Fig. 1. The ultrastructure of a SARS-CoV-2 virion created using our modeling technique. The membrane shape and distribution of the spike proteins are determined from microscopy image data. The internal assembly is a result of an interactive 3D rule specification approach. Left: internal nucleoprotein complex. Middle: RNA condensed within the nucleoprotein. Right: Outer spike distribution.
Link prediction is the task of computing the likelihood that a link exists between two given nodes in a network. With countless applications in different areas of science and engineering, link prediction has received the attention of many researchers working in various disciplines. considerable research efforts have been invested into the development of increasingly accurate prediction methods. Most of the proposed algorithms, however, have limited use in practice because of their high computational requirements. The aim of this work is to develop a scalable link prediction algorithm that offers a higher overall predictive power than existing methods. the proposed solution falls into the class of global, parameter-free similarity-popularity-based methods, and in it, we assume that network topology is governed by three factors: popularity of the nodes, their similarity and the attraction induced by local neighbourhood. in our approach, popularity and neighbourhood-caused attraction are computed directly from the network topology and factored out by introducing a specific weight map, which is then used to estimate the dissimilarity between non-adjacent nodes through shortest path distances. We show through extensive experimental testing that the proposed method produces highly accurate predictions at a fraction of the computational cost required by existing global methods and at a low additional cost compared to local methods. the scalability of the proposed algorithm is demonstrated on several large networks having hundreds of thousands of nodes. The Internet, the World Wide Web, the brain and human society are some examples of systems that, despite seeming completely different at first sight, all share a fundamental property: they are all composed of interacting entities. Individual objects in these systems are not isolated, but rather connected through links or relationships. Mounting scientific evidence shows that these systems are better understood by investigating their properties as networks, where nodes represent individual components, and links refer to relationships, interactions or influences that exist among nodes 1. Network science aims at understanding and creating effective tools for characterizing and quantifying complex systems. The first step in this endeavour is to observe and record the existing interactions in order to build the network. In most cases, however, it is not possible to observe all interactions between the individual components. This can be due either to limitations in the data collection process or because certain relationships have not yet been established 2. The process of identifying the links that are missing from the network is known as link prediction. Recommending new friends or collaborators in social networks 3 , reconstructing networks 2 and discovering unknown interactions in biological networks 4 are few examples of the variety of applications that can benefit from predicting non-existing links. Link prediction has proven to be a challenging problem, and a lot of effor...
Fig. 1: Nanotilus entering the center of the HIV model. Several protein instances are sparsified to reveal the internal part of the model. Left: A grayscale model with highlighted proteins inside the Nanotilus hull is combined with the model's final depiction. The model is dissected by a cutting plane perpendicular to the Nanotilus hull. Right: Resulting view from the Nanotilus perspective.
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