Monodirectional tissue P systems with channel states

Timed Tissue P Systems With Channel States

Tissue P systems with channel states are a variant of tissue P systems that can be employed as highly parallel computing devices, where the channel states can control the movements of objects. In a sense, the time-free approach can improve the robustness of P systems; hence, in this work, we introduce the time-free property into such P systems and explore their computational performances. Specifically, in a time-free manner, it is proved that this type of P systems have Turing universality by using two cells and four channel states with a maximum rule length of 2, or by using two cells and noncooperative symport rules with a maximum rule length of 1. Moreover, in terms of computational efficiency, it is proved that a uniform solution of the satisfiability ( SAT ) problem can be obtained in a time-free manner by applying noncooperative symport rules with a maximum rule length of 1. The research results of this paper show that a highly robust dynamic membrane computing system is constructed. Theoretically, relative to the existing system, our constructed system can enhance robustness and expand its application scope.

Spiking neural P systems with lateral inhibition

As a member of the third generation of artificial neural network models, spiking neural P systems (SN P systems) have gained a hot research spot in recent years. This work introduces the phenomenon of lateral inhibition in biological nervous systems into SN P systems, and proposes SN P systems with lateral inhibition (LISN P systems). LISN P systems add the property of synaptic length to portray the lateral distance between neurons, and adopt a new form of rules, lateral interaction rules, to describe the reception of spikes by postsynaptic neurons with different lateral distances from the presynaptic neuron. Specifically, an excited neuron produces lateral inhibition on surrounding postsynaptic neurons. Postsynaptic neurons close to the excited neuron, i.e., neurons with small lateral distances, are more susceptible to lateral inhibition and either receive a fewer number of spikes generated by the excited neuron or fail to receive spikes. As the lateral distance increases, the lateral inhibition weakens, and the number of spikes received by postsynaptic neurons increases. Based on the above mechanism, four specific LISN P systems are designed for generating arbitrary odd numbers, arbitrary even numbers, arbitrary natural numbers and arithmetic series, respectively, as examples. By designing working modules, LISN P systems provide equivalence in computational power to the universal register machines in both generating and accepting modes. This verifies the computational completeness of LISN P systems. A universal LISN P system using merely 65 neurons is devised for function computation. According to comparisons among several systems, universal LISN P systems require fewer computational resources.

Evolution-communication spiking neural P systems with energy request rules

Evolution-communication spiking neural P systems with energy request rules (ECSNP-ER systems) are proposed and developed as a new variant of evolution-communication spiking neural P systems. In ECSNP-ER systems, in addition to spike-evolution rules and spike-communication rules, neurons also have energy request rules. Energy request rules are used to obtain energy from the environment needed for spike evolution and communication in neurons. The definition, structure and operations of ECSNP-ER systems are presented in detail. ECSNP-ER systems are proved to have the same computing capabilities as Turing machines by using them as number generating/accepting devices and function computing devices. Working non-deterministically, ECSNP-ER systems are used to solve NP-complete problems, using the SAT problem as an example, in linear time.

Spiking Neural P Systems with Membrane Potentials, Inhibitory Rules, and Anti-Spikes

Spiking neural P systems (SN P systems for short) realize the high abstraction and simulation of the working mechanism of the human brain, and adopts spikes for information encoding and processing, which are regarded as one of the third-generation neural network models. In the nervous system, the conduction of excitation depends on the presence of membrane potential (also known as the transmembrane potential difference), and the conduction of excitation on neurons is the conduction of action potentials. On the basis of the SN P systems with polarizations, in which the neuron-associated polarization is the trigger condition of the rule, the concept of neuronal membrane potential is introduced into systems. The obtained variant of the SN P system features charge accumulation and computation within neurons in quantity, as well as transmission between neurons. In addition, there are inhibitory synapses between neurons that inhibit excitatory transmission, and as such, synapses cause postsynaptic neurons to generate inhibitory postsynaptic potentials. Therefore, to make the model better fit the biological facts, inhibitory rules and anti-spikes are also adopted to obtain the spiking neural P systems with membrane potentials, inhibitory rules, and anti-spikes (referred to as the MPAIRSN P systems). The Turing universality of the MPAIRSN P systems as number generating and accepting devices is demonstrated. On the basis of the above working mechanism of the system, a small universal MPAIRSN P system with 95 neurons for computing functions is designed. The comparisons with other SN P models conclude that fewer neurons are required by the MPAIRSN P systems to realize universality.

Stability Based on PI Control of Three-Dimensional Chaotic Oscillatory System via DNA Chemical Reaction Networks

The classical proportional integral (PI) controller of SISO linear system is realized by DNA chemical reaction networks (CRNs) in the previous work. Up to now, few works have been done to realize PI controller of chaotic system through DNA CRNs. In this paper, a three-dimensional chaotic oscillatory system and a PI controller of three-dimensional chaotic oscillatory system are proposed by DNA CRNs. The CRNs of chaotic oscillatory system are made up of catalysis modules, degradation module and annihilation module then chemical reaction equations can be compiled into three-dimensional chaotic oscillatory system by the law of mass action to generate chaotic oscillatory signals. The CRNs of PI controller are designed by an integral module, a proportion module and an addition module, which can be compiled into PI controller for stabilizing chaotic oscillatory signals. The simulations of Matlab and Visual DSD are given to show our design achieving the PI control of a three-variable chaotic oscillatory system.

Prediction of lncRNA-Protein Interactions via the Multiple Information Integration

The long non-coding RNA (lncRNA)-protein interaction plays an important role in the post-transcriptional gene regulation, such as RNA splicing, translation, signaling, and the development of complex diseases. The related research on the prediction of lncRNA-protein interaction relationship is beneficial in the excavation and the discovery of the mechanism of lncRNA function and action occurrence, which are important. Traditional experimental methods for detecting lncRNA-protein interactions are expensive and time-consuming. Therefore, computational methods provide many effective strategies to deal with this problem. In recent years, most computational methods only use the information of the lncRNA-lncRNA or the protein-protein similarity and cannot fully capture all features to identify their interactions. In this paper, we propose a novel computational model for the lncRNA-protein prediction on the basis of machine learning methods. First, a feature method is proposed for representing the information of the network topological properties of lncRNA and protein interactions. The basic composition feature information and evolutionary information based on protein, the lncRNA sequence feature information, and the lncRNA expression profile information are extracted. Finally, the above feature information is fused, and the optimized feature vector is used with the recursive feature elimination algorithm. The optimized feature vectors are input to the support vector machine (SVM) model. Experimental results show that the proposed method has good effectiveness and accuracy in the lncRNA-protein interaction prediction.

RA-UNet: A Hybrid Deep Attention-Aware Network to Extract Liver and Tumor in CT Scans

Automatic extraction of liver and tumor from CT volumes is a challenging task due to their heterogeneous and diffusive shapes. Recently, 2D deep convolutional neural networks have become popular in medical image segmentation tasks because of the utilization of large labeled datasets to learn hierarchical features. However, few studies investigate 3D networks for liver tumor segmentation. In this paper, we propose a 3D hybrid residual attention-aware segmentation method, i.e., RA-UNet, to precisely extract the liver region and segment tumors from the liver. The proposed network has a basic architecture as U-Net which extracts contextual information combining low-level feature maps with high-level ones. Attention residual modules are integrated so that the attention-aware features change adaptively. This is the first work that an attention residual mechanism is used to segment tumors from 3D medical volumetric images. We evaluated our framework on the public MICCAI 2017 Liver Tumor Segmentation dataset and tested the generalization on the 3DIRCADb dataset. The experiments show that our architecture obtains competitive results.