识别药物-靶标相互作用(DTI)是药物再利用和创新药物发现中不可或缺的关键步骤,目前已经有许多基于序列的计算方法被广泛应用于DTI预测;然而,在以往的基于序列的研究中,特征提取通常只关注序列本身,忽视了异构信息网络,如药物-药物相互...识别药物-靶标相互作用(DTI)是药物再利用和创新药物发现中不可或缺的关键步骤,目前已经有许多基于序列的计算方法被广泛应用于DTI预测;然而,在以往的基于序列的研究中,特征提取通常只关注序列本身,忽视了异构信息网络,如药物-药物相互作用网络、药物-靶标相互作用网络等。因此,提出一种基于序列和多视角网络进行DTI预测的新方法 SMN-DTI(prediction of Drug-Target Interactions based on Sequence and Multi-view Networks)。该方法使用变分自编码器(VAE)学习药物SMILES(Simplified Molecular-Input Line-Entry System)字符串和靶标氨基酸序列的嵌入矩阵;随后,利用具有两级注意力机制的异构图注意力网络(HAN)从节点和语义2个视角的网络中聚集来自药物或靶标的不同邻居的信息,并得到最终的嵌入。在2个广泛用于DTI预测的基准数据集Hetero-seq-A和Hetero-seqB上对SMN-DTI和基准方法进行评估的结果表明,在3种不同正负样本比例下SMN-DTI均取得了最优的特征曲线下面积(AUC)和精确召回曲线下面积(AUPR)。可见,SMN-DTI比目前主流的先进预测方法具有更好的性能。展开更多
变分图自编码器是图嵌入研究中重要的深度学习模型,但存在着先验正态分布缺陷、训练过程中容易出现后验塌陷等问题.本文从建立云概念空间与隐空间的映射关系入手,引入云模型数字特征对网络中的节点进行不确定性概念表示,设计了一种基于...变分图自编码器是图嵌入研究中重要的深度学习模型,但存在着先验正态分布缺陷、训练过程中容易出现后验塌陷等问题.本文从建立云概念空间与隐空间的映射关系入手,引入云模型数字特征对网络中的节点进行不确定性概念表示,设计了一种基于多维云模型的变分图自编码器(Variational Graph Autoencoder based on Multidimensional Cloud Model,MCM-VGAE).该模型实现了隐空间的多维云概念嵌入及相应的漂移性损失度量,将先验分布扩展为泛正态分布,利用多维正向云发生器及云包络带修正采样算法实现了重参数化过程,有效缓解了后验塌陷现象.在应用效果上,模型在多类型数据集上的链路预测、节点聚类、图嵌入可视化实验表现均优于基准模型,进一步说明了方法的普适有效性.展开更多
Stocks that are fundamentally connected with each other tend to move together.Considering such common trends is believed to benefit stock movement forecasting tasks.However,such signals are not trivial to model becaus...Stocks that are fundamentally connected with each other tend to move together.Considering such common trends is believed to benefit stock movement forecasting tasks.However,such signals are not trivial to model because the connections among stocks are not physically presented and need to be estimated from volatile data.Motivated by this observation,we propose a framework that incorporates the inter-connection of firms to forecast stock prices.To effectively utilize a large set of fundamental features,we further design a novel pipeline.First,we use variational autoencoder(VAE)to reduce the dimension of stock fundamental information and then cluster stocks into a graph structure(fundamentally clustering).Second,a hybrid model of graph convolutional network and long-short term memory network(GCN-LSTM)with an adjacency graph matrix(learnt from VAE)is proposed for graph-structured stock market forecasting.Experiments on minute-level U.S.stock market data demonstrate that our model effectively captures both spatial and temporal signals and achieves superior improvement over baseline methods.The proposed model is promising for other applications in which there is a possible but hidden spatial dependency to improve time-series prediction.展开更多
Advances on bidirectional intelligence are overviewed along three threads,with extensions and new perspectives.The first thread is about bidirectional learning architecture,exploring five dualities that enable Lmser s...Advances on bidirectional intelligence are overviewed along three threads,with extensions and new perspectives.The first thread is about bidirectional learning architecture,exploring five dualities that enable Lmser six cognitive functions and provide new perspectives on which a lot of extensions and particularlly flexible Lmser are proposed.Interestingly,either or two of these dualities actually takes an important role in recent models such as U-net,ResNet,and Dense Net.The second thread is about bidirectional learning principles unified by best yIng-yAng(IA)harmony in BYY system.After getting insights on deep bidirectional learning from a bird-viewing on existing typical learning principles from one or both of the inward and outward directions,maximum likelihood,variational principle,and several other learning principles are summarised as exemplars of the BYY learning,with new perspectives on advanced topics.The third thread further proceeds to deep bidirectional intelligence,driven by long term dynamics(LTD)for parameter learning and short term dynamics(STD)for image thinking and rational thinking in harmony.Image thinking deals with information flow of continuously valued arrays and especially image sequence,as if thinking was displayed in the real world,exemplified by the flow from inward encoding/cognition to outward reconstruction/transformation performed in Lmser learning and BYY learning.In contrast,rational thinking handles symbolic strings or discretely valued vectors,performing uncertainty reasoning and problem solving.In particular,a general thesis is proposed for bidirectional intelligence,featured by BYY intelligence potential theory(BYY-IPT)and nine essential dualities in architecture,fundamentals,and implementation,respectively.Then,problems of combinatorial solving and uncertainty reasoning are investigated from this BYY IPT perspective.First,variants and extensions are suggested for AlphaGoZero like searching tasks,such as traveling salesman problem(TSP)and attributed graph matching(AGM)that are turned into Go like problems with help of a feature enrichment technique.Second,reasoning activities are summarized under guidance of BYY IPT from the aspects of constraint satisfaction,uncertainty propagation,and path or tree searching.Particularly,causal potential theory is proposed for discovering causal direction,with two roads developed for its implementation.展开更多
Ensuring the safe and efficient operation of self-driving vehicles relies heavily on accurately predicting their future trajectories.Existing approaches commonly employ an encoder-decoder neural network structure to e...Ensuring the safe and efficient operation of self-driving vehicles relies heavily on accurately predicting their future trajectories.Existing approaches commonly employ an encoder-decoder neural network structure to enhance information extraction during the encoding phase.However,these methods often neglect the inclusion of road rule constraints during trajectory formulation in the decoding phase.This paper proposes a novel method that combines neural networks and rule-based constraints in the decoder stage to improve trajectory prediction accuracy while ensuring compliance with vehicle kinematics and road rules.The approach separates vehicle trajectories into lateral and longitudinal routes and utilizes conditional variational autoencoder(CVAE)to capture trajectory uncertainty.The evaluation results demonstrate a reduction of 32.4%and 27.6%in the average displacement error(ADE)for predicting the top five and top ten trajectories,respectively,compared to the baseline method.展开更多
文摘识别药物-靶标相互作用(DTI)是药物再利用和创新药物发现中不可或缺的关键步骤,目前已经有许多基于序列的计算方法被广泛应用于DTI预测;然而,在以往的基于序列的研究中,特征提取通常只关注序列本身,忽视了异构信息网络,如药物-药物相互作用网络、药物-靶标相互作用网络等。因此,提出一种基于序列和多视角网络进行DTI预测的新方法 SMN-DTI(prediction of Drug-Target Interactions based on Sequence and Multi-view Networks)。该方法使用变分自编码器(VAE)学习药物SMILES(Simplified Molecular-Input Line-Entry System)字符串和靶标氨基酸序列的嵌入矩阵;随后,利用具有两级注意力机制的异构图注意力网络(HAN)从节点和语义2个视角的网络中聚集来自药物或靶标的不同邻居的信息,并得到最终的嵌入。在2个广泛用于DTI预测的基准数据集Hetero-seq-A和Hetero-seqB上对SMN-DTI和基准方法进行评估的结果表明,在3种不同正负样本比例下SMN-DTI均取得了最优的特征曲线下面积(AUC)和精确召回曲线下面积(AUPR)。可见,SMN-DTI比目前主流的先进预测方法具有更好的性能。
文摘变分图自编码器是图嵌入研究中重要的深度学习模型,但存在着先验正态分布缺陷、训练过程中容易出现后验塌陷等问题.本文从建立云概念空间与隐空间的映射关系入手,引入云模型数字特征对网络中的节点进行不确定性概念表示,设计了一种基于多维云模型的变分图自编码器(Variational Graph Autoencoder based on Multidimensional Cloud Model,MCM-VGAE).该模型实现了隐空间的多维云概念嵌入及相应的漂移性损失度量,将先验分布扩展为泛正态分布,利用多维正向云发生器及云包络带修正采样算法实现了重参数化过程,有效缓解了后验塌陷现象.在应用效果上,模型在多类型数据集上的链路预测、节点聚类、图嵌入可视化实验表现均优于基准模型,进一步说明了方法的普适有效性.
文摘Stocks that are fundamentally connected with each other tend to move together.Considering such common trends is believed to benefit stock movement forecasting tasks.However,such signals are not trivial to model because the connections among stocks are not physically presented and need to be estimated from volatile data.Motivated by this observation,we propose a framework that incorporates the inter-connection of firms to forecast stock prices.To effectively utilize a large set of fundamental features,we further design a novel pipeline.First,we use variational autoencoder(VAE)to reduce the dimension of stock fundamental information and then cluster stocks into a graph structure(fundamentally clustering).Second,a hybrid model of graph convolutional network and long-short term memory network(GCN-LSTM)with an adjacency graph matrix(learnt from VAE)is proposed for graph-structured stock market forecasting.Experiments on minute-level U.S.stock market data demonstrate that our model effectively captures both spatial and temporal signals and achieves superior improvement over baseline methods.The proposed model is promising for other applications in which there is a possible but hidden spatial dependency to improve time-series prediction.
基金supported by the Zhi-Yuan Chair Professorship Start-up Grant (WF220103010) from Shanghai Jiao Tong University
文摘Advances on bidirectional intelligence are overviewed along three threads,with extensions and new perspectives.The first thread is about bidirectional learning architecture,exploring five dualities that enable Lmser six cognitive functions and provide new perspectives on which a lot of extensions and particularlly flexible Lmser are proposed.Interestingly,either or two of these dualities actually takes an important role in recent models such as U-net,ResNet,and Dense Net.The second thread is about bidirectional learning principles unified by best yIng-yAng(IA)harmony in BYY system.After getting insights on deep bidirectional learning from a bird-viewing on existing typical learning principles from one or both of the inward and outward directions,maximum likelihood,variational principle,and several other learning principles are summarised as exemplars of the BYY learning,with new perspectives on advanced topics.The third thread further proceeds to deep bidirectional intelligence,driven by long term dynamics(LTD)for parameter learning and short term dynamics(STD)for image thinking and rational thinking in harmony.Image thinking deals with information flow of continuously valued arrays and especially image sequence,as if thinking was displayed in the real world,exemplified by the flow from inward encoding/cognition to outward reconstruction/transformation performed in Lmser learning and BYY learning.In contrast,rational thinking handles symbolic strings or discretely valued vectors,performing uncertainty reasoning and problem solving.In particular,a general thesis is proposed for bidirectional intelligence,featured by BYY intelligence potential theory(BYY-IPT)and nine essential dualities in architecture,fundamentals,and implementation,respectively.Then,problems of combinatorial solving and uncertainty reasoning are investigated from this BYY IPT perspective.First,variants and extensions are suggested for AlphaGoZero like searching tasks,such as traveling salesman problem(TSP)and attributed graph matching(AGM)that are turned into Go like problems with help of a feature enrichment technique.Second,reasoning activities are summarized under guidance of BYY IPT from the aspects of constraint satisfaction,uncertainty propagation,and path or tree searching.Particularly,causal potential theory is proposed for discovering causal direction,with two roads developed for its implementation.
基金supported in part by the National Natural Science Foundation of China under Grant 52372393,62003238in part by the DongfengTechnology Center(Research and Application of Next-Generation Low-Carbonntelligent Architecture Technology).
文摘Ensuring the safe and efficient operation of self-driving vehicles relies heavily on accurately predicting their future trajectories.Existing approaches commonly employ an encoder-decoder neural network structure to enhance information extraction during the encoding phase.However,these methods often neglect the inclusion of road rule constraints during trajectory formulation in the decoding phase.This paper proposes a novel method that combines neural networks and rule-based constraints in the decoder stage to improve trajectory prediction accuracy while ensuring compliance with vehicle kinematics and road rules.The approach separates vehicle trajectories into lateral and longitudinal routes and utilizes conditional variational autoencoder(CVAE)to capture trajectory uncertainty.The evaluation results demonstrate a reduction of 32.4%and 27.6%in the average displacement error(ADE)for predicting the top five and top ten trajectories,respectively,compared to the baseline method.
