PhoTorch: a robust and generalized biochemical photosynthesis model fitting package based on PyTorch

Advancements in artificial intelligence (AI) have greatly benefited plant phenotyping and predictive modeling. However, unrealized opportunities exist in leveraging AI advancements in model parameter optimization for parameter fitting in complex biophysical models. This work developed novel software, PhoTorch, for fitting parameters of the Farquhar, von Caemmerer, and Berry (FvCB) biochemical photosynthesis model based on the parameter optimization components of the popular AI framework PyTorch. The primary novelty of the software lies in its computational efficiency, robustness of parameter estimation, and flexibility in handling different types of response curves and sub-model functional forms. PhoTorch can fit both steady-state and non-steady-state gas exchange data with high efficiency and accuracy. Its flexibility allows for optional fitting of temperature and light response parameters, and can simultaneously fit light response curves and standard <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>A</mml:mi> <mml:mo>/</mml:mo> <mml:msub><mml:mi>C</mml:mi> <mml:mi>i</mml:mi></mml:msub> </mml:mrow> </mml:math> curves. These features are not available within presently available <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>A</mml:mi> <mml:mo>/</mml:mo> <mml:msub><mml:mi>C</mml:mi> <mml:mi>i</mml:mi></mml:msub> </mml:mrow> </mml:math> curve fitting packages. Results illustrated the robustness and efficiency of PhoTorch in fitting <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>A</mml:mi> <mml:mo>/</mml:mo> <mml:msub><mml:mi>C</mml:mi> <mml:mi>i</mml:mi></mml:msub> </mml:mrow> </mml:math> curves with high variability and some level of artifacts and noise. PhoTorch is more than four times faster than benchmark software, which may be relevant when processing many non-steady-state <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>A</mml:mi> <mml:mo>/</mml:mo> <mml:msub><mml:mi>C</mml:mi> <mml:mi>i</mml:mi></mml:msub> </mml:mrow> </mml:math> curves with hundreds of data points per curve. PhoTorch provides researchers from various fields with a reliable and efficient tool for analyzing photosynthetic data. The Python package is openly accessible from the repository: https://github.com/GEMINI-Breeding/photorch .