Daniel Schwalbe-Koda

Daniel Schwalbe-Koda, Daniel E. Widdowson, Tuan Anh Pham et al.

Zeolites are inorganic materials known for their diversity of applications, synthesis conditions, and resulting polymorphs. Although their synthesis is controlled both by inorganic and organic synthesis conditions, computational studies of zeolite synthesis have focused mostly on organic template design. In this work, we use a strong distance metric between crystal structures and machine learning (ML) to create inorganic synthesis maps in zeolites. Starting with 253 known zeolites, we show how the continuous distances between frameworks reproduce inorganic synthesis conditions from the literature without using labels such as building units. An unsupervised learning analysis shows that neighboring zeolites according to our metric often share similar inorganic synthesis conditions, even in template-based routes. In combination with ML classifiers, we find synthesis-structure relationships for 14 common inorganic conditions in zeolites, namely Al, B, Be, Ca, Co, F, Ga, Ge, K, Mg, Na, P, Si, and Zn. By explaining the model predictions, we demonstrate how (dis)similarities towards known structures can be used as features for the synthesis space. Finally, we show how these methods can be used to predict inorganic synthesis conditions for unrealized frameworks in hypothetical databases and interpret the outcomes by extracting local structural patterns from zeolites. In combination with template design, this work can accelerate the exploration of the space of synthesis conditions for zeolites.

Joshua A. Vita, Daniel Schwalbe-Koda

Over the last few years, key architectural advances have been proposed for neural network interatomic potentials (NNIPs), such as incorporating message-passing networks, equivariance, or many-body expansion terms. Although modern NNIP models exhibit small differences in energy/forces errors, improvements in accuracy are still considered the main target when developing new NNIP architectures. In this work, we show how architectural and optimization choices influence the generalization of NNIPs, revealing trends in molecular dynamics (MD) stability, data efficiency, and loss landscapes. Using the 3BPA dataset, we show that test errors in NNIP follow a scaling relation and can be robust to noise, but cannot predict MD stability in the high-accuracy regime. To circumvent this problem, we propose the use of loss landscape visualizations and a metric of loss entropy for predicting the generalization power of NNIPs. With a large-scale study on NequIP and MACE, we show that the loss entropy predicts out-of-distribution error and MD stability despite being computed only on the training set. Using this probe, we demonstrate how the choice of optimizers, loss function weighting, data normalization, and other architectural decisions influence the extrapolation behavior of NNIPs. Finally, we relate loss entropy to data efficiency, demonstrating that flatter landscapes also predict learning curve slopes. Our work provides a deep learning justification for the extrapolation performance of many common NNIPs, and introduces tools beyond accuracy metrics that can be used to inform the development of next-generation models.

Benjamin Yu, Vincenzo Lordi, Daniel Schwalbe-Koda

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

Jiawei Guo, Daniel Schwalbe-Koda

Determining atomistic structures from characterization data is one of the most common yet intricate problems in materials science. Particularly in amorphous materials, proposing structures that balance realism and agreement with experiments requires expert guidance, good interatomic potentials, or both. Here, we introduce GLASS, a generative framework that inverts multi-modal spectroscopic measurements into realistic atomistic structures without knowledge of the potential energy surface. A score-based model learns a structural prior from low-fidelity data and samples out-of-distribution structures conditioned on differentiable spectral targets. Reconstructions using pair distribution functions (PDFs), X-ray absorption spectroscopy, and diffraction measurements quantify the complementarity between spectral modalities and demonstrate that PDFs is the most informative probe for our framework. We use GLASS to rationalize three contested experimental problems: paracrystallinity in amorphous silicon, a liquid-liquid phase transition in sulfur, and ball-milled amorphous ice. In each case, generated structures reproduce experimental measurements and reveal mechanisms inaccessible to diffraction analysis alone.

Daniel Schwalbe-Koda, Sebastien Hamel, Babak Sadigh et al.

An accurate description of information is relevant for a range of problems in atomistic machine learning (ML), such as crafting training sets, performing uncertainty quantification (UQ), or extracting physical insights from large datasets. However, atomistic ML often relies on unsupervised learning or model predictions to analyze information contents from simulation or training data. Here, we introduce a theoretical framework that provides a rigorous, model-free tool to quantify information contents in atomistic simulations. We demonstrate that the information entropy of a distribution of atom-centered environments explains known heuristics in ML potential developments, from training set sizes to dataset optimality. Using this tool, we propose a model-free UQ method that reliably predicts epistemic uncertainty and detects out-of-distribution samples, including rare events in systems such as nucleation. This method provides a general tool for data-driven atomistic modeling and combines efforts in ML, simulations, and physical explainability.

Jingru Gan, Peichen Zhong, Yuanqi Du et al.

Crystal structure generation is fundamental to materials science, enabling the discovery of novel materials with desired properties. While existing approaches leverage Large Language Models (LLMs) through extensive fine-tuning on materials databases, we show that pre-trained LLMs can inherently generate novel and stable crystal structures without additional fine-tuning. Our framework employs LLMs as intelligent proposal agents within an evolutionary pipeline that guides them to perform implicit crossover and mutation operations while maintaining chemical validity. We demonstrate that MatLLMSearch achieves a 78.38% metastable rate validated by machine learning interatomic potentials and 31.7% DFT-verified stability, outperforming specialized models such as CrystalTextLLM. Beyond crystal structure generation, we further demonstrate that our framework adapts to diverse materials design tasks, including crystal structure prediction and multi-objective optimization of properties such as deformation energy and bulk modulus, all without fine-tuning. These results establish our framework as a versatile and effective framework for consistent high-quality materials discovery, offering training-free generation of novel stable structures with reduced overhead and broader accessibility.

Kai Yang, Daniel Schwalbe-Koda

Generative models show great promise for the inverse design of molecules and inorganic crystals, but remain largely ineffective within more complex structures such as amorphous materials. Here, we present a diffusion model that reliably generates amorphous structures up to 1000 times faster than conventional simulations across processing conditions, compositions, and data sources. Generated structures recovered the short- and medium-range order, sampling diversity, and macroscopic properties of silica glass, as validated by simulations and an information-theoretical strategy. Conditional generation allowed sampling large structures at low cooling rates of 10$^{-2}$ K/ps to uncover a ductile-to-brittle transition and mesoporous silica structures. Extension to metallic glassy systems accurately reproduced local structures and properties from both computational and experimental datasets, demonstrating how synthetic data can be generated from characterization results. Our methods provide a roadmap for the design and simulation of amorphous materials previously inaccessible to computational methods.

Daniel Schwalbe-Koda, Aik Rui Tan, Rafael Gómez-Bombarelli

Neural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile behavior when extrapolating. Uncertainty quantification approaches can flag atomic configurations for which prediction confidence is low, but arriving at such uncertain regions requires expensive sampling of the NN phase space, often using atomistic simulations. Here, we exploit automatic differentiation to drive atomistic systems towards high-likelihood, high-uncertainty configurations without the need for molecular dynamics simulations. By performing adversarial attacks on an uncertainty metric, informative geometries that expand the training domain of NNs are sampled. When combined to an active learning loop, this approach bootstraps and improves NN potentials while decreasing the number of calls to the ground truth method. This efficiency is demonstrated on sampling of kinetic barriers and collective variables in molecules, and can be extended to any NN potential architecture and materials system.

Daniel Schwalbe-Koda, Rafael Gómez-Bombarelli

Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approaches map properties to structures, thus expediting the design of novel useful compounds. In this chapter, we examine the way in which current deep generative models are addressing the inverse chemical discovery paradigm. We begin by revisiting early inverse design algorithms. Then, we introduce generative models for molecular systems and categorize them according to their architecture and molecular representation. Using this classification, we review the evolution and performance of important molecular generation schemes reported in the literature. Finally, we conclude highlighting the prospects and challenges of generative models as cutting edge tools in materials discovery.