Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison.
Recommendation systems play a vital role to keep users engaged with personalized content in modern online platforms. Deep learning has revolutionized many research fields and there is a recent surge of interest in applying it to collaborative filtering (CF). However, existing methods compose deep learning architectures with the latent factor model ignoring a major class of CF models, neighborhood or memory-based approaches. We propose Collaborative Memory Networks (CMN), a deep architecture to unify the two classes of CF models capitalizing on the strengths of the global structure of latent factor model and local neighborhood-based structure in a nonlinear fashion. Motivated by the success of Memory Networks, we fuse a memory component and neural attention mechanism as the neighborhood component. The associative addressing scheme with the user and item memories in the memory module encodes complex user-item relations coupled with the neural attention mechanism to learn a user-item specific neighborhood. Finally, the output module jointly exploits the neighborhood with the user and item memories to produce the ranking score. Stacking multiple memory modules together yield deeper architectures capturing increasingly complex user-item relations. Furthermore, we show strong connections between CMN components, memory networks and the three classes of CF models. Comprehensive experimental results demonstrate the effectiveness of CMN on three public datasets outperforming competitive baselines. Qualitative visualization of the attention weights provide insight into the model's recommendation process and suggest the presence of higher order interactions.
As the amount of textual data has been rapidly increasing over the past decade, efficient similarity search methods have become a crucial component of large-scale information retrieval systems. A popular strategy is to represent original data samples by compact binary codes through hashing. A spectrum of machine learning methods have been utilized, but they o en lack expressiveness and flexibility in modeling to learn effective representations. e recent advances of deep learning in a wide range of applications has demonstrated its capability to learn robust and powerful feature representations for complex data. Especially, deep generative models naturally combine the expressiveness of probabilistic generative models with the high capacity of deep neural networks, which is very suitable for text modeling. However, li le work has leveraged the recent progress in deep learning for text hashing.In this paper, we propose a series of novel deep document generative models for text hashing. e first proposed model is unsupervised while the second one is supervised by utilizing document labels/tags for hashing. e third model further considers document-specific factors that affect the generation of words. e probabilistic generative formulation of the proposed models provides a principled framework for model extension, uncertainty estimation, simulation, and interpretability. Based on variational inference and reparameterization, the proposed models can be interpreted as encoder-decoder deep neural networks and thus they are capable of learning complex nonlinear distributed representations of the original documents. We conduct a comprehensive set of experiments on four public testbeds. e experimental results have demonstrated the effectiveness of the proposed supervised learning models for text hashing.
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