IBridge: Inferring bridge links that diffuse information across communities

In positive and unlabeled (PU) learning problems, only positive examples are labeled. Unlabeled data contain both positive and negative examples. Studies show that positive examples of (secondary) diagnoses, and clinical conditions, such as sepsis, are present in unlabeled hospital administrative data, potentially distorting hospital reimbursement systems, and negatively affecting hospitals' revenue and profitability. We investigate whether PU learning is suitable for improving the quality of hospital administrative data. We train three models on 313,434 hospital cases using hospital cost features: two based on the two-step "spy" approach and one using a robust PU learning method. For model evaluation, we rely exclusively on positive examples due to the PU setting. To further assess model performance, we perform an external validity check: We relabel unlabeled sepsis cases, derive new sepsis rates, and compare them to those reported in medical record review studies. All models identify true positives well in unseen data. External validity checks show, however, that only the robust PU learner effectively discriminates between positives and negatives in the unlabeled data, yielding new sepsis rates within the range of sepsis rates reported in medical record review studies. PU learning can improve the quality of hospital administrative data, but its effectiveness depends strongly on the choice of learning approach and classifier. The output of a PU learner can potentially improve hospital reimbursement systems, hospital revenue and profitability management, and sensitivity analyses in healthcare management science, health economics, health services research, and disease surveillance.

Many learning techniques have been applied to identify disease-associated genes. At the early, they usually approached this problem as a binary classification, where training set is comprised of positive and negative samples. In which, positive samples are constructed from known disease genes, whereas negative samples are the remaining which are not known to be associated with diseases. This is the limitation of the binary classification-based solutions, since the negative training set should be actual non-disease genes; however, construction of this set is nearly impossible in biomedical researches. Therefore, to reduce this uncertainty, more realistic classification-based methods have been proposed. For instance, unary classification technique based on one-class SVM method was proposed by learning from only positive samples. In addition, the remaining set may contain unknown disease genes; therefore, semi-supervised methods such as binary semi-supervised and positive and unlabeled (PU) learning classifications have been proposed. In particular, PU learning methods, which learn from both known disease genes and the remaining genes, were shown to outperform others. In these studies, data sources are usually represented by vectorial form for binary classifiers, while they are in kernel matrices for unary and PU learning ones. The kernel-based data fusion is only suitable for data with different types and it seems unfair for the comparison based on different data representations. Therefore, in this study, we compared different classification techniques for the disease gene prediction based on vectorial representation of samples. The simulation result showed that the unary classification technique, which combines both density and class probability estimation strategies, achieved the best performance, whereas it is worst for the one-class SVM-based method. Interestingly, performance of the best binary classification technique is comparable with that of biased SVM-based PU learning and binary semi-supervised classification methods. And, they are all better than the multi-level SVM-based one.

Link prediction aims to find the missing link in current networks or estimate the likelihood the link will appear in the future. In many real-world scenarios, networks can be massive and drastically evolving. Many recent works concentrated on how to solve the procession of massive data, which cares less about the effects of the temporal information. In some dynamic networks, the edge that appears a long time ago will have fewer effects on the appearance of edges in the future. The accuracy of link prediction in dynamic networks can be further improved by adding temporal information in prediction measures. In this paper, we mainly explore the effects of the link temporal information in the graph stream link prediction. We design a graph stream-based framework to solve link prediction problems in dynamic networks which can provide a convenient platform to implement different link prediction methods for dynamic networks, and evaluate these methods on a fair basis. Then, we proposed the Time Decay-based Link Prediction (TDLP) method to improve the efficient of link prediction problem in the dynamic networks. TDLP extends the neighborhood-based measure with time decay functions in graph stream scenarios which can handle temporal information and massive data. Experiment results demonstrate that the accuracy of link prediction for dynamic networks can be efficiently improved in our TDLP method.

Among emerging energy materials, halide and chalcogenide perovskites have garnered significant attention over the last decade owing to the abundance of their constituent species, low manufacturing costs, and their highly tunable composition-structure-property space. Navigating the vast perovskite compositional landscape is possible using density functional theory (DFT) computations, but they are not easily extended to predictions of the synthesizability of new materials and their properties. As a result, only a limited number of compositions identified to have desirable optoelectronic properties from these calculations have been realized experimentally. One way to bridge this gap is by learning from the experimental literature about how the perovskite composition-structure space relates to their likelihood of laboratory synthesis. Here, we present our efforts in combining high-throughput DFT data with experimental labels collected from the literature to train classifier models employing various materials descriptors to forecast the synthesizability of any given perovskite compound. Our framework utilizes the positive and unlabeled learning strategy and makes probabilistic estimates of the synthesis likelihood based on DFT-computed energies and the prior existence of similar synthesized compounds. Our data and models can be readily accessed via a findable, accessible, interoperable, and reproducible nanoHUB tool.

Link prediction based on bipartite networks can not only mine hidden relationships between different types of nodes, but also reveal the inherent law of network evolution. Existing bipartite network link prediction is mainly based on the global structure that cannot analyze the role of the local structure in link prediction. To tackle this problem, this paper proposes a deep link-prediction (DLP) method by leveraging the local structure of bipartite networks. The method first extracts the local structure between target nodes and observes structural information between nodes from a local perspective. Then, representation learning of the local structure is performed on the basis of the graph neural network to extract latent features between target nodes. Lastly, a deep-link prediction model is trained on the basis of latent features between target nodes to achieve link prediction. Experimental results on five datasets showed that DLP achieved significant improvement over existing state-of-the-art link prediction methods. In addition, this paper analyzes the relationship between local structure and link prediction, confirming the effectiveness of a local structure in link prediction.

Social network analysis is an approach to the study of social structures. One of the important fields in social networks analyses is link prediction. Link prediction tries to reach an appropriate answer to this question: what kinds of interaction among members of a network would possible form in future, given a snapshot of the network in current time. The main purpose of this paper is to boost the performance of similarity based link prediction methods by using community information. This information is derived from the structure of the graph, based on the number of community levels that two vertices have in common, in a hierarchical representation of communities. To evaluate the performance of the proposed method, four datasets are used as benchmark. The results suggest that the information of communities often increases the efficiency and accuracy of link prediction.

Urban areas are one of the most important components of human society. Their extents have been continuously growing during the last few decades. Accurate and timely measurements of the extents of urban areas can help in analyzing population densities and urban sprawls and in studying environmental issues related to urbanization. Urban extents detected from remotely sensed data are usually a by-product of land use classification results, and their interpretation requires a full understanding of land cover types. In this study, for the first time, we mapped urban extents in the continental United States using a novel one-class classification method, i.e., positive and unlabeled learning (PUL), with multi-temporal Moderate Resolution Imaging Spectroradiometer (MODIS) data for the year 2010. The Defense Meteorological Satellite Program Operational Linescan System (DMSP-OLS) night stable light data were used to calibrate the urban extents obtained from the one-class classification scheme. Our results demonstrated the effectiveness of the use of the PUL algorithm in mapping large-scale urban areas from coarse remote-sensing images, for the first time. The total accuracy of mapped urban areas was 92.9% and the kappa coefficient was 0.85. The use of DMSP-OLS night stable light data can significantly reduce false detection rates from bare land and cropland far from cities. Compared with traditional supervised classification methods, the one-class classification scheme can greatly reduce the effort involved in collecting training datasets, without losing predictive accuracy.

Improving local clustering based top-L link prediction methods via asymmetric link clustering information

Link prediction is a common problem in network science that cuts across many disciplines. The goal is to forecast the appearance of new links or to find links missing in the network. Typical methods for link prediction use the topology of the network to predict the most likely future or missing connections between a pair of nodes. However, network evolution is often mediated by higher-order structures involving more than pairs of nodes; for example, cliques on three nodes (also called triangles) are key to the structure of social networks, but the standard link prediction framework does not directly predict these structures. To address this gap, in recent work, we propose a new link prediction task called “pairwise link prediction” that directly targets the prediction of new triangles, where one is tasked with finding which nodes are most likely to form a triangle with a given edge. We extend this work in this manuscript, and we evaluate a variety of natural extensions to link prediction methods including neighborhood and PageRank-based methods. A key difference from our previous work is the definition of the neighborhood of an edge, which has a surprisingly large impact on the empirical performance. Our experiments on a variety of networks show that diffusion-based methods are less sensitive to the type of graphs used and more consistent in their results. We also show how our pairwise link prediction framework can be used to get better predictions within the context of standard link prediction evaluation.

Link prediction is a key tool for studying the structure and evolution mechanism of complex networks. Recommending new friend relationships through accurate link prediction is one of the important factors in the evolution, development, and popularization of social networks. At present, scholars have proposed many link prediction algorithms based on the similarity of local information and random walks. These algorithms help identify actual missing and false links in various networks. However, the prediction results significantly differ in networks with various structures, and the prediction accuracy is low. This study proposes a method for improving the accuracy of link prediction. Before link prediction, k‐shell decomposition method is used to layer the network, and the nodes that are in 1‐shell and the nodes that are not linked to the high‐shell in the 2‐shell are deleted. The experiments on four real network datasets verify the effectiveness of the proposed method.

Introduction Network representation can give a holistic view of relationships for biomedical entities through network topology. Link prediction estimates the probability of link formation between the pair of unconnected nodes. In the drug discovery process, the link prediction method not only enables the detection of connectivity patterns but also predicts the effects of one biomedical entity to multiple entities simultaneously and vice versa, which is useful for many applications. Areas covered The authors provide a comprehensive overview of network link prediction in drug discovery. Link prediction methodologies such as similarity-based approaches, embedding-based approaches, probabilistic model-based approaches, and preprocessing methods are summarized with examples. In addition to describing their properties and limitations, the authors discuss the applications of link prediction in drug discovery based on the relationship between biomedical concepts. Expert opinion Link prediction is a powerful method to infer the existence of novel relationships in drug discovery. However, link prediction has been hampered by the sparsity of data and the lack of negative links in biomedical networks. With preprocessing to balance positive and negative samples and the collection of more data, the authors believe it is possible to develop more reliable link prediction methods that can become invaluable tools for successful drug discovery.

Link prediction is widely used in network analysis to identify future links between nodes. Link prediction has an important place in terms of being applicable to many real-world networks with dynamic structure. Networks with dynamic structure, such as social networks, scientific collaboration networks and metabolic networks, are networks in which link prediction studies are performed. In addition, it is seen that there are few studies showing the feasibility of link prediction by creating networks from different areas. In this study, in order to show the applicability of link prediction processes in different fields link prediction was made by applying traditional link prediction methods in the networks formed from the data of football competitions played after the groups between the years 2004–2017 in the UEFA European League. The AUC metric was used to measure the success of forecasting. The results show that link prediction methods can be used in sports networks.

Multi-label classification has attracted significant interests in various domains. However, only few positive labels are labeled. Treating unknown labels as negative labels brings the one-side noise, which causes the severe performance degradation. Motivated by this, we present the positive and unlabeled (PU) matrix completion based Multi-Label Classification with Missing Labels called PUMCML, that focus on finding all positive labels and construct a classifier based on completion matrix under instance and label dependencies. More specifically, an asymmetrical PU learning loss function is firstly used to solve the one-side noise from missing labels. Secondly, an instance dependencies assumption is proposed that similar instances in multi-label data will share similar labels. Furthermore, considering the label dependencies, the completion matrix consisting of the predicted labels and origin labels is constrained by a nuclear norm. Finally, the proposed algorithm is optimization problem which is convex but not smooth, so Alternating Direction Multiplier Method is design for handling the optimization problem by dividing the problem into multiple subproblems. Experimental results on four benchmarks demonstrate our method achieves a huge improvement in performance and robustness to missing labels compared to other advanced algorithms.

An efficient link prediction index for complex military organization

Improving embedding-based link prediction performance using clustering