Due to the minimum free energy model, it is very important to predict the RNA secondary structure accurately and efficiently from the suboptimal foldings. Using clustering techniques in analyzing the suboptimal structures could effectively improve the prediction accuracy. An improved k-medoids cluster method is proposed to make this a better accuracy with the RBP score and the incremental candidate set of medoids matrix in this paper. The algorithm optimizes initial medoids through an expanding medoids candidate sets gradually.The predicted results indicated this algorithm could get a higher value of CH and significantly shorten the time for calculating clustering RNA folding structures.
The use of echocardiography ventricle segmentation can obtain ventricular volume parameters, and it is helpful to evaluate cardiac function. However, the ultrasound images have the characteristics of high noise and difficulty in segmentation, bringing huge workload to segment the object region manually. Meanwhile, the automatic segmentation technology cannot guarantee the segmentation accuracy. In order to solve this problem, a novel algorithm framework is proposed to segment the ventricle. Firstly, faster region-based convolutional neural network is used to locate the object to get the region of interest. Secondly, K-means is used to pre-segment the image; then a mean shift with adaptive bandwidth of kernel function is proposed to segment the region of interest. Finally, the region growing algorithm is used to get the object region. By this framework, ventricle is obtained automatically without manual localization. Experiments prove that this framework can segment the object accurately, and the algorithm of adaptive mean shift is more stable and accurate than the mean shift with fixed bandwidth on quantitative evaluation. These results show that the method in this paper is helpful for automatic segmentation of left ventricle in echocardiography.
Sleep stage scoring is a hotspot in the field of medicine and neuroscience. Visual inspection of sleep is laborious and the results may be subjective to different clinicians. Automatic sleep stage classification algorithm can be used to reduce the manual workload. However, there are still limitations when it encounters complicated and changeable clinical cases. The purpose of this paper is to develop an automatic sleep staging algorithm based on the characteristics of actual sleep data. In the proposed improved K-means clustering algorithm, points were selected as the initial centers by using a concept of density to avoid the randomness of the original K-means algorithm. Meanwhile, the cluster centers were updated according to the 'Three-Sigma Rule' during the iteration to abate the influence of the outliers. The proposed method was tested and analyzed on the overnight sleep data of the healthy persons and patients with sleep disorders after continuous positive airway pressure (CPAP) treatment. The automatic sleep stage classification results were compared with the visual inspection by qualified clinicians and the averaged accuracy reached 76%. With the analysis of morphological diversity of sleep data, it was proved that the proposed improved K-means algorithm was feasible and valid for clinical practice.
Accurate segmentation of pulmonary nodules is an important basis for doctors to determine lung cancer. Aiming at the problem of incorrect segmentation of pulmonary nodules, especially the problem that it is difficult to separate adhesive pulmonary nodules connected with chest wall or blood vessels, an improved random walk method is proposed to segment difficult pulmonary nodules accurately in this paper. The innovation of this paper is to introduce geodesic distance to redefine the weights in random walk combining the coordinates of the nodes and seed points in the image with the space distance. The improved algorithm is used to achieve the accurate segmentation of pulmonary nodules. The computed tomography (CT) images of 17 patients with different types of pulmonary nodules were selected for segmentation experiments. The experimental results are compared with the traditional random walk method and those of several literatures. Experiments show that the proposed method has good accuracy in the segmentation of pulmonary nodule, and the accuracy can reach more than 88% with segmentation time is less than 4 seconds. The results could be used to assist doctors in the diagnosis of benign and malignant pulmonary nodules and improve clinical efficiency.
The deoxyribonucleic acid (DNA) molecule damage simulations with an atom level geometric model use the traversal algorithm that has the disadvantages of quite time-consuming, slow convergence and high-performance computer requirement. Therefore, this work presents a density-based spatial clustering of applications with noise (DBSCAN) clustering algorithm based on the spatial distributions of energy depositions and hydroxyl radicals (·OH). The algorithm with probability and statistics can quickly get the DNA strand break yields and help to study the variation pattern of the clustered DNA damage. Firstly, we simulated the transportation of protons and secondary particles through the nucleus, as well as the ionization and excitation of water molecules by using Geant4-DNA that is the Monte Carlo simulation toolkit for radiobiology, and got the distributions of energy depositions and hydroxyl radicals. Then we used the damage probability functions to get the spatial distribution dataset of DNA damage points in a simplified geometric model. The DBSCAN clustering algorithm based on damage points density was used to determine the single-strand break (SSB) yield and double-strand break (DSB) yield. Finally, we analyzed the DNA strand break yield variation trend with particle linear energy transfer (LET) and summarized the variation pattern of damage clusters. The simulation results show that the new algorithm has a faster simulation speed than the traversal algorithm and a good precision result. The simulation results have consistency when compared to other experiments and simulations. This work achieves more precise information on clustered DNA damage induced by proton radiation at the molecular level with high speed, so that it provides an essential and powerful research method for the study of radiation biological damage mechanism.
Our team proposed and constructed an Expert-knowledge and Data-driven Comprehensive Evaluation Model of Chinese Patent Medicine (EDCEM-CPM) using the machine learning algorithm. This model could improve the system of the comprehensive evaluation of the Chinese patent medicine in technology and provide measurement tools for Chinese patent medicine according to its characteristics. The model evaluates the multi-dimensional value of Chinese patent medicine by data pre-treatment, clustering algorithms, and data training steps, such as automatic learning weighting. This evaluation model is already in practice. In this paper, we introduced the establishment of the model with the calculation process for reference.
ObjectiveTo predict the total hospitalization expenses of bronchopneumonia inpatients in a tertiay hospital of Sichuan Province through BP neural network and support vector machine models, and analyze the influencing factors.MethodsThe home page information of 749 cases of bronchopneumonia discharged from a tertiay hospital of Sichuan Province in 2017 was collected and compiled. The BP neural network model and the support vector machine model were simulated by SPSS 20.0 and Clementine softwares respectively to predict the total hospitalization expenses and analyze the influencing factors.ResultsThe accuracy rate of the BP neural network model in predicting the total hospitalization expenses was 81.2%, and the top three influencing factors and their importances were length of hospital stay (0.477), age (0.154), and discharge department (0.083). The accuracy rate of the support vector machine model in predicting the total hospitalization expenses was 93.4%, and the top three influencing factors and their importances were length of hospital stay (0.215), age (0.196), and marital status (0.172), but after stratified analysis by Mantel-Haenszel method, the correlation between marital status and total hospitalization expenses was not statistically significant (χ2=0.137, P=0.711).ConclusionsThe BP neural network model and the support vector machine model can be applied to predicting the total hospitalization expenses and analyzing the influencing factors of patients with bronchopneumonia. In this study, the prediction effect of the support vector machine is better than that of the BP neural network model. Length of hospital stay is an important influencing factor of total hospitalization expenses of bronchopneumonia patients, so shortening the length of hospital stay can significantly lighten the economic burden of these patients.
The traditional method of multi-parameter flow data clustering in flow cytometry is to mainly use professional software to manually set the door and circle out the target cells for analysis. The analysis process is complex and professional. Based on this, a clustering algorithm, which is based on t-distributed stochastic neighbor embedding (t-SNE) algorithm for multi-parameter stream data, is proposed in the paper. In this algorithm, the Euclidean distance of sample data in high dimensional space is transformed into conditional probability to represent similarity, and the data is reduced to low dimensional space. In this paper, the stained human peripheral blood cells were treated by flow cytometry, and the processed data were derived as experimental sample data. Thet-SNE algorithm is compared with the kernel principal component analysis (KPCA) dimensionality reduction algorithm, and the main component data obtained by the dimensionality reduction are classified using K-means algorithm. The results show that thet-SNE algorithm has a good clustering effect on the cell population with asymmetric and trailing distribution, and the clustering accuracy can reach 92.55%, which may be helpful for automatic analysis of multi-color multi-parameter flow data.
Objective To classify the nursing needs of patients undergoing ophthalmic day surgery, to understand the characteristics and needs of different patient groups, and propose specific nursing strategies to further improve the nursing quality of the ophthalmic day wards. Methods A retrospective review was conducted on all archived electronic medical records of patients in the Ophthalmology Day Ward of Beijing Tongren Hospital affiliated to the Capital Medical University from January to September 2023. Statistical description and cluster analysis were used to analyze and cluster all data. Results A total of 52049 patients were included, with an average age of (57.11±19.61) years. The number of nursing items required was 0 for 3104 patients (5.96%), 1 for 9158 patients (17.59%), 2 for 25428 patients (48.85%), 3 for 8812 patients (16.93%), 4 for 5442 patients (10.46%), and 5-11 for 105 patients (0.20%). The number of patients’ comorbidities was 0 for 38653 patients (74.26%), 1 for 10896 patients (20.93%), 2 for 2449 patients (4.71%), and 3-11 for 51 patients (0.10%). Using the number of comorbidities, total required nursing care items, and age as clustering variables, the 52049 patients were divided into 3 groups: low nursing demand group with 11817 patients (22.70%), medium nursing demand group with 24466 patients (47.01%), and high nursing demand group with 15766 patients (30.29%). The results showed that both patient age and the number of comorbidities were closely related to the number of nursing care items needed. Conclusion Classifying and analyzing the nursing needs of patients undergoing ophthalmic day surgery can help understand the needs of different categories of patients, improve nursing strategies specifically, provide support for further improving the accuracy and quality of ophthalmic day care services, and provide reference for clinical nursing work.
The rapid development of high-throughput chromatin conformation capture (Hi-C) technology provides rich genomic interaction data between chromosomal loci for chromatin structure analysis. However, existing methods for identifying topologically associated domains (TADs) based on Hi-C data suffer from low accuracy and sensitivity to parameters. In this context, a TAD identification method based on spatial density clustering was designed and implemented in this paper. The method preprocessed the raw Hi-C data to obtain normalized Hi-C contact matrix data. Then, it computed the distance matrix between loci, generated a reachability graph based on the core distance and reachability distance of loci, and extracted clustering clusters. Finally, it extracted TAD boundaries based on clustering results. This method could identify TAD structures with higher coherence, and TAD boundaries were enriched with more ChIP-seq factors. Experimental results demonstrate that our method has advantages such as higher accuracy and practical significance in TAD identification.
