Spiking neural P systems, shortly named SN P systems, are bio-inspired neural-like computing models, which are obtained by abstracting the way of biological neurons’ spiking and communication by means of spikes in central nervous systems. SN P systems performed well in describing and modeling behaviors that occur simultaneously, yet weak at modeling complex systems with the limits of using a single spike. In this work, drawing on the idea from colored petri nets, SN P systems with colored spikes are proposed, where a finite set of colors is introduced to mark the spikes such that each spike is associated with a unique color. The updated spiking rule is applied by consuming and emitting a number of colored spikes (with the same or different colors). The computation power of the systems is investigated. Specifically, it is shown that SN P systems with colored spikes having 3 neurons are sufficient to compute Turing computable sets of numbers, and such system having 2 neurons is able to compute the family of recursive functions. These results improved the corresponding ones on the number of neurons needed to construct universal SN P systems recently appeared in [Neurocomputing, 2016, 193(12): 193–200]. To our best knowledge, this is the smallest number of neurons used to construct Turing universal SN P systems as number generator and function computing device by far.

MicroRNAs (miRNAs) play critical roles in regulating gene expression at post-transcriptional levels. Numerous experimental studies indicate that alterations and dysregulations in miRNAs are associated with important complex diseases, especially cancers. Predicting potential miRNA-disease association is beneficial not only to explore the pathogenesis of diseases, but also to understand biological processes. In this work, we propose two methods that can effectively predict potential miRNA-disease associations using our reconstructed miRNA and disease similarity networks, which are based on the latest experimental data. We reconstruct a miRNA functional similarity network using the following biological information: the miRNA family information, miRNA cluster information, experimentally valid miRNA-target association and disease-miRNA information. We also reconstruct a disease similarity network using disease functional information and disease semantic information. We present Katz with specific weights and Katz with machine learning, on the comprehensive heterogeneous network. These methods, which achieve corresponding AUC values of 0.897 and 0.919, exhibit performance superior to the existing methods. Comprehensive data networks and reasonable considerations guarantee the high performance of our methods. Contrary to several methods, which cannot work in such situations, the proposed methods also predict associations for diseases without any known related miRNAs. A web service for the download and prediction of relationships between diseases and miRNAs is available at http://lab.malab.cn/soft/MDPredict/.

Infections with many Gram-negative pathogens, including Escherichia coli , Salmonella , Shigella , and Yersinia , rely on type III secretion system (T3SS) effectors. We hypothesized that while hijacking processes within mammalian cells, the effectors operate as a robust network that can tolerate substantial contractions. This was tested in vivo using the mouse pathogen Citrobacter rodentium (encoding 31 effectors). Sequential gene deletions showed that effector essentiality for infection was context dependent and that the network could tolerate 60% contraction while maintaining pathogenicity. Despite inducing very different colonic cytokine profiles (e.g., interleukin-22, interleukin-17, interferon-γ, or granulocyte-macrophage colony-stimulating factor), different networks induced protective immunity. Using data from >100 distinct mutant combinations, we built and trained a machine learning model able to predict colonization outcomes, which were confirmed experimentally. Furthermore, reproducing the human-restricted enteropathogenic E. coli effector repertoire in C. rodentium was not sufficient for efficient colonization, which implicates effector networks in host adaptation. These results unveil the extreme robustness of both T3SS effector networks and host responses.

Spiking neural P systems, namely SN P systems, are a class of distributed and parallel neural-like computing models, inspired from the way neurons communicate by means of spikes. In this research, a new variant of the systems, called SN P systems with learning functions, is introduced. Such systems can dynamically strengthen and weaken connections among neurons during the computation. A class of specific SN P systems with simple Hebbian learning function is constructed to recognize English letters. The experimental results show that the SN P systems achieve average accuracy rate 98.76% in the test case without noise. In the test cases with low, medium and high noise, the SN P systems outperform Back Propagation (BP) neural networks and probabilistic neural networks. Moreover, comparing with spiking neural networks, SN P systems perform a little better in recognizing letters with noise. The result of this study is promising in terms of the fact that it is the first attempt to use SN P systems in pattern recognition after many theoretical advancements of SN P systems, SN P systems exhibit the feasibility for tackling pattern recognition problems.