Global nonlinear kernel prediction for large data set with a particle swarm-optimized interval support vector regression

Multi-kernel support vector regression with improved moth-flame optimization algorithm for software effort estimation

In this paper, a novel Moth-Flame Optimization (MFO) algorithm, namely MFO algorithm enhanced by Multiple Improvement Strategies (MISMFO) is proposed for solving parameter optimization in Multi-Kernel Support Vector Regressor (MKSVR), and the MISMFO-MKSVR model is further employed to deal with the software effort estimation problems. In MISMFO, the logistic chaotic mapping is applied to increase initial population diversity, while the mutation and flame number phased reduction mechanisms are carried out to improve the search efficiency, as well the adaptive weight adjustment mechanism is used to accelerate convergence and balance exploration and exploitation. The MISMFO model is verified on fifteen benchmark functions and CEC 2020 test set. The results show that the MISMFO has advantages over other meta-heuristic algorithms and MFO variants in terms of convergence speed and accuracy. Additionally, the MISMFO-MKSVR model is tested by simulations on five software effort datasets and the results demonstrate that the proposed model has better performance in software effort estimation problem. The Matlab code of MISMFO can be found at https://github.com/loadstar1997/MISMFO .

DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data

Single-cell mass cytometry, also known as cytometry by time of flight (CyTOF) is a powerful high-throughput technology that allows analysis of up to 50 protein markers per cell for the quantification and classification of single cells. Traditional manual gating utilized to identify new cell populations has been inadequate, inefficient, unreliable, and difficult to use, and no algorithms to identify both calibration and new cell populations has been well established. A deep learning with graphic cluster (DGCyTOF) visualization is developed as a new integrated embedding visualization approach in identifying canonical and new cell types. The DGCyTOF combines deep-learning classification and hierarchical stable-clustering methods to sequentially build a tri-layer construct for known cell types and the identification of new cell types. First, deep classification learning is constructed to distinguish calibration cell populations from all cells by softmax classification assignment under a probability threshold, and graph embedding clustering is then used to identify new cell populations sequentially. In the middle of two-layer, cell labels are automatically adjusted between new and unknown cell populations via a feedback loop using an iteration calibration system to reduce the rate of error in the identification of cell types, and a 3-dimensional (3D) visualization platform is finally developed to display the cell clusters with all cell-population types annotated. Utilizing two benchmark CyTOF databases comprising up to 43 million cells, we compared accuracy and speed in the identification of cell types among DGCyTOF, DeepCyTOF, and other technologies including dimension reduction with clustering, including Principal Component Analysis (PCA), Factor Analysis (FA), Independent Component Analysis (ICA), Isometric Feature Mapping (Isomap), t-distributed Stochastic Neighbor Embedding (t-SNE), and Uniform Manifold Approximation and Projection (UMAP) with k-means clustering and Gaussian mixture clustering. We observed the DGCyTOF represents a robust complete learning system with high accuracy, speed and visualization by eight measurement criteria. The DGCyTOF displayed F-scores of 0.9921 for CyTOF1 and 0.9992 for CyTOF2 datasets, whereas those scores were only 0.507 and 0.529 for the t-SNE+k-means; 0.565 and 0.59, for UMAP+ k-means. Comparison of DGCyTOF with t-SNE and UMAP visualization in accuracy demonstrated its approximately 35% superiority in predicting cell types. In addition, observation of cell-population distribution was more intuitive in the 3D visualization in DGCyTOF than t-SNE and UMAP visualization. The DGCyTOF model can automatically assign known labels to single cells with high accuracy using deep-learning classification assembling with traditional graph-clustering and dimension-reduction strategies. Guided by a calibration system, the model seeks optimal accuracy balance among calibration cell populations and unknown cell types, yielding a complete and robust learning system that is highly accurate in the identification of cell populations compared to results using other methods in the analysis of single-cell CyTOF data. Application of the DGCyTOF method to identify cell populations could be extended to the analysis of single-cell RNASeq data and other omics data.

kESVR: An Ensemble Model for Drug Response Prediction in Precision Medicine Using Cancer Cell Lines Gene Expression

Background: Cancer cell lines are frequently used in research as in-vitro tumor models. Genomic data and large-scale drug screening have accelerated the right drug selection for cancer patients. Accuracy in drug response prediction is crucial for success. Due to data-type diversity and big data volume, few methods can integrative and efficiently find the principal low-dimensional manifold of the high-dimensional cancer multi-omics data to predict drug response in precision medicine. Method: A novelty k-means Ensemble Support Vector Regression (kESVR) is developed to predict each drug response values for single patient based on cell-line gene expression data. The kESVR is a blend of supervised and unsupervised learning methods and is entirely data driven. It utilizes embedded clustering (Principal Component Analysis and k-means clustering) and local regression (Support Vector Regression) to predict drug response and obtain the global pattern while overcoming missing data and outliers’ noise. Results: We compared the efficiency and accuracy of kESVR to 4 standard machine learning regression models: (1) simple linear regression, (2) support vector regression (3) random forest (quantile regression forest) and (4) back propagation neural network. Our results, which based on drug response across 610 cancer cells from Cancer Cell Line Encyclopedia (CCLE) and Cancer Therapeutics Response Portal (CTRP v2), proved to have the highest accuracy (smallest mean squared error (MSE) measure). We next compared kESVR with existing 17 drug response prediction models based a varied range of methods such as regression, Bayesian inference, matrix factorization and deep learning. After ranking the 18 models based on their accuracy of prediction, kESVR ranks first (best performing) in majority (74%) of the time. As for the remaining (26%) cases, kESVR still ranked in the top five performing models. Conclusion: In this paper we introduce a novel model (kESVR) for drug response prediction using high dimensional cell-line gene expression data. This model outperforms current existing prediction models in terms of prediction accuracy and speed and overcomes overfitting. This can be used in future to develop a robust drug response prediction system for cancer patients using the cancer cell-lines guidance and multi-omics data.

A Virtual Sensor for Electric Vehicles’ State of Charge Estimation

The estimation of the state of charge is a critical function in the operation of electric vehicles. The battery management system must provide accurate information about the battery state, even in the presence of failures in the vehicle sensors. This article presents a new methodology for the state of charge estimation (SOC) in electric vehicles without the use of a battery current sensor, relying on a virtual sensor, based on other available vehicle measurements, such as speed, battery voltage and acceleration pedal position. The estimator was derived from experimental data, employing support vector regression (SVR), principal component analysis (PCA) and a dual polarization (DP) battery model (BM). It is shown that the obtained model is able to predict the state of charge of the battery with acceptable precision in the case of a failure of the current sensor.

On Selecting Effective Patterns for Fast Support Vector Regression Training

It is time consuming to train support vector regression (SVR) for large-scale problems even with efficient quadratic programming solvers. This issue is particularly serious when tuning the model's parameters. One way to address the issue is to reduce the problem's scale by selecting a subset of the training set. This paper presents a fast pattern selection method by scanning the training data set to reduce a problem's scale. In particular, we find the k-nearest neighbors (kNNs) in a local region around each pattern's target value, and then determine to retain the pattern according to the distribution of its nearest neighbors. There is a high probability that the pattern locates outside the -tube. Since the kNNs of a pattern are found in a very small region, it is fast to scan the whole training data set. The proposed method deals with the year prediction Million Song Data set, which contains 463 715 patterns, within 10 s on a personal computer with an Intel Core i5-4690 CPU at 3.50 GHz and 8GB DRAM. An additional advantage of the proposed method is that it can predefine the size of the selected subset according to the training set. Comprehensive empirical evaluations demonstrate that the proposed method can significantly eliminate redundant patterns for SVR training with only a slight decrease in performance.