Sparks: Multi-Agent Artificial Intelligence Model Discovers Protein Design Principles

• URL: http://arxiv.org/abs/2504.19017v1
• Date: Sat, 26 Apr 2025 20:43:28 GMT
• Title: Sparks: Multi-Agent Artificial Intelligence Model Discovers Protein Design Principles
• Authors: Alireza Ghafarollahi, Markus J. Buehler,
• Abstract summary: We present Sparks, a multi-modal multi-agent AI model that executes the entire discovery cycle.<n>Sparks can independently conduct rigorous scientific inquiry and identify previously unknown scientific principles.
• Score: 0.0
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Advances in artificial intelligence (AI) promise autonomous discovery, yet most systems still resurface knowledge latent in their training data. We present Sparks, a multi-modal multi-agent AI model that executes the entire discovery cycle that includes hypothesis generation, experiment design and iterative refinement to develop generalizable principles and a report without human intervention. Applied to protein science, Sparks uncovered two previously unknown phenomena: (i) a length-dependent mechanical crossover whereby beta-sheet-biased peptides surpass alpha-helical ones in unfolding force beyond ~80 residues, establishing a new design principle for peptide mechanics; and (ii) a chain-length/secondary-structure stability map revealing unexpectedly robust beta-sheet-rich architectures and a "frustration zone" of high variance in mixed alpha/beta folds. These findings emerged from fully self-directed reasoning cycles that combined generative sequence design, high-accuracy structure prediction and physics-aware property models, with paired generation-and-reflection agents enforcing self-correction and reproducibility. The key result is that Sparks can independently conduct rigorous scientific inquiry and identify previously unknown scientific principles.

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