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AI-based Computational Methods in Early Drug Discovery and Post Market Drug Assessment: A Survey. 基于人工智能的计算方法在早期药物发现和上市后药物评估中的应用:调查。
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-06 DOI: 10.1109/TCBB.2024.3492708
Flora Rajaei, Cristian Minoccheri, Emily Wittrup, Richard C Wilson, Brian D Athey, Gilbert S Omenn, Kayvan Najarian

Over the past few years, artificial intelligence (AI) has emerged as a transformative force in drug discovery and development (DDD), revolutionizing many aspects of the process. This survey provides a comprehensive review of recent advancements in AI applications within early drug discovery and post-market drug assessment. It addresses the identification and prioritization of new therapeutic targets, prediction of drug-target interaction (DTI), design of novel drug-like molecules, and assessment of the clinical efficacy of new medications. By integrating AI technologies, pharmaceutical companies can accelerate the discovery of new treatments, enhance the precision of drug development, and bring more effective therapies to market. This shift represents a significant move towards more efficient and cost-effective methodologies in the DDD landscape.

在过去几年中,人工智能(AI)已成为药物发现与开发(DDD)领域的一股变革性力量,彻底改变了药物发现与开发过程的许多方面。本调查全面回顾了人工智能在早期药物发现和上市后药物评估中应用的最新进展。它涉及新治疗靶点的识别和优先排序、药物-靶点相互作用(DTI)预测、新型类药物分子设计以及新药临床疗效评估。通过整合人工智能技术,制药公司可以加快新疗法的发现,提高药物开发的精准度,并将更有效的疗法推向市场。这一转变标志着 DDD 领域正朝着更高效、更具成本效益的方法迈出重要一步。
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引用次数: 0
Enhancing Single-Cell RNA-seq Data Completeness with a Graph Learning Framework. 利用图形学习框架提高单细胞 RNA-seq 数据的完整性。
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-06 DOI: 10.1109/TCBB.2024.3492384
Snehalika Lall, Sumanta Ray, Sanghamitra Bandyopadhyay

Single cell RNA sequencing (scRNA-seq) is a powerful tool to capture gene expression snapshots in individual cells. However, a low amount of RNA in the individual cells results in dropout events, which introduce huge zero counts in the single cell expression matrix. We have developed VAImpute, a variational graph autoencoder based imputation technique that learns the inherent distribution of a large network/graph constructed from the scRNA-seq data leveraging copula correlation ( Ccor) among cells/genes. The trained model is utilized to predict the dropouts events by computing the probability of all non-edges (cell-gene) in the network. We devise an algorithm to impute the missing expression values of the detected dropouts. The performance of the proposed model is assessed on both simulated and real scRNA-seq datasets, comparing it to established single-cell imputation methods. VAImpute yields significant improvements to detect dropouts, thereby achieving superior performance in cell clustering, detecting rare cells, and differential expression. All codes and datasets are given in the github link: https://github.com/sumantaray/VAImputeAvailability.

单细胞 RNA 测序(scRNA-seq)是捕捉单个细胞基因表达快照的强大工具。然而,由于单个细胞中的 RNA 含量较低,因此会出现丢失事件,从而在单细胞表达矩阵中引入大量零计数。我们开发的 VAImpute 是一种基于变异图自动编码器的估算技术,它利用细胞/基因间的 copula correlation ( Ccor) 学习由 scRNA-seq 数据构建的大型网络/图的固有分布。通过计算网络中所有非边(细胞-基因)的概率,利用训练好的模型预测掉线事件。我们还设计了一种算法,对检测到的缺失表达值进行补偿。我们在模拟和真实的 scRNA-seq 数据集上评估了拟议模型的性能,并将其与已有的单细胞估算方法进行了比较。VAImpute 在检测缺失方面有显著改进,因此在细胞聚类、检测稀有细胞和差异表达方面表现出色。所有代码和数据集都在 github 链接中提供:https://github.com/sumantaray/VAImputeAvailability。
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引用次数: 0
Hierarchical hypergraph learning in association-weighted heterogeneous network for miRNA-disease association identification. 用于 miRNA 与疾病关联识别的关联加权异构网络中的层次超图学习
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-30 DOI: 10.1109/TCBB.2024.3485788
Qiao Ning, Yaomiao Zhao, Jun Gao, Chen Chen, Minghao Yin

MicroRNAs (miRNAs) play a significant role in cell differentiation, biological development as well as the occurrence and growth of diseases. Although many computational methods contribute to predicting the association between miRNAs and diseases, they do not fully explore the attribute information contained in associated edges between miRNAs and diseases. In this study, we propose a new method, Hierarchical Hypergraph learning in Association-Weighted heterogeneous network for MiRNA-Disease association identification (HHAWMD). HHAWMD first adaptively fuses multi-view similarities based on channel attention and distinguishes the relevance of different associated relationships according to changes in expression levels of disease-related miRNAs, miRNA similarity information, and disease similarity information. Then, HHAWMD assigns edge weights and attribute features according to the association level to construct an association-weighted heterogeneous graph. Next, HHAWMD extracts the subgraph of the miRNA-disease node pair from the heterogeneous graph and builds the hyperedge (a kind of virtual edge) between the node pair to generate the hypergraph. Finally, HHAWMD proposes a hierarchical hypergraph learning approach, including node-aware attention and hyperedge-aware attention, which aggregates the abundant semantic information contained in deep and shallow neighborhoods to the hyperedge in the hypergraph. Our experiment results suggest that HHAWMD has better performance and can be used as a powerful tool for miRNA-disease association identification. The source code and data of HHAWMD are available at https://github.com/ningq669/HHAWMD/.

微小核糖核酸(miRNA)在细胞分化、生物发育以及疾病的发生和发展中发挥着重要作用。虽然许多计算方法有助于预测 miRNA 与疾病之间的关联,但它们并没有充分挖掘 miRNA 与疾病之间关联边所包含的属性信息。在本研究中,我们提出了一种新方法--用于 MiRNA 与疾病关联识别的关联加权异构网络中的层次超图学习(HHAWMD)。HHAWMD 首先基于通道注意力自适应地融合多视图相似性,并根据疾病相关 miRNA 表达水平的变化、miRNA 相似性信息和疾病相似性信息区分不同关联关系的相关性。然后,HHAWMD 根据关联程度分配边权重和属性特征,构建关联加权异构图。接着,HHAWMD 从异质图中提取 miRNA-疾病节点对的子图,并在节点对之间建立超边(一种虚拟边),生成超图。最后,HHAWMD 提出了一种分层超图学习方法,包括节点感知注意力和超边感知注意力,将深层和浅层邻域中包含的丰富语义信息聚合到超图中的超边。实验结果表明,HHAWMD 具有更好的性能,可作为 miRNA 与疾病关联识别的有力工具。HHAWMD的源代码和数据可在https://github.com/ningq669/HHAWMD/。
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引用次数: 0
LHPre: Phage Host Prediction with VAE-based Class Imbalance Correction and Lyase Sequence Embedding. LHPre:利用基于 VAE 的类不平衡校正和 Lyase 序列嵌入进行噬菌体宿主预测。
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-30 DOI: 10.1109/TCBB.2024.3488059
Jia Wang, Zhenjing Yu, Jianqiang Li

The escalation of antibiotic resistance underscores the need for innovative approaches to combat bacterial infections. Phage therapy has emerged as a promising solution, wherein host determination plays an important role. Phage lysins, characterized by their specificity in targeting and cleaving corresponding host bacteria, serve as key players in this paradigm. In this study, we present a novel approach by leveraging genes of phage-encoded lytic enzymes for host prediction, culminating in the development of LHPre. Initially, gene fragments of phage-encoded lytic enzymes and their respective hosts were collected from the database. Secondly, DNA sequences were encoded using the Frequency Chaos Game Representation (FCGR) method, and pseudo samples were generated employing the Variational Autoencoder (VAE) model to address class imbalance. Finally, a prediction model was constructed using the Vision Transformer(Vit) model. Five-fold cross-validation results demonstrated that LHPre surpassed other state-of-the-art phage host prediction methods, achieving accuracies of 85.04%, 90.01%, and 93.39% at the species, genus, and family levels, respectively.

抗生素耐药性的升级凸显了采用创新方法抗击细菌感染的必要性。噬菌体疗法已成为一种前景广阔的解决方案,其中宿主决定起着重要作用。噬菌体溶菌素具有靶向和裂解相应宿主细菌的特异性,是这一模式中的关键角色。在这项研究中,我们提出了一种新方法,利用噬菌体编码的溶菌酶基因进行宿主预测,最终开发出 LHPre。首先,我们从数据库中收集了噬菌体编码的溶菌酶基因片段及其各自的宿主。其次,利用频率混沌博弈表示法(FCGR)对DNA序列进行编码,并利用变异自动编码器(VAE)模型生成伪样本,以解决类不平衡问题。最后,利用视觉转换器(Vit)模型构建了一个预测模型。五倍交叉验证结果表明,LHPre 超越了其他最先进的噬菌体宿主预测方法,在种、属和科层面的准确率分别达到了 85.04%、90.01% 和 93.39%。
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引用次数: 0
circ2DGNN: circRNA-disease Association Prediction via Transformer-based Graph Neural Network. circ2DGNN:通过基于变换器的图神经网络进行 circRNA-疾病关联预测。
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-30 DOI: 10.1109/TCBB.2024.3488281
Keliang Cen, Zheming Xing, Xuan Wang, Yadong Wang, Junyi Li

Investigating the associations between circRNA and diseases is vital for comprehending the underlying mechanisms of diseases and formulating effective therapies. Computational prediction methods often rely solely on known circRNA-disease data, indirectly incorporating other biomolecules' effects by computing circRNA and disease similarities based on these molecules. However, this approach is limited, as other biomolecules also play significant roles in circRNA-disease interactions. To address this, we construct a comprehensive heterogeneous network incorporating data on human circRNAs, diseases, and other biomolecule interactions to develop a novel computational model, circ2DGNN, which is built upon a heterogeneous graph neural network. circ2DGNN directly takes heterogeneous networks as inputs and obtains the embedded representation of each node for downstream link prediction through graph representation learning. circ2DGNN employs a Transformer-like architecture, which can compute heterogeneous attention score for each edge, and perform message propagation and aggregation, using a residual connection to enhance the representation vector. It uniquely applies the same parameter matrix only to identical meta-relationships, reflecting diverse parameter spaces for different relationship types. After fine-tuning hyperparameters via five-fold cross-validation, evaluation conducted on a test dataset shows circ2DGNN outperforms existing state-of-the-art(SOTA) methods.

研究 circRNA 与疾病之间的关联对于理解疾病的内在机制和制定有效疗法至关重要。计算预测方法通常仅依赖于已知的 circRNA-疾病数据,通过计算基于这些分子的 circRNA 和疾病相似性,间接纳入其他生物分子的影响。然而,这种方法存在局限性,因为其他生物大分子在 circRNA 与疾病的相互作用中也发挥着重要作用。为了解决这个问题,我们构建了一个综合的异构网络,其中包含人类 circRNA、疾病和其他生物分子相互作用的数据,从而开发出一种新型计算模型 circ2DGNN,它建立在异构图神经网络的基础上。circ2DGNN直接将异构网络作为输入,通过图表示学习获得每个节点的嵌入表示,用于下游链接预测。circ2DGNN采用了类似变形器的架构,可以计算每条边的异构关注度得分,并进行信息传播和聚合,利用残差连接增强表示向量。它唯一适用于相同元关系的相同参数矩阵,反映了不同关系类型的不同参数空间。通过五倍交叉验证对超参数进行微调后,在测试数据集上进行的评估显示,circ2DGNN优于现有的最先进(SOTA)方法。
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引用次数: 0
Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets. 利用循环计数技术检测布尔不对称关系及其对分析基因表达数据集异质性的影响
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-29 DOI: 10.1109/TCBB.2024.3487434
Haosheng Zhou, Wei Lin, Sergio R Labra, Stuart A Lipton, Jeremy A Elman, Nicholas J Schork, Aaditya V Rangan

Many traditional methods for analyzing gene-gene relationships focus on positive and negative correlations, both of which are a kind of 'symmetric' relationship. Biclustering is one such technique that typically searches for subsets of genes exhibiting correlated expression among a subset of samples. However, genes can also exhibit 'asymmetric' relationships, such as 'if-then' relationships used in boolean circuits. In this paper we develop a very general method that can be used to detect biclusters within gene-expression data that involve subsets of genes which are enriched for these 'boolean-asymmetric' relationships (BARs). These BAR-biclusters can correspond to heterogeneity that is driven by asymmetric gene-gene interactions, e.g., reflecting regulatory effects of one gene on another, rather than more standard symmetric interactions. Unlike typical approaches that search for BARs across the entire population, BAR-biclusters can detect asymmetric interactions that only occur among a subset of samples. We apply our method to a single-cell RNA-sequencing data-set, demonstrating that the statistically-significant BARbiclusters indeed contain additional information not present within the more traditional 'boolean-symmetric'-biclusters. For example, the BAR-biclusters involve different subsets of cells, and highlight different gene-pathways within the data-set. Moreover, by combining the boolean-asymmetric- and boolean-symmetricsignals, one can build linear classifiers which outperform those built using only traditional boolean-symmetric signals.

许多分析基因-基因关系的传统方法都侧重于正相关和负相关,这两种关系都是一种 "对称 "关系。双聚类就是这样一种技术,它通常在样本子集中搜索表现出相关表达的基因子集。然而,基因也可以表现出 "非对称 "关系,例如布尔电路中使用的 "如果-那么 "关系。在本文中,我们开发了一种非常通用的方法,可用于检测基因表达数据中的双簇,这些数据涉及富集了这些 "布尔-非对称 "关系(BAR)的基因子集。这些 "布尔-非对称 "关系双集群可能对应于由非对称基因-基因相互作用驱动的异质性,例如,反映一个基因对另一个基因的调控作用,而不是更标准的对称相互作用。与在整个群体中搜索 BAR 的典型方法不同,BAR-双簇可以检测到只发生在部分样本中的非对称相互作用。我们将这一方法应用于单细胞 RNA 序列数据集,结果表明,在统计意义上显著的 BAR 双簇确实包含了更传统的 "布尔-对称 "双簇所不具备的额外信息。例如,BAR 双簇涉及不同的细胞子集,并突出了数据集中不同的基因通路。此外,通过结合布尔-非对称信号和布尔-对称信号,我们可以建立线性分类器,其效果优于仅使用传统布尔-对称信号建立的分类器。
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引用次数: 0
Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq. 在单细胞 RNA-Seq 中同时消除批次效应和标注细胞类型的判别域自适应网络
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-29 DOI: 10.1109/TCBB.2024.3487574
Qi Zhu, Aizhen Li, Zheng Zhang, Chuhang Zheng, Junyong Zhao, Jin-Xing Liu, Daoqiang Zhang, Wei Shao

Machine learning techniques have become increasingly important in analyzing single-cell RNA and identifying cell types, providing valuable insights into cellular development and disease mechanisms. However, the presence of batch effects poses major challenges in scRNA-seq analysis due to data distribution variation across batches. Although several batch effect mitigation algorithms have been proposed, most of them focus only on the correlation of local structure embeddings, ignoring global distribution matching and discriminative feature representation in batch correction. In this paper, we proposed the discriminative domain adaption network (D2AN) for joint batch effects correction and type annotation with single-cell RNA-seq. Specifically, we first captured the global low-dimensional embeddings of samples from the source and target domains by adversarial domain adaption strategy. Second, a contrastive loss is developed to preliminarily align the source domain samples. Moreover, the semantic alignment of class centroids in the source and target domains is achieved for further local alignment. Finally, a self-paced learning mechanism based on inter-domain loss is adopted to gradually select samples with high similarity to the target domain for training, which is used to improve the robustness of the model. Experimental results demonstrated that the proposed method on multiple real datasets outperforms several state-of-the-art methods.

机器学习技术在分析单细胞 RNA 和识别细胞类型方面的作用日益重要,为细胞发育和疾病机制提供了宝贵的见解。然而,由于不同批次的数据分布存在差异,批次效应的存在给 scRNA-seq 分析带来了重大挑战。虽然已有多种批次效应缓解算法被提出,但大多数算法只关注局部结构嵌入的相关性,忽略了批次校正中的全局分布匹配和判别特征表示。在本文中,我们提出了用于单细胞 RNA-seq 批次效应校正和类型标注的判别域自适应网络(D2AN)。具体来说,我们首先通过对抗性域自适应策略捕获源域和目标域样本的全局低维嵌入。其次,我们开发了一种对比损失(contrastive loss)来初步对齐源域样本。此外,还实现了源域和目标域中类中心点的语义对齐,以进一步进行局部对齐。最后,采用基于域间损失的自步进学习机制,逐步选择与目标域相似度高的样本进行训练,从而提高模型的鲁棒性。实验结果表明,所提出的方法在多个真实数据集上的表现优于几种最先进的方法。
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引用次数: 0
ESGC-MDA: Identifying miRNA-disease associations using enhanced Simple Graph Convolutional Networks. ESGC-MDA:利用增强型简单图卷积网络识别 miRNA 与疾病的关联。
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-28 DOI: 10.1109/TCBB.2024.3486911
Xuehua Bi, Chunyang Jiang, Cheng Yan, Kai Zhao, Linlin Zhang, Jianxin Wang

MiRNAs play an important role in the occurrence and development of human disease. Identifying potential miRNA-disease associations is valuable for disease diagnosis and treatment. Therefore, it is urgent to develop efficient computational methods for predicting potential miRNA-disease associations to reduce the cost and time associated with biological wet experiments. In addition, high-quality feature representation remains a challenge for miRNA-disease association prediction using graph neural network methods. In this paper, we propose a method named ESGC-MDA, which employs an enhanced Simple Graph Convolution Network to identify miRNA-disease associations. We first construct a bipartite attributed graph for miRNAs and diseases by computing multi-source similarity. Then, we enhance the feature representations of miRNA and disease nodes by applying two strategies in the simple convolution network, which include randomly dropping messages during propagation to ensure the model learns more reliable feature representations, and using adaptive weighting to aggregate features from different layers. Finally, we calculate the prediction scores of miRNA-disease pairs by using a fully connected neural network decoder. We conduct 5-fold cross-validation and 10-fold cross-validation on HDMM v2.0 and HMDD v3.2, respectively, and ESGC-MDA achieves better performance than state-of-the-art baseline methods. The case studies for cardiovascular disease, lung cancer and colon cancer also further confirm the effectiveness of ESGC-MDA. The source codes are available at https://github.com/bixuehua/ESGC-MDA.

miRNA 在人类疾病的发生和发展中发挥着重要作用。识别潜在的 miRNA 与疾病的关联对疾病诊断和治疗非常有价值。因此,当务之急是开发预测潜在 miRNA 与疾病关联的高效计算方法,以减少生物湿实验的成本和时间。此外,高质量的特征表示仍然是使用图神经网络方法预测 miRNA-疾病关联的一个挑战。本文提出了一种名为 ESGC-MDA 的方法,它采用增强型简单图卷积网络来识别 miRNA 与疾病的关联。我们首先通过计算多源相似性为 miRNA 和疾病构建一个双方属性图。然后,我们通过在简单卷积网络中应用两种策略来增强 miRNA 和疾病节点的特征表示,包括在传播过程中随机丢弃信息以确保模型学习到更可靠的特征表示,以及使用自适应加权来聚合不同层的特征。最后,我们使用全连接神经网络解码器计算 miRNA 疾病对的预测得分。我们分别在 HDMM v2.0 和 HMDD v3.2 上进行了 5 倍交叉验证和 10 倍交叉验证,ESGC-MDA 比最先进的基线方法取得了更好的性能。对心血管疾病、肺癌和结肠癌的案例研究也进一步证实了 ESGC-MDA 的有效性。源代码见 https://github.com/bixuehua/ESGC-MDA。
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引用次数: 0
MLW-BFECF: a multi-weighted dynamic cascade forest based on bilinear feature extraction for predicting the stage of Kidney Renal Clear Cell Carcinoma on multi-modal gene data. MLW-BFECF:基于双线性特征提取的多加权动态级联森林,用于在多模态基因数据上预测肾透明细胞癌的分期。
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-25 DOI: 10.1109/TCBB.2024.3486742
Liye Jia, Liancheng Jiang, Junhong Yue, Fang Hao, Yongfei Wu, Xilin Liu

The stage prediction of kidney renal clear cell carcinoma (KIRC) is important for the diagnosis, personalized treatment, and prognosis of patients. Many prediction methods have been proposed, but most of them are based on unimodal gene data, and their accuracy is difficult to further improve. Therefore, we propose a novel multi-weighted dynamic cascade forest based on the bilinear feature extraction (MLW-BFECF) model for stage prediction of KIRC using multimodal gene datasets (RNA-seq, CNA, and methylation). The proposed model utilizes a dynamic cascade framework with shuffle layers to prevent early degradation of the model. In each cascade layer, a voting technique based on three gene selection algorithms is first employed to effectively retain gene features more relevant to KIRC and eliminate redundant information in gene features. Then, two new bilinear models based on the gated attention mechanism are proposed to better extract new intra-modal and inter-modal gene features; Finally, based on the idea of the bagging, a multi-weighted ensemble forest classifiers module is proposed to extract and fuse probabilistic features of the three-modal gene data. A series of experiments demonstrate that the MLW-BFECF model based on the three-modal KIRC dataset achieves the highest prediction performance with an accuracy of 88.92%.

肾透明细胞癌(KIRC)的分期预测对于患者的诊断、个性化治疗和预后都非常重要。目前已提出了许多预测方法,但大多基于单模态基因数据,其准确性难以进一步提高。因此,我们提出了一种基于双线性特征提取的新型多权重动态级联森林(MLW-BFECF)模型,利用多模态基因数据集(RNA-seq、CNA 和甲基化)对 KIRC 进行分期预测。该模型采用动态级联框架和洗牌层,以防止模型的早期退化。在每个级联层中,首先采用基于三种基因选择算法的投票技术,以有效保留与 KIRC 更为相关的基因特征,并消除基因特征中的冗余信息。然后,提出了基于门控注意机制的两个新的双线性模型,以更好地提取新的模内和模间基因特征;最后,基于bagging的思想,提出了多加权集合森林分类器模块,以提取和融合三模态基因数据的概率特征。一系列实验证明,基于三模态 KIRC 数据集的 MLW-BFECF 模型预测准确率高达 88.92%,预测性能最高。
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引用次数: 0
An End-to-end Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction. 用于准确预测蛋白质-蛋白质相互作用的端到端知识图谱融合图神经网络
IF 3.6 3区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-24 DOI: 10.1109/TCBB.2024.3486216
Jie Yang, Yapeng Li, Guoyin Wang, Zhong Chen, Di Wu

Protein-protein interactions (PPIs) are essential to understanding cellular mechanisms, signaling networks, disease processes, and drug development, as they represent the physical contacts and functional associations between proteins. Recent advances have witnessed the achievements of artificial intelligence (AI) methods aimed at predicting PPIs. However, these approaches often handle the intricate web of relationships and mechanisms among proteins, drugs, diseases, ribonucleic acid (RNA), and protein structures in a fragmented or superficial manner. This is typically due to the limitations of non-end-to-end learning frameworks, which can lead to sub-optimal feature extraction and fusion, thereby compromising the prediction accuracy. To address these deficiencies, this paper introduces a novel end-to-end learning model, the Knowledge Graph Fused Graph Neural Network (KGF-GNN). This model comprises three integral components: (1) Protein Associated Network (PAN) Construction: We begin by constructing a PAN that extensively captures the diverse relationships and mechanisms linking proteins with drugs, diseases, RNA, and protein structures. (2) Graph Neural Network for Feature Extraction: A Graph Neural Network (GNN) is then employed to distill both topological and semantic features from the PAN, alongside another GNN designed to extract topological features directly from observed PPI networks. (3) Multi-layer Perceptron for Feature Fusion: Finally, a multi-layer perceptron integrates these varied features through end-to-end learning, ensuring that the feature extraction and fusion processes are both comprehensive and optimized for PPI prediction. Extensive experiments conducted on real-world PPI datasets validate the effectiveness of our proposed KGF-GNN approach, which not only achieves high accuracy in predicting PPIs but also significantly surpasses existing state-of-the-art models. This work not only enhances our ability to predict PPIs with a higher precision but also contributes to the broader application of AI in Bioinformatics, offering profound implications for biological research and therapeutic development.

蛋白质-蛋白质相互作用(PPIs)对于理解细胞机制、信号网络、疾病过程和药物开发至关重要,因为它们代表了蛋白质之间的物理接触和功能关联。近年来,旨在预测 PPIs 的人工智能(AI)方法取得了长足的进步。然而,这些方法往往以零散或肤浅的方式处理蛋白质、药物、疾病、核糖核酸(RNA)和蛋白质结构之间错综复杂的关系和机制。这通常是由于非端到端学习框架的局限性造成的,它可能导致次优特征提取和融合,从而影响预测的准确性。为了解决这些不足,本文介绍了一种新型端到端学习模型--知识图谱融合图神经网络(KGF-GNN)。该模型由三个组成部分组成:(1) 蛋白质关联网络(PAN)构建:我们首先构建一个 PAN,广泛捕捉将蛋白质与药物、疾病、RNA 和蛋白质结构联系起来的各种关系和机制。(2) 用于特征提取的图神经网络:然后使用图神经网络(GNN)从 PAN 中提取拓扑和语义特征,同时使用另一个图神经网络直接从观察到的 PPI 网络中提取拓扑特征。(3) 用于特征融合的多层感知器:最后,多层感知器通过端到端学习整合这些不同的特征,确保特征提取和融合过程既全面又优化了 PPI 预测。在真实世界的 PPI 数据集上进行的大量实验验证了我们提出的 KGF-GNN 方法的有效性,它不仅在预测 PPI 方面实现了高准确率,而且大大超过了现有的先进模型。这项工作不仅提高了我们预测 PPIs 的精度,而且有助于人工智能在生物信息学中的广泛应用,对生物研究和治疗开发具有深远影响。
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IEEE/ACM Transactions on Computational Biology and Bioinformatics
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