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Machine Learning (ML) has the potential to accelerate discovery of new materials and shed light on useful properties of existing materials. A key difficulty when applying ML in Materials Science is that experimental datasets of material properties tend to be small. In this work we show how material descriptors can be learned from the structures present in large scale datasets of material simulations; and how these descriptors can be used to improve the prediction of an experimental property, the energy of formation of a solid. The material descriptors are learned by training a Graph Neural Network to regress simulated formation energies from a materials atomistic structure. Using these learned features for experimental property predictions outperforms existing methods that are based solely on chemical composition. Moreover, we find that the advantage of our approach increases as the generalization requirements of the task are made more stringent, for example when limiting the amount of training data or when generalizing to unseen chemical spaces.
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Graph neural networks (GNN) have been shown to provide substantial performance improvements for representing and modeling atomistic materials compared with descriptor-based machine-learning models. While most existing GNN models for atomistic predictions are based on atomic distance information, they do not explicitly incorporate bond angles, which are critical for distinguishing many atomic structures. Furthermore, many material properties are known to be sensitive to slight changes in bond angles. We present an Atomistic Line Graph Neural Network (ALIGNN), a GNN architecture that performs message passing on both the interatomic bond graph and its line graph corresponding to bond angles. We demonstrate that angle information can be explicitly and efficiently included, leading to improved performance on multiple atomistic prediction tasks. We use ALIGNN models for predicting 52 solid-state and molecular properties available in the JARVIS-DFT, Materials project, and QM9 databases. ALIGNN can outperform some previously reported GNN models on atomistic prediction tasks by up to 85 % in accuracy with better or comparable model training speed.
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a huge number of potential chemical compounds. Machine learning methods for molecular modeling are attractive alternatives, however, the development of expressive, accurate, and scalable graph neural networks for learning molecular representations is still challenging. In this work, we propose a simple and powerful graph neural networks for molecular property prediction. We model a molecular as a directed complete graph in which each atom has a spatial position, and introduce a recursive neural network with simple gating function. We also feed input embeddings for every layers as skip connections to accelerate the training. Experimental results show that our model achieves the state-of-the-art performance on the standard benchmark dataset for molecular property prediction.
The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and bonds significantly affect the chemical properties of a molecule, so an expressive model shall be able to exploit both node (atom) and edge (bond) information simultaneously. Guided by this observation, we present Multi-View Graph Neural Network (MV-GNN), a multi-view message passing architecture to enable more accurate predictions of molecular properties. In MV-GNN, we introduce a shared self-attentive readout component and disagreement loss to stabilize the training process. This readout component also renders the whole architecture interpretable. We further boost the expressive power of MV-GNN by proposing a cross-dependent message passing scheme that enhances information communication of the two views, which results in the MV-GNN^cross variant. Lastly, we theoretically justify the expressiveness of the two proposed models in terms of distinguishing non-isomorphism graphs. Extensive experiments demonstrate that MV-GNN models achieve remarkably superior performance over the state-of-the-art models on a variety of challenging benchmarks. Meanwhile, visualization results of the node importance are consistent with prior knowledge, which confirms the interpretability power of MV-GNN models.
Emergent functionalities of structural and topological defects in ferroelectric materials underpin an extremely broad spectrum of applications ranging from domain wall electronics to high dielectric and electromechanical responses. Many of these have been discovered and quantified via local scanning probe microscopy methods. However, the search for these functionalities has until now been based by either trial and error or using auxiliary information such as topography or domain wall structure to identify potential objects of interest based on the intuition of operator or preexisting hypotheses, with subsequent manual exploration. Here, we report the development and implementation of a machine learning framework that actively discovers relationships between local domain structure and polarization switching characteristics in ferroelectric materials encoded in the hysteresis loop. The latter and descriptors such as nucleation bias, coercive bias, hysteresis loop area, or more complex functionals of hysteresis loop shape and corresponding uncertainties are used to guide the discovery via automated piezoresponse force microscopy (PFM) and spectroscopy experiments. As such, this approach combines the power of machine learning methods to learn the correlative relationships between high dimensional data, and human-based physics insights encoded in the acquisition function. For ferroelectric, this automated workflow demonstrates that the discovery path and sampling points of on-field and off-field hysteresis loops are largely different, indicating the on-field and off-field hysteresis loops are dominated by different mechanisms. The proposed approach is universal and can be applied to a broad range of modern imaging and spectroscopy methods ranging from other scanning probe microscopy modalities to electron microscopy and chemical imaging.
Molecular property prediction plays a fundamental role in drug discovery to discover candidate molecules with target properties. However, molecular property prediction is essentially a few-shot problem which makes it hard to obtain regular models. In this paper, we propose a property-aware adaptive relation networks (PAR) for the few-shot molecular property prediction problem. In comparison to existing works, we leverage the facts that both substructures and relationships among molecules are different considering various molecular properties. Our PAR is compatible with existing graph-based molecular encoders, and are further equipped with the ability to obtain property-aware molecular embedding and model molecular relation graph adaptively. The resultant relation graph also facilitates effective label propagation within each task. Extensive experiments on benchmark molecular property prediction datasets show that our method consistently outperforms state-of-the-art methods and is able to obtain property-aware molecular embedding and model molecular relation graph properly.
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