Symmetry-Aware Bayesian Flow Networks for Crystal Generation

The discovery of new crystalline materials is essential to scientific and technological progress. However, traditional trial-and-error approaches are inefficient due to the vast search space. Recent advancements in machine learning have enabled generative models to predict new stable materials by incorporating structural symmetries and to condition the generation on desired properties. In this work, we introduce SymmBFN, a novel symmetry-aware Bayesian Flow Network (BFN) for crystalline material generation that accurately reproduces the distribution of space groups found in experimentally observed crystals. SymmBFN substantially improves efficiency, generating stable structures at least 50 times faster than the next-best method. Furthermore, we demonstrate its capability for property-conditioned generation, enabling the design of materials with tailored properties. Our findings establish BFNs as an effective tool for accelerating the discovery of crystalline materials.

Temperature-Annealed Boltzmann Generators

Efficient sampling of unnormalized probability densities such as the Boltzmann distribution of molecular systems is a longstanding challenge. Next to conventional approaches like molecular dynamics or Markov chain Monte Carlo, variational approaches, such as training normalizing flows with the reverse Kullback-Leibler divergence, have been introduced. However, such methods are prone to mode collapse and often do not learn to sample the full configurational space. Here, we present temperature-annealed Boltzmann generators (TA-BG) to address this challenge. First, we demonstrate that training a normalizing flow with the reverse Kullback-Leibler divergence at high temperatures is possible without mode collapse. Furthermore, we introduce a reweighting-based training objective to anneal the distribution to lower target temperatures. We apply this methodology to three molecular systems of increasing complexity and, compared to the baseline, achieve better results in almost all metrics while requiring up to three times fewer target energy evaluations. For the largest system, our approach is the only method that accurately resolves the metastable states of the system.

PAL -- Parallel active learning for machine-learned potentials

Constructing datasets representative of the target domain is essential for training effective machine learning models. Active learning (AL) is a promising method that iteratively extends training data to enhance model performance while minimizing data acquisition costs. However, current AL workflows often require human intervention and lack parallelism, leading to inefficiencies and underutilization of modern computational resources. In this work, we introduce PAL, an automated, modular, and parallel active learning library that integrates AL tasks and manages their execution and communication on shared- and distributed-memory systems using the Message Passing Interface (MPI). PAL provides users with the flexibility to design and customize all components of their active learning scenarios, including machine learning models with uncertainty estimation, oracles for ground truth labeling, and strategies for exploring the target space. We demonstrate that PAL significantly reduces computational overhead and improves scalability, achieving substantial speed-ups through asynchronous parallelization on CPU and GPU hardware. Applications of PAL to several real-world scenarios - including ground-state reactions in biomolecular systems, excited-state dynamics of molecules, simulations of inorganic clusters, and thermo-fluid dynamics - illustrate its effectiveness in accelerating the development of machine learning models. Our results show that PAL enables efficient utilization of high-performance computing resources in active learning workflows, fostering advancements in scientific research and engineering applications.

Global Concept Explanations for Graphs by Contrastive Learning

Beyond improving trust and validating model fairness, xAI practices also have the potential to recover valuable scientific insights in application domains where little to no prior human intuition exists. To that end, we propose a method to extract global concept explanations from the predictions of graph neural networks to develop a deeper understanding of the tasks underlying structure-property relationships. We identify concept explanations as dense clusters in the self-explaining Megan models subgraph latent space. For each concept, we optimize a representative prototype graph and optionally use GPT-4 to provide hypotheses about why each structure has a certain effect on the prediction. We conduct computational experiments on synthetic and real-world graph property prediction tasks. For the synthetic tasks we find that our method correctly reproduces the structural rules by which they were created. For real-world molecular property regression and classification tasks, we find that our method rediscovers established rules of thumb. More specifically, our results for molecular mutagenicity prediction indicate more fine-grained resolution of structural details than existing explainability methods, consistent with previous results from chemistry literature. Overall, our results show promising capability to extract the underlying structure-property relationships for complex graph property prediction tasks.

Conditional Normalizing Flows for Active Learning of Coarse-Grained Molecular Representations

Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been used to learn the Boltzmann distribution directly, without samples. However, this approach is susceptible to mode collapse and thus often does not explore the full configurational space. In this work, we address this challenge by separating the problem into two levels, the fine-grained and coarse-grained degrees of freedom. A normalizing flow conditioned on the coarse-grained space yields a probabilistic connection between the two levels. To explore the configurational space, we employ coarse-grained simulations with active learning which allows us to update the flow and make all-atom potential energy evaluations only when necessary. Using alanine dipeptide as an example, we show that our methods obtain a speedup to molecular dynamics simulations of approximately 15.9 to 216.2 compared to the speedup of 4.5 of the current state-of-the-art machine learning approach.

Contextualized Policy Recovery: Modeling and Interpreting Medical Decisions with Adaptive Imitation Learning

Interpretable policy learning seeks to estimate intelligible decision policies from observed actions; however, existing models fall short by forcing a tradeoff between accuracy and interpretability. This tradeoff limits data-driven interpretations of human decision-making process. e.g. to audit medical decisions for biases and suboptimal practices, we require models of decision processes which provide concise descriptions of complex behaviors. Fundamentally, existing approaches are burdened by this tradeoff because they represent the underlying decision process as a universal policy, when in fact human decisions are dynamic and can change drastically with contextual information. Thus, we propose Contextualized Policy Recovery (CPR), which re-frames the problem of modeling complex decision processes as a multi-task learning problem in which complex decision policies are comprised of context-specific policies. CPR models each context-specific policy as a linear observation-to-action mapping, and generates new decision models $\textit{on-demand}$ as contexts are updated with new observations. CPR is compatible with fully offline and partially observable decision environments, and can be tailored to incorporate any recurrent black-box model or interpretable decision model. We assess CPR through studies on simulated and real data, achieving state-of-the-art performance on the canonical tasks of predicting antibiotic prescription in intensive care units ($+22\%$ AUROC vs. previous SOTA) and predicting MRI prescription for Alzheimer's patients ($+7.7\%$ AUROC vs. previous SOTA). With this improvement in predictive performance, CPR closes the accuracy gap between interpretable and black-box methods for policy learning, allowing high-resolution exploration and analysis of context-specific decision models.

Mitigating Molecular Aggregation in Drug Discovery with Predictive Insights from Explainable AI

As the importance of high-throughput screening (HTS) continues to grow due to its value in early stage drug discovery and data generation for training machine learning models, there is a growing need for robust methods for pre-screening compounds to identify and prevent false-positive hits. Small, colloidally aggregating molecules are one of the primary sources of false-positive hits in high-throughput screens, making them an ideal candidate to target for removal from libraries using predictive pre-screening tools. However, a lack of understanding of the causes of molecular aggregation introduces difficulty in the development of predictive tools for detecting aggregating molecules. Herein, we present an examination of the molecular features differentiating datasets of aggregating and non-aggregating molecules, as well as a machine learning approach to predicting molecular aggregation. Our method uses explainable graph neural networks and counterfactuals to reliably predict and explain aggregation, giving additional insights and design rules for future screening. The integration of this method in HTS approaches will help combat false positives, providing better lead molecules more rapidly and thus accelerating drug discovery cycles.

Quantifying the Intrinsic Usefulness of Attributional Explanations for Graph Neural Networks with Artificial Simulatability Studies

Despite the increasing relevance of explainable AI, assessing the quality of explanations remains a challenging issue. Due to the high costs associated with human-subject experiments, various proxy metrics are often used to approximately quantify explanation quality. Generally, one possible interpretation of the quality of an explanation is its inherent value for teaching a related concept to a student. In this work, we extend artificial simulatability studies to the domain of graph neural networks. Instead of costly human trials, we use explanation-supervisable graph neural networks to perform simulatability studies to quantify the inherent usefulness of attributional graph explanations. We perform an extensive ablation study to investigate the conditions under which the proposed analyses are most meaningful. We additionally validate our methods applicability on real-world graph classification and regression datasets. We find that relevant explanations can significantly boost the sample efficiency of graph neural networks and analyze the robustness towards noise and bias in the explanations. We believe that the notion of usefulness obtained from our proposed simulatability analysis provides a dimension of explanation quality that is largely orthogonal to the common practice of faithfulness and has great potential to expand the toolbox of explanation quality assessments, specifically for graph explanations.

Neural networks trained on synthetically generated crystals can extract structural information from ICSD powder X-ray diffractograms

Machine learning techniques have successfully been used to extract structural information such as the crystal space group from powder X-ray diffractograms. However, training directly on simulated diffractograms from databases such as the ICSD is challenging due to its limited size, class-inhomogeneity, and bias toward certain structure types. We propose an alternative approach of generating synthetic crystals with random coordinates by using the symmetry operations of each space group. Based on this approach, we demonstrate online training of deep ResNet-like models on up to a few million unique on-the-fly generated synthetic diffractograms per hour. For our chosen task of space group classification, we achieved a test accuracy of 79.9% on unseen ICSD structure types from most space groups. This surpasses the 56.1% accuracy of the current state-of-the-art approach of training on ICSD crystals directly. Our results demonstrate that synthetically generated crystals can be used to extract structural information from ICSD powder diffractograms, which makes it possible to apply very large state-of-the-art machine learning models in the area of powder X-ray diffraction. We further show first steps toward applying our methodology to experimental data, where automated XRD data analysis is crucial, especially in high-throughput settings. While we focused on the prediction of the space group, our approach has the potential to be extended to related tasks in the future.

Connectivity Optimized Nested Graph Networks for Crystal Structures

Graph neural networks (GNNs) have been applied to a large variety of applications in materials science and chemistry. Here, we recapitulate the graph construction for crystalline (periodic) materials and investigate its impact on the GNNs model performance. We suggest the asymmetric unit cell as a representation to reduce the number of atoms by using all symmetries of the system. With a simple but systematically built GNN architecture based on message passing and line graph templates, we furthermore introduce a general architecture (Nested Graph Network, NGN) that is applicable to a wide range of tasks and systematically improves state-of-the-art results on the MatBench benchmark datasets.