Playing the role of weak clique property in link prediction: A friend recommendation model.
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ABSTRACT:
SUBMITTER: Ma C
PROVIDER: S-EPMC4954950 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:MotivationThe usefulness of supervised molecular property prediction (MPP) is well-recognized in many applications. However, the insufficiency and the imbalance of labeled data make the learning problem difficult. Moreover, the reliability of the predictions is also a huddle in the deployment of MPP models in safety-critical fields.ResultsWe propose the Evidential Meta-model for Molecular Property Prediction (EM3P2) method that returns uncertainty estimates along with its predictions. Our EM3P2 trains an evidential graph isomorphism network classifier using multi-task molecular property datasets under the model-agnostic meta-learning (MAML) framework while addressing the problem of data imbalance.Our results showed better prediction performances compared to existing meta-MPP models. Furthermore, we showed that the uncertainty estimates returned by our EM3P2 can be used to reject uncertain predictions for applications that require higher confidence.Availability and implementationSource code available for download at https://github.com/Ajou-DILab/EM3P2.
| S-EPMC10597608 | biostudies-literature
Project description:Inferring missing links based on the currently observed network is known as link prediction, which has tremendous real-world applications in biomedicine, e-commerce, social media, and criminal intelligence. Numerous methods have been proposed to solve the link prediction problem. Yet, many of these methods are designed for undirected networks only and based on domain-specific heuristics. Here we developed a new link prediction method based on deep generative models, which does not rely on any domain-specific heuristic and works for general undirected or directed complex networks. Our key idea is to represent the adjacency matrix of a network as an image and then learn hierarchical feature representations of the image by training a deep generative model. Those features correspond to structural patterns in the network at different scales, from small subgraphs to mesoscopic communities. When applied to various real-world networks from different domains, our method shows overall superior performance against existing methods.
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Project description:Friend recommendation plays a key role in promoting user experience in online social networks (OSNs). However, existing studies usually neglect users' fine-grained interest as well as the evolving feature of interest, which may cause unsuitable recommendation. In particular, some OSNs, such as the online learning community, even have little work on friend recommendation. To this end, we strive to improve friend recommendation with fine-grained evolving interest in this paper. We take the online learning community as an application scenario, which is a special type of OSNs for people to learn courses online. Learning partners can help improve learners' learning effect and improve the attractiveness of platforms. We propose a learning partner recommendation framework based on the evolution of fine-grained learning interest (LPRF-E for short). We extract a sequence of learning interest tags that changes over time. Then, we explore the time feature to predict evolving learning interest. Next, we recommend learning partners by fine-grained interest similarity. We also refine the learning partner recommendation framework with users' social influence (denoted as LPRF-F for differentiation). Extensive experiments on two real datasets crawled from Chinese University MOOC and Douban Book validate that the proposed LPRF-E and LPRF-F models achieve a high accuracy (i.e., approximate 50% improvements on the precision and the recall) and can recommend learning partners with high quality (e.g., more experienced and helpful). Supplementary Information The online version contains supplementary material available at 10.1007/s11390-021-2124-z.
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Project description:Informative representation of molecules is a crucial prerequisite in AI-driven drug design and discovery. Pharmacophore information including functional groups and chemical reactions can indicate molecular properties, which have not been fully exploited by prior atom-based molecular graph representation. To obtain a more informative representation of molecules for better molecule property prediction, we propose the Pharmacophoric-constrained Heterogeneous Graph Transformer (PharmHGT). We design a pharmacophoric-constrained multi-views molecular representation graph, enabling PharmHGT to extract vital chemical information from functional substructures and chemical reactions. With a carefully designed pharmacophoric-constrained multi-view molecular representation graph, PharmHGT can learn more chemical information from molecular functional substructures and chemical reaction information. Extensive downstream experiments prove that PharmHGT achieves remarkably superior performance over the state-of-the-art models the performance of our model is up to 1.55% in ROC-AUC and 0.272 in RMSE higher than the best baseline model) on molecular properties prediction. The ablation study and case study show that our proposed molecular graph representation method and heterogeneous graph transformer model can better capture the pharmacophoric structure and chemical information features. Further visualization studies also indicated a better representation capacity achieved by our model.
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Project description:BACKGROUND:RNAs can interact and form complexes, which have various biological roles. The secondary structure prediction of those complexes is a first step towards the identification of their 3D structure. We propose an original approach that takes advantage of the high number of RNA secondary structure and RNA-RNA interaction prediction tools. We formulate the problem of RNA complex prediction as the determination of the best combination (according to the free energy) of predicted RNA secondary structures and RNA-RNA interactions. RESULTS:We model those predicted structures and interactions as a graph in order to have a combinatorial optimization problem that is a constrained maximum weight clique problem. We propose an heuristic based on Breakout Local Search to solve this problem and a tool, called RCPred, that returns several solutions, including motifs like internal and external pseudoknots. On a large number of complexes, RCPred gives competitive results compared to the methods of the state of the art. CONCLUSIONS:We propose in this paper a method called RCPred for the prediction of several secondary structures of RNA complexes, including internal and external pseudoknots. As further works we will propose an improved computation of the global energy and the insertion of 3D motifs in the RNA complexes.
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Project description:Institutional Review Boards (IRBs) are a critical component of clinical research and can become a significant bottleneck due to the dramatic increase, in both volume and complexity of clinical research. Despite the interest in developing clinical research informatics (CRI) systems and supporting data standards to increase clinical research efficiency and interoperability, informatics research in the IRB domain has not attracted much attention in the scientific community. The lack of standardized and structured application forms across different IRBs causes inefficient and inconsistent proposal reviews and cumbersome workflows. These issues are even more prominent in multi-institutional clinical research that is rapidly becoming the norm. This paper proposes and evaluates a domain analysis model for electronic IRB (eIRB) systems, paving the way for streamlined clinical research workflow via integration with other CRI systems and improved IRB application throughput via computer-assisted decision support.
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Project description:Various structural features of networks have been applied to develop link prediction methods. However, because different features highlight different aspects of network structural properties, it is very difficult to benefit from all of the features that might be available. In this paper, we investigate the role of network topology in predicting missing links from the perspective of information theory. In this way, the contributions of different structural features to link prediction are measured in terms of their values of information. Then, an information-theoretic model is proposed that is applicable to multiple structural features. Furthermore, we design a novel link prediction index, called Neighbor Set Information (NSI), based on the information-theoretic model. According to our experimental results, the NSI index performs well in real-world networks, compared with other typical proximity indices.
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Project description:RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ?84% Q3 accuracy for 3-state SS, ?72% Q8 accuracy for 8-state SS, ?66% Q3 accuracy for 3-state solvent accessibility, and ?0.89 area under the ROC curve (AUC) for disorder prediction.
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