Machine learning interatomic potentials have become an indispensable tool for materials science, enabling the study of larger systems and longer timescales. State-of-the-art models are generally graph neural networks that employ message passing to iteratively update atomic embeddings that are ultimately used for predicting properties. In this work we extend the message passing formalism with the inclusion of a continuous variable that accounts for fractional atomic existence. This allows us to calculate the gradient of the Gibbs free energy with respect to both the Cartesian coordinates of atoms and their existence. Using this we propose a gradient-based grand canonical optimization method and document its capabilities for a Cu(110) surface oxide.

The use of generative models to sample equilibrium distributions of many-body systems, as first demonstrated by Boltzmann Generators, has attracted substantial interest due to their ability to produce unbiased and uncorrelated samples in `one shot'. Despite their promise and impressive results across the natural sciences, scaling these models to large systems remains a major challenge. In this work, we introduce a Boltzmann Generator architecture that addresses this scalability bottleneck with a focus on applications in materials science. We leverage augmented coupling flows in combination with graph neural networks to base the generation process on local environmental information, while allowing for energy-based training and fast inference. Compared to previous architectures, our model trains significantly faster, requires far less computational resources, and achieves superior sampling efficiencies. Crucially, the architecture is transferable to larger system sizes, which allows for the efficient sampling of materials with simulation cells of unprecedented size. We demonstrate the potential of our approach by applying it to several materials systems, including Lennard-Jones crystals, ice phases of mW water, and the phase diagram of silicon, for system sizes well above one thousand atoms. The trained Boltzmann Generators produce highly accurate equilibrium ensembles for various crystal structures, as well as Helmholtz and Gibbs free energies across a range of system sizes, able to reach scales where finite-size effects become negligible.

The preparation of quantum Gibbs states is a fundamental challenge in quantum computing, essential for applications ranging from modeling open quantum systems to quantum machine learning. Building on the Meta-Variational Quantum Eigensolver framework proposed by Cervera-Lierta et al.(2021) and a problem driven ansatz design, we introduce two meta-learning algorithms: Meta-Variational Quantum Thermalizer (Meta-VQT) and Neural Network Meta-VQT (NN-Meta VQT) for efficient thermal state preparation of parametrized Hamiltonians on Noisy Intermediate-Scale Quantum (NISQ) devices. Meta-VQT utilizes a fully quantum ansatz, while NN Meta-VQT integrates a quantum classical hybrid architecture. Both leverage collective optimization over training sets to generalize Gibbs state preparation to unseen parameters. We validate our methods on upto 8-qubit Transverse Field Ising Model and the 2-qubit Heisenberg model with all field terms, demonstrating efficient thermal state generation beyond training data. For larger systems, we show that our meta-learned parameters when combined with appropriately designed ansatz serve as warm start initializations, significantly outperforming random initializations in the optimization tasks. Furthermore, a 3- qubit Kitaev ring example showcases our algorithm's effectiveness across finite-temperature crossover regimes. Finally, we apply our algorithms to train a Quantum Boltzmann Machine (QBM) on a 2-qubit Heisenberg model with all field terms, achieving enhanced training efficiency, improved Gibbs state accuracy, and a 30-fold runtime speedup over existing techniques such as variational quantum imaginary time (VarQITE)-based QBM highlighting the scalability and practicality of meta-algorithm-based QBMs.

Machine learning interatomic potentials (MLIPs) have become a workhorse of modern atomistic simulations, and recently published universal MLIPs, pre-trained on large datasets, have demonstrated remarkable accuracy and generalizability. However, the computational cost of MLIPs limits their applicability to chemically disordered systems requiring large simulation cells or to sample-intensive statistical methods. Here, we report the use of continuous and differentiable alchemical degrees of freedom in atomistic materials simulations, exploiting the fact that graph neural network MLIPs represent discrete elements as real-valued tensors. The proposed method introduces alchemical atoms with corresponding weights into the input graph, alongside modifications to the message-passing and readout mechanisms of MLIPs, and allows smooth interpolation between the compositional states of materials. The end-to-end differentiability of MLIPs enables efficient calculation of the gradient of energy with respect to the compositional weights. Leveraging these gradients, we propose methodologies for optimizing the composition of solid solutions towards target macroscopic properties and conducting alchemical free energy simulations to quantify the free energy of vacancy formation and composition changes. The approach offers an avenue for extending the capabilities of universal MLIPs in the modeling of compositional disorder and characterizing the phase stabilities of complex materials systems.

We present a machine-learning model based on normalizing flows that is trained to sample from the isobaric-isothermal ensemble. In our approach, we approximate the joint distribution of a fully-flexible triclinic simulation box and particle coordinates to achieve a desired internal pressure. This novel extension of flow-based sampling to the isobaric-isothermal ensemble yields direct estimates of Gibbs free energies. We test our NP T -flow on monatomic water in the cubic and hexagonal ice phases and find excellent agreement of Gibbs free energies and other observables compared with established baselines.

Datasets in the real world are often complex and to some degree hierarchical, with groups and sub-groups of data sharing common characteristics at different levels of abstraction. Understanding and uncovering the hidden structure of these datasets is an important task that has many practical applications. To address this challenge, we present a new and general method for building relational data trees by exploiting the learning dynamics of the Restricted Boltzmann Machine (RBM). Our method is based on the mean-field approach, derived from the Plefka expansion, and developed in the context of disordered systems. It is designed to be easily interpretable. We tested our method in an artificially created hierarchical dataset and on three different real-world datasets (images of digits, mutations in the human genome, and a homologous family of proteins). The method is able to automatically identify the hierarchical structure of the data. This could be useful in the study of homologous protein sequences, where the relationships between proteins are critical for understanding their function and evolution.

We present a new approximate learning algorithm for Boltzmann Machines, using a systematic expansion of the Gibbs free energy to second order in the weights. The linear response correction to the correlations is given by the Hessian of the Gibbs free energy. The computational complexity of the algorithm is cubic in the number of neurons. We compare the performance of the exact BM learning algorithm with first order (Weiss) mean field theory and second order (TAP) mean field theory. The learning task consists of a fully connected Ising spin glass model on 10 neurons.

The adoption of deep learning techniques in genomics has been hindered by the difficulty of mechanistically interpreting the models that these techniques produce. In recent years, a variety of post-hoc attribution methods have been proposed for addressing this neural network interpretability problem in the context of gene regulation. Here we describe a complementary way of approaching this problem. Our strategy is based on the observation that two large classes of biophysical models of cis-regulatory mechanisms can be expressed as deep neural networks in which nodes and weights have explicit physiochemical interpretations. We also demonstrate how such biophysical networks can be rapidly inferred, using modern deep learning frameworks, from the data produced by certain types of massively parallel reporter assays (MPRAs). These results suggest a scalable strategy for using MPRAs to systematically characterize the biophysical basis of gene regulation in a wide range of biological contexts. They also highlight gene regulation as a promising venue for the development of scientifically interpretable approaches to deep learning.