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Protein function prediction is critical for understanding the cellular physiological and biochemical processes, and it opens up new possibilities for advancements in fields such as disease research and drug discovery. During the past decades, with the exponential growth of protein sequence data, many computational methods for predicting protein function have been proposed. Therefore, a systematic review and comparison of these methods are necessary. In this study, we divide these methods into four different categories, including sequence-based methods, 3D structure-based methods, PPI network-based methods and hybrid information-based methods. Furthermore, their advantages and disadvantages are discussed, and then their performance is comprehensively evaluated and compared. Finally, we discuss the challenges and opportunities present in this field. [ABSTRACT FROM AUTHOR]

With the booming development of the Internet of Things (IoT) industry, millions of data are generated every day. How to use and manage these data safely and efficiently has become a hot issue of concern to people. Due to the accumulation of IoT data, the isolated data island phenomenon makes it difficult to connect and interact with each data owner, and the security and privacy of IoT data also become a challenge. Blockchain is a decentralized database technology that uses distributed accounting to ensure reliable data transmission and access, along with smart contracts that can be executed automatically to program and manipulate data. At the same time, blockchain techniques have stronger security and privacy, which can better meet the needs of users. In this paper, we analyze the current management mode and challenges of IoT data and propose an IoT data platform based on blockchain. The proposed platform takes into account important factors including IoT data traceability, IoT data trusted transactions, etc. Our IoT data platform achieves the trusted management and transaction of IoT data. We also propose follow-up optimization solutions to expand the application scope of our platform and achieve more efficient management of IoT data. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy (DR), the main cause of irreversible blindness, is one of the most common complications of diabetes. At present, deep convolutional neural networks have achieved promising performance in automatic DR detection tasks. The convolution operation of methods is a local cross‐correlation operation, whose receptive field determines the size of the local neighbourhood for processing. However, for retinal fundus photographs, there is not only the local information but also long‐distance dependence between the lesion features (e.g. hemorrhages and exudates) scattered throughout the whole image. The proposed method incorporates correlations between long‐range patches into the deep learning framework to improve DR detection. Patch‐wise relationships are used to enhance the local patch features since lesions of DR usually appear as plaques. The Long‐Range unit in the proposed network with a residual structure can be flexibly embedded into other trained networks. Extensive experimental results demonstrate that the proposed approach can achieve higher accuracy than existing state‐of‐the‐art models on Messidor and EyePACS datasets. [ABSTRACT FROM AUTHOR]

In this paper, we study the problem of privacy-preserving data synthesis (PPDS) for tabular data in a distributed multi-party environment. In a decentralized setting, for PPDS, federated generative models with differential privacy are used by the existing methods. Unfortunately, the existing models apply only to images or text data and not to tabular data. Unlike images, tabular data usually consist of mixed data types (discrete and continuous attributes) and real-world datasets with highly imbalanced data distributions. Existing methods hardly model such scenarios due to the multimodal distributions in the decentralized continuous columns and highly imbalanced categorical attributes of the clients. To solve these problems, we propose a federated generative model for decentralized tabular data synthesis (HT-Fed-GAN). There are three important parts of HT-Fed-GAN: the federated variational Bayesian Gaussian mixture model (Fed-VB-GMM), which is designed to solve the problem of multimodal distributions; federated conditional one-hot encoding with conditional sampling for global categorical attribute representation and rebalancing; and a privacy consumption-based federated conditional GAN for privacy-preserving decentralized data modeling. The experimental results on five real-world datasets show that HT-Fed-GAN obtains the best trade-off between the data utility and privacy level. For the data utility, the tables generated by HT-Fed-GAN are the most statistically similar to the original tables and the evaluation scores show that HT-Fed-GAN outperforms the state-of-the-art model in terms of machine learning tasks. [ABSTRACT FROM AUTHOR]

Protein remote homology detection is a fundamental and important task for protein structure and function analysis. Several search methods have been proposed to improve the detection performance of the remote homologues and the accuracy of ranking lists. The position-specific scoring matrix (PSSM) profile and hidden Markov model (HMM) profile can contribute to improving the performance of the state-of-the-art search methods. In this paper, we improved the profile-link (PL) information for constructing PSSM or HMM profiles, and proposed a PL-based search method (PL-search). In PL-search, more robust PLs are constructed through the double-link and iterative extending strategies, and an accurate similarity score of sequence pairs is calculated from the two-level Jaccard distance for remote homologues. We tested our method on two widely used benchmark datasets. Our results show that whether HHblits, JackHMMER or position-specific iterated-BLAST is used, PL-search obviously improves the search performance in terms of ranking quality as well as the number of detected remote homologues. For ease of use of PL-search, both its stand-alone tool and the web server are constructed, which can be accessed at http://bliulab.net/PL-search/. [ABSTRACT FROM AUTHOR]

Motivation As one of the most important and widely used mainstream iterative search tool for protein sequence search, an accurate Position-Specific Scoring Matrix (PSSM) is the key of PSI-BLAST. However, PSSMs containing non-homologous information obviously reduce the performance of PSI-BLAST for protein remote homology. Results To further study this problem, we summarize three types of Incorrectly Selected Homology (ISH) errors in PSSMs. A new search tool Supervised-Manner-based Iterative BLAST (SMI-BLAST) is proposed based on PSI-BLAST for solving these errors. SMI-BLAST obviously outperforms PSI-BLAST on the Structural Classification of Proteins-extended (SCOPe) dataset. Compared with PSI-BLAST on the ISH error subsets of SCOPe dataset, SMI-BLAST detects 1.6–2.87 folds more remote homologous sequences, and outperforms PSI-BLAST by 35.66% in terms of ROC1 scores. Furthermore, this framework is applied to JackHMMER, DELTA-BLAST and PSI-BLASTexB, and their performance is further improved. Availability and implementation User-friendly webservers for SMI-BLAST, JackHMMER, DELTA-BLAST and PSI-BLASTexB are established at http://bliulab.net/SMI-BLAST/ , by which the users can easily get the results without the need to go through the mathematical details. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]