BackgroundComparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most widely used indicators for protein interaction. Among the various approaches proposed, those based on the vector space model are relatively simple, but their effectiveness is far from satisfying.ResultsWe propose a Hierarchical Vector Space Model (HVSM) for computing semantic similarity between different genes or their products, which enhances the basic vector space model by introducing the relation between GO terms. Besides the directly annotated terms, HVSM also takes their ancestors and descendants related by “is_a” and “part_of” relations into account. Moreover, HVSM introduces the concept of a Certainty Factor to calibrate the semantic similarity based on the number of terms annotated to genes. To assess the performance of our method, we applied HVSM to Homo sapiens and Saccharomyces cerevisiae protein-protein interaction datasets. Compared with TCSS, Resnik, and other classic similarity measures, HVSM achieved significant improvement for distinguishing positive from negative protein interactions. We also tested its correlation with sequence, EC, and Pfam similarity using online tool CESSM.ConclusionsHVSM showed an improvement of up to 4% compared to TCSS, 8% compared to IntelliGO, 12% compared to basic VSM, 6% compared to Resnik, 8% compared to Lin, 11% compared to Jiang, 8% compared to Schlicker, and 11% compared to SimGIC using AUC scores. CESSM test showed HVSM was comparable to SimGIC, and superior to all other similarity measures in CESSM as well as TCSS. Supplementary information and the software are available at https://github.com/kejia1215/HVSM.
Graphene is a promising THz magneto-optical material. However, high Faraday rotation is only achievable at a low THz frequency range in single layer graphene. In this paper, we report simultaneous Faraday rotation and optical transmission enhancement in Au grating/graphene/silicon hybrid plasmonic structures across a wide frequency range from 0.43 to 24 THz using extraordinary transmission of THz spoof surface plasmons. In a broad frequency range up to 13.1 THz, the Faraday rotation and magneto-optical figure of merit in this hybrid structure can exceed the maximum value of single layer graphene at the low THz frequency range. Numerical analysis on the device dispersion relation indicates that the mechanism of simultaneous Faraday rotation and transmission enhancement is due to coupling of the TE waveguide mode with the TM hybrid waveguide-plasmon mode. Our work demonstrates the hybrid plasmonic structure as a promising candidate for THz nonreciprocal photonic device applications.
Support Vector Regression (SVR) has been a long standing problem in machine learning, and gains its popularity on various computer vision tasks. In this paper, we propose a structured support vector regression framework by extending the max-margin principle to incorporate spatial correlations among neighboring pixels. The objective function in our framework considers both label information and pairwise features, helping to achieve better cross-smoothing over neighboring nodes. With the bundle method, we effectively reduce the number of constraints and alleviate the adverse effect of outliers, leading to an efficient and robust learning algorithm. Moreover, we conduct a thorough analysis for the loss function used in structured regression, and provide a principled approach for defining proper loss functions and deriving the corresponding solvers to find the most violated constraint. We demonstrate that our method outperforms the state-of-the-art regression approaches on various testbeds of synthetic images and real-world scenes. Abstract. Support Vector Regression (SVR) has been a long standing problem in machine learning, and gains its popularity on various computer vision tasks. In this paper, we propose a structured support vector regression framework by extending the max-margin principle to incorporate spatial correlations among neighboring pixels. The objective function in our framework considers both label information and pairwise features, helping to achieve better cross-smoothing over neighboring nodes. With the bundle method, we effectively reduce the number of constraints and alleviate the adverse effect of outliers, leading to an efficient and robust learning algorithm. Moreover, we conduct a thorough analysis for the loss function used in structured regression, and provide a principled approach for defining proper loss functions and deriving the corresponding solvers to find the most violated constraint. We demonstrate that our method outperforms the state-of-the-art regression approaches on various testbeds of synthetic images and real-world scenes.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.