapt to all scenarios. Due to this…

Computing systems form the backbone of many aspects of our life, hence they are becoming as vital as water, electricity, and road infrastructures for our society. Yet, engineering long running computing systems that achieve their goals in…

The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension…