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Background: Protein–protein interaction (PPI) is vital for life processes, disease treatment, and drug discovery. The computational prediction of PPI is relatively inexpensive and efficient when compared to traditional wet-lab experiments. Given a new protein, one may wish to find whether the protein has any PPI relationship with other existing proteins. Current computational PPI prediction methods usually compare the new protein to existing proteins one by one in a pairwise manner. This is time consuming. Results: In this work, we propose a more efficient model, called deep hash learning protein-and-protein interaction (DHL-PPI), to predict all-against-all PPI relationships in a database of proteins. First, DHL-PPI encodes a protein sequence into a binary hash code based on deep features extracted from the protein sequences using deep learning techniques. This encoding scheme enables us to turn the PPI discrimination problem into a much simpler searching problem. The binary hash code for a protein sequence can be regarded as a number. Thus, in the pre-screening stage of DHL-PPI, the string matching problem of comparing a protein sequence against a database with M proteins can be transformed into a much more simpler problem: to find a number inside a sorted array of length M. This pre-screening process narrows down the search to a much smaller set of candidate proteins for further confirmation. As a final step, DHL-PPI uses the Hamming distance to verify the final PPI relationship. Conclusions: The experimental results confirmed that DHL-PPI is feasible and effective. Using a dataset with strictly negative PPI examples of four species, DHL-PPI is shown to be superior or competitive when compared to the other state-of-the-art methods in terms of precision, recall or F1 score. Furthermore, in the prediction stage, the proposed DHL-PPI reduced the time complexity from O (M 2) to O (M log M) for performing an all-against-all PPI prediction for a database with M proteins. With the proposed approach, a protein database can be preprocessed and stored for later search using the proposed encoding scheme. This can provide a more efficient way to cope with the rapidly increasing volume of protein datasets. [ABSTRACT FROM AUTHOR]

Recommendation efficiency and data sparsity problems have been regarded as two challenges of improving performance for online recommendation. Most of the previous related work focus on improving recommendation accuracy instead of efficiency. In this paper, we propose a Deep Pairwise Hashing (DPH) to map users and items to binary vectors in Hamming space, where a user's preference for an item can be efficiently calculated by Hamming distance, which significantly improves the efficiency of online recommendation. To alleviate data sparsity and cold-start problems, the user-item interactive information and item content information are unified to learn effective representations of items and users. Specifically, we first pre-train robust item representation from item content data by a Denoising Auto-encoder instead of other deterministic deep learning frameworks; then we finetune the entire framework by adding a pairwise loss objective with discrete constraints; moreover, DPH aims to minimize a pairwise ranking loss that is consistent with the ultimate goal of recommendation. Finally, we adopt the alternating optimization method to optimize the proposed model with discrete constraints. Extensive experiments on three different datasets show that DPH can significantly advance the state-of-the-art frameworks regarding data sparsity and item cold-start recommendation. [ABSTRACT FROM AUTHOR]