Factorial HMMs with Collapsed Gibbs Sampling for Optimizing Long-term HIV Therapy

Amit Gruber, Chen Yanover, Tal El-Hay, Anders Sönnerborg, Vanni Borghi, Francesca Incardona, Yaara Goldschmidt
Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics, PMLR 84:317-326, 2018.

Abstract

Combined antiretroviral therapies can successfully suppress HIV in the serum and bring its viral load below detection rate. However, drug resistance remains a major challenge. As resistance patterns vary between patients, therapy personalization is required. Automatic systems for therapy personalization exist and were shown to better predict therapy outcome than HIV experts in some settings. However, these systems focus only on selecting the therapy most likely to suppress the virus for several weeks, a choice that may be suboptimal over the longer term due to evolution of drug resistance. We present a novel generative model for HIV drug resistance evolution. This model is based on factorial HMMs, applying a novel collapsed Gibbs Sampling algorithm for approximate learning. Using the suggested model, we obtain better therapy outcome predictions than existing methods and recommend therapies that may be more effective in the long term. We demonstrate our results using simulated data and using real data from the EuResist dataset.

Cite this Paper

BibTeX
@InProceedings{pmlr-v84-gruber18a, title = {Factorial HMMs with Collapsed Gibbs Sampling for Optimizing Long-term HIV Therapy}, author = {Gruber, Amit and Yanover, Chen and El-Hay, Tal and Sönnerborg, Anders and Borghi, Vanni and Incardona, Francesca and Goldschmidt, Yaara}, booktitle = {Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics}, pages = {317--326}, year = {2018}, editor = {Storkey, Amos and Perez-Cruz, Fernando}, volume = {84}, series = {Proceedings of Machine Learning Research}, month = {09--11 Apr}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v84/gruber18a/gruber18a.pdf}, url = {https://proceedings.mlr.press/v84/gruber18a.html}, abstract = {Combined antiretroviral therapies can successfully suppress HIV in the serum and bring its viral load below detection rate. However, drug resistance remains a major challenge. As resistance patterns vary between patients, therapy personalization is required. Automatic systems for therapy personalization exist and were shown to better predict therapy outcome than HIV experts in some settings. However, these systems focus only on selecting the therapy most likely to suppress the virus for several weeks, a choice that may be suboptimal over the longer term due to evolution of drug resistance. We present a novel generative model for HIV drug resistance evolution. This model is based on factorial HMMs, applying a novel collapsed Gibbs Sampling algorithm for approximate learning. Using the suggested model, we obtain better therapy outcome predictions than existing methods and recommend therapies that may be more effective in the long term. We demonstrate our results using simulated data and using real data from the EuResist dataset. } }
Endnote
%0 Conference Paper %T Factorial HMMs with Collapsed Gibbs Sampling for Optimizing Long-term HIV Therapy %A Amit Gruber %A Chen Yanover %A Tal El-Hay %A Anders Sönnerborg %A Vanni Borghi %A Francesca Incardona %A Yaara Goldschmidt %B Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics %C Proceedings of Machine Learning Research %D 2018 %E Amos Storkey %E Fernando Perez-Cruz %F pmlr-v84-gruber18a %I PMLR %P 317--326 %U https://proceedings.mlr.press/v84/gruber18a.html %V 84 %X Combined antiretroviral therapies can successfully suppress HIV in the serum and bring its viral load below detection rate. However, drug resistance remains a major challenge. As resistance patterns vary between patients, therapy personalization is required. Automatic systems for therapy personalization exist and were shown to better predict therapy outcome than HIV experts in some settings. However, these systems focus only on selecting the therapy most likely to suppress the virus for several weeks, a choice that may be suboptimal over the longer term due to evolution of drug resistance. We present a novel generative model for HIV drug resistance evolution. This model is based on factorial HMMs, applying a novel collapsed Gibbs Sampling algorithm for approximate learning. Using the suggested model, we obtain better therapy outcome predictions than existing methods and recommend therapies that may be more effective in the long term. We demonstrate our results using simulated data and using real data from the EuResist dataset.
APA
Gruber, A., Yanover, C., El-Hay, T., Sönnerborg, A., Borghi, V., Incardona, F. & Goldschmidt, Y.. (2018). Factorial HMMs with Collapsed Gibbs Sampling for Optimizing Long-term HIV Therapy. Proceedings of the Twenty-First International Conference on Artificial Intelligence and Statistics, in Proceedings of Machine Learning Research 84:317-326 Available from https://proceedings.mlr.press/v84/gruber18a.html.

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