Tiarnan A. S. Doherty

Shreshth A Malik, Tiarnan Doherty, Panagiotis Tigas et al.

Existing benchmarks for computational materials discovery primarily evaluate static predictive tasks or isolated computational sub-tasks. While valuable, these evaluations neglect the inherently iterative and adaptive nature of scientific discovery. We introduce MAterials Discovery Environments (MADE), a novel framework for benchmarking end-to-end autonomous materials discovery pipelines. MADE simulates closed-loop discovery campaigns in which an agent or algorithm proposes, evaluates, and refines candidate materials under a constrained oracle budget, capturing the sequential and resource-limited nature of real discovery workflows. We formalize discovery as a search for thermodynamically stable compounds relative to a given convex hull, and evaluate efficacy and efficiency via comparison to baseline algorithms. The framework is flexible; users can compose discovery agents from interchangeable components such as generative models, filters, and planners, enabling the study of arbitrary workflows ranging from fixed pipelines to fully agentic systems with tool use and adaptive decision making. We demonstrate this by conducting systematic experiments across a family of systems, enabling ablation of components in discovery pipelines, and comparison of how methods scale with system complexity.

Shreshth A. Malik, Tiarnan A. S. Doherty, Benjamin Colmey et al.

High-fidelity electron microscopy simulations required for quantitative crystal structure refinements face a fundamental challenge: while physical interactions are well-described theoretically, real-world experimental effects are challenging to model analytically. To address this gap, we present a novel hybrid physics-machine learning framework that integrates differentiable physical simulations with neural networks. By leveraging automatic differentiation throughout the simulation pipeline, our method enables gradient-based joint optimization of physical parameters and neural network components representing experimental variables, offering superior scalability compared to traditional second-order methods. We demonstrate this framework through application to three-dimensional electron diffraction (3D-ED) structure refinement, where our approach learns complex thickness distributions directly from diffraction data rather than relying on simplified geometric models. This method achieves state-of-the-art refinement performance across synthetic and experimental datasets, recovering atomic positions, thermal displacements, and thickness profiles with high fidelity. The modular architecture proposed can naturally be extended to accommodate additional physical phenomena and extended to other electron microscopy techniques. This establishes differentiable hybrid modeling as a powerful new paradigm for quantitative electron microscopy, where experimental complexities have historically limited analysis.