We propose a unified framework based on persistent homology (PH) to characterize both local and global structures in disordered systems. It can simultaneously generate local and global descriptors using the same algorithm and data structure, and has shown to be highly effective and interpretable in predicting particle rearrangements and classifying global phases. We also demonstrated that using a single variable enables a linear SVM to achieve nearly perfect three-phase classification. Inspired by this discovery, we define a non-parametric metric, the Separation Index (SI), which not only achieves this classification without sacrificing significant performance but also establishes a connection between particle environments and the global phase structure. Our methods provide an effective framework for understanding and analyzing the properties of disordered materials, with broad potential applications in materials science and even wider studies of complex systems.

Crystallization processes at the mesoscopic scale, where faceted, dendritic growth, and multigrain formation can be observed, are of particular interest within materials science and metallurgy. These processes are highly nonlinear, stochastic, and sensitive to small perturbations of system parameters and initial conditions. Methods for the simulation of these processes have been developed using discrete numerical models, but these are computationally expensive. This work aims to scale crystal growth simulation with a machine learning emulator. Specifically, autoregressive latent variable models are well suited for modeling the joint distribution over system parameters and the crystallization trajectories. However, successfully training such models is challenging due to the stochasticity and sensitivity of the system. Existing approaches consequently fail to produce diverse and faithful crystallization trajectories. In this paper, we introduce the Crystal Growth Neural Emulator (CGNE), a probabilistic model for efficient crystal growth emulation at the mesoscopic scale that overcomes these challenges. We validate CGNE results using the morphological properties of the crystals produced by numerical simulation. CGNE delivers a factor of 11 improvement in inference time and performance gains compared with recent state-of-the-art probabilistic models for dynamical systems.

Automation can transform productivity in research activities that use liquid handling, such as organic synthesis, but it has made less impact in materials laboratories, which require sample preparation steps and a range of solid-state characterization techniques. For example, powder X-ray diffraction (PXRD) is a key method in materials and pharmaceutical chemistry, but its end-to-end automation is challenging because it involves solid powder handling and sample processing. Here we present a fully autonomous solid-state workflow for PXRD experiments that can match or even surpass manual data quality. The workflow involves 12 steps performed by a team of three multipurpose robots, illustrating the power of flexible, modular automation to integrate complex, multitask laboratories.

Crystallization of the amorphous phases into metastable crystals plays a fundamental role in the formation of new matter, from geological to biological processes in nature to synthesis and development of new materials in the laboratory. Predicting the outcome of such phase transitions reliably would enable new research directions in these areas, but has remained beyond reach with molecular modeling or ab-initio methods. Here, we show that crystallization products of amorphous phases can be predicted in any inorganic chemistry by sampling the crystallization pathways of their local structural motifs at the atomistic level using universal deep learning potentials. We show that this approach identifies the crystal structures of polymorphs that initially nucleate from amorphous precursors with high accuracy across a diverse set of material systems, including polymorphic oxides, nitrides, carbides, fluorides, chlorides, chalcogenides, and metal alloys. Our results demonstrate that Ostwald's rule of stages can be exploited mechanistically at the molecular level to predictably access new metastable crystals from the amorphous phase in material synthesis.

Most existing digital twins rely on data-driven black-box models, predominantly using deep neural recurrent, and convolutional neural networks (DNNs, RNNs, and CNNs) to capture the dynamics of chemical systems. However, these models have not seen the light of day, given the hesitance of directly deploying a black-box tool in practice due to safety and operational issues. To tackle this conundrum, hybrid models combining first-principles physics-based dynamics with machine learning (ML) models have increased in popularity as they are considered a 'best of both worlds' approach. That said, existing simple DNN models are not adept at long-term time-series predictions and utilizing contextual information on the trajectory of the process dynamics. Recently, attention-based time-series transformers (TSTs) that leverage multi-headed attention mechanism and positional encoding to capture long-term and short-term changes in process states have shown high predictive performance. Thus, a first-of-a-kind, TST-based hybrid framework has been developed for batch crystallization, demonstrating improved accuracy and interpretability compared to traditional black-box models. Specifically, two different configurations (i.e., series and parallel) of TST-based hybrid models are constructed and compared, which show a normalized-mean-square-error (NMSE) in the range of $[10, 50]\times10^{-4}$ and an $R^2$ value over 0.99. Given the growing adoption of digital twins, next-generation attention-based hybrid models are expected to play a crucial role in shaping the future of chemical manufacturing.

Members of the Google Brain team today announced that they have crafted computer vision for the identification of protein crystallization, claiming accuracy rates around 94 percent. Protein crystallization determines the shape of cells and can play a role in discovery of drugs to treat various illnesses. "Hundreds of experiments are typically run for each protein, and while the setup and imaging are mostly automated, finding individual protein crystals remains largely performed through visual inspection and thus prone to human error," Google Brain principal scientist Vincent Vanhoucke said in a blog post today. "Critically, missing these structures can result in lost opportunity for important biomedical discoveries for advancing the state of medicine." To train the AI model, Google researchers worked with the Machine Recognition of Crystallization Outcomes (MARCO) initiative, a partnership between pharmaceutical companies and academics.

Case-based reasoning (CBR) is a computational reasoning paradigm that involves the storage and retrieval of past experiences to solve novel problems. It is an approach that is particularly relevant in scientific domains, where there is a wealth of data but often a lack of theories or general principles. This article describes several CBR systems that have been developed to carry out planning, analysis, and prediction in the domain of molecular biology. Experts remember positive experiences for possible reuse of solutions; negative experiences are used to avoid potentially unsuccessful outcomes. Similar to other scientific domains, problem solving in molecular biology can benefit from systematic knowledge management using techniques from AI. Case-based reasoning (CBR) is particularly applicable to this problem domain because it (1) supports rich and evolvable representation of experiences--problems, solutions, and feedback; (2) provides efficient and flexible ways to retrieve these experiences; and (3) applies analogical reasoning to solve novel problems.

Obtaining a protein's 3D structure is crucial to the understanding of its functions and interactions with other proteins. It is critical to accelerate the protein crystallization process with improved accuracy for understanding cancer and designing drugs. Systematic high-throughput approaches in protein crystallization have been widely applied, generating a large number of protein crystallization-trial images. Therefore, an efficient and effective automatic analysis for these images is a top priority. In this paper, we present a novel system, CrystalNet, for automatically labeling outcomes of protein crystallization-trial images. CrystalNet is a deep convolutional neural network that automatically extracts features from X-ray protein crystallization images for classification. We show that (1) CrystalNet can provide real-time labels for crystallization images effectively, requiring approximately 2 seconds to provide labels for all 1536 images of crystallization microassay on each plate; (2) compared with the state-of-the-art classification systems in crystallization image analysis, our technique demonstrates an improvement of 8% in accuracy, and achieve 90.8% accuracy in classification. As a part of the high-throughput pipeline which generates millions of images a year, CrystalNet can lead to a substantial reduction of labor-intensive screening.

Thus, one of the primary goals of a CBR system is to find the most similar, or most relevant, cases for new input problems. The effectiveness of CBR depends on the quality and quantity of cases in a case base. In some domains, even a small number of cases provide good solutions, but in other domains, an increased number of unique cases improves problemsolving capabilities of CBR systems because there are more experiences to draw on. The reader can find detailed complete theories, and rapid evolution; reasoning descriptions of the CBR process and systems in is often based on experience rather Kolodner (1993). Experts remember are presented in Leake (1996), and practically positive experiences for possible reuse of solutions; negative experiences are used to avoid oriented descriptions of CBR can be potentially unsuccessful outcomes.