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EuResist is a Pharmacogenomics project that integrates viral genomics with clinical data to predict responses to anti-HIV treatment. The system will provide the clinicians with a prediction of response to antiretroviral treatment in HIV patients, thus helping them choose the best drugs and drug combinations for any given HIV genetic variant.
Two groups in HRL are participating in the project: ours and the Healthcare & Life Sciences group. Our group is in charge of the machine learning activities of the project, while the Healthcare and Life Sciences group is in charge of creating a unified database which will be used for training.
Prediction engines
The EuResist project includes the development of several prediction engines of different flavors. Each engine is being designed to predict the efficiency of possible drug combinations and to recommend an optimal treatment. The prediction is based on data input for a specific HIV patient, including samples of the virus` genotype, past treatments, and various clinical measures.
The engine development requires data for training. To this end, a huge European integrated data set is being created to link some of the largest existing databases containing the required attributes.
The final system will allow the treating physician to specify patient data, which will be fed to all, or some, of the engines. The engines' answers will be consolidated in a single recommendation. It is believed this method will produce results that are more accurate than those obtained from any single engine. The development plans include five different kinds of prediction engines, including: evolutionary models, graph theoretical models, mutual-information based data mining, case-based reasoning, and machine learning.
Our team's contribution
Our team's main task is to develop a prediction engine based on machine learning techniques. More specifically, we plan to use a combination of generative and discriminative techniques.
The general time frame is as follows:
- End of 2006: Complete engine specification
- 2007: Deploy prediction engine
- 2008: Integrated system is expected to be fully operational
The other partners of the EuResist project include:
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