A novel approach for blast-induced flyrock prediction based on imperialist competitive algorithm and artificial neural network.
Ontology highlight
ABSTRACT:
SUBMITTER: Marto A
PROVIDER: S-EPMC4132322 | biostudies-other | 2014
REPOSITORIES: biostudies-other
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Project description:BackgroundThe major histocompatibility complex (MHC) molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event.ResultsHere, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods.ConclusionThe NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.
| S-EPMC2753847 | biostudies-literature
Project description:Background: Identifying large vessel occlusion (LVO) patients in the prehospital triage stage to avoid unnecessary and costly delays is important but still challenging. We aim to develop an artificial neural network (ANN) algorithm to predict LVO using prehospital accessible data including demographics, National Institutes of Health Stroke Scale (NIHSS) items and vascular risk factors. Methods: Consecutive acute ischemic stroke patients who underwent CT angiography (CTA) or time of flight MR angiography (TOF-MRA) and received reperfusion therapy within 8 h from symptom onset were included. The diagnosis of LVO was defined as occlusion of the intracranial internal carotid artery (ICA), M1 and M2 segments of the middle cerebral artery (MCA) and basilar artery on CTA or TOF-MRA before treatment. Patients with and without LVO were randomly selected at a 1:1 ratio. The ANN model was developed using backpropagation algorithm, and 10-fold cross-validation was used to validate the model. The comparison of diagnostic parameters between the ANN model and previously established prehospital prediction scales were performed. Results: Finally, 300 LVO and 300 non-LVO patients were randomly selected for the training and validation of the ANN model. The mean Youden index, sensitivity, specificity and accuracy of the ANN model based on the 10-fold cross-validation analysis were 0.640, 0.807, 0.833 and 0.820, respectively. The area under the curve (AUC), Youden index and accuracy of the ANN model were all higher than other prehospital prediction scales. Conclusions: The ANN can be an effective tool for the recognition of LVO in the prehospital triage stage.
| S-EPMC6028566 | biostudies-literature
Project description:An mRNA transcript contains many potential antisense oligodeoxynucleotide target sites. Identification of the most efficacious targets remains an important and challenging problem. Building on separate work that revealed a strong correlation between the inclusion of short sequence motifs and the activity level of an oligo, we have developed a predictive artificial neural network system for mapping tetranucleotide motif content to antisense oligo activity. Trained for high-specificity prediction, the system has been cross-validated against a database of 348 oligos from the literature and a larger proprietary database of 908 oligos. In cross- validation tests the system identified effective oligos (i.e. oligos capable of reducing target mRNA expression to <25% that of the control) with 53% accuracy, in contrast to the <10% success rates commonly reported for trial-and-error oligo selection, suggesting a possible 5-fold reduction in the in vivo screening required to find an active oligo. We have implemented a web interface to a trained neural network. Given an RNA transcript as input, the system identifies the most likely oligo targets and provides estimates of the probabilities that oligos targeted against these sites will be effective.
| S-EPMC140555 | biostudies-literature
Project description:BACKGROUND:Accurate prediction of operative transfusions is essential for resource allocation and identifying patients at risk of postoperative adverse events. This research examines the efficacy of using artificial neural networks (ANNs) to predict transfusions for all inpatient operations. METHODS:Over 1.6 million surgical cases over a two year period from the NSQIP-PUF database are used. Data from 2014 (750937 records) are used for model development and data from 2015 (885502 records) are used for model validation. ANN and regression models are developed to predict perioperative transfusions for surgical patients. RESULTS:Various ANN models and logistic regression, using four variable sets, are compared. The best performing ANN models with respect to both sensitivity and area under the receiver operator characteristic curve outperformed all of the regression models (p < .001) and achieved a performance of 70-80% specificity with a corresponding 75-62% sensitivity. CONCLUSION:ANNs can predict >75% of the patients who will require transfusion and 70% of those who will not. Increasing specificity to 80% still enables a sensitivity of almost 67%. The unique contribution of this research is the utilization of a single ANN model to predict transfusions across a broad range of surgical procedures.
| S-EPMC7039514 | biostudies-literature
Project description:ObjectivesTo compare two statistical models, namely logistic regression and artificial neural network (ANN), in prediction of vestibular schwannoma (VS) recurrence.MethodsSeven hundred eighty-nine patients with VS diagnosis completed an online survey. Potential predictors for recurrence were derived from univariate analysis by reaching the cut off P value of .05. Those nine potential predictors were years since treatment, surgeon's specialty, resection amount, and having incomplete eye closure, dry eye, double vision, facial pain, seizure, and voice/swallowing problem as a complication following treatment. Multivariate binary logistic regression model was compared with a four-layer 9-5-10-1 feedforward backpropagation ANN for prediction of recurrence.ResultsThe overall recurrence rate was 14.5%. Significant predictors of recurrence in the regression model were years since treatment and resection amount (both P < .001). The regression model did not show an acceptable performance (area under the curve [AUC] = 0.64; P = .27). The regression model's sensitivity and specificity were 44% and 69%, respectively and correctly classified 56% of cases. The ANN showed a superior performance compared to the regression model (AUC = 0.79; P = .001) with higher sensitivity (61%) and specificity (81%), and correctly classified 70% of cases.ConclusionThe constructed ANN model was superior to logistic regression in predicting patient-answered VS recurrence in an anonymous survey with higher sensitivity and specificity. Since artificial intelligence tools such as neural networks can have higher predictive abilities compared to logistic regression models, continuous investigation into their utility as complementary clinical tools in predicting certain surgical outcomes is warranted.
| S-EPMC7178452 | biostudies-literature
Project description:This paper presents an approach to predicting the intrinsic self-healing in concrete using a hybrid genetic algorithm-artificial neural network (GA-ANN). A genetic algorithm was implemented in the network as a stochastic optimizing tool for the initial optimal weights and biases. This approach can assist the network in achieving a global optimum and avoid the possibility of the network getting trapped at local optima. The proposed model was trained and validated using an especially built database using various experimental studies retrieved from the open literature. The model inputs include the cement content, water-to-cement ratio (w/c), type and dosage of supplementary cementitious materials, bio-healing materials, and both expansive and crystalline additives. Self-healing indicated by means of crack width is the model output. The results showed that the proposed GA-ANN model is capable of capturing the complex effects of various self-healing agents (e.g., biochemical material, silica-based additive, expansive and crystalline components) on the self-healing performance in cement-based materials.
| S-EPMC5459209 | biostudies-other
Project description:This paper presents a novel approach to predicting self-calibration in a pressure sensor using a proposed Levenberg Marquardt Back Propagation Artificial Neural Network (LMBP-ANN) model. The self-calibration algorithm should be able to fix major problems in the pressure sensor such as hysteresis, variation in gain and lack of linearity with high accuracy. The traditional calibration process for this kind of sensor is a time-consuming task because it is usually done through manual and repetitive identification. Furthermore, a traditional computational method is inadequate for solving the problem since it is extremely difficult to resolve the mathematical formula among multiple confounding pressure variables. Accordingly, this paper describes a new self-calibration methodology for nonlinear pressure sensors based on an LMBP-ANN model. The proposed method was achieved using a collected dataset from pressure sensors in real time. The load cell will be used as a reference for measuring the applied force. The proposed method was validated by comparing the output pressure of the trained network with the experimental target pressure (reference). This paper also shows that the proposed model exhibited a remarkable performance than traditional methods with a max mean square error of 0.17325 and an R-value over 0.99 for the total response of training, testing and validation. To verify the proposed model's capability to build a self-calibration algorithm, the model was tested using an untrained input data set. As a result, the proposed LMBP-ANN model for self-calibration purposes is able to successfully predict the desired pressure over time, even the uncertain behaviour of the pressure sensors due to its material creep. This means that the proposed model overcomes the problems of hysteresis, variation in gain and lack of linearity over time. In return, this can be used to enhance the durability of the grasping mechanism, leading to a more robust and secure grasp for paralyzed hands. Furthermore, the exposed analysis approach in this paper can be a useful methodology for the user to evaluate the performance of any measurement system in a real-time environment.
| S-EPMC6111596 | biostudies-literature
Project description:Background and Purpose- Computed tomography perfusion (CTP) is a useful tool in the evaluation of acute ischemic stroke, where it can provide an estimate of the ischemic core and the ischemic penumbra. The optimal CTP parameters to identify the ischemic core remain undetermined. Methods- We used artificial neural networks (ANNs) to optimally predict the ischemic core in acute stroke patients, using diffusion-weighted imaging as the gold standard. We first designed an ANN based on CTP data alone and next designed an ANN based on clinical and CTP data. Results- The ANN based on CTP data predicted the ischemic core with a mean absolute error of 13.8 mL (SD, 13.6 mL) compared with diffusion-weighted imaging. The area under the receiver operator characteristic curve was 0.85. At the optimal threshold, the sensitivity for predicting the ischemic core was 0.90 and the specificity was 0.62. Combining CTP data with clinical data available at time of presentation resulted in the same mean absolute error (13.8 mL) but lower SD (12.4 mL). The area under the curve, sensitivity, and specificity were 0.87, 0.91, and 0.65, respectively. The maximal Dice coefficient was 0.48 in the ANN based on CTP data exclusively. Conclusions- An ANN that integrates clinical and CTP data predicts the ischemic core with accuracy.
| S-EPMC6538437 | biostudies-literature
Project description:BACKGROUND: Large amounts of data are being generated by high-throughput genome sequencing methods. But the rate of the experimental functional characterization falls far behind. To fill the gap between the number of sequences and their annotations, fast and accurate automated annotation methods are required. Many methods, such as GOblet, GOFigure, and Gotcha, are designed based on the BLAST search. Unfortunately, the sequence coverage of these methods is low as they cannot detect the remote homologues. Adding to this, the lack of annotation specificity advocates the need to improve automated protein function prediction. RESULTS: We designed a novel automated protein functional assignment method based on the neural response algorithm, which simulates the neuronal behavior of the visual cortex in the human brain. Firstly, we predict the most similar target protein for a given query protein and thereby assign its GO term to the query sequence. When assessed on test set, our method ranked the actual leaf GO term among the top 5 probable GO terms with accuracy of 86.93%. CONCLUSIONS: The proposed algorithm is the first instance of neural response algorithm being used in the biological domain. The use of HMM profiles along with the secondary structure information to define the neural response gives our method an edge over other available methods on annotation accuracy. Results of the 5-fold cross validation and the comparison with PFP and FFPred servers indicate the prominent performance by our method. The program, the dataset, and help files are available at http://www.jjwanglab.org/NRProF/.
| S-EPMC3403322 | biostudies-literature
Project description:Multiplex quantitative polymerase chain reaction (qPCR) has found an increasing range of applications. The construction of a reliable and dynamic mathematical model for multiplex qPCR that analyzes the effects of interactions between variables is therefore especially important. This work aimed to analyze the effects of interactions between variables through response surface method (RSM) for uni- and multiplex qPCR, and further optimize the parameters by constructing two mathematical models via RSM and back-propagation neural network-genetic algorithm (BPNN-GA) respectively. The statistical analysis showed that Mg2+ was the most important factor for both uni- and multiplex qPCR. Dynamic models of uni- and multiplex qPCR could be constructed using both RSM and BPNN-GA methods. But RSM was better than BPNN-GA on prediction performance in terms of the mean absolute error (MAE), the mean square error (MSE) and the Coefficient of Determination (R2). Ultimately, optimal parameters of uni- and multiplex qPCR were determined by RSM.
| S-EPMC6059488 | biostudies-literature