12,956 research outputs found

    ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

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    Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches

    Zero Shot Learning with the Isoperimetric Loss

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    We introduce the isoperimetric loss as a regularization criterion for learning the map from a visual representation to a semantic embedding, to be used to transfer knowledge to unknown classes in a zero-shot learning setting. We use a pre-trained deep neural network model as a visual representation of image data, a Word2Vec embedding of class labels, and linear maps between the visual and semantic embedding spaces. However, the spaces themselves are not linear, and we postulate the sample embedding to be populated by noisy samples near otherwise smooth manifolds. We exploit the graph structure defined by the sample points to regularize the estimates of the manifolds by inferring the graph connectivity using a generalization of the isoperimetric inequalities from Riemannian geometry to graphs. Surprisingly, this regularization alone, paired with the simplest baseline model, outperforms the state-of-the-art among fully automated methods in zero-shot learning benchmarks such as AwA and CUB. This improvement is achieved solely by learning the structure of the underlying spaces by imposing regularity.Comment: Accepted to AAAI-2
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