MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention.

Identifying drug-target interactions (DTIs) holds significant importance in drug discovery and development, playing a crucial role in various areas such as virtual screening, drug repurposing and identification of potential drug side effects. However, existing methods commonly exploit only a single type of feature from drugs and targets, suffering from miscellaneous challenges such as high sparsity and cold-start problems. We propose a novel framework called MSI-DTI (Multi-Source Information-based Drug-Target Interaction Prediction) to enhance prediction performance, which obtains feature representations from different views by integrating biometric features and knowledge graph representations from multi-source information. Our approach involves constructing a Drug-Target Knowledge Graph (DTKG), obtaining multiple feature representations from diverse information sources for SMILES sequences and amino acid sequences, incorporating network features from DTKG and performing an effective multi-source information fusion. Subsequently, we employ a multi-head self-attention mechanism coupled with residual connections to capture higher-order interaction information between sparse features while preserving lower-order information. Experimental results on DTKG and two benchmark datasets demonstrate that our MSI-DTI outperforms several state-of-the-art DTIs prediction methods, yielding more accurate and robust predictions. The source codes and datasets are publicly accessible at https://github.com/KEAML-JLU/MSI-DTI.

AGF-PPIS: A protein-protein interaction site predictor based on an attention mechanism and graph convolutional networks.

Protein-protein interactions play an important role in various biological processes. Interaction among proteins has a wide range of applications. Therefore, the correct identification of protein-protein interactions sites is crucial. In this paper, we propose a novel predictor for protein-protein interactions sites, AGF-PPIS, where we utilize a multi-head self-attention mechanism (introducing a graph structure), graph convolutional network, and feed-forward neural network. We use the Euclidean distance between each protein residue to generate the corresponding protein graph as the input of AGF-PPIS. On the independent test dataset Test_60, AGF-PPIS achieves superior performance over comparative methods in terms of seven different evaluation metrics (ACC, precision, recall, F1-score, MCC, AUROC, AUPRC), which fully demonstrates the validity and superiority of the proposed AGF-PPIS model. The source codes and the steps for usage of AGF-PPIS are available at https://github.com/fxh1001/AGF-PPIS.

A semi-supervised approach for the integration of multi-omics data based on transformer multi-head self-attention mechanism and graph convolutional networks.

BACKGROUND AND OBJECTIVES: Comprehensive analysis of multi-omics data is crucial for accurately formulating effective treatment plans for complex diseases. Supervised ensemble methods have gained popularity in recent years for multi-omics data analysis. However, existing research based on supervised learning algorithms often fails to fully harness the information from unlabeled nodes and overlooks the latent features within and among different omics, as well as the various associations among features. Here, we present a novel multi-omics integrative method MOSEGCN, based on the Transformer multi-head self-attention mechanism and Graph Convolutional Networks(GCN), with the aim of enhancing the accuracy of complex disease classification. MOSEGCN first employs the Transformer multi-head self-attention mechanism and Similarity Network Fusion (SNF) to separately learn the inherent correlations of latent features within and among different omics, constructing a comprehensive view of diseases. Subsequently, it feeds the learned crucial information into a self-ensembling Graph Convolutional Network (SEGCN) built upon semi-supervised learning methods for training and testing, facilitating a better analysis and utilization of information from multi-omics data to achieve precise classification of disease subtypes. RESULTS: The experimental results show that MOSEGCN outperforms several state-of-the-art multi-omics integrative analysis approaches on three types of omics data: mRNA expression data, microRNA expression data, and DNA methylation data, with accuracy rates of 83.0% for Alzheimer's disease and 86.7% for breast cancer subtyping. Furthermore, MOSEGCN exhibits strong generalizability on the GBM dataset, enabling the identification of important biomarkers for related diseases. CONCLUSION: MOSEGCN explores the significant relationship information among different omics and within each omics' latent features, effectively leveraging labeled and unlabeled information to further enhance the accuracy of complex disease classification. It also provides a promising approach for identifying reliable biomarkers, paving the way for personalized medicine.

MHCRoBERTa: pan-specific peptide-MHC class I binding prediction through transfer learning with label-agnostic protein sequences.

Predicting the binding of peptide and major histocompatibility complex (MHC) plays a vital role in immunotherapy for cancer. The success of Alphafold of applying natural language processing (NLP) algorithms in protein secondary struction prediction has inspired us to explore the possibility of NLP methods in predicting peptide-MHC class I binding. Based on the above motivations, we propose the MHCRoBERTa method, RoBERTa pre-training approach, for predicting the binding affinity between type I MHC and peptides. Analysis of the results on benchmark dataset demonstrates that MHCRoBERTa can outperform other state-of-art prediction methods with an increase of the Spearman rank correlation coefficient (SRCC) value. Notably, our model gave a significant improvement on IC50 value. Our method has achieved SRCC value and AUC value as 0.785 and 0.817, respectively. Our SRCC value is 14.3% higher than NetMHCpan3.0 (the second highest SRCC value on pan-specific) and is 3% higher than MHCflurry (the second highest SRCC value on all methods). The AUC value is also better than any other pan-specific methods. Moreover, we visualize the multi-head self-attention for the token representation across the layers and heads by this method. Through the analysis of the representation of each layer and head, we can show whether the model has learned the syntax and semantics necessary to perform the prediction task well. All these results demonstrate that our model can accurately predict the peptide-MHC class I binding affinity and that MHCRoBERTa is a powerful tool for screening potential neoantigens for cancer immunotherapy. MHCRoBERTa is available as an open source software at github (https://github.com/FuxuWang/MHCRoBERTa).

iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism.

The location of microRNAs (miRNAs) in cells determines their function in regulation activity. Studies have shown that miRNAs are stable in the extracellular environment that mediates cell-to-cell communication and are located in the intracellular region that responds to cellular stress and environmental stimuli. Though in situ detection techniques of miRNAs have made great contributions to the study of the localization and distribution of miRNAs, miRNA subcellular localization and their role are still in progress. Recently, some machine learning-based algorithms have been designed for miRNA subcellular location prediction, but their performance is still far from satisfactory. Here, we present a new data partitioning strategy that categorizes functionally similar locations for the precise and instructive prediction of miRNA subcellular location in Homo sapiens. To characterize the localization signals, we adopted one-hot encoding with post padding to represent the whole miRNA sequences, and proposed a deep bidirectional long short-term memory with the multi-head self-attention algorithm to model. The algorithm showed high selectivity in distinguishing extracellular miRNAs from intracellular miRNAs. Moreover, a series of motif analyses were performed to explore the mechanism of miRNA subcellular localization. To improve the convenience of the model, a user-friendly web server named iLoc-miRNA was established (http://iLoc-miRNA.lin-group.cn/).

A miRNA-disease association prediction model based on tree-path global feature extraction and fully connected artificial neural network with multi-head self-attention mechanism.

BACKGROUND: MicroRNAs (miRNAs) emerge in various organisms, ranging from viruses to humans, and play crucial regulatory roles within cells, participating in a variety of biological processes. In numerous prediction methods for miRNA-disease associations, the issue of over-dependence on both similarity measurement data and the association matrix still hasn't been improved. In this paper, a miRNA-Disease association prediction model (called TP-MDA) based on tree path global feature extraction and fully connected artificial neural network (FANN) with multi-head self-attention mechanism is proposed. The TP-MDA model utilizes an association tree structure to represent the data relationships, multi-head self-attention mechanism for extracting feature vectors, and fully connected artificial neural network with 5-fold cross-validation for model training. RESULTS: The experimental results indicate that the TP-MDA model outperforms the other comparative models, AUC is 0.9714. In the case studies of miRNAs associated with colorectal cancer and lung cancer, among the top 15 miRNAs predicted by the model, 12 in colorectal cancer and 15 in lung cancer were validated respectively, the accuracy is as high as 0.9227. CONCLUSIONS: The model proposed in this paper can accurately predict the miRNA-disease association, and can serve as a valuable reference for data mining and association prediction in the fields of life sciences, biology, and disease genetics, among others.

TRANS-CNN-Based Gesture Recognition for mmWave Radar.

In order to improve the real-time performance of gesture recognition by a micro-Doppler map of mmWave radar, the point cloud based gesture recognition for mmWave radar is proposed in this paper. Two steps are carried out for mmWave radar-based gesture recognition. The first step is to estimate the point cloud of the gestures by 3D-FFT and the peak grouping. The second step is to train the TRANS-CNN model by combining the multi-head self-attention and the 1D-convolutional network so as to extract the features in the point cloud data at a deeper level to categorize the gestures. In the experiments, TI mmWave radar sensor IWR1642 is used as a benchmark to evaluate the feasibility of the proposed approach. The results show that the accuracy of the gesture recognition reaches 98.5%. In order to prove the effectiveness of our approach, a simply 2Tx2Rx radar sensor is developed in our lab, and the accuracy of recognition reaches 97.1%. The results show that our proposed gesture recognition approach achieves the best performance in real time with limited training data in comparison with the existing methods.

A Remote Sensing Image Super-Resolution Reconstruction Model Combining Multiple Attention Mechanisms.

Remote sensing images are characterized by high complexity, significant scale variations, and abundant details, which present challenges for existing deep learning-based super-resolution reconstruction methods. These algorithms often exhibit limited convolutional receptive fields and thus struggle to establish global contextual information, which can lead to an inadequate utilization of both global and local details and limited generalization capabilities. To address these issues, this study introduces a novel multi-branch residual hybrid attention block (MBRHAB). This innovative approach is part of a proposed super-resolution reconstruction model for remote sensing data, which incorporates various attention mechanisms to enhance performance. First, the model employs window-based multi-head self-attention to model long-range dependencies in images. A multi-branch convolution module (MBCM) is then constructed to enhance the convolutional receptive field for improved representation of global information. Convolutional attention is subsequently combined across channels and spatial dimensions to strengthen associations between different features and areas containing crucial details, thereby augmenting local semantic information. Finally, the model adopts a parallel design to enhance computational efficiency. Generalization performance was assessed using a cross-dataset approach involving two training datasets (NWPU-RESISC45 and PatternNet) and a third test dataset (UCMerced-LandUse). Experimental results confirmed that the proposed method surpassed the existing super-resolution algorithms, including Bicubic interpolation, SRCNN, ESRGAN, Real-ESRGAN, IRN, and DSSR in the metrics of PSNR and SSIM across various magnifications scales.

MCL-DTI: using drug multimodal information and bi-directional cross-attention learning method for predicting drug-target interaction.

BACKGROUND: Prediction of drug-target interaction (DTI) is an essential step for drug discovery and drug reposition. Traditional methods are mostly time-consuming and labor-intensive, and deep learning-based methods address these limitations and are applied to engineering. Most of the current deep learning methods employ representation learning of unimodal information such as SMILES sequences, molecular graphs, or molecular images of drugs. In addition, most methods focus on feature extraction from drug and target alone without fusion learning from drug-target interacting parties, which may lead to insufficient feature representation. MOTIVATION: In order to capture more comprehensive drug features, we utilize both molecular image and chemical features of drugs. The image of the drug mainly has the structural information and spatial features of the drug, while the chemical information includes its functions and properties, which can complement each other, making drug representation more effective and complete. Meanwhile, to enhance the interactive feature learning of drug and target, we introduce a bidirectional multi-head attention mechanism to improve the performance of DTI. RESULTS: To enhance feature learning between drugs and targets, we propose a novel model based on deep learning for DTI task called MCL-DTI which uses multimodal information of drug and learn the representation of drug-target interaction for drug-target prediction. In order to further explore a more comprehensive representation of drug features, this paper first exploits two multimodal information of drugs, molecular image and chemical text, to represent the drug. We also introduce to use bi-rectional multi-head corss attention (MCA) method to learn the interrelationships between drugs and targets. Thus, we build two decoders, which include an multi-head self attention (MSA) block and an MCA block, for cross-information learning. We use a decoder for the drug and target separately to obtain the interaction feature maps. Finally, we feed these feature maps generated by decoders into a fusion block for feature extraction and output the prediction results. CONCLUSIONS: MCL-DTI achieves the best results in all the three datasets: Human, C. elegans and Davis, including the balanced datasets and an unbalanced dataset. The results on the drug-drug interaction (DDI) task show that MCL-DTI has a strong generalization capability and can be easily applied to other tasks.

CRMSNet: A deep learning model that uses convolution and residual multi-head self-attention block to predict RBPs for RNA sequence.

RNA-binding proteins (RBPs) play significant roles in many biological life activities, many algorithms and tools are proposed to predict RBPs for researching biological mechanisms of RNA-protein binding sites. Deep learning algorithms based on traditional machine learning get better result for predicting RBPs. Recently, deep learning method fused with attention mechanism has attracted huge attention in many fields and gets competitive result. Thus, attention mechanism module may also improve model performance for predicting RNA-protein binding sites. In this study, we propose convolutional residual multi-head self-attention network (CRMSNet) that combines convolutional neural network (CNN), ResNet, and multi-head self-attention blocks to find RBPs for RNA sequence. First, CRMSNet incorporates convolutional neural networks, recurrent neural networks, and multi-head self-attention block. Second, CRMSNet can draw binding motif pictures from the convolutional layer parameters. Third, attention mechanism module combines the local and global RNA sequence information for capturing long sequence feature. CRMSNet gets competitive AUC (area under the receiver operating characteristic [ROC] curve) result in a large-scale dataset RBP-24. And CRMSNet experiment result is also compared with other state-of-the-art methods. The source code of our proposed CRMSNet method can be found in https://github.com/biomg/CRMSNet.

Hepatic vessel segmentation based on 3D swin-transformer with inductive biased multi-head self-attention.

PURPOSE: Segmentation of liver vessels from CT images is indispensable prior to surgical planning and aroused a broad range of interest in the medical image analysis community. Due to the complex structure and low-contrast background, automatic liver vessel segmentation remains particularly challenging. Most of the related researches adopt FCN, U-net, and V-net variants as a backbone. However, these methods mainly focus on capturing multi-scale local features which may produce misclassified voxels due to the convolutional operator's limited locality reception field. METHODS: We propose a robust end-to-end vessel segmentation network called Inductive BIased Multi-Head Attention Vessel Net(IBIMHAV-Net) by expanding swin transformer to 3D and employing an effective combination of convolution and self-attention. In practice, we introduce voxel-wise embedding rather than patch-wise embedding to locate precise liver vessel voxels and adopt multi-scale convolutional operators to gain local spatial information. On the other hand, we propose the inductive biased multi-head self-attention which learns inductively biased relative positional embedding from initialized absolute position embedding. Based on this, we can gain more reliable queries and key matrices. RESULTS: We conducted experiments on the 3DIRCADb dataset. The average dice and sensitivity of the four tested cases were 74.8[Formula: see text] and 77.5[Formula: see text], which exceed the results of existing deep learning methods and improved graph cuts method. The Branches Detected(BD)/Tree-length Detected(TD) indexes also proved the global/local feature capture ability better than other methods. CONCLUSION: The proposed model IBIMHAV-Net provides an automatic, accurate 3D liver vessel segmentation with an interleaved architecture that better utilizes both global and local spatial features in CT volumes. It can be further extended for other clinical data.

Fusing Self-Attention and CoordConv to Improve the YOLOv5s Algorithm for Infrared Weak Target Detection.

Convolutional neural networks have achieved good results in target detection in many application scenarios, but convolutional neural networks still face great challenges when facing scenarios with small target sizes and complex background environments. To solve the problem of low accuracy of infrared weak target detection in complex scenes, and considering the real-time requirements of the detection task, we choose the YOLOv5s target detection algorithm for improvement. We add the Bottleneck Transformer structure and CoordConv to the network to optimize the model parameters and improve the performance of the detection network. Meanwhile, a two-dimensional Gaussian distribution is used to describe the importance of pixel points in the target frame, and the normalized Guassian Wasserstein distance (NWD) is used to measure the similarity between the prediction frame and the true frame to characterize the loss function of weak targets, which will help highlight the targets with flat positional deviation transformation and improve the detection accuracy. Finally, through experimental verification, compared with other mainstream detection algorithms, the improved algorithm in this paper significantly improves the target detection accuracy, with the mAP reaching 96.7 percent, which is 2.2 percentage points higher compared with Yolov5s.

LFLDNet: Lightweight Fingerprint Liveness Detection Based on ResNet and Transformer.

With the rapid development of fingerprint recognition systems, fingerprint liveness detection is gradually becoming regarded as the main countermeasure to protect the fingerprint identification system from spoofing attacks. Convolutional neural networks have shown great potential in fingerprint liveness detection. However, the generalization ability of the deep network model for unknown materials, and the computational complexity of the network, need to be further improved. A new lightweight fingerprint liveness detection network is here proposed to distinguish fake fingerprints from real ones. The method includes mainly foreground extraction, fingerprint image blocking, style transfer based on CycleGan and an improved ResNet with multi-head self-attention mechanism. The proposed method can effectively extract ROI and obtain the end-to-end data structure, which increases the amount of data. For false fingerprints generated from unknown materials, the use of CycleGan network improves the model generalization ability. The introduction of Transformer with MHSA in the improved ResNet improves detection performance and reduces computing overhead. Experiments on the LivDet2011, LivDet2013 and LivDet2015 datasets showed that the proposed method achieves good results. For example, on the LivDet2015 dataset, our methods achieved an average classification error of 1.72 across all sensors, while significantly reducing network parameters, and the overall parameter number was only 0.83 M. At the same time, the experiment on small-area fingerprints yielded an accuracy of 95.27%.

SE-VisionTransformer: Hybrid Network for Diagnosing Sugarcane Leaf Diseases Based on Attention Mechanism.

Sugarcane is an important raw material for sugar and chemical production. However, in recent years, various sugarcane diseases have emerged, severely impacting the national economy. To address the issue of identifying diseases in sugarcane leaf sections, this paper proposes the SE-VIT hybrid network. Unlike traditional methods that directly use models for classification, this paper compares threshold, K-means, and support vector machine (SVM) algorithms for extracting leaf lesions from images. Due to SVM's ability to accurately segment these lesions, it is ultimately selected for the task. The paper introduces the SE attention module into ResNet-18 (CNN), enhancing the learning of inter-channel weights. After the pooling layer, multi-head self-attention (MHSA) is incorporated. Finally, with the inclusion of 2D relative positional encoding, the accuracy is improved by 5.1%, precision by 3.23%, and recall by 5.17%. The SE-VIT hybrid network model achieves an accuracy of 97.26% on the PlantVillage dataset. Additionally, when compared to four existing classical neural network models, SE-VIT demonstrates significantly higher accuracy and precision, reaching 89.57% accuracy. Therefore, the method proposed in this paper can provide technical support for intelligent management of sugarcane plantations and offer insights for addressing plant diseases with limited datasets.

TranStutter: A Convolution-Free Transformer-Based Deep Learning Method to Classify Stuttered Speech Using 2D Mel-Spectrogram Visualization and Attention-Based Feature Representation.

Stuttering, a prevalent neurodevelopmental disorder, profoundly affects fluent speech, causing involuntary interruptions and recurrent sound patterns. This study addresses the critical need for the accurate classification of stuttering types. The researchers introduce "TranStutter", a pioneering Convolution-free Transformer-based DL model, designed to excel in speech disfluency classification. Unlike conventional methods, TranStutter leverages Multi-Head Self-Attention and Positional Encoding to capture intricate temporal patterns, yielding superior accuracy. In this study, the researchers employed two benchmark datasets: the Stuttering Events in Podcasts Dataset (SEP-28k) and the FluencyBank Interview Subset. SEP-28k comprises 28,177 audio clips from podcasts, meticulously annotated into distinct dysfluent and non-dysfluent labels, including Block (BL), Prolongation (PR), Sound Repetition (SR), Word Repetition (WR), and Interjection (IJ). The FluencyBank subset encompasses 4144 audio clips from 32 People Who Stutter (PWS), providing a diverse set of speech samples. TranStutter's performance was assessed rigorously. On SEP-28k, the model achieved an impressive accuracy of 88.1%. Furthermore, on the FluencyBank dataset, TranStutter demonstrated its efficacy with an accuracy of 80.6%. These results highlight TranStutter's significant potential in revolutionizing the diagnosis and treatment of stuttering, thereby contributing to the evolving landscape of speech pathology and neurodevelopmental research. The innovative integration of Multi-Head Self-Attention and Positional Encoding distinguishes TranStutter, enabling it to discern nuanced disfluencies with unparalleled precision. This novel approach represents a substantial leap forward in the field of speech pathology, promising more accurate diagnostics and targeted interventions for individuals with stuttering disorders.

DPACFuse: Dual-Branch Progressive Learning for Infrared and Visible Image Fusion with Complementary Self-Attention and Convolution.

Infrared and visible image fusion aims to generate a single fused image that not only contains rich texture details and salient objects, but also facilitates downstream tasks. However, existing works mainly focus on learning different modality-specific or shared features, and ignore the importance of modeling cross-modality features. To address these challenges, we propose Dual-branch Progressive learning for infrared and visible image fusion with a complementary self-Attention and Convolution (DPACFuse) network. On the one hand, we propose Cross-Modality Feature Extraction (CMEF) to enhance information interaction and the extraction of common features across modalities. In addition, we introduce a high-frequency gradient convolution operation to extract fine-grained information and suppress high-frequency information loss. On the other hand, to alleviate the CNN issues of insufficient global information extraction and computation overheads of self-attention, we introduce the ACmix, which can fully extract local and global information in the source image with a smaller computational overhead than pure convolution or pure self-attention. Extensive experiments demonstrated that the fused images generated by DPACFuse not only contain rich texture information, but can also effectively highlight salient objects. Additionally, our method achieved approximately 3% improvement over the state-of-the-art methods in MI, Qabf, SF, and AG evaluation indicators. More importantly, our fused images enhanced object detection and semantic segmentation by approximately 10%, compared to using infrared and visible images separately.

Text Sentiment Classification Based on BERT Embedding and Sliced Multi-Head Self-Attention Bi-GRU.

In the task of text sentiment analysis, the main problem that we face is that the traditional word vectors represent lack of polysemy, the Recurrent Neural Network cannot be trained in parallel, and the classification accuracy is not high. We propose a sentiment classification model based on the proposed Sliced Bidirectional Gated Recurrent Unit (Sliced Bi-GRU), Multi-head Self-Attention mechanism, and Bidirectional Encoder Representations from Transformers embedding. First, the word vector representation obtained by the BERT pre-trained language model is used as the embedding layer of the neural network. Then the input sequence is sliced into subsequences of equal length. And the Bi-sequence Gated Recurrent Unit is applied to extract the subsequent feature information. The relationship between words is learned sequentially via the Multi-head Self-attention mechanism. Finally, the emotional tendency of the text is output by the Softmax function. Experiments show that the classification accuracy of this model on the Yelp 2015 dataset and the Amazon dataset is 74.37% and 62.57%, respectively. And the training speed of the model is better than most existing models, which verifies the effectiveness of the model.

AMMVF-DTI: A Novel Model Predicting Drug-Target Interactions Based on Attention Mechanism and Multi-View Fusion.

Accurate identification of potential drug-target interactions (DTIs) is a crucial task in drug development and repositioning. Despite the remarkable progress achieved in recent years, improving the performance of DTI prediction still presents significant challenges. In this study, we propose a novel end-to-end deep learning model called AMMVF-DTI (attention mechanism and multi-view fusion), which leverages a multi-head self-attention mechanism to explore varying degrees of interaction between drugs and target proteins. More importantly, AMMVF-DTI extracts interactive features between drugs and proteins from both node-level and graph-level embeddings, enabling a more effective modeling of DTIs. This advantage is generally lacking in existing DTI prediction models. Consequently, when compared to many of the start-of-the-art methods, AMMVF-DTI demonstrated excellent performance on the human, C. elegans, and DrugBank baseline datasets, which can be attributed to its ability to incorporate interactive information and mine features from both local and global structures. The results from additional ablation experiments also confirmed the importance of each module in our AMMVF-DTI model. Finally, a case study is presented utilizing our model for COVID-19-related DTI prediction. We believe the AMMVF-DTI model can not only achieve reasonable accuracy in DTI prediction, but also provide insights into the understanding of potential interactions between drugs and targets.

Long-distance dependency combined multi-hop graph neural networks for protein-protein interactions prediction.

BACKGROUND: Protein-protein interactions are widespread in biological systems and play an important role in cell biology. Since traditional laboratory-based methods have some drawbacks, such as time-consuming, money-consuming, etc., a large number of methods based on deep learning have emerged. However, these methods do not take into account the long-distance dependency information between each two amino acids in sequence. In addition, most existing models based on graph neural networks only aggregate the first-order neighbors in protein-protein interaction (PPI) network. Although multi-order neighbor information can be aggregated by increasing the number of layers of neural network, it is easy to cause over-fitting. So, it is necessary to design a network that can capture long distance dependency information between amino acids in the sequence and can directly capture multi-order neighbor information in protein-protein interaction network. RESULTS: In this study, we propose a multi-hop neural network (LDMGNN) model combining long distance dependency information to predict the multi-label protein-protein interactions. In the LDMGNN model, we design the protein amino acid sequence encoding (PAASE) module with the multi-head self-attention Transformer block to extract the features of amino acid sequences by calculating the interdependence between every two amino acids. And expand the receptive field in space by constructing a two-hop protein-protein interaction (THPPI) network. We combine PPI network and THPPI network with amino acid sequence features respectively, then input them into two identical GIN blocks at the same time to obtain two embeddings. Next, the two embeddings are fused and input to the classifier for predict multi-label protein-protein interactions. Compared with other state-of-the-art methods, LDMGNN shows the best performance on both the SHS27K and SHS148k datasets. Ablation experiments show that the PAASE module and the construction of THPPI network are feasible and effective. CONCLUSIONS: In general terms, our proposed LDMGNN model has achieved satisfactory results in the prediction of multi-label protein-protein interactions.

DeepMHADTA: Prediction of Drug-Target Binding Affinity Using Multi-Head Self-Attention and Convolutional Neural Network.

Drug-target interactions provide insight into the drug-side effects and drug repositioning. However, wet-lab biochemical experiments are time-consuming and labor-intensive, and are insufficient to meet the pressing demand for drug research and development. With the rapid advancement of deep learning, computational methods are increasingly applied to screen drug-target interactions. Many methods consider this problem as a binary classification task (binding or not), but ignore the quantitative binding affinity. In this paper, we propose a new end-to-end deep learning method called DeepMHADTA, which uses the multi-head self-attention mechanism in a deep residual network to predict drug-target binding affinity. On two benchmark datasets, our method outperformed several current state-of-the-art methods in terms of multiple performance measures, including mean square error (MSE), consistency index (CI), rm2, and PR curve area (AUPR). The results demonstrated that our method achieved better performance in predicting the drug-target binding affinity.