Spatio Temporal forecasting of

Dengue Outbreaks using Machine

Learning
Preliminary Findings - Lasantha Fernando

Problem Statement and Motivation

Dengue is a mosquito vector borne viral disease and a major health concern
Predicting dengue outbreaks before it occurs can help to take preventive
measures and direct available resources more efficiently
Current research into predicting dengue outbreaks use

Statistical models
Neural Networks
Support Vector machines
Agent based modeling
Other computational methods

Limited research that incorporates human mobility

These studies did not address both spatial and temporal dimensions
Some studies do not give quantitative results

Parameters affecting Spread of Dengue

Temperature
Humidity
Rainfall
Land cover/vegetation
Human population size
Vector population size
Human mobility
Immunology of the population
Urban vs Rural

Statistical Models

Meta population model described in [1]

takes Ordinary Differential Equation to
model the population dynamics of vectors
and hosts
Ento-epidemiological model is used and
combined with human mobility data [2]
Most of them consider a SEIR-SEI model or
a similar derivative for Human-Vector
population dynamics [3-5]

Image Source: [5] M. K. Enduri and S. Jolad, Spatial Patterns of Spread of Dengue with Human and Vector Mobility, pp. 13, 2014.

Least Squares - Support Vector Machines

Study done in Malaysia for predicting dengue outbreaks for 5 provinces [6]
Has temporal aspects, not spatial aspects of prediction
LS-SVM has a better generalization

Input parameters for the model

Empirical risk minimization vs Structural risk minimization

Dengue fever cases
Neighbourhood dengue cases
Total rainfall

Decimal point normalization was used

LS-SVM - MSE - 0.00632, Accuracy - 86.84
LS-SVM trained faster than NN (0.13694 s vs 452.94 s)

Neural Networks

In the study done for 5 provinces of Malaysia [6] that used LS-SVM, neural
networks also used for comparison. It had less accuracy (MSE - 0.0331,
Accuracy - 65.58)
Predicting using 2 years worth of data in Singapore and training using NN has
good results [6]

3 parameters (temperature, humidity, rainfall): Correlation - 0.46

4 parameters (additionally dengue confirmed cases): Correlation - 0.91; RMS error - 50.7
Model with lesser accuracy when considering training data is selected to avoid overfitting

Validated with 4 years of data

Accuracy is good when predicting unseen data

Correlation - 0.86 - RMS error - 82.39 for predicting year 2005

Entropy and Neural Networks

Research done in Thailand with weekly data from 1999-2007 [8]

Entropy for the input data is calculated by classifying all range of values of
data into equal intervals and calculating the probability
Entropy equation from information theory is used

This transformed data is used as a feature vector for a feed forward NN

Temperature, Rainfall, humidity data are taken as input for calculating entropy
Simply a classification - Risk of outbreak vs No risk
Accuracy 85.92% with entropy vs 78.19% w/o entropy

Human Mobility

Has been established as a critical factor for the spread of Dengue virus [9-11]
Modeling human mobility for spreading of diseases

Models based on physics

Radiation model - considers population in between source and destination and does not
assume uniform distribution of population
Probabilistic models using mobile phone data (CDR data)
Agent based models that make use of CDR data

Gravity model - Assumes that the movement is proportional to populations at source

and destination and the distance between them

Vector Population

Primary vectors are mosquito species aedes aegypti and aedes albopictus
Mathematical models would involve estimating parameters using available
data [2]
Can also use a machine learning technique to estimate vector population

Using BRT to predict occurrence of a vector [13]

Need data like temperature, rainfall, land cover, vegetation
Need occurrence of vector population also to train/validate the model

Cellular Automata

Cellular automata based approach tried for Ahmedabad [5]

Considered SEIR-SEI model for humans and vectors
Reaction/diffusion based approach for modeling vector mobility
Run simulations with and without human mobility
Mobility parameters for humans were simply assigned
Results point that the spread of the disease is inhibited when considering
human mobility
Dengue case data from 2006-2012 is used only for validation of the model

Agent Based Modeling

Research describes of the H1N1 Influenza outbreak at Mexico 2009 [12]

3 seperate models for different dynamics of spreading of the disease

No quantitative results

Disease Model - SEIR model

Mobility model - Probability that agent n is at BTS Voronoi cell i on a given weekday
Social network model - list of reciprocal contacts for a weekday/weekend
2 simulations were run (with and without artificially controlling mobility)
Shown that government actions delayed the peak of the outbreak by 40 hours

EpiSimDemics algorithm was used (EpiFast is an improved version of the

algorithm)
If agent based models are used, performance will become a factor

Other Computational Methods

Random forest method to predict using suspected dengue cases of telephone

triage service [16]

Genetic Algorithms to identify transition rules of CA Lattice [17]

Fuzzy Association Rule Mining [18]

Temperature, rainfall, humidity, awareness level taken as inputs (Median RMSE - 0.63,
Correlation - 0.88 when predicting 2 weeks ahead)
Uses Generalized Linear Model for comparison (Media RMSE - 1.14, Correlation - 0.51)

Uses weather data and classifies into cells for spatial information
Classifiers are built automatically and best is selected using case data for validation

Entropy information extraction and pattern recognition [19]

Modeling dengue transmission in Colombo using a wavelet and cross-wavelet
approach [20]

Currently available platforms for modeling

spread of diseases

GLEAMviz [14] - Used by Bulcan et. al [9] for modeling

Simulation engine runs on server side

Model is done on client side
C++ code base for simulation engine
Could not find any information on the technical details of the engine

AIME - Claims to be able to predict to accuracy of 86.32% [15]

Research is not available publicly

Quoted in a newspaper article by Dr Dhesi Raja (Founder of the system) - The a

different variables such as wind direction, velocity, rainfall, thunderstorms, solar radiation,
construction sites and altitude,"

Modeling dengue outbreaks - Considerations

Sub models to consider

Disease model
Incubation period
Recovery period
Symptomatic vs asymptomatic hosts
Probability of transmission from vector-to-host/host-to-vector
Percentage of infected vectors
Vector population
Human mobility

Suitability of dengue transmission

Is considering the suitability of the vector population to survive enough?

Will have to be a spatio temporal measure

Modeling dengue outbreaks - Considerations

Do we consider different serotypes?

Which mobility model to use?

In Sri Lanka, most common serotypes are DENV-2 and DENV-3 []

What is the actual population size for an MOH area?
Percentage of infected that is travelling
If it is an agent based model, do we model the vector population as well?

What is the percentage of population that is already immune due to previous

outbreaks?

References
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mobility on the emergence of dengue epidemics in Pakistan, Proc. Natl. Acad. Sci., vol. 112, no. 38, pp. 1188711892, 2015.
[3] J. Loureno and M. Recker, The 2012 Madeira Dengue Outbreak: Epidemiological Determinants and Future Epidemic Potential, PLoS Negl.
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[11] D. Brockmann, Human Mobility and Spatial Disease Dynamics, Rev. Nonlinear Dyn. Complex., vol. 2, pp. 124, 2010.

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Discussion