MODELING THE EPIDEMIOLOGY OF HIV/AIDS USING HIGH PERFORMANCE COMPUTING

Abstract
HIV/AIDS is a global pandemic and it poses a serious threat to public healthcare systems at all levels. HIV is more complex than other infectious disease because it is spreads as a direct consequence of social behavior which involves varying and unique personalities. The spread of HIV is dynamic, it is not based on geographical area, proximity to the infectious contagion nor demographics. It is based on complex social interaction networks that lead to sexual transmission. Existing models of computational epidemiology are either not scalable or not adaptable to the HIV contagion. They are better customized for epidemics such as influenza, SARS, malaria, asthma, diabetes and tuberculosis. They lack the scientific precision required when considering the impact of such studies on society. The model in this paper is an evolution of the first model which was concerned specifically with the HIV contagion. By using the Message Passing Interface (MPI) middleware the efficiency of the model for parallel computing can be optimized. As well as enhancing the structure and dynamics of the social interaction networks to be a more precise representation of the actual environment. The enhancements should also make the model scalable to different populations. Inferences are drawn from the work on the original model.

1.0 INTRODUCTION
It is paramount to understand the spatio-temporal diffusion or propagation of disease through populations, in order to mitigate the spread. This has been the aim of computational epidemiology. The data intensiveness of the task requires several terabytes and MIPS (Millions of instructions per second) of memory and processing power respectively. Such performances are the capabilities of distributed computing infrastructures and are way beyond those of multi-core processors. The networked computers may form a cluster, a GRID, or a cloud. For the purpose of modeling an epidemic a highperformance cluster is suitable, just as well as a GRID or cloud.

HIV/AIDS is responsible for more deaths than any other disease in the past two decades. More than 20 million people have already died and approximately 50 million people are infected with the disease. There are several data and statistics regarding other impacts of HIV/AIDS. The general trend is good impacts are affected negatively and bad impacts are affected positively. There is an obvious emergency. Statistics alone cannot facilitate executive counter-active decisions. There is also a tendency of statistics

to deviate from what was expected, as is the case with HIV/AIDS. Therefore epidemiology tools need to be continually renewed to meet the current state-of-the-matter. The demand for new tools simply indicates the lack of customization and standardization of existing tools. The naivety of existing tools is based on the complexity of using mathematics, statistics, cellular automata or agent based modeling to simulate the actual demographics, psychographics or geography of a disease spread. There are inherent complexities in maintaining attributes and parameters that are adaptable, available, modifiable and verifiable. Functions need to be based on sound theoretical principles developed in research. When principles advance existing models become more and more obsolete. The dynamic nature of HIV/AIDS makes it a prime consumer of new tools, but yet the extent of research in such tools does not meet the demand.

There are a lot of startling factors that result in sexual contact and the influence of social networks. Considering the stigma associated with the disease mentioning them is unethical. The resulting network of disease spread is a challenge to computerize. The endpoints of each network are dynamically determined. A computerized active network has to be a simplification and green prototype of HIV transmission in a population. Interactions between end points known as agents are modeled in an agent-based system. The representation of sexual interaction in the agents is modeled using messages between agents based on the characteristics of environment in which such interactions occur. For instance is the interaction in a high risk or hazardous environment, with presence of STDs, drugs and alcohol, lack of condom usage, commercial sex etc. The interactions are controlled by locality of the agents and likelihood of interaction based on age profile and profession. Agents will interact with more than one other agent over the course of time. Agents will be classified as positives, negatives and neutrals, to be described in section 5, the methodology of this paper. The agents are heterogeneous and the social networks dynamically evolve linearly as well as with a feedback mechanism to re-initializing the starting configurations for added dynamism. Hence behavior can be heterogeneous within the agents.

The probability of transmission function is used to determine the contraction of the disease from one agent to another during interactions of agents. This is based on several factors including CD4 count and viral load of the infected individual, basically the morbidity of the infected individual. Findings of interest are the prevalence of HIV in a given population, the number of new infections observed over a period of time and the effects of various factors and containment strategies, such as safe male circumcision and Anti-Retroviral therapy (ART).

The Message Passing Interface (MPI) will be used for the inter-process and intra-process communication. The processes will be parallel on a cluster of more than fifty (50) PCs. MPI is yet to be employed in computational epidemiology due to the limited high performance computing models.

However MPI is a common programming model in cluster computing. MPI allows for heterogeneity and therefore is suitable for the stochastic manner of disease spread. The results are expected to be consistent with the format of a combination of other epidemiology models. One observation is of the number of new infections, which should show a decline as more efforts towards prevention are put in place. Another observation is the HIV prevalence. The effects of various factors on the spread, the rates of transmission etc. are also form part of the findings.

2.0 RELATED WORK

Several infectious and highly communicable diseases have led to the research on the epidemiology of such diseases. By using computer models researchers have been able to forecast the demographic and geographic environments during an epidemic. These models take into consideration the transmission of the diseases as well as the prevention policies for the disease. The concern is the diseases would lead to fatality if not prevented and treated. In most cases even with adequate treatment strategies or prevention policies there are always a number of fatalities.

Smallpox is a highly communicable disease and its spread at county level was modeled using an individual-based computational approach. The purpose was to come up with a containment strategy especially in case of a bioterror attack on a small European county. The model permits generalization to multiple levels of social structure [1]. For instance a county could be composed of towns, hospitals, households, schools and work places. The structure used in the model divides a modeling day into daytime and nighttime [1] which determines the current location of individuals and their interactions. An individual can be said to be active that is when he/she is contacted by other individuals. Transmission of the disease may result from a contact. Individuals maintain a current status of infection, they are either Susceptible, Infected but asymptomatic and Non-contagious, Infected and contagious with early rash, Infected and contagious with rash, Dead, or Recovered. The parameters are strictly based on smallpox transmission and data. Various intervention strategies applied in smallpox can be simulated in the model hence providing policy makers better decision making mechanisms. The model is applicable to a population of only 800 and it can simulate runs for 82 days. The period may be adequate for smallpox since after 23 days of infection individuals have a 30% chance of mortality. For modeling the spread of the HIV contagion simulations will require several years, and of course larger populations.

Another agent-based simulation was built to model the social impacts of HIV/AIDS in villages in the Sekhukhune district of the Limpopo province in South Africa. The key to the model is that the networks are dynamic and co-evolving. [2] The model does not look at the epidemiology of the disease but it looks at the issue of how HIV/AIDS influences the livelihood and the household structure of a rural community. The model uses agents to represent individuals with a set of characteristics. The individuals age and may be born during the run of the simulation. The model adopts a distribution-based approach

to model the HIV/AIDS spread [2]. This is owing to the sensitivity of the issue of modeling sexual interactions and the lack of data concerning it. The model considers 100% transmission between spouses if one becomes infected as a result of migration. Agents are given a health status which is measured as the proportion of full fitness. After a patient is exposed to HIV/AIDS their health status declines more rapidly after an incubation period and a Sigmoid function is used to model the decay in health. The simulation uses a probability of 30% for mother to child transmission. The model further attempts to model the concept of families either nuclear or extended. These families represented as households can be created due to marriage or other factors. Households are assigned income resources and other resources that determine their livelihood. The households may then form neighborhoods that may provide mutual support to each other in case of hunger, bereavement etc. The agents or individuals may also be a part of an association such as a stokvel or funeral club. The model also enables agents to be assigned a migrated status, based on pre-conditions for migration. The model is used to run a simulation of a village with initially a 100 households and 600 to 900 agents. The model was used show the role of social networks in accommodating dissolved households. It could also be used to tell the impact on households composition due to HIV/AIDS and migration. The economy of households was also derived from simulations. The research carried out in this model is of interest because using the agent-based approach a dynamic social network of a typical village was abstracted. The research however does not address policies and intervention strategies aimed at fighting the spread of HIV/AIDS. It is not high performance computing oriented hence simulating thousands of individuals is unreasonably time consuming. There are several equations which have been proposed for the rate of transmission of pathogens including HIV/AIDS one equation is given below. Disease propagation is modeled by (1)

(1)

Where pi is the probability that a particular susceptible individual i is infected, is the duration of exposure, R is the set of infectivities of the infected individuals at the location, Nr is the number of infectious individuals with infectivity r, si is the susceptibility of i, and is the transmissibility [7].

3.0 METHODOLOGY
Firstly we begin with an analysis of influencing characteristics in a human population. A critical characteristic is health status this should include HIV result. Some people may fall severely ill warranting an HIV test. Others test voluntarily or other various reasons. Lets look at two categories of people. HIV positive people (from hence forth known as positives) who are aware of their status, do not loose belief in life. Therefore they continue to survive with as much hope and vigor as HIV negative people (negatives) who are aware of their status. The positives are still part of the heart and soul of society. With instances where they end in marital unions, because the difference in the variation of the behavior of the positives is micrometers away from the variation in the behavior of the negatives. The gap in the variations needs to be made constantly incrementing. The behavior of the positives and that of the negatives are the two influencing outcomes and parameters that policies and prevention strategies could be aimed at. One counter spread strategy may have to look at broadcasting in an even tone to both negatives and positives to induce favorable attitudes.

The next characteristic that is considered is that though human populations are entirely heterogeneous we can say there are homogenous trends which are at a higher hierarchy. These result in a uniform progression of life, regardless of the heterogeneous nature of the population or century. Indeed time cannot be a lacking factor in a model prototype. Hence the population of the agents should be modeled to have common behavior which can be viewed to an abstraction level as destiny. There are possibilities of the number of tiers in the hierarchy increasing.

The model uniquely models the transition of the Living status i.e. Dead or Alive from life to death. Hence the epidemiology of HIV/AIDS can be visualized on any population whilst the natural cycle of life progresses. This gives us several indications of the impact and pandemic prevalence of the disease.

The model is implemented with a feedback mechanism that reconfigures the initial statuses based on milestones reached in a population. This adds a level of dynamism that is non-existent in current models that maintain a single dimension of heterogeneity. It also gives the added advantage that it logically values human life, i.e. does not recklessly process the spread of the HIV/AIDS virus in a population. It does so by not attributing inherent characteristics to agents rather they are able to change behavior therefore undesirable behavior cannot be attributed to an agent permanently, preemptively condemning it to doom. The agent should however retain identifying traits.

Along with the positives and negatives in the population there is also a third key category. People who are either positive or negative but are unaware of their status (neutrals). The objectives of strategies

aimed at neutrals include encouraging HIV testing and Safe Male Circumcision. The neutrals also have defining behavior in our abstraction, which have their own influences on the spread of the disease. The pool of positives and negatives is joined from the pool of neutrals.

Another layer of categorization is the profession with the likelihood of sexual interactions between certain professions very limited.

We will choose an applicable function for the probability of infection of susceptible individuals. The model will have a meta-structure that places socially interacting agents in varying environments that have different levels of prevalence, different levels of transmission rates and different levels of risk. The risk factor will result in environments such as where there is drug and alcohol abuse, environments where individuals commit adultery or cheating, environments where individuals have casual sexual encounters, environments of faithful marriage or relationship . Generally agents will exist in any environment from very hazardous environments to safe environments whenever they interact. Agents frequently in hazardous environments are likely to be infected.

The model will use sections of other previously developed models of social interaction networks. For example from the related work of this paper, the model from [1] has levels of social structure where a county/district is composed of towns, hospitals, households, etc. The implementation of the function of the social structure is embedded in the function of the environments. Hospitals and Morgues since they serve a unique purpose from that of the environments may be included in the structure. The hospitals being responsible for testing, treatment, and prevention. Treatment will be for AIDS related diseases as well as Anti-Retroviral Therapy.

The model will allow for births and mother-to-child transmission. The child agents remain in a safe environment until an age yet to be determined. The child agents are also in pools of positives, negatives, often with limited neutrals. Once the age limit of safety is reached the child agents are now able to exist in hazardous environments. The model is enhanced with the core nature of the spread of the HIV/AIDS virus while retaining existing epidemiological modeling. Thus creating a model better representative of the HIV/AIDS spread, even considering ethical issues. The work done by [3] forms the basis of the transmission model of this model. There are several highlights of that model which have led to this implementation. Therefore the model will be described as is in the subsection below. The modifications may not serve the purpose of this paper if mentioned, though they are targeted at more realistic transmission, prevalence and impact of policies.

Further characteristics of a useful nature will be in constant development and may form part of the final prototype or as upgrades.

3.1 TRANSMISSION
During an interaction between a male and a female, the probability of transmission is calculated if one of the individuals is HIV infected. This probability is then used to determine if transmission is successful. Once transmission takes place the infected individual experiences progression of the infection according to the graph shown in Figure 3.1.0 Anti-Retroviral Therapy (ART) is also introduced in the model and its effect on the viral load and CD4+T cell count is consistent with that shown in Figure 3.1.1 and Figure 3.1.2.

Figure 3.1.0 Changes in HIV Viral Load and CD4+ T cell count in an infected person [4]

Figure

3.1.1

Decline

in

HIV

Viral

Load

Resulting

From

ARV

Therapy

[4]

Figure 3.1.2 Increase In CD4+ T Cell Count As A Result Of ARV Therapy [4]

The probability of successful transmission from male to female has been given as:

Where

= HIV-1 RNA NSI Count per ejaculation, which is the concentration of the virus in the = CD4+CCR5 count, which is the number of receptor cells in the mucosal

sexual secretions, and

layer of the cervical canal (in females) [5]

3.2 MPI
MPI has been applied in research in cluster computing. MPI provides message passing through a set of libraries that users can use to develop parallel and distributed applications [6]. MPI with support from C++ with a VIA (Virtual Interface Architecture) for low latency communication on the network, makes up an example of a cluster programming model. The operating system required is Linux. This cluster programming model is now being adopted to implement the high demands of processes of computational epidemiology. MPI is used to initialize a set of processes at start up. A processor will run a single process but different processes can be run on each processor. MPI allows grouping of processes to perform global operations. The message exchanges of the processes will convey the communication context in which they too place. Furthermore the processes will be able to communicate synchronously and asynchronously, as they can probe the environment and probe for messages.

4.0 EVALUATION
The parameters of the model are customizable to give preset environments based on their characteristics. Several environments can be modeled based on the nature of the actual environment such as population, disease prevalence, containment strategies etc. The model is initialized to an environment then agents interactions are moderated and their status is monitored. A number of agents are generated at start up. Firstly the population can be represented as is or it can be over projected to allow for births depending on the implementation. The environments broadcast messages to the agents. When agents have entered an environment, based on the characteristics of the environment they interact. The spread of the disease is modeled as a result of these interactions. The simulation is run for a number or years. Data is collected on demographics of agents, and epidemiology of the disease.

5.0 RESULTS
The results will be representative of some of the following graphs typically observable and of interest in a study of this study.

Figure 5.1 The Epidemic curve The size of the epidemic is analyzed based on the number of new infections as shown in Figure 5.1. This is useful for research on the effectiveness of no new infections strategies. A class of similar curves based on different characteristics of the epidemiology of HIV/AIDS can be generated. The other results are the number of deaths of either males of females in a category such as age group. This is shown in Figure 5.2 below.

Figure 5.2 Modeled estimates of Male/Female deaths in 2012.

Another result derivable is the prevalence of the disease among populations with different demographics. A graph of this nature is shown in Figure 5.3. below.

Figure 5.3 Observed and Modeled HIV prevalence in women who visit antenatal clinics

More indicators are shown in Figure 5.4 for example c shows the increase in the crude mortality rate due to AIDS, or the percentage of the population dying due to AIDS in each year. The results can be used to analyze the difference between intervention scenarios over time.

Figure 5.4 HIV incidence, HIV prevalence, and impact of HIV/AIDS on demographic indicators Figure 5.5 below shows trends in the age profile of newly infected individuals and trends in the morbidity profile of the infected adult population, for two intervention scenarios. The morbidity profile of the HIV infected adult population also changes over the course of the epidemic.

Figure 5.5 Trends in the age profile of new HIV infections and the morbidity profile of adult HIV infections, for intervention scenarios.

The morbidity profile in a year 2015 for instance can be further analyzed by age shown in Figure 5.6.

Figure 5.6 Percentage of population infected by age, split by disease stage, in 2015, for two intervention scenarios

Figure 5.7 shows an estimated population. While Figure 5.8 shows the risk of HIV infection. Figure 5.9 shows awareness level in population, and Figure 5.10 shows the effect on a certain factor on the risk of HIV infection.

Figure 5.7 Estimated population

Figure 5.8 Risk of infection

Figure 5.9 Awareness level

Figure 5.10 Effect of FSW on risk

6.0 CONCLUSION
Being able to accurately predict the spatio-temporal diffusion of a disease in stochastic social interaction networks is paramount to the study of any epidemic. HIV/AIDS is no exception, and it is wide spread throughout the world with Sub Saharan Africa being the most affected. The model in this paper arises to serve the need for a more suitable and up to date epidemiology of HIV/AIDS. It does so by incorporating several benefits of models for other diseases with the HIV/AIDS transmission dynamics. In addition the model uses a high performance computing platform to execute. The social interaction networks are uniquely modeled. The implementation tools are also for a first time applied to computational epidemiology. An important outcome of this work is evidence that very large epidemic simulations can be realized with significant speedup using large parallel computing platforms. Also being

incorporated are prevention, mitigation and intervention mechanisms and their effects. The resultant infection and morbidity rates can be valuable to domain (epidemiological) experts.

0.0 REFERENCES [1] Joshua M. Epstein, Derek A. T. Cummings, Shubha Chakravarty, Ramesh M. Singa, and Donald S. Burke. Toward a Containment Strategy for Smallpox Bioterror: An Individual-Based Computational Approach. Center on Social and Economic Dynamics. December 2002 [2] Shah J. Alam, Ruth Meyer, Emma Norling. Using Agent-Based Modeling to Understand the Impact of HIV/Aids in the Context of Socio-Economic Stressors. Centre for Policy Modeling. Manchester University with Metropolitan University [3] Tau T., Anderson G., Masizana-Katongo A., Mpoeleng D. Understanding HIV/AIDS Pandemic by High Performance Computing Epidemiology. Computer Science Department, University of Botswana. Gaborone, BOTSWANA. [4] Hoffmann C., Rockstroh J. K. and Kamps B. S. HIV Medicine 2006. Flying Publisher. 2006. [5] Chakraborty, Hrishikesh; Sen, Pranab K., Helms, Ronald W., Vernazza, Pietro L., Fiscus, Susan A., Eron, Joseph J., Patterson, Bruce K., Coombs, Robert W., Krieger, John N., and Cohen, Myron S. Viral Burden In Genital Secretions Determines Male-To-Female Sexual Transmission Of HIV-1: A Probabilistic Empiric Model. AIDS. 15(5):621-627, March 30, 2001. [6] Chee Shin Yeo, Rajkumar Buyya, Hossein Pourreza, Rasit Eskicioglu, Peter Graham, Frank Sommers. Cluster Computing: High-Performance, High-Availability, and High-Throughput Processing on a Network of Computers. The University of Melbourne, Australia. The University of Manitoba, Canada. [7] Keith R. Bisset, Xizhou Feng, Madhav Marathe, Shrirang Yardi. Modeling Interaction Between Individuals, Social Networks And Public Policy To Support Public Health Epidemiology. Virginia State University and Polytechnic Institute. Blacksburg, VA, 24061 USA