Using gene expression programming to infer gene regulatory networks from time-series data

Gene regulatory networks inference is currently a topic under heavy research in the systems biology field. In this paper, gene regulatory networks are inferred via evolutionary model based on time-series microarray data. A non-linear differential equation model is adopted. Gene expression programming (GEP) is applied to identify the structure of the model and least mean square (LMS) is used to optimize the parameters in ordinary differential equations (ODEs). The proposed work has been first verified by synthetic data with noise-free and noisy time-series data, respectively, and then its effectiveness is confirmed by three real time-series expression datasets. Finally, a gene regulatory network was constructed with 12 Yeast genes. Experimental results demonstrate that our model can improve the prediction accuracy of microarray time-series data effectively.     

A hybrid Bayesian network learning method for constructing gene networks

A Bayesian network (BN) is a knowledge representation formalism that has proven to be a promising tool for analyzing gene expression data. Several problems still restrict its successful applications. Typical gene expression databases contain measurements for thousands of genes and no more than several hundred samples, but most existing BNs learning algorithms do not scale more than a few hundred variables. Current methods result in poor quality BNs when applied in such high-dimensional datasets. We propose a hybrid constraint-based scored-searching method that is effective for learning gene networks from DNA microarray data. In the first phase of this method, a novel algorithm is used to generate a skeleton BN based on dependency analysis. Then the resulting BN structure is searched by a scoring metric combined with the knowledge learned from the first phase. Computational tests have shown that the proposed method achieves more accurate results than state-of-the-art methods. This method can also be scaled beyond datasets with several hundreds of variables.     

基于改进BP神经网络的煤催化气化预测模型研究

采用改进的三层BP神经网络建立了煤催化气化反应失重率、气化初始温度和最大气化速率所对应温度的预测模型。结果表明,采用改进BP神经网络模型在此研究中可达到较高的精度,其最大预测误差分别为5.18% 、5.65% 、2.33%,明显小于归回公式的预测误差。
     

Predicting chain dimensions from an artificial neural network model

Artificial neural network models are used to investigate polymer chain dimensions. In our model, the input nodes are glass transition temperature (T_g), entanglement molecular weight (M_e), and melt density (ρ). The number of nodes in the hidden layer is eight. We found that the relative error for prediction of the characteristic ratio ranges from 0.77 to 7.5% and that the overall average error is 3.57%. Artificial neural network models may provide a new method for studying statistics properties of polymer chains. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 3163–3167, 2000     

Reconstructing gene regulatory networks from knock-out data using Gaussian Noise Model and Pearson Correlation Coefficient

A gene regulatory network (GRN) is a large and complex network consisting of interacting elements that, over time, affect each other’s state. The dynamics of complex gene regulatory processes are difficult to understand using intuitive approaches alone. To overcome this problem, we propose an algorithm for inferring the regulatory interactions from knock-out data using a Gaussian model combines with Pearson Correlation Coefficient (PCC). There are several problems relating to GRN construction that have been outlined in this paper. We demonstrated the ability of our proposed method to (1) predict the presence of regulatory interactions between genes, (2) their directionality and (3) their states (activation or suppression). The algorithm was applied to network sizes of 10 and 50 genes from DREAM3 datasets and network sizes of 10 from DREAM4 datasets. The predicted networks were evaluated based on AUROC and AUPR. We discovered that high false positive values were generated by our GRN prediction methods because the indirect regulations have been wrongly predicted as true relationships. We achieved satisfactory results as the majority of sub-networks achieved AUROC values above 0.5.     

Quantitative fuzzy neural network for analytical determination

A quantitative fuzzy neural network (Q-FNN) for pattern recognition in analytical determination is reported in this paper. The fuzzy neural network (FNN) combines a fuzzy logic system with an artificial neural network (ANN) so that it has both advantages of a high training speed and strong anti-interference. Importantly, the analytical concept of relative error (RE) in quantitative determination has been integrated into FNN so that the Q-FNN provides a very good quantitative capability in chemical analysis, and prevents the system from an over-fitting problem. The logarithm curve with noise in terms of analytical response versus concentration is calibrated by trained FNN and a close approximation to the ideal one without noise is obtained. The Q-FNN has been applied to the concentration determination of freon in the presence of interference gases. The prediction error for a test set in quantification is less than 10% while no qualitative mistake is observed, implying that the quantitative FNN has sustained the feature of pattern recognition. The results indicate that the Q-FNN has obvious advantages not only in converging speed, but also in the quantitative accuracy over the ANN.     

Predicting coal ash fusion temperature based on its chemical composition using ACO-BP neural network

Coal ash fusion temperature is important to boiler designers and operators of power plants. Fusion temperature is determined by the chemical composition of coal ash, however, their relationships are not precisely known. A novel neural network, ACO-BP neural network, is used to model coal ash fusion temperature based on its chemical composition. Ant colony optimization (ACO) is an ecological system algorithm, which draws its inspiration from the foraging behavior of real ants. A three-layer network is designed with 10 hidden nodes. The oxide contents consist of the inputs of the network and the fusion temperature is the output. Data on 80 typical Chinese coal ash samples were used for training and testing. Results show that ACO-BP neural network can obtain better performance compared with empirical formulas and BP neural network. The well-trained neural network can be used as a useful tool to predict coal ash fusion temperature according to the oxide contents of the coal ash.     

GanDTI: A multi-task neural network for drug-target interaction prediction

Drug discovery processes require drug-target interaction (DTI) prediction by virtual screenings with high accuracy. Compared with traditional methods, the deep learning method requires less time and domain expertise, while achieving higher accuracy. However, there is still room for improvement for higher performance with simplified structures. Meanwhile, this field is calling for multi-task models to solve different tasks. Here we report the GanDTI, an end-to-end deep learning model for both interaction classification and binding affinity prediction tasks. This model employs the compound graph and protein sequence data. It only consists of a graph neural network, an attention module and a multiple-layer perceptron, yet outperforms the state-of-the art methods to predict binding affinity and interaction classification on the DUD-E, human, and bindingDB benchmark datasets. This demonstrates our refined model is highly effective and efficient for DTI prediction and provides a new strategy for performance improvement.     

A neural network approach based on gold‐nanoparticle enzyme biosensor

Gold nanoparticles have demonstrated to be a very useful material for the construction of stable and sensitive glucose oxidase (GOx) amperometric biosensors. However, as for other enzyme electrodes, the lack of specificity for glucose limits their practical applications. Coupling biosensor responses with chemometric tools can be used to solve complex analytical signals from mixtures of species with similar properties. In this work, an amperometric biosensor based on a colloidal gold—cysteamine—gold disk electrode with the enzyme GOx and a redox mediator, tetrathiafulvalene (TTF), co‐immobilised atop the modified electrode, was used for the simultaneous determination of glucose and its common interferences, ascorbic acid and uric acid, in mixtures. Analytical data obtained from cyclic voltammograms generated with the biosensor were processed using an artificial neural network (ANN), and the separate quantification of the analytes over a range of 0.1–1 mM each was performed without any pretreatment. In all cases, the correlation coefficients obtained were higher than 0.99 and the mean prediction error was less than 1.7%. Copyright © 2007 John Wiley & Sons, Ltd.     

Evaluation of a mathematical model using experimental data and artificial neural network for prediction of gas separation

In recent times, membranes have found wide applications in gas separation processes. As most of the industrial membrane separation units use hollow fiber modules, having a proper model for simulating this type of membrane module is very useful in achieving guidelines for design and characterization of membrane separation units. In this study, a model based on Coker, Freeman, and Fleming＇s study was used for estimating the required membrane area. This model could simulate a multicomponent gas mixture separation by solving the governing differential mass balance equations with numerical methods. Results of the model were validated using some binary and multicomponent experimental data from the literature. Also, the artificial neural network （ANN） technique was applied to predict membrane gas separation behavior and the results of the ANN simulation were compared with the simulation results of the model and the experimental data. Good consistency between these results shows that ANN method can be successfully used for prediction of the separation behavior after suitable training of the network     

一种改进BP网络结构用于化学中的非线性校正

针对化学领域中的非线性关系特点,在常规BP网络基础上,提出了一种“杂交”型BP网络,包含两个隐层,并有输入层到输出层的直连接。它可很好地解释数据中同时存在的线性及非线性关系,效果优于多元回归法及普通BP算法。     

Application of probabilistic neural network in the clinical diagnosis of cancers based on clinical chemistry data

As a recently developed and powerful classification tool, probabilistic neural network was used to distinguish cancer patients from healthy persons according to the levels of nucleosides in human urine. Two datasets (containing 32 and 50 patterns, respectively) were investigated and the total consistency rate obtained was 100% for dataset 1 and 94% for dataset 2. To evaluate the performance of probabilistic neural network, linear discriminant analysis and learning vector quantization network were also applied to the classification problem. The results showed that the predictive ability of the probabilistic neural network is stronger than the others in this study. Moreover, the recognition rate for dataset 2 can achieve to 100% if combining these three methods together, which indicated the promising potential of clinical diagnosis by combining different methods.     

Quantitative prediction of substituted products based on quantum-chemical parameters and neural network method

The criterion of orientating group of electrophilic aromatic nitration was discussed by means of pattern recognition method with quantum-chemical parameters as features, and the product ratios of the reactions were quantitatively calculated using artificial neural network (ANN) method with the same parameters as inputs, based on the ab initio calculation of quantum chemistry. The quantum-chemical parameters involved orbital energy, orbital electron population, atomic total electron density and atomic net charge. The predicted values are in agreement with experimental results and (he predicted error of the ANN with quantum-chemical parameters for the reaction is the smallest among the all methods.