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EndNote: Feature-based classification of networks.

ABSTRACT: Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural features. These features tend to be shared by networks belonging to the same broad class, such as the class of social networks or the class of biological networks. Within each such class, networks describing similar systems tend to have similar features. This occurs presumably because networks representing similar systems would be expected to be generated by a shared set of domain specific mechanisms, and it should therefore be possible to classify networks based on their features at various structural levels. Here we describe and demonstrate a new hybrid approach that combines manual selection of network features of potential interest with existing automated classification methods. In particular, selecting well-known network features that have been studied extensively in social network analysis and network science literature, and then classifying networks on the basis of these features using methods such as random forest, which is known to handle the type of feature collinearity that arises in this setting, we find that our approach is able to achieve both higher accuracy and greater interpretability in shorter computation time than other methods.

SUBMITTER: Barnett I

PROVIDER: S-EPMC6980283 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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EndNote: Feature-based classification of networks.

Barnett Ian I Malik Nishant N Kuijjer Marieke L ML Mucha Peter J PJ Onnela Jukka-Pekka JP

Network science (Cambridge University Press) 20190923 3

Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural features. These features tend to be shared by networks belonging to the same broad class, such as the class of social networks or the class of biological networks. Within each such class, networks describing similar systems tend to have similar features. This occurs presumably because networks representing similar syst ...[more]

PMID: 31984135

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Project description:BackgroundReliable prediction of stability changes in protein variants is an important aspect of computational protein design. A number of machine learning methods that allow a classification of stability changes knowing only the sequence of the protein emerged. However, their performance on amino acid substitutions of previously unseen non-homologous proteins is rather limited. Moreover, the performance varies for different types of mutations based on the secondary structure or accessible surface area of the mutation site.ResultsWe proposed feature-based multiple models with each model designed for a specific type of mutations. The new method is composed of five models trained for mutations in exposed, buried, helical, sheet, and coil residues. The classification of a mutation as stabilising or destabilising is made as a consensus of two models, one selected based on the predicted accessible surface area and the other based on the predicted secondary structure of the mutation site. We refer to our new method as Evolutionary, Amino acid, and Structural Encodings with Multiple Models (EASE-MM). Cross-validation results show that EASE-MM provides a notable improvement to our previous work reaching a Matthews correlation coefficient of 0.44. EASE-MM was able to correctly classify 73% and 75% of stabilising and destabilising protein variants, respectively. Using an independent test set of 238 mutations, we confirmed our results in a comparison with related work.ConclusionsEASE-MM not only outperformed other related methods but achieved more balanced results for different types of mutations based on the accessible surface area, secondary structure, or magnitude of stability changes. This can be attributed to using multiple models with the most relevant features selected for the given type of mutations. Therefore, our results support the presumption that different interactions govern stability changes in the exposed and buried residues or in residues with a different secondary structure.

Dataset Information

EndNote: Feature-based classification of networks.

Publications

EndNote: Feature-based classification of networks.

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