Information theory unifies atomistic machine learning, uncertainty quantification, and materials thermodynamics

An accurate description of information is relevant for a range of problems in atomistic modeling, such as sampling methods, detecting rare events, analyzing datasets, or performing uncertainty quantification (UQ) in machine learning (ML)-driven simulations. Although individual methods have been proposed for each of these tasks, they lack a common theoretical background integrating their solutions. Here, we introduce an information theoretical framework that unifies predictions of phase transformations, kinetic events, dataset optimality, and model-free UQ from atomistic simulations, thus bridging materials modeling, ML, and statistical mechanics. We first demonstrate that, for a proposed representation, the information entropy of a distribution of atom-centered environments is a surrogate value for thermodynamic entropy. Using molecular dynamics (MD) simulations, we show that information entropy differences from trajectories can be used to build phase diagrams, identify rare events, and recover classical theories of nucleation. Building on these results, we use this general concept of entropy to quantify information in datasets for ML interatomic potentials (IPs), informing compression, explaining trends in testing errors, and evaluating the efficiency of active learning strategies. Finally, we propose a model-free UQ method for MLIPs using information entropy, showing it reliably detects extrapolation regimes, scales to millions of atoms, and goes beyond model errors. This method is made available as the package QUESTS: Quick Uncertainty and Entropy via STructural Similarity, providing a new unifying theory for data-driven atomistic modeling and combining efforts in ML, first-principles thermodynamics, and simulations.

LTAU-FF: Loss Trajectory Analysis for Uncertainty in Atomistic Force Fields

Model ensembles are simple and effective tools for estimating the prediction uncertainty of deep learning atomistic force fields. Despite this, widespread adoption of ensemble-based uncertainty quantification (UQ) techniques is limited by the high computational costs incurred by ensembles during both training and inference. In this work we leverage the cumulative distribution functions (CDFs) of per-sample errors obtained over the course of training to efficiently represent the model ensemble, and couple them with a distance-based similarity search in the model latent space. Using these tools, we develop a simple UQ metric (which we call LTAU) that leverages the strengths of ensemble-based techniques without requiring the evaluation of multiple models during either training or inference. As an initial test, we apply our method towards estimating the epistemic uncertainty in atomistic force fields (LTAU-FF) and demonstrate that it can be easily calibrated to accurately predict test errors on multiple datasets from the literature. We then illustrate the utility of LTAU-FF in two practical applications: 1) tuning the training-validation gap for an example dataset, and 2) predicting errors in relaxation trajectories on the OC20 IS2RS task. Though in this work we focus on the use of LTAU with deep learning atomistic force fields, we emphasize that it can be readily applied to any regression task, or any ensemble-generation technique, to provide a reliable and easy-to-implement UQ metric.

Spectroscopy-Guided Discovery of Three-Dimensional Structures of Disordered Materials with Diffusion Models

The ability to rapidly develop materials with desired properties has a transformative impact on a broad range of emerging technologies. In this work, we introduce a new framework based on the diffusion model, a recent generative machine learning method to predict 3D structures of disordered materials from a target property. For demonstration, we apply the model to identify the atomic structures of amorphous carbons ($a$-C) as a representative material system from the target X-ray absorption near edge structure (XANES) spectra--a common experimental technique to probe atomic structures of materials. We show that conditional generation guided by XANES spectra reproduces key features of the target structures. Furthermore, we show that our model can steer the generative process to tailor atomic arrangements for a specific XANES spectrum. Finally, our generative model exhibits a remarkable scale-agnostic property, thereby enabling generation of realistic, large-scale structures through learning from a small-scale dataset (i.e., with small unit cells). Our work represents a significant stride in bridging the gap between materials characterization and atomic structure determination; in addition, it can be leveraged for materials discovery in exploring various material properties as targeted.

Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments

The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets. A novel method that combines the linear mapping hash function and multiple sequence alignment (MSA) was developed. This method takes advantage of the already sorted by similarity sequences from the MSA output, and identifies the optimal number of clusters, clusters cut-offs, and clusters centroids that can represent reference gene vouchers for the different species. The linear mapping hash function can map an already ordered by similarity distance matrix to indices to reveal gaps in the values around which the optimal cut-offs of the different clusters can be identified. The method was evaluated using sets of closely related (16S rRNA gene sequences of Nocardia species) and highly variable (VP1 genomic region of Enterovirus 71) sequences and outperformed existing unsupervised machine learning clustering methods and dimensionality reduction methods. This method does not require prior knowledge of the number of clusters or the distance between clusters, handles clusters of different sizes and shapes, and scales linearly with the dataset. The combination of MSA with the linear mapping hash function is a computationally efficient way of gene sequence clustering and can be a valuable tool for the assessment of similarity, clustering of different microbial genomes, identifying reference sequences, and for the study of evolution of bacteria and viruses.

Score dynamics: scaling molecular dynamics with picosecond timesteps via conditional diffusion model

We propose score dynamics (SD), a general framework for learning effective evolution operators for atomistic as well as coarse-grained dynamics from molecular-dynamics (MD) simulations. SD is centered around scores, or derivatives of the transition log-probability with respect to the dynamical degrees of freedom. The latter play the same role as force fields in MD but are used in denoising diffusion probability models to generate discrete transitions of the dynamical variables in an SD timestep, which can be orders of magnitude larger than a typical MD timestep. In this work, we construct graph neural network based score dynamics models of realistic molecular systems that are evolved with 1~ps timesteps. We demonstrate the efficacy of score dynamics with case studies of alanine dipeptide and short alkanes in aqueous solution. Both equilibrium predictions derived from the stationary distributions of the conditional probability and kinetic predictions for the transition rates and transition paths are in good agreement with MD at about 8-18 fold wall-clock speedup. Open challenges and possible future remedies to improve score dynamics are also discussed.

Learning dislocation dynamics mobility laws from large-scale MD simulations

The computational method of discrete dislocation dynamics (DDD), used as a coarse-grained model of true atomistic dynamics of lattice dislocations, has become of powerful tool to study metal plasticity arising from the collective behavior of dislocations. As a mesoscale approach, motion of dislocations in the DDD model is prescribed via the mobility law; a function which specifies how dislocation lines should respond to the driving force. However, the development of traditional hand-crafted mobility laws can be a cumbersome task and may involve detrimental simplifications. Here we introduce a machine-learning (ML) framework to streamline the development of data-driven mobility laws which are modeled as graph neural networks (GNN) trained on large-scale Molecular Dynamics (MD) simulations of crystal plasticity. We illustrate our approach on BCC tungsten and demonstrate that our GNN mobility implemented in large-scale DDD simulations accurately reproduces the challenging tension/compression asymmetry observed in ground-truth MD simulations while correctly predicting the flow stress at lower straining rate conditions unseen during training, thereby demonstrating the ability of our method to learn relevant dislocation physics. Our DDD+ML approach opens new promising avenues to improve fidelity of the DDD model and to incorporate more complex dislocation motion behaviors in an automated way, providing a faithful proxy for dislocation dynamics several orders of magnitude faster than ground-truth MD simulations.

Collaborative Auto-encoding for Blind Image Quality Assessment

Blind image quality assessment (BIQA) is a challenging problem with important real-world applications. Recent efforts attempting to exploit powerful representations by deep neural networks (DNN) are hindered by the lack of subjectively annotated data. This paper presents a novel BIQA method which overcomes this fundamental obstacle. Specifically, we design a pair of collaborative autoencoders (COAE) consisting of a content autoencoder (CAE) and a distortion autoencoder (DAE) that work together to extract content and distortion representations, which are shown to be highly descriptive of image quality. While the CAE follows a standard codec procedure, we introduce the CAE-encoded feature as an extra input to the DAE's decoder for reconstructing distorted images, thus effectively forcing DAE's encoder to extract distortion representations. The self-supervised learning framework allows the COAE including two feature extractors to be trained by almost unlimited amount of data, thus leaving limited samples with annotations to finetune a BIQA model. We will show that the proposed BIQA method achieves state-of-the-art performance and has superior generalization capability over other learning based models. The codes are available at: https://github.com/Macro-Zhou/NRIQA-VISOR/.

One-Stage Cascade Refinement Networks for Infrared Small Target Detection

Single-frame InfraRed Small Target (SIRST) detection has been a challenging task due to a lack of inherent characteristics, imprecise bounding box regression, a scarcity of real-world datasets, and sensitive localization evaluation. In this paper, we propose a comprehensive solution to these challenges. First, we find that the existing anchor-free label assignment method is prone to mislabeling small targets as background, leading to their omission by detectors. To overcome this issue, we propose an all-scale pseudo-box-based label assignment scheme that relaxes the constraints on scale and decouples the spatial assignment from the size of the ground-truth target. Second, motivated by the structured prior of feature pyramids, we introduce the one-stage cascade refinement network (OSCAR), which uses the high-level head as soft proposals for the low-level refinement head. This allows OSCAR to process the same target in a cascade coarse-to-fine manner. Finally, we present a new research benchmark for infrared small target detection, consisting of the SIRST-V2 dataset of real-world, high-resolution single-frame targets, the normalized contrast evaluation metric, and the DeepInfrared toolkit for detection. We conduct extensive ablation studies to evaluate the components of OSCAR and compare its performance to state-of-the-art model-driven and data-driven methods on the SIRST-V2 benchmark. Our results demonstrate that a top-down cascade refinement framework can improve the accuracy of infrared small target detection without sacrificing efficiency. The DeepInfrared toolkit, dataset, and trained models are available at https://github.com/YimianDai/open-deepinfrared to advance further research in this field.

Score-based denoising for atomic structure identification

We propose an accurate method for removing thermal vibrations that complicate the task of analyzing complex dynamics in atomistic simulation of condensed matter. Our method iteratively subtracts thermal noises or perturbations in atomic positions using a denoising score function trained on synthetically noised but otherwise perfect crystal lattices. The resulting denoised structures clearly reveal underlying crystal order while retaining disorder associated with crystal defects. Purely geometric, agnostic to interatomic potentials, and trained without inputs from explicit simulations, our denoiser can be applied to simulation data generated from vastly different interatomic interactions. Followed by a simple phase classification tool such as the Common Neighbor Analysis, the denoiser outperforms other existing methods and reaches perfect classification accuracy on a recently proposed benchmark dataset consisting of perturbed crystal structures (DC3). Demonstrated here in a wide variety of atomistic simulation contexts, the denoiser is general, robust, and readily extendable to delineate order from disorder in structurally and chemically complex materials.