scholarly journals DeepSeqPanII: an interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction

2019 ◽  
Author(s):  
Zhonghao Liu ◽  
Jing Jin ◽  
Yuxin Cui ◽  
Zheng Xiong ◽  
Alireza Nasiri ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Prediction Models ◽  
State Of The Art ◽  
Human Leukocyte ◽  
Class Ii ◽  
Hla Class Ii ◽  
Attention Mechanism ◽  
Binding Prediction

AbstractHuman leukocyte antigen (HLA) complex molecules play an essential role in immune interactions by presenting peptides on the cell surface to T cells. With significant progress in deep learning, a series of neural network based models have been proposed and demonstrated with their good performances for peptide-HLA class I binding prediction. However, there still lack effective binding prediction models for HLA class II protein binding with peptides due to its inherent challenges. In this work, we present a novel sequence-based pan-specific neural network structure, DeepSeaPanII, for peptide-HLA class II binding prediction. Compared with existing pan-specific models, our model is an end-to-end neural network model without the need for pre- or post-processing on input samples. Besides state-of-the-art peformance in binding affinity prediction, DeepSeqPanII can also extract biological insight on the binding mechanism over the peptide and HLA sequences by its attention mechanism based binding core prediction capability. The leave-one-allele-out cross validation and benchmark evaluation results show that our proposed network model achieved state-of-the-art performance in HLA-II peptide binding. The source code and trained models are freely available at https://github.com/pcpLiu/DeepSeqPanII.

scholarly journals DeepSeqPanII: an interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction

2020 ◽  
Author(s):  
ZHONGHAO LIU ◽  
Jing Jin ◽  
Yuxin Cui ◽  
Zheng Xiong ◽  
Alireza Nasiri ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Network Structure ◽  
State Of The Art ◽  
Class Ii ◽  
Hla Class Ii ◽  
Binding Prediction ◽  
Neural Network Structure ◽  
Art Performance

Abstract Background: Human leukocyte antigen (HLA) complex molecules play an essential role in immune interactions by presenting peptides on the cell surface to T cells. With significant progress in deep learning, a series of neural network based models have been proposed and demonstrated with their good performances for peptide-HLA class I binding prediction. However, there still lack effective binding prediction models for HLA class II protein binding with peptides due to its inherent challenges. In this work, we present a novel sequence-based pan-specific neural network structure, DeepSeaPanII, for peptide-HLA class II binding prediction. Compared with existing pan-specific models, our model is an end-to-end neural network model without the need for pre- or post-processing on input samples. Results: The leave-one-allele-out cross validation and benchmark evaluation results show that our proposed network model achieved state-of-the-art performance in HLA-II peptide binding. Besides state-of-the-art performance in binding affinity prediction, DeepSeqPanII can also extract biological insight on the binding mechanism over the peptide and HLA sequences by its attention mechanism based binding core prediction capability. Conclusions: In this work, we present a novel neural network structure for peptide-HLA class II binding prediction. It has state-of-the-art performance and could display insightful information it learned benefiting from attention module we carefully designed. Without requiring additional data, this structure could be applied to other related sequence problems. The source code and trained models are freely available at https://github.com/pcpLiu/DeepSeqPanII.

scholarly journals AI-MHC: an allele-integrated deep learning framework for improving Class I & Class II HLA-binding predictions

2018 ◽  
Author(s):  
John-William Sidhom ◽  
Drew Pardoll ◽  
Alexander Baras
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Immune System ◽  
State Of The Art ◽  
Class Ii ◽  
Class I ◽  
Binding Prediction ◽  
Translational Invariance ◽  
Mhc Molecules ◽  
Improved Performance

AbstractMotivationThe immune system has potential to present a wide variety of peptides to itself as a means of surveillance for pathogenic invaders. This means of surveillances allows the immune system to detect peptides derives from bacterial, viral, and even oncologic sources. However, given the breadth of the epitope repertoire, in order to study immune responses to these epitopes, investigators have relied on in-silico prediction algorithms to help narrow down the list of candidate epitopes, and current methods still have much in the way of improvement.ResultsWe present Allele-Integrated MHC (AI-MHC), a deep learning architecture with improved performance over the current state-of-the-art algorithms in human Class I and Class II MHC binding prediction. Our architecture utilizes a convolutional neural network that improves prediction accuracy by 1) allowing one neural network to be trained on all peptides for all alleles of a given class of MHC molecules by making the allele an input to the net and 2) introducing a global max pooling operation with an optimized kernel size that allows the architecture to achieve translational invariance in MHC-peptide binding analysis, making it suitable for sequence analytics where a frame of interest needs to be learned in a longer, variable length sequence. We assess AI-MHC against internal independent test sets and compare against all algorithms in the IEDB automated server benchmarks, demonstrating our algorithm achieves state-of-the-art for both Class I and Class II prediction.Availability and ImplementationAI-MHC can be used via web interface at baras.pathology.jhu.edu/[email protected]

scholarly journals PresB-Net: parametric binarized neural network with learnable activations and shuffled grouped convolution

2022 ◽  
Vol 8 ◽  
pp. e842
Author(s):  
Jungwoo Shin ◽  
HyunJin Kim
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
State Of The Art ◽  
Classification Performance ◽  
Performance Degradation ◽  
Critical Problem ◽  
Hardware Costs ◽  
Performance Enhancing

In this study, we present a novel performance-enhancing binarized neural network model called PresB-Net: Parametric Binarized Neural Network. A binarized neural network (BNN) model can achieve fast output computation with low hardware costs by using binarized weights and features. However, performance degradation is the most critical problem in BNN models. Our PresB-Net combines several state-of-the-art BNN structures including the learnable activation with additional trainable parameters and shuffled grouped convolution. Notably, we propose a new normalization approach, which reduces the imbalance between the shuffled groups occurring in shuffled grouped convolutions. Besides, the proposed normalization approach helps gradient convergence so that the unstableness of the learning can be amortized when applying the learnable activation. Our novel BNN model enhances the classification performance compared with other existing BNN models. Notably, the proposed PresB-Net-18 achieves 73.84% Top-1 inference accuracy for the CIFAR-100 dataset, outperforming other existing counterparts.

scholarly journals MHCSeqNet: a deep neural network model for universal MHC binding prediction

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Poomarin Phloyphisut ◽  
Natapol Pornputtapong ◽  
Sira Sriswasdi ◽  
Ekapol Chuangsuwanich
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Deep Neural Network ◽  
Binding Prediction

Prediction Models of Short-Term Traffic Flow Based on Neural Network

2013 ◽  
Vol 671-674 ◽  
pp. 2908-2911 ◽  
Author(s):  
Chao Jun Dong ◽  
Ang Cui
Keyword(s):  
Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Network Topology ◽  
Bp Neural Network ◽  
Prediction Models ◽  
Measured Data ◽  
Short Term ◽  
Hidden Layer ◽  
Bp Neural Network Model

For the city’s road conditions, a nonlinear regression prediction model based on BP Neural Network was built. The simulation shows it has good adaptability and strong nonlinear mapping ability. Using the wavelet basis function as hidden layer nodes transfer function, a BP-Neural- Network-topology-based Wavelet Neural Network model was proposed. The model can overcome the defects of the BP Neural Network model that easy to fall into local minimum and cannot perform global search. The feasibility of the model was proved using measured data from yingbin avenue in jiangmen city.

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