GPU-accelerated Modeling of Biological Regulatory Networks
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arXiv
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| Main Authors: | , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866914493810868224 |
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| author | Reimer, Joyce Saha, Pranta Chen, Chris Dhar, Neeraj Byrns, Brook Rayan, Steven Broderick, Gordon |
| author_facet | Reimer, Joyce Saha, Pranta Chen, Chris Dhar, Neeraj Byrns, Brook Rayan, Steven Broderick, Gordon |
| contents | The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are suitable for proposing logic models that explain the data and make predictions about how the system will behave under varying conditions. Considering the large scale of the parameter search spaces associated with these regulatory systems, performance optimizations on the level of both hardware and software are necessary for making this a practical tool for in silico pharmaceutical research. We show here how the implementation of these global optimization algorithms in a GPU-computing environment can accelerate the solution of these parameter search problems considerably. We carry out parameter searches on two model biological regulatory systems that represent almost an order of magnitude scale-up in complexity, and we find the gains in efficiency from GPU to be a 33%-43% improvement compared to multi-thread CPU implementations and a 33%-1866% increase compared to CPU in serial. These improvements make global optimization of logic model identification a far more attractive and feasible method for in silico hypothesis generation and design of experiments. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2506_19866 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | GPU-accelerated Modeling of Biological Regulatory Networks Reimer, Joyce Saha, Pranta Chen, Chris Dhar, Neeraj Byrns, Brook Rayan, Steven Broderick, Gordon Molecular Networks Performance Optimization and Control Quantitative Methods The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are suitable for proposing logic models that explain the data and make predictions about how the system will behave under varying conditions. Considering the large scale of the parameter search spaces associated with these regulatory systems, performance optimizations on the level of both hardware and software are necessary for making this a practical tool for in silico pharmaceutical research. We show here how the implementation of these global optimization algorithms in a GPU-computing environment can accelerate the solution of these parameter search problems considerably. We carry out parameter searches on two model biological regulatory systems that represent almost an order of magnitude scale-up in complexity, and we find the gains in efficiency from GPU to be a 33%-43% improvement compared to multi-thread CPU implementations and a 33%-1866% increase compared to CPU in serial. These improvements make global optimization of logic model identification a far more attractive and feasible method for in silico hypothesis generation and design of experiments. |
| title | GPU-accelerated Modeling of Biological Regulatory Networks |
| topic | Molecular Networks Performance Optimization and Control Quantitative Methods |
| url | https://arxiv.org/abs/2506.19866 |