An open challenge to advance probabilistic forecasting for dengue epidemics.

A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project-integration with public health needs, a common forecasting framework, shared and standardized data, and open participation-can help advance infectious disease forecasting beyond dengue.

Predicting influenza with dynamical methods.

BACKGROUND: Prediction of influenza weeks in advance can be a useful tool in the management of cases and in the early recognition of pandemic influenza seasons. METHODS: This study explores the prediction of influenza-like-illness incidence using both epidemiological and climate data. It uses Lorenz's well-known Method of Analogues, but with two novel improvements. Firstly, it determines internal parameters using the implicit near-neighbor distances in the data, and secondly, it employs climate data (mean dew point) to screen analogue near-neighbors and capture the hidden dynamics of disease spread. RESULTS: These improvements result in the ability to forecast, four weeks in advance, the total number of cases and the incidence at the peak with increased accuracy. In most locations the total number of cases per year and the incidence at the peak are forecast with less than 15 % root-mean-square (RMS) Error, and in some locations with less than 10 % RMS Error. CONCLUSIONS: The use of additional variables that contribute to the dynamics of influenza spread can greatly improve prediction accuracy.

Fuzzy association rule mining and classification for the prediction of malaria in South Korea.

BACKGROUND: Malaria is the world's most prevalent vector-borne disease. Accurate prediction of malaria outbreaks may lead to public health interventions that mitigate disease morbidity and mortality. METHODS: We describe an application of a method for creating prediction models utilizing Fuzzy Association Rule Mining to extract relationships between epidemiological, meteorological, climatic, and socio-economic data from Korea. These relationships are in the form of rules, from which the best set of rules is automatically chosen and forms a classifier. Two classifiers have been built and their results fused to become a malaria prediction model. Future malaria cases are predicted as Low, Medium or High, where these classes are defined as a total of 0-2, 3-16, and above 17 cases, respectively, for a region in South Korea during a two-week period. Based on user recommendations, HIGH is considered an outbreak. RESULTS: Model accuracy is described by Positive Predictive Value (PPV), Sensitivity, and F-score for each class, computed on test data not previously used to develop the model. For predictions made 7-8 weeks in advance, model PPV and Sensitivity are 0.842 and 0.681, respectively, for the HIGH classes. The F0.5 and F3 scores (which combine PPV and Sensitivity) are 0.804 and 0.694, respectively, for the HIGH classes. The overall FARM results (as measured by F-scores) are significantly better than those obtained by Decision Tree, Random Forest, Support Vector Machine, and Holt-Winters methods for the HIGH class. For the Medium class, Random Forest and FARM obtain comparable results, with FARM being better at F0.5, and Random Forest obtaining a higher F3. CONCLUSIONS: A previously described method for creating disease prediction models has been modified and extended to build models for predicting malaria. In addition, some new input variables were used, including indicators of intervention measures. The South Korea malaria prediction models predict Low, Medium or High cases 7-8 weeks in the future. This paper demonstrates that our data driven approach can be used for the prediction of different diseases.

Biological Subtypes of Breast Cancer and Sentinel Lymph Node Biopsy.

OBJECTIVE: Breast cancer subtypes are used as prognostic and predictive factors considering the genomic profile of the disease. This study is designed to investigate the Sentinel Lymph Node (SLN) detection rate in breast cancer for different biological characteristics. MATERIAL AND METHODS: Patients on whom we performed the methylene blue method alone were named as Group I, radiocolloid substance method alone as Group II and both methylene blue and radiocolloid method as Group III. The results of biological tumor characteristics and characteristics of the patients on different SLN biopsy techniques were investigated. RESULTS: The overall SLN detecting success rate was 83.3%. When considered for each group, success rate was 80% for group I, 84.9% for group II and 90.6% for group III. While a success rate of 94.6% was achieved with radiocolloid only in the patients in Luminal A and B subgroup, 90% success rate was achieved in Her2 (+) and triple negative (TN) patients with combined method. CONCLUSION: While successful results could be achieved by using radiocolloid substances alone in patients with Luminal A and B subtypes, combined methods should be used in HER2 (+) and TN patients.

Completion Thyroidectomy: Safer than Thought.

BACKGROUND: The aim of this study was to find out whether a substantial difference in terms of complication rates exists between primary and completion thyroidectomies following initial bilateral subtotal thyroidectomy in the light of current literature and our series. PATIENTS AND METHODS: Total number of 696 patients who received completion thyroidectomy (Group 1, n = 289) and total thyroidectomy for differentiated thyroid cancer (Group 2, n = 407) and their data were reviewed and postoperative complications were compared between the groups and with the literature. RESULTS: Transient and permanent hypocalcaemia rates were 20% and 5.8% in Group 1 and 10.5% and 5.1% for Group 2 respectively. Unilateral transient, bilateral transient and unilateral permanent recurrent laryngeal nerve palsy rates were 6.2%, 1.3% and 4.4% for patients in Group 1 whereas same complications were seen in 4.6%, 0.7% and 3.6% of patients in Group 2. When groups were compared for complications; temporary hypocalcaemia, unilateral temporary nerve palsy, and minor wound infection rates were statistically higher in Group 1, with no significant difference in permanent complications. CONCLUSION: When complication rates of re-operation after bilateral subtotal thyroidectomy and primary total thyroidectomy for differentiated thyroid cancer were compared in an unbiased fashion, completion thyroidectomy was shown to be as safe as a primary operation with regard to permanent complications.

Ensemble method for dengue prediction.

BACKGROUND: In the 2015 NOAA Dengue Challenge, participants made three dengue target predictions for two locations (Iquitos, Peru, and San Juan, Puerto Rico) during four dengue seasons: 1) peak height (i.e., maximum weekly number of cases during a transmission season; 2) peak week (i.e., week in which the maximum weekly number of cases occurred); and 3) total number of cases reported during a transmission season. A dengue transmission season is the 12-month period commencing with the location-specific, historical week with the lowest number of cases. At the beginning of the Dengue Challenge, participants were provided with the same input data for developing the models, with the prediction testing data provided at a later date. METHODS: Our approach used ensemble models created by combining three disparate types of component models: 1) two-dimensional Method of Analogues models incorporating both dengue and climate data; 2) additive seasonal Holt-Winters models with and without wavelet smoothing; and 3) simple historical models. Of the individual component models created, those with the best performance on the prior four years of data were incorporated into the ensemble models. There were separate ensembles for predicting each of the three targets at each of the two locations. PRINCIPAL FINDINGS: Our ensemble models scored higher for peak height and total dengue case counts reported in a transmission season for Iquitos than all other models submitted to the Dengue Challenge. However, the ensemble models did not do nearly as well when predicting the peak week. CONCLUSIONS: The Dengue Challenge organizers scored the dengue predictions of the Challenge participant groups. Our ensemble approach was the best in predicting the total number of dengue cases reported for transmission season and peak height for Iquitos, Peru.

Prediction of Peaks of Seasonal Influenza in Military Health-Care Data.

Influenza is a highly contagious disease that causes seasonal epidemics with significant morbidity and mortality. The ability to predict influenza peak several weeks in advance would allow for timely preventive public health planning and interventions to be used to mitigate these outbreaks. Because influenza may also impact the operational readiness of active duty personnel, the US military places a high priority on surveillance and preparedness for seasonal outbreaks. A method for creating models for predicting peak influenza visits per total health-care visits (ie, activity) weeks in advance has been developed using advanced data mining techniques on disparate epidemiological and environmental data. The model results are presented and compared with those of other popular data mining classifiers. By rigorously testing the model on data not used in its development, it is shown that this technique can predict the week of highest influenza activity for a specific region with overall better accuracy than other methods examined in this article.

Prediction of high incidence of dengue in the Philippines.

BACKGROUND: Accurate prediction of dengue incidence levels weeks in advance of an outbreak may reduce the morbidity and mortality associated with this neglected disease. Therefore, models were developed to predict high and low dengue incidence in order to provide timely forewarnings in the Philippines. METHODS: Model inputs were chosen based on studies indicating variables that may impact dengue incidence. The method first uses Fuzzy Association Rule Mining techniques to extract association rules from these historical epidemiological, environmental, and socio-economic data, as well as climate data indicating future weather patterns. Selection criteria were used to choose a subset of these rules for a classifier, thereby generating a Prediction Model. The models predicted high or low incidence of dengue in a Philippines province four weeks in advance. The threshold between high and low was determined relative to historical incidence data. PRINCIPAL FINDINGS: Model accuracy is described by Positive Predictive Value (PPV), Negative Predictive Value (NPV), Sensitivity, and Specificity computed on test data not previously used to develop the model. Selecting a model using the F0.5 measure, which gives PPV more importance than Sensitivity, gave these results: PPV = 0.780, NPV = 0.938, Sensitivity = 0.547, Specificity = 0.978. Using the F3 measure, which gives Sensitivity more importance than PPV, the selected model had PPV = 0.778, NPV = 0.948, Sensitivity = 0.627, Specificity = 0.974. The decision as to which model has greater utility depends on how the predictions will be used in a particular situation. CONCLUSIONS: This method builds prediction models for future dengue incidence in the Philippines and is capable of being modified for use in different situations; for diseases other than dengue; and for regions beyond the Philippines. The Philippines dengue prediction models predicted high or low incidence of dengue four weeks in advance of an outbreak with high accuracy, as measured by PPV, NPV, Sensitivity, and Specificity.