Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based me...Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.展开更多
The progressive edge-growth(PEG)al-gorithm is a general method to construct short low-density parity-check(LDPC)codes and it is a greedy method to place each edge with large girths.In order to improve the performance ...The progressive edge-growth(PEG)al-gorithm is a general method to construct short low-density parity-check(LDPC)codes and it is a greedy method to place each edge with large girths.In order to improve the performance of LDPC codes,many im-proved PEG(IPEG)algorithms employ multi metrics to select surviving edges in turn.In this paper,the pro-posed edges metric(EM)based on message-passing algorithm(MPA)is introduced to PEG algorithm and the proposed EM constrained PEG(EM-PEG)algo-rithm mainly considers the independence of message passing from different nodes in Tanner graph.The numerical results show that our EM-PEG algorithm brings better bit error rate(BER)performance gains to LDPC codes than the traditional PEG algorithm and the powerful multi-edge multi-metric constrained PEG algorithm(MM-PEGA)proposed recently.In ad-dition,the multi-edge EM constrained PEG(M-EM-PEG)algorithm which adopts multi-edge EM may fur-ther improve the BER performance.展开更多
Low-density parity-check(LDPC)codes are not only capacity-approaching,but also greatly suitable for high-throughput implementation.Thus,they are the most popular codes for high-speed data transmission in the past two ...Low-density parity-check(LDPC)codes are not only capacity-approaching,but also greatly suitable for high-throughput implementation.Thus,they are the most popular codes for high-speed data transmission in the past two decades.Thanks to the low-density property of their parity-check matrices,the optimal maximum a posteriori probability decoding of LDPC codes can be approximated by message-passing decoding with linear complexity and highly parallel nature.Then,it reveals that the approximation has to carry on Tanner graphs without short cycles and small trapping sets.Last,it demonstrates that well-designed LDPC codes with the aid of computer simulation and asymptotic analysis tools are able to approach the channel capacity.Moreover,quasi-cyclic(QC)structure is introduced to significantly facilitate their high-throughput implementation.In fact,compared to the other capacity-approaching codes,QC-LDPC codes can provide better area-efficiency and energy-efficiency.As a result,they are widely applied in numerous communication systems,e.g.,Landsat satellites,Chang’e Chinese Lunar mission,5G mobile communications and so on.What’s more,its extension to non-binary Galois fields has been adopted as the channel coding scheme for BeiDou navigation satellite system.展开更多
Directed networks such as gene regulation networks and neural networks are connected by arcs（directed links）. The nodes in a directed network are often strongly interwound by a huge number of directed cycles, which ...Directed networks such as gene regulation networks and neural networks are connected by arcs（directed links）. The nodes in a directed network are often strongly interwound by a huge number of directed cycles, which leads to complex information-processing dynamics in the network and makes it highly challenging to infer the intrinsic direction of information flow. In this theoretical paper, based on the principle of minimum-feedback, we explore the node hierarchy of directed networks and distinguish feedforward and feedback arcs. Nearly optimal node hierarchy solutions, which minimize the number of feedback arcs from lower-level nodes to higher-level nodes, are constructed by belief-propagation and simulated-annealing methods. For real-world networks, we quantify the extent of feedback scarcity by comparison with the ensemble of direction-randomized networks and identify the most important feedback arcs. Our methods are also useful for visualizing directed networks.展开更多
Object-oriented model possesses inherent concurrency. Integration of concurrency and object-orientation is a promising new field. MPI is a message-passing standard and has been adopted by more and more systems. This p...Object-oriented model possesses inherent concurrency. Integration of concurrency and object-orientation is a promising new field. MPI is a message-passing standard and has been adopted by more and more systems. This paper proposes a novel approach to realize concurrent object-oriented programming based on Message-passing interface(MPI) in which future method communication is adopted between concurrent objects. A state behavior set is proposed to solve inheritance anomaly, and a bounded buffer is taken as an example to illustrate this proposal. The definition of ParaMPI class, which is the most important class in the concurrent class library, and implementation issues are briefly described.展开更多
The Fourier transform is very important to numerous applications in science and engineering. However, its usefulness is hampered by its computational expense. In this paper, in an attempt to develop a faster method fo...The Fourier transform is very important to numerous applications in science and engineering. However, its usefulness is hampered by its computational expense. In this paper, in an attempt to develop a faster method for computing Fourier transforms, the authors present parallel implementations of two new algorithms developed for the type IV Discrete Cosine Transform （DCT-IV） which support the new interleaved fast Fourier transform method. The authors discuss the realizations of their implementations using two paradigms. The first involved commodity equipment and the Message-Passing Interface （MPI） library. The second utilized the RapidMind development platform and the Cell Broadband Engine （BE） processor. These experiments indicate that the authors＇ rotation-based algorithm is preferable to their lifting-based algorithm on the platforms tested, with increased efficiency demonstrated by their MPI implementation for large data sets. Finally, the authors outline future work by discussing an architecture-oriented method for computing DCT-IVs which promises further optimization. The results indicate a promising fresh direction in the search for efficient ways to compute Fourier transforms.展开更多
The distributed computer system described in this paper is a set of computernodes interconnected in an interconnection network via packet-switching interfaces.The nodes communicate with each other by means of message-...The distributed computer system described in this paper is a set of computernodes interconnected in an interconnection network via packet-switching interfaces.The nodes communicate with each other by means of message-passing protocols. Thispaper presents the implementation of rendezvous facilities as highlevel prhoitives provided by a parallel programming language to support interprocess cornmunication andsynchronisation.展开更多
Area-efficient design methodology is proposed for the analog decoding implementations of the rate-l/2 accumulate repeat-4 jagged-accumulate （AR4JA） low density parity check （LDPC） code. The proposed approach is de...Area-efficient design methodology is proposed for the analog decoding implementations of the rate-l/2 accumulate repeat-4 jagged-accumulate （AR4JA） low density parity check （LDPC） code. The proposed approach is designed using optimized decoding architecture and regularized routing network, in such a way that the overall wiring overhead is minimized and the silicon area utilization is significantly improved. The prototyping chip used to verily the approach is tully integrated in a four-metal double-poly 0.35 lam complementary metal oxide semiconductor （CMOS） technology, and includes an input-output interface that maximizes the decoder throughput. The decoding core area is 2.02 mm2 with a post-layout area utilization of 80%. The decoder was successfully tested at the maximum data rate of 10 Mbit/s, with a core power consumption of 6.78 mW at 3.3 V, which corresponds to an energy per decoded bit of 0.677 nJ. The proposed analog LDPC decoder with low processing power and high-reliability is suitable lbr space- and power-constrained spacecraft system.展开更多
基金supported by Macao Science and Technology Development Fund,Macao SAR,China(Grant No.:0043/2023/AFJ)the National Natural Science Foundation of China(Grant No.:22173038)Macao Polytechnic University,Macao SAR,China(Grant No.:RP/FCA-01/2022).
文摘Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.
文摘The progressive edge-growth(PEG)al-gorithm is a general method to construct short low-density parity-check(LDPC)codes and it is a greedy method to place each edge with large girths.In order to improve the performance of LDPC codes,many im-proved PEG(IPEG)algorithms employ multi metrics to select surviving edges in turn.In this paper,the pro-posed edges metric(EM)based on message-passing algorithm(MPA)is introduced to PEG algorithm and the proposed EM constrained PEG(EM-PEG)algo-rithm mainly considers the independence of message passing from different nodes in Tanner graph.The numerical results show that our EM-PEG algorithm brings better bit error rate(BER)performance gains to LDPC codes than the traditional PEG algorithm and the powerful multi-edge multi-metric constrained PEG algorithm(MM-PEGA)proposed recently.In ad-dition,the multi-edge EM constrained PEG(M-EM-PEG)algorithm which adopts multi-edge EM may fur-ther improve the BER performance.
基金supported in part by the National Natural Science Foundation of China(No.62071026,No.62201152 and No.61941106)the Natural Science Foundation of Fujian Province(No.2021J05034)Key Project of Science and Technology Innovation of Fujian Province(No.2021G02006)。
文摘Low-density parity-check(LDPC)codes are not only capacity-approaching,but also greatly suitable for high-throughput implementation.Thus,they are the most popular codes for high-speed data transmission in the past two decades.Thanks to the low-density property of their parity-check matrices,the optimal maximum a posteriori probability decoding of LDPC codes can be approximated by message-passing decoding with linear complexity and highly parallel nature.Then,it reveals that the approximation has to carry on Tanner graphs without short cycles and small trapping sets.Last,it demonstrates that well-designed LDPC codes with the aid of computer simulation and asymptotic analysis tools are able to approach the channel capacity.Moreover,quasi-cyclic(QC)structure is introduced to significantly facilitate their high-throughput implementation.In fact,compared to the other capacity-approaching codes,QC-LDPC codes can provide better area-efficiency and energy-efficiency.As a result,they are widely applied in numerous communication systems,e.g.,Landsat satellites,Chang’e Chinese Lunar mission,5G mobile communications and so on.What’s more,its extension to non-binary Galois fields has been adopted as the channel coding scheme for BeiDou navigation satellite system.
基金Project by the National Basic Research Program of China(Grant No.2013CB932804)the National Natural Science Foundations of China(Grant Nos.11121403 and 11225526)support by Fondazione CRT under project SIBYL,initiative "La Ricerca dei Talenti"
文摘Directed networks such as gene regulation networks and neural networks are connected by arcs（directed links）. The nodes in a directed network are often strongly interwound by a huge number of directed cycles, which leads to complex information-processing dynamics in the network and makes it highly challenging to infer the intrinsic direction of information flow. In this theoretical paper, based on the principle of minimum-feedback, we explore the node hierarchy of directed networks and distinguish feedforward and feedback arcs. Nearly optimal node hierarchy solutions, which minimize the number of feedback arcs from lower-level nodes to higher-level nodes, are constructed by belief-propagation and simulated-annealing methods. For real-world networks, we quantify the extent of feedback scarcity by comparison with the ensemble of direction-randomized networks and identify the most important feedback arcs. Our methods are also useful for visualizing directed networks.
文摘Object-oriented model possesses inherent concurrency. Integration of concurrency and object-orientation is a promising new field. MPI is a message-passing standard and has been adopted by more and more systems. This paper proposes a novel approach to realize concurrent object-oriented programming based on Message-passing interface(MPI) in which future method communication is adopted between concurrent objects. A state behavior set is proposed to solve inheritance anomaly, and a bounded buffer is taken as an example to illustrate this proposal. The definition of ParaMPI class, which is the most important class in the concurrent class library, and implementation issues are briefly described.
文摘The Fourier transform is very important to numerous applications in science and engineering. However, its usefulness is hampered by its computational expense. In this paper, in an attempt to develop a faster method for computing Fourier transforms, the authors present parallel implementations of two new algorithms developed for the type IV Discrete Cosine Transform （DCT-IV） which support the new interleaved fast Fourier transform method. The authors discuss the realizations of their implementations using two paradigms. The first involved commodity equipment and the Message-Passing Interface （MPI） library. The second utilized the RapidMind development platform and the Cell Broadband Engine （BE） processor. These experiments indicate that the authors＇ rotation-based algorithm is preferable to their lifting-based algorithm on the platforms tested, with increased efficiency demonstrated by their MPI implementation for large data sets. Finally, the authors outline future work by discussing an architecture-oriented method for computing DCT-IVs which promises further optimization. The results indicate a promising fresh direction in the search for efficient ways to compute Fourier transforms.
文摘The distributed computer system described in this paper is a set of computernodes interconnected in an interconnection network via packet-switching interfaces.The nodes communicate with each other by means of message-passing protocols. Thispaper presents the implementation of rendezvous facilities as highlevel prhoitives provided by a parallel programming language to support interprocess cornmunication andsynchronisation.
文摘Area-efficient design methodology is proposed for the analog decoding implementations of the rate-l/2 accumulate repeat-4 jagged-accumulate （AR4JA） low density parity check （LDPC） code. The proposed approach is designed using optimized decoding architecture and regularized routing network, in such a way that the overall wiring overhead is minimized and the silicon area utilization is significantly improved. The prototyping chip used to verily the approach is tully integrated in a four-metal double-poly 0.35 lam complementary metal oxide semiconductor （CMOS） technology, and includes an input-output interface that maximizes the decoder throughput. The decoding core area is 2.02 mm2 with a post-layout area utilization of 80%. The decoder was successfully tested at the maximum data rate of 10 Mbit/s, with a core power consumption of 6.78 mW at 3.3 V, which corresponds to an energy per decoded bit of 0.677 nJ. The proposed analog LDPC decoder with low processing power and high-reliability is suitable lbr space- and power-constrained spacecraft system.
