Identifying pre-outbreak signals of hand, foot and mouth disease based on landscape dynamic network marker

Complex network analysis techniques for the early detection of the outbreak of pandemics transmitted through air traffic

Air transport has been identified as one of the primary means whereby COVID-19 spread throughout Europe during the early stages of the pandemic. In this paper we analyse two categories of methods - dynamic network markers (DNMs) and network analysis-based methods - as potential early warning signals for detecting and anticipating COVID-19 outbreaks in Europe on the basis of accuracy regarding the daily confirmed cases. The analysis was carried out from 15 February 2020, around two weeks before the first COVID-19 cases appeared in Europe, and 1 May 2020, approximately two weeks after all the air traffic in Europe had been shut down. Daily European COVID-19 information sourced from the World Health Organization was used, whereas air traffic data from Flightradar24 has been incorporated into the analyses by means of four alternative adjacency matrices. Some DNMs have been discarded since they output multiple time series, which makes it very difficult to interpret their results. The only DNM outputting a single time series does not emulate the COVID-19 trend: it does not detect all the main peaks, which means that peak heights do not match up with the increase in the number of infected people. However, many combinations of network analysis based methods and adjacency matrices output good results (with high accuracy and 20-day advance forecasts), with only minor differences from one to another. The number of edges and the network density methods are slightly better when dynamic flight frequency information is used.

Research on hand, foot and mouth disease incidence forecasting using hybrid model in mainland China

BACKGROUND

This study aimed to construct a more accurate model to forecast the incidence of hand, foot, and mouth disease (HFMD) in mainland China from January 2008 to December 2019 and to provide a reference for the surveillance and early warning of HFMD.

METHODS

We collected data on the incidence of HFMD in mainland China between January 2008 and December 2019. The SARIMA, SARIMA-BPNN, and SARIMA-PSO-BPNN hybrid models were used to predict the incidence of HFMD. The prediction performance was compared using the mean absolute error(MAE), mean squared error(MSE), root mean square error (RMSE), mean absolute percentage error (MAPE), and correlation analysis.

RESULTS

The incidence of HFMD in mainland China from January 2008 to December 2019 showed fluctuating downward trends with clear seasonality and periodicity. The optimal SARIMA model was SARIMA(1,0,1)(2,1,2)_[12], with Akaike information criterion (AIC) and Bayesian Schwarz information criterion (BIC) values of this model were 638.72, 661.02, respectively. The optimal SARIMA-BPNN hybrid model was a 3-layer BPNN neural network with nodes of 1, 10, and 1 in the input, hidden, and output layers, and the R-squared, MAE, and RMSE values were 0.78, 3.30, and 4.15, respectively. For the optimal SARIMA-PSO-BPNN hybrid model, the number of particles is 10, the acceleration coefficients c1 and c2 are both 1, the inertia weight is 1, the probability of change is 0.95, and the values of R-squared, MAE, and RMSE are 0.86, 2.89, and 3.57, respectively.

CONCLUSIONS

Compared with the SARIMA and SARIMA-BPNN hybrid models, the SARIMA-PSO-BPNN model can effectively forecast the change in observed HFMD incidence, which can serve as a reference for the prevention and control of HFMD.

Explanation of hand, foot, and mouth disease cases in Japan using Google Trends before and during the COVID-19: infodemiology study

Background

Coronavirus Disease 2019 (COVID-19) pandemic affects common diseases, but its impact on hand, foot, and mouth disease (HFMD) is unclear. Google Trends data is beneficial for approximate real-time statistics and because of ease in access, is expected to be used for infection explanation from an information-seeking behavior perspective. We aimed to explain HFMD cases before and during COVID-19 using Google Trends.

Methods

HFMD cases were obtained from the National Institute of Infectious Diseases, and Google search data from 2009 to 2021 in Japan were downloaded from Google Trends. Pearson correlation coefficients were calculated between HFMD cases and the search topic “HFMD” from 2009 to 2021. Japanese tweets containing “HFMD” were retrieved to select search terms for further analysis. Search terms with counts larger than 1000 and belonging to ranges of infection sources, susceptible sites, susceptible populations, symptoms, treatment, preventive measures, and identified diseases were retained. Cross-correlation analyses were conducted to detect lag changes between HFMD cases and search terms before and during the COVID-19 pandemic. Multiple linear regressions with backward elimination processing were used to identify the most significant terms for HFMD explanation.

Results

HFMD cases and Google search volume peaked around July in most years, excluding 2020 and 2021. The search topic “HFMD” presented strong correlations with HFMD cases, except in 2020 when the COVID-19 outbreak occurred. In addition, the differences in lags for 73 (72.3%) search terms were negative, which might indicate increasing public awareness of HFMD infections during the COVID-19 pandemic. The results of multiple linear regression demonstrated that significant search terms contained the same meanings but expanded informative search content during the COVID-19 pandemic.

Conclusions

The significant terms for the explanation of HFMD cases before and during COVID-19 were different. Awareness of HFMD infections in Japan may have improved during the COVID-19 pandemic. Continuous monitoring is important to promote public health and prevent resurgence. The public interest reflected in information-seeking behavior can be helpful for public health surveillance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07790-9.

Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer

Finding personalized biomarkers for disease prediction of patients with cancer remains a massive challenge in precision medicine. Most methods focus on one subnetwork or module as a network biomarker; however, this ignores the early warning capabilities of other modules with different configurations of biomarkers (i.e. multi-modal personalized biomarkers). Identifying such modules would not only predict disease but also provide effective therapeutic drug target information for individual patients. To solve this problem, we developed a novel model (denoted multi-modal personalized dynamic network biomarkers (MMPDNB)) based on a multi-modal optimization mechanism and personalized dynamic network biomarker (PDNB) theory, which can provide multiple modules of personalized biomarkers and unveil their multi-modal properties. Using the genomics data of patients with breast or lung cancer from The Cancer Genome Atlas database, we validated the effectiveness of the MMPDNB model. The experimental results showed that compared with other advanced methods, MMPDNB can more effectively predict the critical state with the highest early warning signal score during cancer development. Furthermore, MMPDNB more significantly identified PDNBs containing driver and biomarker genes specific to cancer tissues. More importantly, we validated the biological significance of multi-modal PDNBs, which could provide effective drug targets of individual patients as well as markers for predicting early warning signals of the critical disease state. In conclusion, multi-modal optimization is an effective method to identify PDNBs and offers a new perspective for understanding tumor heterogeneity in cancer precision medicine.

Network Control Models With Personalized Genomics Data for Understanding Tumor Heterogeneity in Cancer

Due to rapid development of high-throughput sequencing and biotechnology, it has brought new opportunities and challenges in developing efficient computational methods for exploring personalized genomics data of cancer patients. Because of the high-dimension and small sample size characteristics of these personalized genomics data, it is difficult for excavating effective information by using traditional statistical methods. In the past few years, network control methods have been proposed to solve networked system with high-dimension and small sample size. Researchers have made progress in the design and optimization of network control principles. However, there are few studies comprehensively surveying network control methods to analyze the biomolecular network data of individual patients. To address this problem, here we comprehensively surveyed complex network control methods on personalized omics data for understanding tumor heterogeneity in precision medicine of individual patients with cancer.