MHADTI: predicting drug-target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms.

MOTIVATION: Discovering the drug-target interactions (DTIs) is a crucial step in drug development such as the identification of drug side effects and drug repositioning. Since identifying DTIs by web-biological experiments is time-consuming and costly, many computational-based approaches have been proposed and have become an efficient manner to infer the potential interactions. Although extensive effort is invested to solve this task, the prediction accuracy still needs to be improved. More especially, heterogeneous network-based approaches do not fully consider the complex structure and rich semantic information in these heterogeneous networks. Therefore, it is still a challenge to predict DTIs efficiently. RESULTS: In this study, we develop a novel method via Multiview heterogeneous information network embedding with Hierarchical Attention mechanisms to discover potential Drug-Target Interactions (MHADTI). Firstly, MHADTI constructs different similarity networks for drugs and targets by utilizing their multisource information. Combined with the known DTI network, three drug-target heterogeneous information networks (HINs) with different views are established. Secondly, MHADTI learns embeddings of drugs and targets from multiview HINs with hierarchical attention mechanisms, which include the node-level, semantic-level and graph-level attentions. Lastly, MHADTI employs the multilayer perceptron to predict DTIs with the learned deep feature representations. The hierarchical attention mechanisms could fully consider the importance of nodes, meta-paths and graphs in learning the feature representations of drugs and targets, which makes their embeddings more comprehensively. Extensive experimental results demonstrate that MHADTI performs better than other SOTA prediction models. Moreover, analysis of prediction results for some interested drugs and targets further indicates that MHADTI has advantages in discovering DTIs. AVAILABILITY AND IMPLEMENTATION: https://github.com/pxystudy/MHADTI.

Identification and candidate analysis of a new brown planthopper resistance locus in an Indian landrace of rice, paedai kalibungga.

The brown planthopper (Nilaparvata lugens Stål, BPH) is the most destructive pest of rice (Oryza sativa L.). Utilizing resistant rice cultivars that harbor resistance gene/s is an effective strategy for integrated pest management. Due to the co-evolution of BPH and rice, a single resistance gene may fail because of changes in the virulent BPH population. Thus, it is urgent to explore and map novel BPH resistance genes in rice germplasm. Previously, an indica landrace from India, Paedai kalibungga (PK), demonstrated high resistance to BPH in both in Wuhan and Fuzhou, China. To map BPH resistance genes from PK, a BC1F2:3 population derived from crosses of PK and a susceptible parent, Zhenshan 97 (ZS97), was developed and evaluated for BPH resistance. A novel BPH resistance locus, BPH39, was mapped on the short arm of rice chromosome 6 using next-generation sequencing-based bulked segregant analysis (BSA-seq). BPH39 was validated using flanking markers within the locus. Furthermore, near-isogenic lines carrying BPH39 (NIL-BPH39) were developed in the ZS97 background. NIL-BPH39 exhibited the physiological mechanisms of antibiosis and preference toward BPH. BPH39 was finally delimited to an interval of 84 Kb ranging from 1.07 to 1.15 Mb. Six candidate genes were identified in this region. Two of them (LOC_Os06g02930 and LOC_Os06g03030) encode proteins with a similar short consensus repeat (SCR) domain, which displayed many variations leading to amino acid substitutions and showed higher expression levels in NIL-BPH39. Thus, these two genes are considered reliable candidate genes for BPH39. Additionally, transcriptome sequencing, DEGs analysis, and gene RT-qPCR verification preliminary revealed that BPH39 may be involved in the jasmonic acid (JA) signaling pathway, thus mediating the molecular mechanism of BPH resistance. This work will facilitate map-based cloning and marker-assisted selection for the locus in breeding programs targeting BPH resistance. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-024-01485-6.

A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology.

BACKGROUND: Recently, with the foundation and development of gene ontology (GO) resources, numerous works have been proposed to compute functional similarity of genes and achieved series of successes in some research fields. Focusing on the calculation of the information content (IC) of terms is the main idea of these methods, which is essential for measuring functional similarity of genes. However, most approaches have some deficiencies, especially when measuring the IC of both GO terms and their corresponding annotated term sets. To this end, measuring functional similarity of genes accurately is still challenging. RESULTS: In this article, we proposed a novel gene functional similarity calculation method, which especially encapsulates the specificity of terms and edges (STE). The proposed method mainly contains three steps. Firstly, a novel computing model is put forward to compute the IC of terms. This model has the ability to exploit the specific structural information of GO terms. Secondly, the IC of term sets are computed by capturing the genetic structure between the terms contained in the set. Lastly, we measure the gene functional similarity according to the IC overlap ratio of the corresponding annotated genes sets. The proposed method accurately measures the IC of not only GO terms but also the annotated term sets by leveraging the specificity of edges in the GO graph. CONCLUSIONS: We conduct experiments on gene functional classification in biological pathways, gene expression datasets, and protein-protein interaction datasets. Extensive experimental results show the better performances of our proposed STE against several baseline methods.

A Joint Symbol-Detection, Channel-Estimation and Decoding Scheme under Few-Bit ADCs in mmWave Communications.

Few-bit analog-to-digital converter (ADC) is regarded as a promising technique to greatly reduce power consumption of Internet of Things (IoT) devices in millimeter-wave (mmWave) communications. In this work, based on the recently proposed parametric bilinear generalized approximate message passing (PBiGAMP), we propose a new scheme to perform joint symbol detection, channel estimation and decoding. The proposed scheme is flexible to deal with discrete prior on symbols, Gaussian mixture prior on channels and quantized likelihood on observations. Furthermore, we introduce doping factor to control the portion of "extrinsic" and "posterior" information with negligible complexity increase. Since this joint scheme can be implemented via fast Fourier transformation (FFT), the complexity grows only logarithmically. Compared to the benchmark algorithms, numerical results show that the proposed joint scheme can achieve significant performance gain, and demonstrate the effectiveness in dealing with the nonlinear distortion from few-bit ADC.

A Survey on Information Bottleneck.

This survey is for the remembrance of one of the creators of the information bottleneck theory, Prof. Naftali Tishby, passing away at the age of 68 on August, 2021. Information bottleneck (IB), a novel information theoretic approach for pattern analysis and representation learning, has gained widespread popularity since its birth in 1999. It provides an elegant balance between data compression and information preservation, and improves its prediction or representation ability accordingly. This survey summarizes both the theoretical progress and practical applications on IB over the past 20-plus years, where its basic theory, optimization, extensive models and task-oriented algorithms are systematically explored. Existing IB methods are roughly divided into two parts: traditional and deep IB, where the former contains the IBs optimized by traditional machine learning analysis techniques without involving any neural networks, and the latter includes the IBs involving the interpretation, optimization and improvement of deep neural works (DNNs). Specifically, based on the technique taxonomy, traditional IBs are further classified into three categories: Basic, Informative and Propagating IB; While the deep IBs, based on the taxonomy of problem settings, contain Debate: Understanding DNNs with IB, Optimizing DNNs Using IB, and DNN-based IB methods. Furthermore, some potential issues deserving future research are discussed. This survey attempts to draw a more complete picture of IB, from which the subsequent studies can benefit.

Multitask Image Clustering via Deep Information Bottleneck.

Multitask image clustering approaches intend to improve the model accuracy on each task by exploring the relationships of multiple related image clustering tasks. However, most existing multitask clustering (MTC) approaches isolate the representation abstraction from the downstream clustering procedure, which makes the MTC models unable to perform unified optimization. In addition, the existing MTC relies on exploring the relevant information of multiple related tasks to discover their latent correlations while ignoring the irrelevant information between partially related tasks, which may also degrade the clustering performance. To tackle these issues, a multitask image clustering method named deep multitask information bottleneck (DMTIB) is devised, which aims at conducting multiple related image clustering by maximizing the relevant information of multiple tasks while minimizing the irrelevant information among them. Specifically, DMTIB consists of a main-net and multiple subnets to characterize the relationships across tasks and the correlations hidden in a single clustering task. Then, an information maximin discriminator is devised to maximize the mutual information (MI) measurement of positive samples and minimize the MI of negative ones, in which the positive and negative sample pairs are constructed by a high-confidence pseudo-graph. Finally, a unified loss function is devised for the optimization of task relatedness discovery and MTC simultaneously. Empirical comparisons on several benchmark datasets, NUS-WIDE, Pascal VOC, Caltech-256, CIFAR-100, and COCO, show that our DMTIB approach outperforms more than 20 single-task clustering and MTC approaches.

Deep Multiview Clustering by Pseudo-Label Guided Contrastive Learning and Dual Correlation Learning.

Deep multiview clustering (MVC) is to learn and utilize the rich relations across different views to enhance the clustering performance under a human-designed deep network. However, most existing deep MVCs meet two challenges. First, most current deep contrastive MVCs usually select the same instance across views as positive pairs and the remaining instances as negative pairs, which always leads to inaccurate contrastive learning (CL). Second, most deep MVCs only consider learning feature or cluster correlations across views, failing to explore the dual correlations. To tackle the above challenges, in this article, we propose a novel deep MVC framework by pseudo-label guided CL and dual correlation learning. Specifically, a novel pseudo-label guided CL mechanism is designed by using the pseudo-labels in each iteration to help removing false negative sample pairs, so that the CL for the feature distribution alignment can be more accurate, thus benefiting the discriminative feature learning. Different from most deep MVCs learning only one kind of correlation, we investigate both the feature and cluster correlations among views to discover the rich and comprehensive relations. Experiments on various datasets demonstrate the superiority of our method over many state-of-the-art compared deep MVCs. The source implementation code will be provided at https://github.com/ShizheHu/Deep-MVC-PGCL-DCL.

GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes.

The measurement of gene functional similarity plays a critical role in numerous biological applications, such as gene clustering, the construction of gene similarity networks. However, most existing approaches still rely heavily on traditional computational strategies, which are not guaranteed to achieve satisfactory performance. In this study, we propose a novel computational approach called GOGCN to measure gene functional similarity by modeling the Gene Ontology (GO) through Graph Convolutional Network (GCN). GOGCN is a graph-based approach that performs sufficient representation learning for terms and relations in the GO graph. First, GOGCN employs the GCN-based knowledge graph embedding (KGE) model to learn vector representations (i.e., embeddings) for all entities (i.e., terms). Second, GOGCN calculates the semantic similarity between two terms based on their corresponding vector representations. Finally, GOGCN estimates gene functional similarity by making use of the pair-wise strategy. During the representation learning period, GOGCN promotes semantic interaction between terms through GCN, thereby capturing the rich structural information of the GO graph. Further experimental results on various datasets suggest that GOGCN is superior to the other state-of-the-art approaches, which shows its reliability and effectiveness.

Learning From the Future: Light Cone Modeling for Sequential Recommendation.

Modeling sequential behaviors is the core of sequential recommendation. As users visit items in chronological order, existing methods typically capture a user's present interests from his/her past-to-present behaviors, i.e., making recommendations with only the unidirectional past information. This article argues that future information is another critical factor for the sequential recommendation. However, directly learning from future-to-present behaviors inevitably causes data leakage. Here, it is pointed out that future information can be learned from users' collaborative behaviors. Toward this end, this article introduces sequential graphs to depict item transition relationships: where and how each item transits from and will transit to. This temporal evolution information is called the light cone in special and general relativity. Then, a bidirectional sequential graph convolutional network (BiSGCN) is proposed to learn item representations by encoding past and future light cones. Finally, a manifold translating embedding (MTE) method is proposed to model item transition patterns in Riemannian manifolds, which helps to better capture the geometric structures of light cones and item transition patterns. Experimental comparisons and ablation studies verify the outstanding performance of BiSGCN, the benefits of learning from the future, and the improvements of learning in Riemannian manifolds.

Cross-Modal Clustering With Deep Correlated Information Bottleneck Method.

Cross-modal clustering (CMC) intends to improve the clustering accuracy (ACC) by exploiting the correlations across modalities. Although recent research has made impressive advances, it remains a challenge to sufficiently capture the correlations across modalities due to the high-dimensional nonlinear characteristics of individual modalities and the conflicts in heterogeneous modalities. In addition, the meaningless modality-private information in each modality might become dominant in the process of correlation mining, which also interferes with the clustering performance. To tackle these challenges, we devise a novel deep correlated information bottleneck (DCIB) method, which aims at exploring the correlation information between multiple modalities while eliminating the modality-private information in each modality in an end-to-end manner. Specifically, DCIB treats the CMC task as a two-stage data compression procedure, in which the modality-private information in each modality is eliminated under the guidance of the shared representation of multiple modalities. Meanwhile, the correlations between multiple modalities are preserved from the aspects of feature distributions and clustering assignments simultaneously. Finally, the objective of DCIB is formulated as an objective function based on a mutual information measurement, in which a variational optimization approach is proposed to ensure its convergence. Experimental results on four cross-modal datasets validate the superiority of the DCIB. Code is released at https://github.com/Xiaoqiang-Yan/DCIB.

GCRec: Graph-Augmented Capsule Network for Next-Item Recommendation.

Next-item recommendation has been a hot research, which aims at predicting the next action by modeling users' behavior sequences. While previous efforts toward this task have been made in capturing complex item transition patterns, we argue that they still suffer from three limitations: 1) they have difficulty in explicitly capturing the impact of inherent order of item transition patterns; 2) only a simple and crude embedding is insufficient to yield satisfactory long-term users' representations from limited training sequences; and 3) they are incapable of dynamically integrating long-term and short-term user interest modeling. In this work, we propose a novel solution named graph-augmented capsule network (GCRec), which exploits sequential user behaviors in a more fine-grained manner. Specifically, we employ a linear graph convolution module to learn informative long-term representations of users. Furthermore, we devise a user-specific capsule module and a position-aware gating module, which are sensitive to the relative sequential order of the recently interacted items, to capture sequential patterns at union-level and point-level. To aggregate the long-term and short-term user interests as a representative vector, we design a dual-gating mechanism, which could decide the contribution ratio of each module given different contextual information. Through extensive experiments on four benchmarks, we validate the rationality and effectiveness of GCRec on the next-item recommendation task.

Multiview Clustering With Propagating Information Bottleneck.

In many practical applications, massive data are observed from multiple sources, each of which contains multiple cohesive views, called hierarchical multiview (HMV) data, such as image-text objects with different types of visual and textual features. Naturally, the inclusion of source and view relationships offers a comprehensive view of the input HMV data and achieves an informative and correct clustering result. However, most existing multiview clustering (MVC) methods can only process single-source data with multiple views or multisource data with single type of feature, failing to consider all the views across multiple sources. Observing the rich closely related multivariate (i.e., source and view) information and the potential dynamic information flow interacting among them, in this article, a general hierarchical information propagation model is first built to address the above challenging problem. It describes the process from optimal feature subspace learning (OFSL) of each source to final clustering structure learning (CSL). Then, a novel self-guided method named propagating information bottleneck (PIB) is proposed to realize the model. It works in a circulating propagation fashion, so that the resulting clustering structure obtained from the last iteration can "self-guide" the OFSL of each source, and the learned subspaces are in turn used to conduct the subsequent CSL. We theoretically analyze the relationship between the cluster structures learned in the CSL phase and the preservation of relevant information propagated from the OFSL phase. Finally, a two-step alternating optimization method is carefully designed for optimization. Experimental results on various datasets show the superiority of the proposed PIB method over several state-of-the-art methods.

DMIB: Dual-Correlated Multivariate Information Bottleneck for Multiview Clustering.

Multiview clustering (MVC) has recently been the focus of much attention due to its ability to partition data from multiple views via view correlations. However, most MVC methods only learn either interfeature correlations or intercluster correlations, which may lead to unsatisfactory clustering performance. To address this issue, we propose a novel dual-correlated multivariate information bottleneck (DMIB) method for MVC. DMIB is able to explore both interfeature correlations (the relationship among multiple distinct feature representations from different views) and intercluster correlations (the close agreement among clustering results obtained from individual views). For the former, we integrate both view-shared feature correlations discovered by learning a shared discriminative feature subspace and view-specific feature information to fully explore the interfeature correlation. This allows us to attain multiple reliable local clustering results of different views. Following this, we explore the intercluster correlations by learning the shared mutual information over different local clusterings for an improved global partition. By integrating both correlations, we formulate the problem as a unified information maximization function and further design a two-step method for optimization. Moreover, we theoretically prove the convergence of the proposed algorithm, and discuss the relationships between our method and several existing clustering paradigms. The experimental results on multiple datasets demonstrate the superiority of DMIB compared to several state-of-the-art clustering methods.

View-Wise Versus Cluster-Wise Weight: Which Is Better for Multi-View Clustering?

Weighted multi-view clustering (MVC) aims to combine the complementary information of multi-view data (such as image data with different types of features) in a weighted manner to obtain a consistent clustering result. However, when the cluster-wise weights across views are vastly different, most existing weighted MVC methods may fail to fully utilize the complementary information, because they are based on view-wise weight learning and can not learn the fine-grained cluster-wise weights. Additionally, extra parameters are needed for most of them to control the weight distribution sparsity or smoothness, which are hard to tune without prior knowledge. To address these issues, in this paper we propose a novel and effective Cluster-weighted mUlti-view infoRmation bottlEneck (CURE) clustering algorithm, which can automatically learn the cluster-wise weights to discover the discriminative clusters across multiple views and thus can enhance the clustering performance by properly exploiting the cluster-level complementary information. To learn the cluster-wise weights, we design a new weight learning scheme by exploring the relation between the mutual information of the joint distribution of a specific cluster (containing a group of data samples) and the weight of this cluster. Finally, a novel draw-and-merge method is presented to solve the optimization problem. Experimental results on various multi-view datasets show the superiority and effectiveness of our cluster-wise weighted CURE over several state-of-the-art methods.

Rank-based pooling for deep convolutional neural networks.

Pooling is a key mechanism in deep convolutional neural networks (CNNs) which helps to achieve translation invariance. Numerous studies, both empirically and theoretically, show that pooling consistently boosts the performance of the CNNs. The conventional pooling methods are operated on activation values. In this work, we alternatively propose rank-based pooling. It is derived from the observations that ranking list is invariant under changes of activation values in a pooling region, and thus rank-based pooling operation may achieve more robust performance. In addition, the reasonable usage of rank can avoid the scale problems encountered by value-based methods. The novel pooling mechanism can be regarded as an instance of weighted pooling where a weighted sum of activations is used to generate the pooling output. This pooling mechanism can also be realized as rank-based average pooling (RAP), rank-based weighted pooling (RWP) and rank-based stochastic pooling (RSP) according to different weighting strategies. As another major contribution, we present a novel criterion to analyze the discriminant ability of various pooling methods, which is heavily under-researched in machine learning and computer vision community. Experimental results on several image benchmarks show that rank-based pooling outperforms the existing pooling methods in classification performance. We further demonstrate better performance on CIFAR datasets by integrating RSP into Network-in-Network.