Related papers: The Reconstruction of Science Phylogeny
Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our…
The emergence of large language models offers new possibilities for structured exploration of scientific knowledge. Rather than viewing scientific discovery as isolated ideas or content, we propose a structured approach that emphasizes the…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
The rapid expansion of Earth Science data from satellite observations, reanalysis products, and numerical simulations has created a critical bottleneck in scientific discovery, namely identifying relevant datasets for a given research…
Science is essential to innovation and economic prosperity. Although studies have shown that national scientific development is affected by geographic, historic, and economic factors, it remains unclear whether there are universal…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…
The concept of (auto)catalytic systems has become a cornerstone in understanding evolutionary processes in various fields. The common ground is the observation that for the production of new species/goods/ideas/elements etc. the…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
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…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
Nature's many varied complex systems (including galaxies, stars, planets, life, and society) are islands of order within the increasingly disordered universe. All organized systems are subject to physical, biological or cultural evolution,…
Classic economic science is reaching the limits of its explanatory powers. Complexity science uses an increasingly larger set of different methods to analyze physical, biological, cultural, social, and economic factors, providing a broader…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
We apply bio-inspired methods for the analysis of different dynamic bibliometric networks (linking papers by citation, authors, and keywords, respectively). Biological species are clusters of individuals defined by widely different criteria…
Whereas the research program of the measurement of scientific communications emerged in a context where the delineations among academia, government, and industry were institutionalized, the systemic development of these relations during the…
Systems evolving according to the standard concept of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find a deep relationship to classical…
Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized to influence…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…