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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Paddy: an evolutionary optimization algorithm for chemical systems and spaces.

Armen G Beck¹, Sanjay Iyer¹, Jonathan Fine¹

¹Department of Chemistry, Purdue University 720 Clinic Drive West Lafayette IN 47907 USA gchopra@purdue.edu.

Digital Discovery

|May 9, 2025

Summary

This summary is machine-generated.

The new Paddy software package, based on a biologically inspired algorithm, efficiently optimizes chemical systems. It demonstrates robust performance across various benchmarks, avoiding local minima for better global solutions in automated experimentation.

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Area of Science:

Computational chemistry
Chemical process optimization
Algorithm development

Background:

Chemical systems and processes require efficient optimization methods.
Existing algorithms often need numerous experiments and can converge on local minima.
Complexity in chemical systems necessitates advanced experimental design algorithms.

Purpose of the Study:

To introduce the Paddy software package and its underlying Paddy field algorithm.
To benchmark Paddy against diverse optimization approaches for chemical and mathematical tasks.
To evaluate Paddy's ability to optimize objectives, sample parameter space, and avoid local optima.

Main Methods:

Development of the Paddy software package utilizing the biologically inspired Paddy field algorithm.
Benchmarking Paddy against Tree of Parzen Estimator (Hyperopt), Bayesian optimization (Ax framework), and EvoTorch algorithms.
Testing performance on mathematical tasks (bimodal distribution, function interpolation) and chemical tasks (ANN hyperparameter optimization, molecule generation, experimental planning).

Main Results:

Paddy demonstrated robust and versatile performance across all tested optimization benchmarks.
Paddy maintained strong performance compared to other algorithms with varying results.
The algorithm effectively avoided early convergence and bypassed local optima, searching for global solutions.

Conclusions:

Paddy offers a facile, versatile, robust, and open-source toolkit for chemical problem-solving.
The software is well-suited for automated experimentation, prioritizing exploratory sampling.
Paddy's resistance to early convergence aids in identifying optimal solutions for complex chemical systems.