A new gene regulatory network model based on BP algorithm for interrogating differentially expressed genes of Sea Urchin

scBPGRN: Integrating single-cell multi-omics data to construct gene regulatory networks based on BP neural network

The deterioration and metastasis of cancer involve various aspects of genomic changes, including genomic DNA changes, epigenetic modifications, gene expression, and other complex interactions. Therefore, integrating single-cell multi-omics data to construct gene regulatory networks containing more omics information is of great significance for understanding the pathogenesis of cancer. In this article, an algorithm integrating single-cell RNA sequencing data and DNA methylation data to construct a gene regulatory network based on the back-propagation (BP) neural network (scBPGRN) is proposed. This algorithm uses biweight extreme correlation coefficients to measure the correlation between factors and uses neural networks to calculate generalized weights to construct gene regulation networks. Finally, the node strength is calculated to identify the genes associated with cancer. We apply the scBPGRN algorithm to hepatocellular carcinoma (HCC) data. We construct a regulatory network and identify top-ranked genes, such as MYCBP, KLHL35, PRKCZ, and SERPINA6, as the key HCC-related genes. We analyze the top 100 genes, and the HCC-related genes are concentrated in the top 20. In addition, the single cell data is found to consist of two subpopulations. We also apply scBPGRN to two subpopulations. We analyze the top 50 genes in them, and the HCC-related genes are concentrated in the top 20. The consequences of functional enrichment analysis indicate that the gene regulatory network we have constructed is valid. Our results have been verified in several pieces of literature. This study provides a reference for the integration of single-cell multi-omics data to construct gene regulatory networks.

Different Data Mining Approaches Based Medical Text Data

The amount of medical text data is increasing dramatically. Medical text data record the progress of medicine and imply a large amount of medical knowledge. As a natural language, they are characterized by semistructured, high-dimensional, high data volume semantics and cannot participate in arithmetic operations. Therefore, how to extract useful knowledge or information from the total available data is very important task. Using various techniques of data mining can extract valuable knowledge or information from data. In the current study, we reviewed different approaches to apply for medical text data mining. The advantages and shortcomings for each technique compared to different processes of medical text data were analyzed. We also explored the applications of algorithms for providing insights to the users and enabling them to use the resources for the specific challenges in medical text data. Further, the main challenges in medical text data mining were discussed. Findings of this paper are benefit for helping the researchers to choose the reasonable techniques for mining medical text data and presenting the main challenges to them in medical text data mining.

Prediction of Mumps Incidence Trend in China Based on Difference Grey Model and Artificial Neural Network Learning

Background:

We aimed to compare the prediction efficiency of back propagation (BP) network and grey model (GM) (1.1) for mumps infectious diseases and compare the application effect of the two models.

Methods:

By calculating the average incidence rate of mumps in January 2014 –2016, we conducted the modeling of the BP time series, GM (1,1) grey model and the combination models of them, and predicted the incidence rate in June 2016 in comparison with the actual one. We compared the quarterly incidence rate to test the two prediction models, and compared the advantages and disadvantages of these models.

Results:

R value of BP model was 68.45%, for GM (1,1) was 58.49%, and for combined forecasting model was 86.95%. We used the principal component analysis clustering method to control the samples, and found that the samples were close to the population mean. We found that the GM (1.1) model was more suitable for the prediction of mumps infection mode. We carried out dimension reduction analysis on the model data, and the accuracy of the data after dimension reduction is within the range of Da. For the discrete degree of the data in the combined model, matlab pipeline was used to verify the reliability of the data and results. By calculation after manifold optimization small error probability was P=0.875 and semi mean relative error 2.43%.

Conclusion:

BP, GM (1,1) is a better method for modeling the epidemic trend of mumps in China, but the efficiency of prediction is not as high as the combination of them.

A novel model-based on FCM-LM algorithm for prediction of protein folding rate

The prediction of protein folding rates is of paramount importance in describing the protein folding mechanism, which has broad applications in fields such as enzyme engineering and protein engineering. Therefore, predicting protein folding rates using the first-order of protein sequence, secondary structure and amino acid properties has become a very active research topic in recent years. This paper presents a new fuzzy cognitive map (FCM) model based on deep learning neural networks which uses data obtained from biological experiments to predict the protein folding rate. FCM extracts the important data features from the protein sequence which then initializes the deep neural networks effectively. It was found that the Levenberg-Marquardt (LM) algorithm for deep neural networks can improve the prediction accuracy of the protein folding rates. The correlation coefficient between the predicted values and those real values obtained from experiments reached 0.94 and 0.9 in two independent numerical tests.