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Cryo-electron microscopy (cryo-EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically improved to generate high-resolution three-dimensional (3D) maps that contain detailed structural information about macromolecules, the computational methods for using the data to automatically build structure models are lagging far behind. The traditional cryo-EM model building approach is template-based homology modeling. Manual de novo modeling is very time-consuming when no template model is found in the database. In recent years, de novo cryo-EM modeling using machine learning (ML) and deep learning (DL) has ranked among the top-performing methods in macromolecular structure modeling. Deep-learning-based de novo cryo-EM modeling is an important application of artificial intelligence, with impressive results and great potential for the next generation of molecular biomedicine. Accordingly, we systematically review the representative ML/DL-based de novo cryo-EM modeling methods. And their significances are discussed from both practical and methodological viewpoints. We also briefly describe the background of cryo-EM data processing workflow. Overall, this review provides an introductory guide to modern research on artificial intelligence (AI) for de novo molecular structure modeling and future directions in this emerging field.

Music-to-dance translation is a brand-new and powerful feature in recent role-playing games. Players can now let their characters dance along with specified music clips and even generate fan-made dance videos. Previous works of this topic consider music-to-dance as a supervised motion generation problem based on time-series data. However, these methods suffer from limited training data pairs and the degradation of movements. This paper provides a new perspective for this task where we re-formulate the translation problem as a piece-wise dance phrase retrieval problem based on the choreography theory. With such a design, players are allowed to further edit the dance movements on top of our generation while other regression based methods ignore such user interactivity. Considering that the dance motion capture is an expensive and time-consuming procedure which requires the assistance of professional dancers, we train our method under a semi-supervised learning framework with a large unlabeled dataset (20x than labeled data) collected. A co-ascent mechanism is introduced to improve the robustness of our network. Using this unlabeled dataset, we also introduce self-supervised pre-training so that the translator can understand the melody, rhythm, and other components of music phrases. We show that the pre-training significantly improves the translation accuracy than that of training from scratch. Experimental results suggest that our method not only generalizes well over various styles of music but also succeeds in expert-level choreography for game players., Comment: 14 pages, 8 figures

Quantifying success in science plays a key role in guiding funding allocations, recruitment decisions, and rewards. Recently, a significant amount of progresses have been made towards quantifying success in science. This lack of detailed analysis and summary continues a practical issue. The literature reports the factors influencing scholarly impact and evaluation methods and indices aimed at overcoming this crucial weakness. We focus on categorizing and reviewing the current development on evaluation indices of scholarly impact, including paper impact, scholar impact, and journal impact. Besides, we summarize the issues of existing evaluation methods and indices, investigate the open issues and challenges, and provide possible solutions, including the pattern of collaboration impact, unified evaluation standards, implicit success factor mining, dynamic academic network embedding, and scholarly impact inflation. This paper should help the researchers obtaining a broader understanding of quantifying success in science, and identifying some potential research directions.

Predicting the impact of research institutions is an important tool for decision makers, such as resource allocation for funding bodies. Despite significant effort of adopting quantitative indicators to measure the impact of research institutions, little is known that how the impact of institutions evolves in time. Previous researches have focused on using the historical relevance scores of different institutions to predict potential future impact for these institutions. In this paper, we explore the factors that can drive the changes of the impact of institutions, finding that the impact of an institution, as measured by the number of the accepted papers of the institution, more is determined by the authors' influence of the institution. Geographic location of institution feature and state GDP can drive the changes of the impact of institutions. Identifying these features allows us to formulate a predictive model that integrates the effects of individual ability, location of institution, and state GDP. The model unveils the underlying factors driving the future impact of institutions, which can be used to accurately predict the future impact of institutions.

Facial appearance matters in social networks. Individuals frequently make trait judgments from facial clues. Although these face-based impressions lack the evidence to determine validity, they are of vital importance, because they may relate to human network-based social behavior, such as seeking certain individuals for help, advice, dating, and cooperation, and thus they may relate to centrality in social networks. However, little to no work has investigated the apparent facial traits that influence network centrality, despite the large amount of research on attributions of the central position including personality and behavior. In this paper, we examine whether perceived traits based on facial appearance affect network centrality by exploring the initial stage of social network formation in a first-year college residential area. We took face photos of participants who are freshmen living in the same residential area, and we asked them to nominate community members linking to different networks. We then collected facial perception data by requiring other participants to rate facial images for three main attributions: dominance, trustworthiness, and attractiveness. Meanwhile, we proposed a framework to discover how facial appearance affects social networks. Our results revealed that perceived facial traits were correlated with the network centrality and that they were indicative to predict the centrality of people in different networks. Our findings provide psychological evidence regarding the interaction between faces and network centrality. Our findings also offer insights in to a combination of psychological and social network techniques, and they highlight the function of facial bias in cuing and signaling social traits. To the best of our knowledge, we are the first to explore the influence of facial perception on centrality in social networks., Comment: 11 pages, 8 figures

Quantifying the impact of a scholarly paper is of great significance, yet the effect of geographical distance of cited papers has not been explored. In this paper, we examine 30,596 papers published in Physical Review C, and identify the relationship between citations and geographical distances between author affiliations. Subsequently, a relative citation weight is applied to assess the impact of a scholarly paper. A higher-order weighted quantum PageRank algorithm is also developed to address the behavior of multiple step citation flow. Capturing the citation dynamics with higher-order dependencies reveals the actual impact of papers, including necessary self-citations that are sometimes excluded in prior studies. Quantum PageRank is utilized in this paper to help differentiating nodes whose PageRank values are identical.

Science of science has become a popular topic that attracts great attentions from the research community. The development of data analytics technologies and the readily available scholarly data enable the exploration of data-driven prediction, which plays a pivotal role in finding the trend of scientific impact. In this paper, we analyse methods and applications in data-driven prediction in the science of science, and discuss their significance. First, we introduce the background and review the current state of the science of science. Second, we review data-driven prediction based on paper citation count, and investigate research issues in this area. Then, we discuss methods to predict scholar impact, and we analyse different approaches to promote the scholarly collaboration in the collaboration network. This paper also discusses open issues and existing challenges, and suggests potential research directions., Comment: 17 pages, 6 figures

Hydrogen (H) induced damage in metals has been a long-standing woe for many industrial applications. One form of such damage is linked to H clustering, for which the atomic origin remains contended, particularly for non-hydride forming metals. In this work, we systematically studied H clustering behavior in bcc metals represented by W, Fe, Mo, and Cr, combining first-principles calculations, atomistic and Monte Carlo simulations. H clustering has been shown to be energetically favorable, and can be strongly facilitated by anisotropic stress field, dominated by the tensile component along one of the <001> crystalline directions. We showed that the stress effect can be well predicted by the continuum model based on H formation volume tensor, and that H clustering is thermodynamically possible at edge dislocations, evidenced by nanohydride formation at rather low levels of H concentration. Moreover, anisotropy in the stress effect is well reflected in nanohydride morphology around dislocations, with nanohydride growth occurring in the form of thin platelet structures that maximize one <001> tension. In particular, the <001> type edge dislocation, with the <001> tensile component maximized, has been shown to be highly effective in facilitating H aggregation, thus expected to play an important role in H clustering in bcc metals, in close agreement with recent experimental observations. This work explicitly and quantitatively clarifies the anisotropic nature of stress effect on H energetics and H clustering behaviors, offering mechanistic insights critical towards understanding H-induced damages in metals.

Arbitrary shape text detection is a challenging task due to the high variety and complexity of scenes texts. In this paper, we propose a novel unified relational reasoning graph network for arbitrary shape text detection. In our method, an innovative local graph bridges a text proposal model via Convolutional Neural Network (CNN) and a deep relational reasoning network via Graph Convolutional Network (GCN), making our network end-to-end trainable. To be concrete, every text instance will be divided into a series of small rectangular components, and the geometry attributes (e.g., height, width, and orientation) of the small components will be estimated by our text proposal model. Given the geometry attributes, the local graph construction model can roughly establish linkages between different text components. For further reasoning and deducing the likelihood of linkages between the component and its neighbors, we adopt a graph-based network to perform deep relational reasoning on local graphs. Experiments on public available datasets demonstrate the state-of-the-art performance of our method., Comment: 10 pages, Accepted by CVPR2020 Oral

Knowledge on structures and energetics of nanovoids is fundamental to understand defect evolution in metals. Yet there remain no reliable methods able to determine essential structural details or to provide accurate assessment of energetics for general nanovoids. Here, we performed systematic first-principles investigations to examine stable structures and energetics of nanovoids in bcc metals, explicitly demonstrated the stable structures can be precisely determined by minimizing their Wigner-Seitz area, and revealed a linear relationship between formation energy and Wigner-Seitz area of nanovoids. We further developed a new physics-based model to accurately predict stable structures and energetics for arbitrary-sized nanovoids. This model was well validated by first-principles calculations and recent nanovoid annealing experiments, and showed distinct advantages over the widely used spherical approximation. The present work offers mechanistic insights that crucial for understanding nanovoid formation and evolution, being a critical step towards predictive control and prevention of nanovoid related damage processes in structural metals.