Comprehending biological reproduction and cellular metabolism is facilitated by the Enzyme Commission, which matches protein sequences to the biochemical reactions they catalyse through EC numbers. In recent years, several methods have been proposed for predicting enzyme function. However, these methods still encounter challenges. Firstly, traditional methods for manually designing enzyme features are complex and cumbersome, lacking an effective generalized method for embedding enzyme sequences. Secondly, the distribution gap between different enzymes is significant, which resulting in existing methods struggling to predict multilevel enzyme functions. Thirdly, traditional enzyme function prediction models only extract single view feature of enzyme, so there is still room for further improving the ability of these models to extract enzyme data. To address these challenges, a new multilevel enzyme function prediction model (SMENET) based on multi-view semantics is proposed. This method uses protein large language model to extract semantic information. Subsequently, this semantic information is fed into multiple information extraction network modules, followed by using Biologic Sematic Attention to integrate these views' information. Finally, a multi-view adaptive fusion network is designed to extract the best common representation between multiple semantic views. Extensive experiments were conducted on multiple datasets to validate the effectiveness of SMENET.

With the explosive growth of graph data in scale, noise, and structural complexity, existing graph neural networks (GNNs) are reaching a performance bottleneck when simultaneously modelling uncertainty and long-range dependencies. To overcome this limitation, we introduce FGMMa, a two-stage framework composed of node-level Fuzzy Graph Message Passing (FGMP) and subgraph-level Fuzzy NeuralSort Graph Mamba. FGMP assigns a learnable fuzzy membership degree to each edge and employs a fuzzy-max aggregator to suppress noise at its source, thereby enhancing the robustness and interpretability of node representations. The Fuzzy NeuralSort Graph Mamba subsequently applies NeuralSort to order fuzzy subgraph features and utilises the linear-time Graph Mamba to dynamically regulate inter-subgraph information flow, generating high-quality sequential embeddings that capture long-range dependencies. Consequently, FGMMa offers a principled integration of fuzzy theory and graph representation learning. The node, fuzzy, and sequential subgraph embeddings are then fused to perform node classification and other downstream tasks. Across seven public benchmark datasets, FGMMa attains state-of-the-art node-classification accuracies of 93.42% on Amazon-Photo and 96.83% on Reddit, surpasses strong baselines on the remaining datasets, and yields lower average running time together with higher$F_{1}$scores. Moreover, on a schizophrenia functional-connectivity dataset, FGMMa identifies multiple clinically relevant brain regions and achieves superior classification accuracy.

Multi-view fuzzy clustering has attracted increasing attention owing to its strong clustering performance and inherent ability to effectively model uncertainty. However, most existing methods rely on the unrealistic assumption that all views are fully observed, which rarely holds in practice. Although several methods have been proposed to address incomplete multi-view data, they typically focus only on extracting shared information across views while overlooking view-specific information. Moreover, they often tend to neglect missing views imputation, a key mechanism for handling incomplete data. Furthermore, by separating representation learning from clustering, many existing frameworks yield representations that are not necessarily optimal for clustering, thus compromising robustness. To address these limitations and based on fuzzy clustering, a novel enhanced one step incomplete multi-view clustering method (IMVFCM_DRL) is proposed in this paper. First, to effectively handle incomplete multi-view data, we construct a new representation learning framework that explicitly integrates missing-view imputation. Second, to fully exploit the multi-view information, a dual information learning strategy is introduced to jointly capture both common and view-specific information. Finally, a unified one-step fuzzy clustering framework with weighted structure preservation is developed, ensuring that representation learning and fuzzy clustering are jointly optimized. The experiments conducted on various multi-view datasets demonstrate the effectiveness of IMVFCM_DRL. The codes are available at https://github.com/BBKing49/IMVFCM_DRL.

Effectively extracting discriminative information from multi-view data remains a key challenge in multi-view learning. Existing methods typically focus on exploring inter-view consistency via linear or nonlinear transformation. While nonlinear methods tend to yield better performance, their limited transparency and interpretability limit their practical applications. Takagi-Sugeno-Kang Fuzzy Systems (TSK-FS), as a rule-based model with high interpretability, have been applied to multi-view tasks. However, prior methods either rely solely on antecedent components for nonlinear modeling or integrate deep neural networks into the consequent part, thereby compromising model interpretability. To address these challenges, we propose Fuzzy Rule-guided Multi-view Differentiable Representation Learning (FRMVDRL). Specifically, in our framework, antecedent parameters of TSK-FS are first used to map data into highdimensional fuzzy space. Then during the learning of consequent parameters, a dual information extraction mechanism is proposed to jointly capture shared knowledge across views and view-specific knowledge. Moreover, a second-order geometric structure preservation mechanism is constructed to exploit structural information at both the instance and the instance-pair level. To enhance discriminability of the learned representations, a biorthogonal constraint alongside a Shannon entropy mechanism is introduced. Finally, to balance model performance and interpretability, we introduce a novel multi-view differentiable optimization strategy that incorporates learnable parameters to expand the solution space while preserving the structure of traditional optimization. Extensive experiments on benchmark multi-view datasets demonstrate the effectiveness of the FRMVDRL.

Artificial intelligence has shown great promise in noninvasive recognition of vulnerable coronary plaques. However, practical data issues in multicenter studies, such as inconsistent data distribution and insufficient or missing data labels, could significantly affect the recognition accuracy. Unsupervised domain adaptation (UDA) can be introduced to address this challenge, but several limits still remain. First, many existing UDA models are black boxes, hindering healthcare professionals' ability to interpret and trust the model's decision. Second, some methods use pseudolabel to enhance performance, but often overlook the quality assessment of these pseudolabels, potentially leading to negative knowledge transfer. To this end, based on the interpretable Takagi–Sugeno–Kang fuzzy system (TSK-FS), a novel domain adaptive method is proposed to improve model generalizability for vulnerable coronary plaques recognition in multicenter data. First of all, TSK-FS is employed to construct a shared fuzzy feature space for the source domain and the target domain, aiming to better align data distribution. To make full use of the information of unlabeled target domain data and further reduce the negative knowledge transfer, the enhanced pseudolabel learning mechanism is further introduced by combining the graph-based random walking and label filtering. Moreover, Multicenter data of 910 patients with suspected or diagnosed coronary artery disease were collected from three hospitals for experiments. Experimental results demonstrate that the proposed DA-TSK-PLR-FS achieves the promising generalizability across multicenter datasets

Generative models (GMs), particularly large language models (LLMs), have garnered significant attention in machine learning and artificial intelligence for their ability to generate new data by learning the statistical properties of training data and creating data that resemble the original data. This capability offers a wide range of applications across various domains. However, the complex structures and numerous model parameters of GMs obscure the input-output processes and complicate the understanding and control of the outputs. Moreover, the purely data-driven learning mechanism limits GMs' abilities to acquire broader knowledge. There remains substantial potential for enhancing the robustness and generalization capabilities of GMs. In this work, we leverage fuzzy system, a classical modeling method, to combine both data-driven and knowledge-driven mechanisms for generative tasks. We propose a novel generative fuzzy system framework, named GenFS, which integrates the deep learning capabilities of GMs with the term-based interpretability and dual-driven mechanisms of fuzzy systems. Specifically, we propose an end-to-end GenFS-based model for sequence generation, called FuzzyS2S. A series of test studies were conducted on 12 datasets, covering three distinct categories of generative tasks: machine translation, code generation, and summary generation. The results demonstrate that FuzzyS2S outperforms the transformer in terms of accuracy and fluency. Furthermore, it exhibits better performance than state-of-the-art models T5 and CodeT5 for some application scenarios.

Representation learning is a key area in machine learning and deep learning, focusing on extracting meaningful features to support downstream tasks such as classification and clustering. Current mainstream representation learning methods primarily rely on nonlinear data mining techniques such as kernel methods and deep neural networks (DNNs) to extract abstract knowledge from complex datasets. However, most of them are "black-box" methods, lacking transparency and interpretability in the learning process, which constrain their practical utility. To this end, this article introduces a novel representation learning method called fuzzy rule-based differentiable representation learning (FRDRL), which is grounded in an interpretable fuzzy rule-based model. Specifically, it is built upon the Takagi-Sugeno-Kang fuzzy system (TSK-FS) to map input data to a high-dimensional fuzzy feature space through the antecedent part of the TSK-FS. Subsequently, a novel differentiable optimization method is proposed for learning in the consequent part, which preserves interpretability and transparency while effectively capturing nonlinear relationships in the data. By retaining the essence of traditional optimization and parameterizing key components as differentiable modules, the method improves performance without sacrificing interpretability. Moreover, a second-order geometry preservation strategy is incorporated to further improve robustness. Extensive evaluations conducted on various benchmark datasets validate the superiority of the proposed method. The source codes are available at https://github.com/BBKing49/FEDRL.

The enzyme turnover number is a key metric for catalytic efficiency. While recent deep learning models have integrated enzyme and substrate modal information for predicting turnover numbers, the following challenges remain. First, existing datasets are limited in scale, inconsistent, and lack standardization. Second, current models emphasize consistency information across modalities while ignoring the specific information within each modality. Third, the imbalanced distribution of measured turnover numbers leads to poor performance of existing methods in extreme value ranges. To address these challenges, we first construct Kinetic-DB, a large, standardized dataset compiled from public sources. Based on this, we propose a novel method, ADKcat, for enzyme turnover number prediction. Specifically, to mitigate the challenge of imbalanced data, an adaptive data augmentation module is first constructed to enrich both enzyme and substrate sequences. Then, two pretrained language models-ESM-2 for enzymes and Mole-BERT for substrates-are used for embedding extraction. Furthermore, to fully explore common and specific information, we introduce a dual information exploration module and enhance it with domain classification and distribution alignment loss functions. Finally, an adaptive density weighted network is further applied to improve prediction accuracy and robustness. Experiments show that ADKcat outperforms state-of-the-art methods, especially in extreme turnover ranges. This makes it a promising tool for enzyme engineering, drug discovery, and synthetic biology.

MOTIVATION: Spatial clustering is a key analytical technique for exploring spatial transcriptomics data. Recent graph neural network-based methods have shown promise in spatial clustering but face notable challenges. One significant issue is that analyzing the functions and complex mechanisms of organisms from a single scale is difficult and most methods focus exclusively on the single-scale representation of transcriptomic data, potentially limiting the discriminative power of extracted features for spatial domain clustering. Furthermore, classical clustering algorithms are often applied directly to latent representation, making it a worthwhile endeavor to explore a tailored clustering method to further improve the accuracy of spatial domain annotation. RESULTS: To address these limitations, we propose m2ST, a novel dual multi-scale graph clustering method. m2ST first uses a multi-scale masked graph autoencoder to extract representations across different scales from spatial transcriptomic data. To effectively compress and distill meaningful knowledge embedded in the data, m2ST introduces a random masking mechanism for node features and uses a scaled cosine error as the loss function. Additionally, we introduce a tailored multi-scale clustering framework that integrates scale-common and scale-specific information exploration into the clustering process, achieving more robust annotation performance. Shannon entropy is finally utilized to dynamically adjust the importance of different scales. Extensive experiments on multiple spatial transcriptomic datasets demonstrate the superior performance of m2ST compared to existing methods. AVAILABILITY AND IMPLEMENTATION: https://github.com/BBKing49/m2ST.

Traditional biological experimental methods to determine enzyme properties are time-consuming and costly, leading to an increasing interest in computational models for enzyme function prediction. However, the existing computational methods are insufficient and inefficient to exploit enzyme structure. In this work, we introduce SEFP, a novel method leveraging enzyme point clouds for enzyme function prediction. The structure encoder of SEFP uses a tailored enzyme point cloud network to analyze the three-dimensional arrangement of atoms within the enzyme, integrating hierarchical residue global features through a residue feature adapter to extract detailed enzyme point features. Additionally, the Bio-BCS residue feature encoder extracts enzyme residue features with channel and spatial weights using a specially designed attention mechanism. Finally, SEFP fuses point and residue features to generate the final prediction results. Comparative evaluations show that SEFP outperforms various recent computational methods, demonstrating superior performance. On the RSCB enzyme structure dataset, SEFP achieves an f1-score of 95.85, outperforming two representative structure-based methods, EnzyNet and DeepFri. On the HECNet dataset, SEFP maintains its superiority over all comparison sequence-based methods, yielding an f1-score of 94.29. Ablation studies are conducted to confirm the effectiveness of individual modules within SEFP. These findings underscore the potential of SEFP for reliable and precise enzyme function prediction, offering advancements in bioinformatics and computational biology.

The rapid advancement of medical imaging technologies has led to an exponential increase in medical image data, making efficient retrieval from large-scale datasets critical for improving diagnostic accuracy and speed. However, two key challenges hinder this process: first, the presence of uncertain and subtle lesions in medical images that are often difficult to discern, and second, class imbalance across different case types within medical image databases. These inherent challenges significantly degrade the performance of existing hashing algorithms. In recent years, methods based on the Takagi–Sugeno–Kang fuzzy system (TSK-FS) have shown promising performance in medical image modeling. Inspired by these advances, this article proposes a novel fuzzy hashing network (FHN) based on TSK-FS to enhance retrieval performance by effectively handling both uncertainty and data imbalance in medical imaging. The FHN first introduces a novel fuzzification mechanism that incorporates the concept of a self-attention mechanism to effectively capture the complex underlying features in medical images, thereby enhancing the data discriminability in fuzzy spaces. Meanwhile, a new consequent parameter learning mechanism is developed for defuzzification by introducing the Transformer network, which aims to improve the inference efficiency and generalization capability of the FHN. Based on these two mechanisms, FHN's capability of analyzing and handling uncertain data is significantly enhanced. Furthermore, a novel hash center loss is designed to capture global relationships while emphasizing local structural information, thereby improving the handling of imbalanced data and significantly enhancing retrieval performance.

The federated Fuzzy C-means (federated FCM) extends the traditional Fuzzy C-means (FCM) to the federated learning (FL) scenario, aiming to address the data privacy preservation issue of soft clustering in distributed environments. However, a significant challenge persists with existing federated FCM algorithms, i.e., they struggle to converge effectively in complex heterogeneous scenarios, leading to unstable clustering outcomes. Here the complex heterogeneous scenarios stem from the combination of non-independently and identically distributed (non-IID) data across different clients (statistical heterogeneity), coupled with the involvement of only some clients in each iteration (systematic heterogeneity). While prior research has attempted to address the impact of statistical heterogeneity in FL scenarios, it has overlooked the issue of system heterogeneity. In response, this paper proposes a novel federated FCM algorithm (SC-FFCM) that remains robust even in such complex heterogeneous scenarios. Firstly, the client-side clustering module of SC-FFCM adopts a Gradient-Based FCM algorithm, facilitating corrections to the direction of local optimization. Secondly, the algorithm introduces a control variates technique to rectify update bias during the iteration process, thereby mitigating the adverse effects of random client sampling and non-IID data distribution on the algorithm convergence. Finally, the proposed algorithm approximates the ideal federated FCM algorithm. Experimental studies verify the effectiveness of the proposed method. The source code of the proposed SC-FFCM algorithm is available from the following website https://github.com/Creazy-MR/SC-FFCM.

Multiview anchor graph clustering has been a prominent research area in recent years, leading to the development of several effective and efficient methods. However, three challenges are faced by current multiview anchor graph clustering methods. First, real-world data often exhibit uncertainty and poor discriminability, leading to suboptimal anchor graphs when directly extracted from the original data. Second, most existing methods assume the presence of common information between views and primarily explore it for clustering, thus neglecting view-specific information. Third, further exploration and exploitation of the learned anchor graph to enhance clustering performance remains an open research question. To address these issues, a novel dual anchor graph fuzzy clustering method is proposed in this article. First, a novel matrix factorization-based dual anchor graph learning method is proposed to address the first two issues by extracting highly discriminative hidden representations for each view and subsequently deriving both common and specific anchor graphs from these hidden representations. Then, to address the third issue, a novel anchor graph fuzzy clustering method is developed with cooperative learning to exploit and utilize the common and specific anchor graphs fully. Meanwhile, a fuzzy membership structure preservation mechanism with dual anchor graphs is constructed to enhance clustering performance. Finally, negative Shannon entropy is further introduced to adaptively adjust the view weighing. Extensive experiments on several datasets demonstrate the effectiveness of the proposed method.

Biological datasets, such as gene expression data, often suffer from high dimensionality, containing numerous irrelevant or redundant features that can lead to overfitting and increased computational complexity. Effective feature selection is essential for reducing dimensionality, enhancing model performance, and improving interpretability. While deep neural networks, such as autoencoders, have shown promise in feature selection, their performance often diminishes when confronted with noisy data. To address these challenges, we propose a novel feature selection method that leverages multigranularity fuzzy autoencoders (FAEs). This approach integrates fuzzy theory with autoencoder models to effectively manage noise and outliers in data. The FAE method introduces a feature selection layer that approximates discrete feature selection using continuous probability distributions. To further enhance the discriminative power of the selected features, we incorporate a coarse-grained loss function designed to exploit clustering structures. In addition, intuitionistic fuzzy weights are applied to account for uncertainty by computing membership and nonmembership degrees for each sample, thereby mitigating the impact of noise and outliers. Test results validate the effectiveness of our approach, demonstrating significant improvements over existing feature selection techniques across 20 public datasets and a real-world schizophrenia dataset. These findings highlight the potential of our method to enhance classification accuracy and robustness, particularly in the context of schizophrenia research.

Contrastive multiview clustering (MVC) has emerged as a mainstream approach in MVC due to its superior representation learning capabilities. Traditional contrastive multiview learning methods extract both low- and high-level information from raw data. However, only high-level information is utilized for clustering. Since both types of information are essential for effective clustering, this limitation hampers performance. Moreover, effectively quantifying the importance of different views remains a critical challenge in contrastive MVC. Additionally, the absence of structural information during clustering further weakens clustering performance. To address these issues, this article proposes a multigranularity (MG) information fused contrastive learning with MVC (MGCMVC). Inspired by the concept of MG, low- and high-level features are reconstructed into fine- and coarse-granularity features. First, an MG adaptive weighting sample-level contrastive learning mechanism is introduced to fuse MG features to enhance clustering performance and mitigate clustering performance degradation caused by variations in view quality. Second, a structure-oriented cluster-level contrastive learning approach is designed to preserve structural information and enforce cross-view clustering consistency. Extensive and comprehensive experiments on ten widely used datasets demonstrate that MGCMVC achieves the state-of-the-art performance. The source code is available at https://github.com/Luyangabc/MGCMVC.

As a class of extremely significant of biocatalysts, enzymes play an important role in the process of biological reproduction and metabolism. Therefore, the prediction of enzyme function is of great significance in biomedicine fields. Recently, computational methods for predicting enzyme function have been proposed, and they effectively reduce the cost of enzyme function prediction. However, there are still deficiencies for effectively mining the discriminant information for enzyme function recognition in existing methods. In this study, we present MVDINET, a novel method for multi-level enzyme function prediction. First, the initial multi-view feature data is extracted by the enzyme sequence. Then, the above initial views are fed into various deep specific network modules to learn the depth-specificity information. Further, a deep view interaction network is designed to extract the interaction information. Finally, the specificity information and interaction information are fed into a multi-view adaptively weighted classification. We compressively evaluate MVDINET on benchmark datasets and demonstrate that MVDINET is superior to existing methods.

Predicting biomolecular interactions is significant for understanding biological systems. Most existing methods for link prediction are based on graph convolution. Although graph convolution methods are advantageous in extracting structure information of biomolecular interactions, two key challenges still remain. One is how to consider both the immediate and high-order neighbors. Another is how to reduce noise when aggregating high-order neighbors. To address these challenges, we propose a novel method, called mixed high-order graph convolution with filter network via LSTM and channel attention (HGLA), to predict biomolecular interactions. Firstly, the basic and high-order features are extracted respectively through the traditional graph convolutional network (GCN) and the two-layer Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing (MixHop). Secondly, these features are mixed and input into the filter network composed of LayerNorm, SENet and LSTM to generate filtered features, which are concatenated and used for link prediction. The advantages of HGLA are: 1) HGLA processes high-order features separately, rather than simply concatenating them; 2) HGLA better balances the basic features and high-order features; 3) HGLA effectively filters the noise from high-order neighbors. It outperforms state-of-the-art networks on four benchmark datasets.

Automatic analysis of epileptic encephalography signals with intelligent models can greatly reduce the workload of doctors. However, the lack of data, insufficient labels, and inconsistent data distribution in real-world scenarios significantly affect the performance of intelligent models. Transfer learning plays an important role in solving the above problems but some challenges remain. First, while various feature extraction methods are available to extract features from the original epilepsy signal, it is difficult to determine which features are effective. Second, transfer learning may lead to domain information loss since the original feature representation from different domains is changed. Third, most of the existing models lack transparency to provide medical practitioners confidence of use. To this end, this article proposes the novel method Multiview Information Preservation Transfer Representation Learning based on Fuzzy Systems (MIP-TRL-FS) to address the issues. First, MIP-TRL-FS utilizes multiple views to get rid of the feature selection process. Second, information preservation techniques are utilized to maintain the data information from the aspects of sample level and feature level, thus minimizing information loss during the transfer learning process. Third, by using Takagi–Sugeno–Kang fuzzy systems as the base model, the output of the proposed method can be interpreted linguistically with IF-THEN rules to makes the model transparent. Extensive experiments were conducted on the CHB-MIT dataset and the results demonstrate the effectiveness of the proposed method.

Heterogeneous feature transfer (HeFT) learning can leverage the semantically related source domain from a different feature space for modeling the target domain with insufficient information. Although HeFT learning has made significant progress, it still faces two major challenges: weak interpretability of the transfer process and underutilization of the hidden information of the heterogeneous source and target domains. To address these two challenges, a framework called heterogeneous feature transfer using fuzzy inference rules (HeFT-FIR) is proposed. The HeFT-FIR framework has two parts: First, design of Takagi–Sugeno–Kang fuzzy systems (TSK-FSs) for the source and target domains, respectively, to achieve HeFT and enhance the interpretability of the transfer process; and second, integration of the HeFT learning mechanism with fuzzy inference rules to optimize the parameters of TSK-FSs and mine the hidden information of the two domains. Based on the framework, a TSK-FS-based heterogeneous feature transfer learning method is then developed with three fuzzy feature space-based learning mechanisms for joint distribution adaptation, local geometric property preservation, and heterogeneous discriminant information extraction, respectively. The mechanisms reduce the difference in distribution between the heterogeneous source and target domains in a common feature subspace, preserve the local geometric properties of two domains, and extract the global discriminant information of them. Extensive analyses are conducted to verify the superiority of the proposed framework and method.

Multiview clustering has received great attention in recent years for the potential in clustering performance improvement by using cooperative learning of different views. Despite the considerable progress, a few issues remain: 1) real multiview data contains redundant features and noises that lead to unsatisfactory clustering performance; 2) most existing multiview clustering methods only mine the shared information between views and ignore the specific information within views; and 3) most multiview clustering methods are based on a two-step framework that learn the hidden view representation and then perform clustering, overlooking the correlation between the two processes. Although some approaches have been proposed to deal with these issues, they cannot them simultaneously. To this end, we propose an end-to-end multiview fuzzy clustering. First, we construct a multiview fuzzy clustering framework to mine the specific information of the visible views. Second, to reduce the impact of redundant features and noises on clustering performance, we introduce the orthogonal projection matrix into the clustering framework to learn the low-dimensional representation of the visible views. Meanwhile, this procedure is integrated into the clustering framework. Third, we explore the shared hidden view representation between the visible views by multiview non-negative matrix factorization and integrate it into the clustering framework to realize visible-hidden view cooperation learning. Finally, the shared hidden view representation learning between visible views, the low-dimensional representation learning of visible views, and the clustering partition of multiview data negotiate with each other in the end-to-end learning framework. Extensive experiments on benchmark multiview datasets indicate the superiority of the proposed method over state-of-the-art methods.

Multiview fuzzy c-means clustering has garnered significant attention in recent years, leading to the development of various multiview fuzzy clustering algorithms. However, existing algorithms still exhibit room for improvement. First, most existing algorithms only utilize the shallow information of the view data and fail to delve into the mining and utilization of deeper representations. Second, existing algorithms tend to extract common representations among the views first and then implement clustering separately, which may lack a collaborative linkage between two tasks. Finally, multiview clustering algorithms based on representation learning often overlook the importance of effectively preserving similarity information within the views. To address these limitations, we propose a novel algorithm called pseudolabel enhanced multiview deep concept factorization fuzzy clustering (PE-MV-DCFCM). The algorithm first introduces a deep concept factorization method to uncover the deep information of the view data. Subsequently, it employs pseudolabel learning to preserve intraview similarity information during the learning of common representations among the views, based on non-negative matrix factorization. Finally, this algorithm integrates deep concept factorization, representation learning, and fuzzy clustering into a unified framework to enhance the collaboration among the various substeps of the algorithm. Experiments on several benchmark datasets show that the proposed PE-MV-DCFCM algorithm outperformed other state-of-the-art algorithms.

Unsupervised multi-view representation learning has been extensively studied for mining multi-view data. However, some critical challenges remain. On the one hand, the existing methods cannot explore multi-view data comprehensively since they usually learn a common representation between views, given that multi-view data contains both the common information between views and the specific information within each view. On the other hand, to mine the nonlinear relationship between data, kernel or neural network methods are commonly used for multi-view representation learning. However, these methods are lacking in interpretability. To this end, this paper proposes a new multi-view fuzzy representation learning method based on the interpretable Takagi-Sugeno-Kang (TSK) fuzzy system (MVRL_FS). The method realizes multi-view representation learning from two aspects. First, multi-view data are transformed into a high-dimensional fuzzy feature space, while the common information between views and specific information of each view are explored simultaneously. Second, a new regularization method based on L2,1-norm regression is proposed to mine the consistency information between views, while the geometric structure of the data is preserved through the Laplacian graph. Finally, extensive experiments on many benchmark multi-view datasets are conducted to validate the superiority of the proposed method.

Multiview data are widespread in real-world applications, and multiview clustering is a commonly used technique to effectively mine the data. Most of the existing algorithms perform multiview clustering by mining the commonly hidden space between views. Although this strategy is effective, there are two challenges that still need to be addressed to further improve the performance. First, how to design an efficient hidden space learning method so that the learned hidden spaces contain both shared and specific information of multiview data. Second, how to design an efficient mechanism to make the learned hidden space more suitable for the clustering task. In this study, a novel one-step multiview fuzzy clustering (OMFC-CS) method is proposed to address the two challenges by collaborative learning between the common and specific space information. To tackle the first challenge, we propose a mechanism to extract the common and specific information simultaneously based on matrix factorization. For the second challenge, we design a one-step learning framework to integrate the learning of common and specific spaces and the learning of fuzzy partitions. The integration is achieved in the framework by performing the two learning processes alternately and thereby yielding mutual benefit. Furthermore, the Shannon entropy strategy is introduced to obtain the optimal views weight assignment during clustering. The experimental results based on benchmark multiview datasets demonstrate that the proposed OMFC-CS outperforms many existing methods.

Protein is the most important component in organisms and plays an indispensable role in life activities. In recent years, a large number of intelligent methods have been proposed to predict protein function. These methods obtain different types of protein information, including sequence, structure and interaction network. Among them, protein sequences have gained significant attention where methods are investigated to extract the information from different views of features. However, how to fully exploit the views for effective protein sequence analysis remains a challenge. In this regard, we propose a multi-view, multi-scale and multi-attention deep neural model (MMSMA) for protein function prediction. First, MMSMA extracts multi-view features from protein sequences, including one-hot encoding features, evolutionary information features, deep semantic features and overlapping property features based on physiochemistry. Second, a specific multi-scale multi-attention deep network model (MSMA) is built for each view to realize the deep feature learning and preliminary classification. In MSMA, both multi-scale local patterns and long-range dependence from protein sequences can be captured. Third, a multi-view adaptive decision mechanism is developed to make a comprehensive decision based on the classification results of all the views. To further improve the prediction performance, an extended version of MMSMA, MMSMAPlus, is proposed to integrate homology-based protein prediction under the framework of multi-view deep neural model. Experimental results show that the MMSMAPlus has promising performance and is significantly superior to the state-of-the-art methods. The source code can be found at https://github.com/wzy-2020/MMSMAPlus.

MOTIVATION: CircRNAs play a critical regulatory role in physiological processes, and the abnormal expression of circRNAs can mediate the processes of diseases. Therefore, exploring circRNAs-disease associations is gradually becoming an important area of research. Due to the high cost of validating circRNA-disease associations using traditional wet-lab experiments, novel computational methods based on machine learning are gaining more and more attention in this field. However, current computational methods suffer to insufficient consideration of latent features in circRNA-disease interactions. RESULTS: In this study, a multilayer attention neural graph-based collaborative filtering (MLNGCF) is proposed. MLNGCF first enhances multiple biological information with autoencoder as the initial features of circRNAs and diseases. Then, by constructing a central network of different diseases and circRNAs, a multilayer cooperative attention-based message propagation is performed on the central network to obtain the high-order features of circRNAs and diseases. A neural network-based collaborative filtering is constructed to predict the unknown circRNA-disease associations and update the model parameters. Experiments on the benchmark datasets demonstrate that MLNGCF outperforms state-of-the-art methods, and the prediction results are supported by the literature in the case studies. AVAILABILITY AND IMPLEMENTATION: The source codes and benchmark datasets of MLNGCF are available at https://github.com/ABard0/MLNGCF.

The purpose of multiview fuzzy clustering is to integrate fuzzy partitions of multiple complete views and obtain the optimal clustering partition. However, multiview data collected in the real world are often incomplete. To address this problem, partial view-based methods and missing view imputation-based methods have been proposed in recent years and achieved some success. However, these two groups of methods still have the following issues. First, since missing view processing and clustering are handled separately, the processed data lack relevance for clustering. Second, either hidden or visible information is explored for clustering, which precludes cooperative learning between these two types of information. Third, the within view and between view information is not fully explored. This article proposes a new end-to-end incomplete multiview fuzzy clustering method to deal with the issues. Based on traditional multiview fuzzy clustering, we construct a new end-to-end clustering framework to integrate the three tasks—missing view imputation, hidden view learning and clustering—as a single process. The framework not only enables mutual coordination of the three tasks, but also cooperative learning between the hidden and visible views. Next, we explore the within and between view information and propose two enhanced learning mechanisms to improve the quality of the imputed missing views and the learned hidden views. Finally, we introduce an adaptive view weighting mechanism to further improve the robustness of the model. Experiments on real-world datasets demonstrate the superiority of the proposed method.

Multiview fuzzy systems aim to deal with fuzzy modeling in multiview scenarios effectively and to obtain the interpretable model through multiview learning. However, current studies of multiview fuzzy systems still face several challenges, one of which is how to achieve efficient collaboration between multiple views when there are few labeled data. To address this challenge, this article explores a novel transductive multiview fuzzy modeling method. The dependency on labeled data is reduced by integrating transductive learning into the fuzzy model to simultaneously learn both the model and the labels using a novel learning criterion. Matrix factorization is incorporated to further improve the performance of the fuzzy model. In addition, collaborative learning between multiple views is used to enhance the robustness of the model. The experimental results indicate that the proposed method is highly competitive with other multiview learning methods.

Multiview clustering is an important topic in multiview learning, where the cooperation of different views is used to improve clustering performance. Although multiview clustering has made considerable progress, most existing methods only utilize the information of the original visible views, or only consider some hidden space information shared by different views. Two of the challenges are: 1) insufficient exploitation of cooperative learning between visible and hidden information despite some preliminary attempts, and 2) inadequate consideration of topological information for improving multiview clustering. To meet the challenges, we propose the cooperation enhanced multiview fuzzy clustering method (CE-MVFC) in this article. First, we characterize multiview data with two hidden views, which are obtained by adaptive multiview non-negative matrix factorization (NMF) and fuzzy partition information of each sample in different clusters. Then, we integrated the hidden views and the original visible views to realize visible-hidden cooperation learning. Furthermore, we establish a similarity matrix for each visible view and the hidden view obtained through NMF to describe the data topology in these views. Based on the spatial topological relationship of the samples and the representation of hidden view obtained by fuzzy partition, the network least absolute shrinkage and selection operator is constructed to constrain multiview learning. Finally, we develop the multiview clustering method by exploiting the visible-hidden information cooperation and the spatial topological information constraints. Experiments on benchmark multiview datasets are conducted to demonstrate the highly competitive performance of the proposed CE-MVFC against the state-of-the-art methods.

Advancement of technology has made available data of different modalities that can be integrated effectively through multiple view learning for modeling real-world problems. Although multiple view learning has achieved great success in many applications, it still faces several challenges. One of them is how to reduce the negative impact of the missing views in incomplete multiple view datasets by fully exploiting the information available. Another challenge is how to enhance the interpretability of the multiple view model for scenarios with high transparency requirement. To address these challenges, this article proposes a novel modeling method for incomplete multiple view fuzzy system. Based on fuzzy interpretable rules, the method integrates missing view imputation and hidden view learning as one single process to yield a model of high interpretability, where cooperative learning is used to mine the complementary information between the visible views and the hidden view. The proposed method has four advantages when compared with existing approaches: 1) the method is more interpretable, attributed to the fuzzy interpretable rules that it is based on, 2) missing view imputation is integrated into the modeling to make it more efficient than the existing two-step strategy, 3) the method not only imputes missing views, but also mines the hidden view shared by the multiple visible views, and 4) cooperative learning is used to mine the complementary information, which significantly reduces the negative impact of missing views. Experiments on real datasets demonstrate the advantages of the proposed method.

Multi-view data are becoming common in real-world applications and many multi-view clustering algorithms have thus been proposed. The existing algorithms usually focus on the cooperation of different visible views in the original space but neglect the influence of the hidden information among these visible views, or they only consider the hidden information among the views. The algorithms are therefore not efficient since the available information is not fully exploited, particularly the otherness information in different views and the consistency information among them. In practice, the otherness and consistency information in multi-view data are both very useful for effective clustering analyses. In this study, a Multi-View clustering algorithm with the Cooperation of Visible and Hidden views, i.e., MV-Co-VH, is proposed. The MV-Co-VH algorithm first projects the multiple views from different visible spaces to the common hidden space by using non-negative matrix factorization to obtain the common hidden view data. Collaborative learning is then implemented in the clustering procedure based on the visible views and the shared hidden view. The experimental results of extensive experiments on UCI multi-view datasets and real-world image multi-view datasets show that the clustering performance of the proposed algorithm is competitive with or even better than that of the existing algorithms.