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Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
Understanding the changing structure of science over time is essential to elucidating how science evolves. We develop diachronic embeddings of scholarly periodicals to quantify "semantic changes" of periodicals across decades, allowing us…
To enable efficient exploration of Web-scale scientific knowledge, it is necessary to organize scientific publications into a hierarchical concept structure. In this work, we present a large-scale system to (1) identify hundreds of…
Scientific knowledge is growing rapidly, making it difficult to track progress and high-level conceptual links across broad disciplines. While tools like citation networks and search engines help retrieve related papers, they lack the…
Concepts in a certain domain of science are linked via intrinsic connections reflecting the structure of knowledge. To get a qualitative insight and a quantitative description of this structure, we perform empirical analysis and modeling of…
A complex system comprises multiple interacting entities whose interdependencies form a unified whole, exhibiting emergent behaviours not present in individual components. Examples include the human brain, living cells, soft matter, Earth's…
Blended mathematical sensemaking in science (blended MSS) involves deep conceptual understanding of quantitative relationships describing phenomena in science and has been studies in various disciplines. However, no unified characterization…
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…
The paradigm of Big Data has been established as a solid field of studies in many areas such as healthcare, science, transport, education, government services, among others. Despite widely discussed, there is no agreed definition about the…
The paper proposes a text-mining based analytical framework aiming at the cognitive organization of complex scientific discourses. The approach is based on models recently developed in science mapping, being a generalization of the…
The evolution of scientific fields has been attracting much attention in recent years. One of the key issues in evolution of scientific field is to quantify the dissimilarity between two collections of scientific publications in literature.…
Bibliometrics have become commonplace and widely used by authors and journals to monitor, to evaluate and to identify their readership in an ever-increasingly publishing scientific world. With this contribution, we aim to investigate the…
Classifying journals or publications into research areas is an essential element of many bibliometric analyses. Classification usually takes place at the level of journals, where the Web of Science subject categories are the most popular…
The two Journal Citation Reports of the Science Citation Index 2004 and the Social Science Citation Index 2004 were combined in order to analyze and map journals and specialties at the edges and in the overlap between the two databases. For…
The highly influential framework of conceptual spaces provides a geometric way of representing knowledge. Instances are represented by points in a high-dimensional space and concepts are represented by regions in this space. Our recent…
This paper reports on the state-of-the-art in application of multidimensional scaling (MDS) techniques to create semantic maps in linguistic research. MDS refers to a statistical technique that represents objects (lexical items, linguistic…
There is no much doubt that biotic interactions shape community assembly and ultimately the spatial co-variations between species. There is a hope that the signal of these biotic interactions can be observed and retrieved by investigating…
We present a novel approach to visually locate bodies of research within the sciences, both at each moment of time and dynamically. This article describes how this approach fits with other efforts to locally and globally map scientific…
Simplified representations of macromolecules help in rationalising and understanding the outcome of atomistic simulations, and serve to the construction of effective, coarse-grained models. The number and distribution of coarse-grained…
Approaches form the foundation for conducting scientific research. Querying approaches from a vast body of scientific papers is extremely time-consuming, and without a well-organized management framework, researchers may face significant…