Gene regulatory network inference based on causal discovery integrating with graph neural network

Gene regulatory network (GRN) inference from gene expression data is asignificant approach to understanding aspects of the biological system.Compared with generalized correlation-based methods, causality-inspiredones seem more rational to infer regulatory relationships. We proposeGRINCD, a novel GRN inference framework empowered by graph representationlearning and causal asymmetric learning, considering both linearand non-linear regulatory relationships. First, high-quality representation ofeach gene is generated using graph neural network. Then, we apply theadditive noise model to predict the causal regulation of each regulator-targetpair. Additionally, we design two channels and finally assemble them forrobust prediction. Through comprehensive comparisons of our frameworkwith state-of-the-art methods based on different principles on numerousdatasets of diverse types and scales, the experimental results show that ourframework achieves superior or comparable performance under variousevaluation metrics. Our work provides a new clue for constructing GRNs,and our proposed framework GRINCD also shows potential in identifyingkey factors affecting cancerdevelopment.

Visualization of flatness pattern recognition based on T-S cloud inference network

Flatness pattern recognition is the key of the flatness control. The accuracy of the present flatness pattern recognition is limited and the shape defects cannot be reflected intuitively. In order to improve it, a novel method via T-S cloud inference network optimized by genetic algorithm(GA) is proposed. T-S cloud inference network is constructed with T-S fuzzy neural network and the cloud model. So, the rapid of fuzzy logic and the uncertainty of cloud model for processing data are both taken into account. What's more, GA possesses good parallel design structure and global optimization characteristics. Compared with the simulation recognition results of traditional BP Algorithm, GA is more accurate and effective. Moreover, virtual reality technology is introduced into the field of shape control by Lab VIEW, MATLAB mixed programming. And virtual flatness pattern recognition interface is designed.Therefore, the data of engineering analysis and the actual model are combined with each other, and the shape defects could be seen more lively and intuitively.

Unicast Network Topology Inference Algorithm Based on Hierarchical Clustering

Network topology inference is one of the important applications of network tomography.Traditional network topology inference may impact network normal operation due to its generation of huge data traffic.A unicast network topology inference is proposed to use time to live(TTL)for layering and classify nodes layer by layer based on the similarity of node pairs.Finally,the method infers logical network topology effectively with self-adaptive combination of previous results.Simulation results show that the proposed method holds a high accuracy of topology inference while decreasing network measuring flow,thus improves measurement efficiency.

Study of Synthesis Identification in Cutting Process with Fuzzy Neural Network

With the development of industrial production modernization, FMS and CIMS will become more and more popularized. For its control system is increasingly modeled, intellectualized and automatized, in order to raise the reliability and stability in the manufacturing process, the comprehensive monitoring and diagnosis aimed at cutting tool wear and chatter become more and more important and get rapid development. The paper tried to discuss of the intellectual status identification method based on acoustics-vibra characteristics of machining process, and propose that the working conditions may be taken as a core, complex fuzzy inference neural network model based on artificial neural network theory, and by using various kinds of modernized signal processing method to abstract enough characteristics parameters which will reflect overall processing status from machining acoustics-vibra signal as information source, to identify different working condition, and provide guarantee for automation and intelligence in machining process. The complex network is composed of NNw and NNs, Each of them is composed of BP model network, NNw is weight network at rule condition, NNs is decision-making network of each status. Y out is final inference result which is to take subordinate degree as weight from NNw, to weight reflecting result from NNs and obtain status inference of monitoring system. In the process of machining, the acoustics-vibor signal were gotten by the acoustimeter and the acceleration piezoelectricity detector, the date is analysed by the signal processing software in time and frequency domain, then form multi feature parameter vector of criterion pattern samples for the different stage of cutting chatter and acoustics-vibra multi feature parameter vector. The vector can give a accurate and comprehensive description for the cutting process, and have the characteristic which are speediness of time domain and veracity of frequency domain. The research works have been practically applied in identification of tool wear, cutting chatter, experiment results showed that it is practicable to identify the cutting chatter based on fuzzy neural network, and the new method based on fuzzy neural network can be applied to other state identification in machining process.

Fundamental Boolean network modelling for childhood acute lymphoblastic leukaemia pathways

Background:A novel data-driven Boolean model,namely,the fundamental Boolean model(FBM),has been proposed to draw genetic regulatory insights into gene activation,inhibition,and protein decay,published in 2018.This novel Boolean model facilitates the analysis of the activation and inhibition pathways.However,the novel model does not handle the situation well,where genetic regulation might require more time steps to complete.Methods:Here,we propose extending the fundamental Boolean modelling to address the issue that some gene regulations might require more time steps to complete than others.We denoted this extension model as the temporal fundamental Boolean model(TFBM)and related networks as the temporal fundamental Boolean networks(TFBNs).The leukaemia microarray datasets downloaded from the National Centre for Biotechnology Information have been adopted to demonstrate the utility of the proposed TFBM and TFBNs.Results:We developed the TFBNs that contain 285 components and 2775 Boolean rules based on TFBM on the leukaemia microarray datasets,which are in the form of short-time series.The data contain gene expression measurements for 13 GC-sensitive children under therapy for acute lymphoblastic leukaemia,and each sample has three time points:0 hour(before GC treatment),6/8 hours(after GC treatment)and 24 hours(after GC treatment).Conclusion:We conclude that the proposed TFBM unlocks their predecessor’s limitation,Le.,FBM,that could help pharmaceutical agents identify any side effects on clinic-related data.New hypotheses could be identified by analysing the extracted fundamental Boolean networks and analysing their up-regulatory and down-regulatory pathways.

Inferring gene regulatory networks by PCA-CMI using Hill climbing algorithm based on MIT score and SORDER method

Inferring gene regulatory networks （GRNs） is a challenging task in Bioinformatics. In this paper, an algorithm, PCHMS, is introduced to infer GRNs. This method applies the path consistency （PC） algorithm based on conditional mutual information test （PCA-CMI）. In the PC-based algorithms the separator set is determined to detect the dependency between variables. The PCHMS algorithm attempts to select the set in the smart way. For this purpose, the edges of resulted skeleton are directed based on PC algorithm direction rule and mutual information test （MIT） score. Then the separator set is selected according to the directed network by considering a suitable sequential order of genes. The effectiveness of this method is benchmarked through several networks from the DREAM challenge and the widely used SOS DNA repair network of Escherichia coll. Results show that applying the PCHMS algorithm improves the precision of learning the structure of the GRNs in comparison with current popular approaches.

supported by the National Natural Science Foundation of China(Nos.62172051,61772085,and 61877005)and Jiangsu Agriculture Science and Technology Innovation Fund(No.CX(18)3054).

Numerous neural network(NN)applications are now being deployed to mobile devices.These applications usually have large amounts of calculation and data while requiring low inference latency,which poses challenges to the computing ability of mobile devices.Moreover,devices’life and performance depend on temperature.Hence,in many scenarios,such as industrial production and automotive systems,where the environmental temperatures are usually high,it is important to control devices’temperatures to maintain steady operations.In this paper,we propose a thermal-aware channel-wise heterogeneous NN inference algorithm.It contains two parts,the thermal-aware dynamic frequency(TADF)algorithm and the heterogeneous-processor single-layer workload distribution(HSWD)algorithm.Depending on a mobile device’s architecture characteristics and environmental temperature,TADF can adjust the appropriate running speed of the central processing unit and graphics processing unit,and then the workload of each layer in the NN model is distributed by HSWD in line with each processor’s running speed and the characteristics of the layers as well as heterogeneous processors.The experimental results,where representative NNs and mobile devices were used,show that the proposed method can considerably improve the speed of the on-device inference by 21%–43%over the traditional inference method.

Navigation of Non-holonomic Mobile Robot Using Neuro-fuzzy Logic with Integrated Safe Boundary Algorithm

In the present work, autonomous mobile robot（AMR） system is intended with basic behaviour, one is obstacle avoidance and the other is target seeking in various environments. The AMR is navigated using fuzzy logic, neural network and adaptive neurofuzzy inference system（ANFIS） controller with safe boundary algorithm. In this method of target seeking behaviour, the obstacle avoidance at every instant improves the performance of robot in navigation approach. The inputs to the controller are the signals from various sensors fixed at front face, left and right face of the AMR. The output signal from controller regulates the angular velocity of both front power wheels of the AMR. The shortest path is identified using fuzzy, neural network and ANFIS techniques with integrated safe boundary algorithm and the predicted results are validated with experimentation. The experimental result has proven that ANFIS with safe boundary algorithm yields better performance in navigation, in particular with curved/irregular obstacles.