Population-Based Black-Box Optimization for Biological Sequence Design

Christof Angermueller, David Belanger, Andreea Gane, Zelda Mariet, David Dohan, Kevin Murphy, Lucy Colwell, D Sculley
Proceedings of the 37th International Conference on Machine Learning, PMLR 119:324-334, 2020.

Abstract

The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences — a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose Population-Based Black-Box Optimization (P3BO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing P3BO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the hyper-parameters of each of the methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that P3BO outperforms any single method in its population, proposing higher quality sequences as well as more diverse batches. As such, P3BO and Adaptive-P3BO are a crucial step towards deploying ML to real-world sequence design.

Cite this Paper

BibTeX
@InProceedings{pmlr-v119-angermueller20a, title = {Population-Based Black-Box Optimization for Biological Sequence Design}, author = {Angermueller, Christof and Belanger, David and Gane, Andreea and Mariet, Zelda and Dohan, David and Murphy, Kevin and Colwell, Lucy and Sculley, D}, booktitle = {Proceedings of the 37th International Conference on Machine Learning}, pages = {324--334}, year = {2020}, editor = {III, Hal Daumé and Singh, Aarti}, volume = {119}, series = {Proceedings of Machine Learning Research}, month = {13--18 Jul}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v119/angermueller20a/angermueller20a.pdf}, url = {https://proceedings.mlr.press/v119/angermueller20a.html}, abstract = {The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences — a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose Population-Based Black-Box Optimization (P3BO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing P3BO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the hyper-parameters of each of the methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that P3BO outperforms any single method in its population, proposing higher quality sequences as well as more diverse batches. As such, P3BO and Adaptive-P3BO are a crucial step towards deploying ML to real-world sequence design.} }
Endnote
%0 Conference Paper %T Population-Based Black-Box Optimization for Biological Sequence Design %A Christof Angermueller %A David Belanger %A Andreea Gane %A Zelda Mariet %A David Dohan %A Kevin Murphy %A Lucy Colwell %A D Sculley %B Proceedings of the 37th International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2020 %E Hal Daumé III %E Aarti Singh %F pmlr-v119-angermueller20a %I PMLR %P 324--334 %U https://proceedings.mlr.press/v119/angermueller20a.html %V 119 %X The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences — a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose Population-Based Black-Box Optimization (P3BO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing P3BO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the hyper-parameters of each of the methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that P3BO outperforms any single method in its population, proposing higher quality sequences as well as more diverse batches. As such, P3BO and Adaptive-P3BO are a crucial step towards deploying ML to real-world sequence design.
APA
Angermueller, C., Belanger, D., Gane, A., Mariet, Z., Dohan, D., Murphy, K., Colwell, L. & Sculley, D.. (2020). Population-Based Black-Box Optimization for Biological Sequence Design. Proceedings of the 37th International Conference on Machine Learning, in Proceedings of Machine Learning Research 119:324-334 Available from https://proceedings.mlr.press/v119/angermueller20a.html.

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