Efficient shortest-path-tree computation in network routing based on pulse-coupled neural networks

How to Analyze the Neurodynamic Characteristics of Pulse-Coupled Neural Networks? A Theoretical Analysis and Case Study of Intersecting Cortical Model

The intersecting cortical model (ICM), initially designed for image processing, is a special case of the biologically inspired pulse-coupled neural-network (PCNN) models. Although the ICM has been widely used, few studies concern the internal activities and firing conditions of the neuron, which may lead to an invalid model in the application. Furthermore, the lack of theoretical analysis has led to inappropriate parameter settings and consequent limitations on ICM applications. To address this deficiency, we first study the continuous firing condition of ICM neurons to determine the restrictions that exist between network parameters and the input signal. Second, we investigate the neuron pulse period to understand the neural firing mechanism. Third, we derive the relationship between the continuous firing condition and the neural pulse period, and the relationship can prove the validity of the continuous firing condition and the neural pulse period as well. A solid understanding of the neural firing mechanism is helpful in setting appropriate parameters and in providing a theoretical basis for widespread applications to use the ICM model effectively. Extensive experiments of numerical tests with a common image reveal the rationality of our theoretical results.

Neural Network Optimal Routing Algorithm Based on Genetic Ant Colony in IPv6 Environment

The traditional IPv6 routing algorithm has problems such as network congestion, excessive energy consumption of nodes, and shortening the life cycle of the network. In response to this phenomenon, we proposed a routing optimization algorithm based on genetic ant colony in IPv6 environment. The algorithm analyzes and studies the genetic algorithm and the ant colony algorithm systematically. We use neural network to build the initial model and combine the constraints of QoS routing. We effectively integrate the genetic algorithm and ant colony algorithm that maximize their respective advantages and apply them to the IPv6 network. At the same time, in order to avoid the accumulation of a lot of pheromones by the ant colony algorithm in the later stage of the network, we have introduced an anticongestion reward and punishment mechanism. By comparing the search path with the optimal path, rewards and punishments are based on whether the network path is smooth or not. Finally, it is judged whether the result meets the condition, and the optimal solution obtained is passed to the BP neural network for training; otherwise, iterative iterations are required until the optimal solution is satisfied. The experimental results show that the algorithm can effectively adapt to the IPv6 routing requirements and can effectively solve the user's needs for network service quality, network performance, and other aspects.

A Highly Effective and Robust Membrane Potential-Driven Supervised Learning Method for Spiking Neurons

Spiking neurons are becoming increasingly popular owing to their biological plausibility and promising computational properties. Unlike traditional rate-based neural models, spiking neurons encode information in the temporal patterns of the transmitted spike trains, which makes them more suitable for processing spatiotemporal information. One of the fundamental computations of spiking neurons is to transform streams of input spike trains into precisely timed firing activity. However, the existing learning methods, used to realize such computation, often result in relatively low accuracy performance and poor robustness to noise. In order to address these limitations, we propose a novel highly effective and robust membrane potential-driven supervised learning (MemPo-Learn) method, which enables the trained neurons to generate desired spike trains with higher precision, higher efficiency, and better noise robustness than the current state-of-the-art spiking neuron learning methods. While the traditional spike-driven learning methods use an error function based on the difference between the actual and desired output spike trains, the proposed MemPo-Learn method employs an error function based on the difference between the output neuron membrane potential and its firing threshold. The efficiency of the proposed learning method is further improved through the introduction of an adaptive strategy, called skip scan training strategy, that selectively identifies the time steps when to apply weight adjustment. The proposed strategy enables the MemPo-Learn method to effectively and efficiently learn the desired output spike train even when much smaller time steps are used. In addition, the learning rule of MemPo-Learn is improved further to help mitigate the impact of the input noise on the timing accuracy and reliability of the neuron firing dynamics. The proposed learning method is thoroughly evaluated on synthetic data and is further demonstrated on real-world classification tasks. Experimental results show that the proposed method can achieve high learning accuracy with a significant improvement in learning time and better robustness to different types of noise.

A time-delay neural network for solving time-dependent shortest path problem

This paper concerns the time-dependent shortest path problem, which is difficult to come up with global optimal solution by means of classical shortest path approaches such as Dijkstra, and pulse-coupled neural network (PCNN). In this study, we propose a time-delay neural network (TDNN) framework that comes with the globally optimal solution when solving the time-dependent shortest path problem. The underlying idea of TDNN comes from the following mechanism: the shortest path depends on the earliest auto-wave (from start node) that arrives at the destination node. In the design of TDNN, each node on a network is considered as a neuron, which comes in the form of two units: time-window unit and auto-wave unit. Time-window unit is used to generate auto-wave in each time window, while auto-wave unit is exploited here to update the state of auto-wave. Whether or not an auto-wave leaves a node (neuron) depends on the state of auto-wave. The evaluation of the performance of the proposed approach was carried out based on online public Cordeau instances and New York Road instances. The proposed TDNN was also compared with the quality of classical approaches such as Dijkstra and PCNN.

Finishing monkeypox genomes from short reads: assembly analysis and a neural network method

BACKGROUND

Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emerging, untreatable infectious disease, killing 1 to 10 % of its human victims. In the case of poxviruses, the emergence of monkeypox outbreaks in humans and the need to monitor potential malicious release of smallpox virus requires development of methods for rapid virus identification. Whole-genome sequencing (WGS) is an emergent technology with increasing application to the diagnosis of diseases and the identification of outbreak pathogens. But "finishing" such a genome is a laborious and time-consuming process, not easily automated. To date the large, complete poxvirus genomes have not been studied comprehensively in terms of applying WGS techniques and evaluating genome assembly algorithms.

RESULTS

To explore the limitations to finishing a poxvirus genome from short reads, we first analyze the repetitive regions in a monkeypox genome and evaluate genome assembly on the simulated reads. We also report on procedures and insights relevant to the assembly (from realistically short reads) of genomes. Finally, we propose a neural network method (namely Neural-KSP) to "finish" the process by closing gaps remaining after conventional assembly, as the final stage in a protocol to elucidate clinical poxvirus genomic sequences.

CONCLUSIONS

The protocol may prove useful in any clinical viral isolate (regardless if a reference-strain sequence is available) and especially useful in genomes confounded by many global and local repetitive sequences embedded in them. This work highlights the feasibility of finishing real, complex genomes by systematically analyzing genetic characteristics, thus remedying existing assembly shortcomings with a neural network method. Such finished sequences may enable clinicians to track genetic distance between viral isolates that provides a powerful epidemiological tool.

Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia

Pediatric acute lymphoblastic leukemia (ALL) accounts for over one-quarter of all pediatric cancers. Interacting genes and proteins within the larger human gene interaction network of the human genome are rarely investigated by studies investigating pediatric ALL. In the present study, interaction networks were constructed using the empirical Bayesian approach and the Search Tool for the Retrieval of Interacting Genes/proteins database, based on the differentially-expressed (DE) genes in pediatric ALL, which were identified using the RankProd package. Enrichment analysis of the interaction network was performed using the network-based methods EnrichNet and PathExpand, which were compared with the traditional expression analysis systematic explored (EASE) method. In total, 398 DE genes were identified in pediatric ALL, and LIF was the most significantly DE gene. The co-expression network consisted of 272 nodes, which indicated genes and proteins, and 602 edges, which indicated the number of interactions adjacent to the node. Comparison between EASE and PathExpand revealed that PathExpand detected more pathways or processes that were closely associated with pediatric ALL compared with the EASE method. There were 294 nodes and 1,588 edges in the protein-protein interaction network, with the processes of hematopoietic cell lineage and porphyrin metabolism demonstrating a close association with pediatric ALL. Network enrichment analysis based on the PathExpand algorithm was revealed to be more powerful for the analysis of interaction networks in pediatric ALL compared with the EASE method. LIF and MLLT11 were identified as the most significantly DE genes in pediatric ALL. The process of hematopoietic cell lineage was the pathway most significantly associated with pediatric ALL.