Using Neural Networks to Predict Secondary Structure for Protein Folding

Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate prediction results. The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from its primary amino acid sequence by using five models of Neural Network (NN). These models are Feed Forward Neural Network (FNN), Learning Vector Quantization (LVQ), Probabilistic Neural Network (PNN), Convolutional Neural Network (CNN), and CNN Fine Tuning for PSSP. To evaluate our approaches two datasets have been used. The first one contains 114 protein samples, and the second one contains 1845 protein samples.

Performance comparison of three artificial neural network methods for classification of electroencephalograph signals of five mental tasks

In this paper, performance of three classifiers for classification of five mental tasks were investigated. Wavelet Packet Transform (WPT) was used for feature extraction of the relevant frequency bands from raw Electroencephalograph (EEG) signal. The three classifiers namely used were Multilayer Back propagation Neural Network, Support Vector Machine and Radial Basis Function Neural Network. In MLP-BP NN five training methods used were a) Gradient Descent Back Propagation b) Levenberg-Marquardt c) Resilient Back Propagation d) Conjugate Learning Gradient Back Propagation and e) Gradient Descent Back Propagation with movementum.

Neural Network-Powered License Plate Recognition System Design

The development of scientific inquiry and research has yielded numerous benefits in the realm of intelligent traffic control systems, particularly in the realm of automatic license plate recognition for vehicles. The design of license plate recognition algorithms has undergone digitalization through the utilization of neural networks. In contemporary times, there is a growing demand for vehicle surveillance due to the need for efficient vehicle processing and traffic management. The design, development, and implementation of a license plate recognition system hold significant social, economic, and academic importance. The study aims to present contemporary methodologies and empirical findings pertaining to automated license plate recognition. The primary focus of the automatic license plate recognition algorithm was on image extraction, character segmentation, and recognition. The task of character segmentation has been identified as the most challenging function based on my observations. The license plate recognition project that we designed demonstrated the effectiveness of this method across various observed conditions. Particularly in low-light environments, such as during periods of limited illumination or inclement weather characterized by precipitation. The method has been subjected to testing using a sample size of fifty images, resulting in a 100% accuracy rate. The findings of this study demonstrate the project’s ability to effectively determine the optimal outcomes of simulations.

Application of Convolutional Neural Networks in Classification of GBM for Enhanced Prognosis

The lethal brain tumor “Glioblastoma” has the propensity to grow over time. To improve patient outcomes, it is essential to classify GBM accurately and promptly in order to provide a focused and individualized treatment plan. Despite this, deep learning methods, particularly Convolutional Neural Networks (CNNs), have demonstrated a high level of accuracy in a myriad of medical image analysis applications as a result of recent technical breakthroughs. The overall aim of the research is to investigate how CNNs can be used to classify GBMs using data from medical imaging, to improve prognosis precision and effectiveness. This research study will demonstrate a suggested methodology that makes use of the CNN architecture and is trained using a database of MRI pictures with this tumor. The constructed model will be assessed based on its overall performance. Extensive experiments and comparisons with conventional machine learning techniques and existing classification methods will also be made. It will be crucial to emphasize the possibility of early and accurate prediction in a clinical workflow because it can have a big impact on treatment planning and patient outcomes. The paramount objective is to not only address the classification challenge but also to outline a clear pathway towards enhancing prognosis precision and treatment effectiveness.

DDoS Attack Detection Scheme Based on Entropy and PSO-BP Neural Network in SDN

SDN (Software Defined Network) has many security problems, and DDoS attack is undoubtedly the most serious harm to SDN architecture network. How to accurately and effectively detect DDoS attacks has always been a difficult point and focus of SDN security research. Based on the characteristics of SDN, a DDoS attack detection method combining generalized entropy and PSOBP neural network is proposed. The traffic is pre-detected by the generalized entropy method deployed on the switch, and the detection result is divided into normal and abnormal. Locate the switch that issued the abnormal alarm. The controller uses the PSO-BP neural network to detect whether a DDoS attack occurs by further extracting the flow features of the abnormal switch. Experiments show that compared with other methods, the detection accurate rate is guaranteed while the CPU load of the controller is reduced, and the detection capability is better.

Neural network-based model for prediction of permanent deformation of unbound granular materials

Several available mechanistic-empirical pavement design methods fail to include predictive model for permanent deformation(PD)of unbound granular materials(UGMs),which make these methods more conservative.In addition,there are limited regression models capable of predicting the PD under multistress levels,and these models have regression limitations and generally fail to cover the complexity of UGM behaviour.Recent researches are focused on using new methods of computational intelligence systems to address the problems,such as artificial neural network(ANN).In this context,we aim to develop an artificial neural model to predict the PD of UGMs exposed to repeated loads.Extensive repeated load triaxial tests(RLTTs)were conducted on base and subbase materials locally available in Victoria,Australia to investigate the PD properties of the tested materials and to prepare the database of the neural networks.Specimens were prepared over different moisture contents and gradations to cover a wide testing matrix.The ANN model consists of one input layer with five neurons,one hidden layer with twelve neurons,and one output layer with one neuron.The five inputs were the number of load cycles,deviatoric stress,moisture content,coefficient of uniformity,and coefficient of curvature.The sensitivity analysis showed that the most important indicator that impacts PD is the number of load cycles with influence factor of 41%.It shows that the ANN method is rapid and efficient to predict the PD,which could be implemented in the Austroads pavement design method.

Deep learning with convolutional neural networks for identification of liver masses and hepatocellular carcinoma: A systematic review

BACKGROUND Artificial intelligence,such as convolutional neural networks(CNNs),has been used in the interpretation of images and the diagnosis of hepatocellular cancer(HCC)and liver masses.CNN,a machine-learning algorithm similar to deep learning,has demonstrated its capability to recognise specific features that can detect pathological lesions.AIM To assess the use of CNNs in examining HCC and liver masses images in the diagnosis of cancer and evaluating the accuracy level of CNNs and their performance.METHODS The databases PubMed,EMBASE,and the Web of Science and research books were systematically searched using related keywords.Studies analysing pathological anatomy,cellular,and radiological images on HCC or liver masses using CNNs were identified according to the study protocol to detect cancer,differentiating cancer from other lesions,or staging the lesion.The data were extracted as per a predefined extraction.The accuracy level and performance of the CNNs in detecting cancer or early stages of cancer were analysed.The primary outcomes of the study were analysing the type of cancer or liver mass and identifying the type of images that showed optimum accuracy in cancer detection.RESULTS A total of 11 studies that met the selection criteria and were consistent with the aims of the study were identified.The studies demonstrated the ability to differentiate liver masses or differentiate HCC from other lesions(n=6),HCC from cirrhosis or development of new tumours(n=3),and HCC nuclei grading or segmentation(n=2).The CNNs showed satisfactory levels of accuracy.The studies aimed at detecting lesions(n=4),classification(n=5),and segmentation(n=2).Several methods were used to assess the accuracy of CNN models used.CONCLUSION The role of CNNs in analysing images and as tools in early detection of HCC or liver masses has been demonstrated in these studies.While a few limitations have been identified in these studies,overall there was an optimal level of accuracy of the CNNs used in segmentation and classification of liver cancers images.

Effect of sevoflurane preconditioning on astrocytic dynamics and neural network formation after cerebral ischemia and reperfusion in rats

Astrocytes, the major component of blood-brain barriers, have presented paradoxical profiles after cerebral ischemia and reperfusion in vivo and in vitro. Our previous study showed that sevoflurane preconditioning improved the integrity of blood-brain barriers after ischemia and reperfusion injury in rats. This led us to investigate the effects of sevoflurane preconditioning on the astrocytic dynamics in ischemia and reperfusion rats, in order to explore astrocytic cell-based mechanisms of sevoflurane preconditioning. In the present study, 2,3,5-triphenyltetrazolium chloride staining and Garcia behavioral scores were utilized to evaluate cerebral infarction and neurological outcome from day 1 to day 3 after transient middle cerebral artery occlusion surgery. Using immunofluorescent staining, we found that sevoflurane preconditioning substantially promoted the astrocytic activation and migration from the penumbra to the infarct with microglial activation from day 3 after middle cerebral artery occlusion. The formation of astrocytic scaffolds facilitated neuroblasts migrating from the subventricular zone to the lesion sites on day 14 after injury. Neural networks increased in the infarct of sevoflurane preconditioned rats, consistent with decreased infarct volume and improved neurological scores after ischemia and reperfusion injury. These findings demonstrate that sevoflurane preconditioning confers neuroprotection, not only by accelerating astrocytic spatial and temporal dynamics, but also providing astrocytic scaffolds for neuroblasts migration to ischemic regions, which facilitates neural reconstruction after brain ischemia.

Adaptive Control Based on Neural Networks for an Uncertain 2-DOF Helicopter System With Input Deadzone and Output Constraints

In this paper, a study of control for an uncertain2-degree of freedom(DOF) helicopter system is given. The2-DOF helicopter is subject to input deadzone and output constraints. In order to cope with system uncertainties and input deadzone, the neural network technique is introduced because of its capability in approximation. In order to update the weights of the neural network, an adaptive control method is utilized to improve the system adaptability. Furthermore, the integral barrier Lyapunov function(IBLF) is adopt in control design to guarantee the condition of output constraints and boundedness of the corresponding tracking errors. The Lyapunov direct method is applied in the control design to analyze system stability and convergence. Finally, numerical simulations are conducted to prove the feasibility and effectiveness of the proposed control based on the model of Quanser's 2-DOF helicopter.

Performance Comparison of Neural Networks for HRTFs Approximation

In order to approach to head related transfer functions (HRTFs), this paper employs and compares three kinds of one input neural network models, namely, multi layer perceptron (MLP) networks, radial basis function (RBF) networks and wavelet neural networks (WNN) so as to select the best network model for further HRTFs approximation. Experimental results demonstrate that wavelet neural networks are more efficient and useful.

High-resolution Image Reconstruction by Neural Network and Its Application in Infrared Imaging

As digital image techniques have been widely used, the requirements for high-resolution images become increasingly stringent. Traditional single-frame interpolation techniques cannot add new high frequency information to the expanded images, and cannot improve resolution in deed. Multiframe-based techniques are effective ways for high-resolution image reconstruction, but their computation complexities and the difficulties in achieving image sequences limit their applications. An original method using an artificial neural network is proposed in this paper. Using the inherent merits in neural network, we can establish the mapping between high frequency components in low-resolution images and high-resolution images. Example applications and their results demonstrated the images reconstructed by our method are aesthetically and quantitatively (using the criteria of MSE and MAE) superior to the images acquired by common methods. Even for infrared images this method can give satisfactory results with high definition. In addition, a single-layer linear neural network is used in this paper, the computational complexity is very low, and this method can be realized in real time.

Comparative Appraisal of Response Surface Methodology and Artificial Neural Network Method for Stabilized Turbulent Confined Jet Diffusion Flames Using Bluff-Body Burners

The present study was conducted to present the comparative modeling, predictive and generalization abilities of response surface methodology (RSM) and artificial neural network (ANN) for the thermal structure of stabilized confined jet diffusion flames in the presence of different geometries of bluff-body burners. Two stabilizer disc burners tapered at 30° and 60° and another frustum cone of 60°/30° inclination angle were employed all having the same diameter of 80 (mm) acting as flame holders. The measured radial mean temperature profiles of the developed stabilized flames at different normalized axial distances (x/dj) were considered as the model example of the physical process. The RSM and ANN methods analyze the effect of the two operating parameters namely (r), the radial distance from the center line of the flame, and (x/dj) on the measured temperature of the flames, to find the predicted maximum temperature and the corresponding process variables. A three-layered Feed Forward Neural Network in conjugation with the hyperbolic tangent sigmoid (tansig) as transfer function and the optimized topology of 2:10:1 (input neurons: hidden neurons: output neurons) was developed. Also the ANN method has been employed to illustrate such effects in the three and two dimensions and shows the location of the predicted maximum temperature. The results indicated the superiority of ANN in the prediction capability as the ranges of R2 and F Ratio are 0.868 - 0.947 and 231.7 - 864.1 for RSM method compared to 0.964 - 0.987 and 2878.8 7580.7 for ANN method beside lower values for error analysis terms.

No-reference image quality assessment based on AdaBoost_BP neural network in wavelet domain

Considering the relatively poor robustness of quality scores for different types of distortion and the lack of mechanism for determining distortion types, a no-reference image quality assessment(NR-IQA) method based on the Ada Boost BP neural network in the wavelet domain(WABNN) is proposed. A 36-dimensional image feature vector is constructed by extracting natural scene statistics(NSS) features and local information entropy features of the distorted image wavelet sub-band coefficients in three scales. The ABNN classifier is obtained by learning the relationship between image features and distortion types. The ABNN scorer is obtained by learning the relationship between image features and image quality scores. A series of contrast experiments are carried out in the laboratory of image and video engineering(LIVE) database and TID2013 database. Experimental results show the high accuracy of the distinguishing distortion type, the high consistency with subjective scores and the high robustness of the method for distorted images. Experiment results also show the independence of the database and the relatively high operation efficiency of this method.

Robust Sliding Mode Control for Nonlinear Discrete-Time Delayed Systems Based on Neural Network

This paper presents a robust sliding mode controller for a class of unknown nonlinear discrete-time systems in the presence of fixed time delay. A neural-network approximation and the Lyapunov-Krasovskii functional theory into the sliding-mode technique is used and a neural-network based sliding mode control scheme is proposed. Because of the novality of Chebyshev Neural Networks (CNNs), that it requires much less computation time as compare to multi layer neural network (MLNN), is preferred to approximate the unknown system functions. By means of linear matrix inequalities, a sufficient condition is derived to ensure the asymptotic stability such that the sliding mode dynamics is restricted to the defined sliding surface. The proposed sliding mode control technique guarantees the system state trajectory to the designed sliding surface. Finally, simulation results illustrate the main characteristics and performance of the proposed approach.

An Efficient and Robust Fall Detection System Using Wireless Gait Analysis Sensor with Artificial Neural Network (ANN) and Support Vector Machine (SVM) Algorithms

In this work, a total of 322 tests were taken on young volunteers by performing 10 different falls, 6 different Activities of Daily Living (ADL) and 7 Dynamic Gait Index (DGI) tests using a custom-designed Wireless Gait Analysis Sensor (WGAS). In order to perform automatic fall detection, we used Back Propagation Artificial Neural Network (BP-ANN) and Support Vector Machine (SVM) based on the 6 features extracted from the raw data. The WGAS, which includes a tri-axial accelerometer, 2 gyroscopes, and a MSP430 microcontroller, is worn by the subjects at either T4 (at back) or as a belt-clip in front of the waist during the various tests. The raw data is wirelessly transmitted from the WGAS to a near-by PC for real-time fall classification. The BP ANN is optimized by varying the training, testing and validation data sets and training the network with different learning schemes. SVM is optimized by using three different kernels and selecting the kernel for best classification rate. The overall accuracy of BP ANN is obtained as 98.20% with LM and RPROP training from the T4 data, while from the data taken at the belt, we achieved 98.70% with LM and SCG learning. The overall accuracy using SVM was 98.80% and 98.71% with RBF kernel from the T4 and belt position data, respectively.

Feed-Forward Artificial Neural Network Model for Air Pollutant Index Prediction in the Southern Region of Peninsular Malaysia

This paper describes the application of principal component analysis (PCA) and artificial neural network (ANN) to predict the air pollutant index (API) within the seven selected Malaysian air monitoring stations in the southern region of Peninsular Malaysia based on seven years database (2005-2011). Feed-forward ANN was used as a prediction method. The feed-forward ANN analysis demonstrated that the rotated principal component scores (RPCs) were the best input parameters to predict API. From the 4 RPCs, only 10 (CO, O3, PM10, NO2, CH4, NmHC, THC, wind direction, humidity and ambient temp) out of 12 prediction variables were the most significant parameters to predict API. The results proved that the ANN method can be applied successfully as tools for decision making and problem solving for better atmospheric management.

A Self-Organizing Memory Neural Network for Aerosol Concentration Prediction

Haze-fog,which is an atmospheric aerosol caused by natural or man-made factors,seriously affects the physical and mental health of human beings.PM2.5(a particulate matter whose diameter is smaller than or equal to 2.5 microns)is the chief culprit causing aerosol.To forecast the condition of PM2.5,this paper adopts the related the meteorological data and air pollutes data to predict the concentration of PM2.5.Since the meteorological data and air pollutes data are typical time series data,it is reasonable to adopt a machine learning method called Single Hidden-Layer Long Short-Term Memory Neural Network(SSHL-LSTMNN)containing memory capability to implement the prediction.However,the number of neurons in the hidden layer is difficult to decide unless manual testing is operated.In order to decide the best structure of the neural network and improve the accuracy of prediction,this paper employs a self-organizing algorithm,which uses Information Processing Capability(IPC)to adjust the number of the hidden neurons automatically during a learning phase.In a word,to predict PM2.5 concentration accurately,this paper proposes the SSHL-LSTMNN to predict PM2.5 concentration.In the experiment,not only the hourly precise prediction but also the daily longer-term prediction is taken into account.At last,the experimental results reflect that SSHL-LSTMNN performs the best.

Recovery of saturated signal waveform acquired from high-energy particles with artificial neural networks

Artificial neural networks(ANNs)are a core component of artificial intelligence and are frequently used in machine learning.In this report,we investigate the use of ANNs to recover the saturated signals acquired in highenergy particle and nuclear physics experiments.The inherent properties of the detector and hardware imply that particles with relatively high energies probably often generate saturated signals.Usually,these saturated signals are discarded during data processing,and therefore,some useful information is lost.Thus,it is worth restoring the saturated signals to their normal form.The mapping from a saturated signal waveform to a normal signal waveform constitutes a regression problem.Given that the scintillator and collection usually do not form a linear system,typical regression methods such as multi-parameter fitting are not immediately applicable.One important advantage of ANNs is their capability to process nonlinear regression problems.To recover the saturated signal,three typical ANNs were tested including backpropagation(BP),simple recurrent(Elman),and generalized radial basis function(GRBF)neural networks(NNs).They represent a basic network structure,a network structure with feedback,and a network structure with a kernel function,respectively.The saturated waveforms were produced mainly by the environmental gamma in a liquid scintillation detector for the China Dark Matter Detection Experiment(CDEX).The training and test data sets consisted of 6000 and 3000 recordings of background radiation,respectively,in which saturation was simulated by truncating each waveform at 40%of the maximum signal.The results show that the GBRF-NN performed best as measured using a Chi-squared test to compare the original and reconstructed signals in the region in which saturation was simulated.A comparison of the original and reconstructed signals in this region shows that the GBRF neural network produced the best performance.This ANN demonstrates a powerful efficacy in terms of solving the saturation recovery problem.The proposed method outlines new ideas and possibilities for the recovery of saturated signals in high-energy particle and nuclear physics experiments.This study also illustrates an innovative application of machine learning in the analysis of experimental data in particle physics.

Unlocking the future:Mitochondrial genes and neural networks in predicting ovarian cancer prognosis and immunotherapy response

BACKGROUND Mitochondrial genes are involved in tumor metabolism in ovarian cancer(OC)and affect immune cell infiltration and treatment responses.AIM To predict prognosis and immunotherapy response in patients diagnosed with OC using mitochondrial genes and neural networks.METHODS Prognosis,immunotherapy efficacy,and next-generation sequencing data of patients with OC were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus.Mitochondrial genes were sourced from the MitoCarta3.0 database.The discovery cohort for model construction was created from 70% of the patients,whereas the remaining 30% constituted the validation cohort.Using the expression of mitochondrial genes as the predictor variable and based on neural network algorithm,the overall survival time and immunotherapy efficacy(complete or partial response)of patients were predicted.RESULTS In total,375 patients with OC were included to construct the prognostic model,and 26 patients were included to construct the immune efficacy model.The average area under the receiver operating characteristic curve of the prognostic model was 0.7268[95% confidence interval(CI):0.7258-0.7278]in the discovery cohort and 0.6475(95%CI:0.6466-0.6484)in the validation cohort.The average area under the receiver operating characteristic curve of the immunotherapy efficacy model was 0.9444(95%CI:0.8333-1.0000)in the discovery cohort and 0.9167(95%CI:0.6667-1.0000)in the validation cohort.CONCLUSION The application of mitochondrial genes and neural networks has the potential to predict prognosis and immunotherapy response in patients with OC,providing valuable insights into personalized treatment strategies.

Synthetic well logs generation via Recurrent Neural Networks

To supplement missing logging information without increasing economic cost, a machine learning method to generate synthetic well logs from the existing log data was presented, and the experimental verification and application effect analysis were carried out. Since the traditional Fully Connected Neural Network(FCNN) is incapable of preserving spatial dependency, the Long Short-Term Memory(LSTM) network, which is a kind of Recurrent Neural Network(RNN), was utilized to establish a method for log reconstruction. By this method, synthetic logs can be generated from series of input log data with consideration of variation trend and context information with depth. Besides, a cascaded LSTM was proposed by combining the standard LSTM with a cascade system. Testing through real well log data shows that: the results from the LSTM are of higher accuracy than the traditional FCNN; the cascaded LSTM is more suitable for the problem with multiple series data; the machine learning method proposed provides an accurate and cost effective way for synthetic well log generation.