Mapping Materials and Molecules.

The visualization of data is indispensable in scientific research, from the early stages when human insight forms to the final step of communicating results. In computational physics, chemistry and materials science, it can be as simple as making a scatter plot or as straightforward as looking through the snapshots of atomic positions manually. However, as a result of the "big data" revolution, these conventional approaches are often inadequate. The widespread adoption of high-throughput computation for materials discovery and the associated community-wide repositories have given rise to data sets that contain an enormous number of compounds and atomic configurations. A typical data set contains thousands to millions of atomic structures, along with a diverse range of properties such as formation energies, band gaps, or bioactivities.It would thus be desirable to have a data-driven and automated framework for visualizing and analyzing such structural data sets. The key idea is to construct a low-dimensional representation of the data, which facilitates navigation, reveals underlying patterns, and helps to identify data points with unusual attributes. Such data-intensive maps, often employing machine learning methods, are appearing more and more frequently in the literature. However, to the wider community, it is not always transparent how these maps are made and how they should be interpreted. Furthermore, while these maps undoubtedly serve a decorative purpose in academic publications, it is not always apparent what extra information can be garnered from reading or making them.This Account attempts to answer such questions. We start with a concise summary of the theory of representing chemical environments, followed by the introduction of a simple yet practical conceptual approach for generating structure maps in a generic and automated manner. Such analysis and mapping is made nearly effortless by employing the newly developed software tool ASAP. To showcase the applicability to a wide variety of systems in chemistry and materials science, we provide several illustrative examples, including crystalline and amorphous materials, interfaces, and organic molecules. In these examples, the maps not only help to sift through large data sets but also reveal hidden patterns that could be easily missed using conventional analyses.The explosion in the amount of computed information in chemistry and materials science has made visualization into a science in itself. Not only have we benefited from exploiting these visualization methods in previous works, we also believe that the automated mapping of data sets will in turn stimulate further creativity and exploration, as well as ultimately feed back into future advances in the respective fields.

Analyzing global utilization and missed opportunities in debt-for-nature swaps with generative AI.

We deploy a prompt-augmented GPT-4 model to distill comprehensive datasets on the global application of debt-for-nature swaps (DNS), a pivotal financial tool for environmental conservation. Our analysis includes 195 nations and identifies 21 countries that have not yet used DNS before as prime candidates for DNS. A significant proportion demonstrates consistent commitments to conservation finance (0.86 accuracy as compared to historical swaps records). Conversely, 35 countries previously active in DNS before 2010 have since been identified as unsuitable. Notably, Argentina, grappling with soaring inflation and a substantial sovereign debt crisis, and Poland, which has achieved economic stability and gained access to alternative EU conservation funds, exemplify the shifting suitability landscape. The study's outcomes illuminate the fragility of DNS as a conservation strategy amid economic and political volatility.

Generative model-enhanced human motion prediction.

The task of predicting human motion is complicated by the natural heterogeneity and compositionality of actions, necessitating robustness to distributional shifts as far as out-of-distribution (OoD). Here, we formulate a new OoD benchmark based on the Human3.6M and Carnegie Mellon University (CMU) motion capture datasets, and introduce a hybrid framework for hardening discriminative architectures to OoD failure by augmenting them with a generative model. When applied to current state-of-the-art discriminative models, we show that the proposed approach improves OoD robustness without sacrificing in-distribution performance, and can theoretically facilitate model interpretability. We suggest human motion predictors ought to be constructed with OoD challenges in mind, and provide an extensible general framework for hardening diverse discriminative architectures to extreme distributional shift. The code is available at: https://github.com/bouracha/OoDMotion.

Data-driven discovery of molecular photoswitches with multioutput Gaussian processes.

Photoswitchable molecules display two or more isomeric forms that may be accessed using light. Separating the electronic absorption bands of these isomers is key to selectively addressing a specific isomer and achieving high photostationary states whilst overall red-shifting the absorption bands serves to limit material damage due to UV-exposure and increases penetration depth in photopharmacological applications. Engineering these properties into a system through synthetic design however, remains a challenge. Here, we present a data-driven discovery pipeline for molecular photoswitches underpinned by dataset curation and multitask learning with Gaussian processes. In the prediction of electronic transition wavelengths, we demonstrate that a multioutput Gaussian process (MOGP) trained using labels from four photoswitch transition wavelengths yields the strongest predictive performance relative to single-task models as well as operationally outperforming time-dependent density functional theory (TD-DFT) in terms of the wall-clock time for prediction. We validate our proposed approach experimentally by screening a library of commercially available photoswitchable molecules. Through this screen, we identified several motifs that displayed separated electronic absorption bands of their isomers, exhibited red-shifted absorptions, and are suited for information transfer and photopharmacological applications. Our curated dataset, code, as well as all models are made available at https://github.com/Ryan-Rhys/The-Photoswitch-Dataset.

Constrained Bayesian optimization for automatic chemical design using variational autoencoders.

Automatic Chemical Design is a framework for generating novel molecules with optimized properties. The original scheme, featuring Bayesian optimization over the latent space of a variational autoencoder, suffers from the pathology that it tends to produce invalid molecular structures. First, we demonstrate empirically that this pathology arises when the Bayesian optimization scheme queries latent space points far away from the data on which the variational autoencoder has been trained. Secondly, by reformulating the search procedure as a constrained Bayesian optimization problem, we show that the effects of this pathology can be mitigated, yielding marked improvements in the validity of the generated molecules. We posit that constrained Bayesian optimization is a good approach for solving this kind of training set mismatch in many generative tasks involving Bayesian optimization over the latent space of a variational autoencoder.