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Creators/Authors contains: "Deagen, Michael E."

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  1. ; ; ; ; ; ; ; ( , Macromolecules)
    Defining the similarity between chemical entities is an essential task in polymer informatics, enabling ranking, clustering, and classification. Despite its importance, the pairwise chemical similarity of polymers remains an open problem. Here, a similarity function for polymers with well-defined backbones is designed based on polymers’ stochastic graph representations generated from canonical BigSMILES, a structurally based line notation for describing macromolecules. The stochastic graph representations are separated into three parts: repeat units, end groups, and polymer topology. The earth mover’s distance is utilized to calculate the similarity of the repeat units and end groups, while the graph edit distance is used to calculate the similarity of the topology. These three values can be linearly or nonlinearly combined to yield an overall pairwise chemical similarity score for polymers that is largely consistent with the chemical intuition of expert users and is adjustable based on the relative importance of different chemical features for a given similarity problem. This method gives a reliable solution to quantitatively calculate the pairwise chemical similarity score for polymers and represents a vital step toward building search engines and quantitative design tools for polymer data. 
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    Free, publicly-accessible full text available September 26, 2024
  2. ; ; ; ; ; ; ; ; ( , Cell Reports Physical Science)
    Autonomous experimental systems offer a compelling glimpse into a future where closed-loop, iterative cycles—performed by machines and guided by artificial intelligence (AI) and machine learning (ML)—play a foundational role in materials research and development. This perspective draws attention to the roles of networks and interfaces—of and between humans and machines—for the purpose of generating knowledge and accelerating innovation. Polymers, a class of materials with massive global impact, present a unique opportunity for the application of informatics and automation to pressing societal challenges. To develop these networks and interfaces in polymer science, the Community Resource for Innovation in Polymer Technology (CRIPT)—a polymer data ecosystem based on novel polymer data model, representation, search, and visualization technologies—is introduced. The ongoing co-design efforts engage stakeholders in industry, academia, and government to uncover rapidly actionable, high-impact opportunities to build networks, bridge interfaces, and catalyze innovation in polymer technology. 
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    Full Text Available 
  3. ; ; ; ; ; ; ( , Scientific Data)
    Abstract

    Graph databases capture richly linked domain knowledge by integrating heterogeneous data and metadata into a unified representation. Here, we present the use of bespoke, interactive data graphics (bar charts, scatter plots, etc.) for visual exploration of a knowledge graph. By modeling a chart as a set of metadata that describes semantic context (SPARQL query) separately from visual context (Vega-Lite specification), we leverage the high-level, declarative nature of the SPARQL and Vega-Lite grammars to concisely specify web-based, interactive data graphics synchronized to a knowledge graph. Resources with dereferenceable URIs (uniform resource identifiers) can employ the hyperlink encoding channel or image marks in Vega-Lite to amplify the information content of a given data graphic, and published charts populate a browsable gallery of the database. We discuss design considerations that arise in relation to portability, persistence, and performance. Altogether, this pairing of SPARQL and Vega-Lite—demonstrated here in the domain of polymer nanocomposite materials science—offers an extensible approach to FAIR (findable, accessible, interoperable, reusable) scientific data visualization within a knowledge graph framework.

     
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  4. ; ; ; ; ; ; ; ; ( , ACS Polymers Au)
  5. ; ; ; ( , MRS Bulletin)
    Abstract

    For over three decades, the materials tetrahedron has captured the essence of materials science and engineering with its interdependent elements of processing, structure, properties, and performance. As modern computational and statistical techniques usher in a new paradigm of data-intensive scientific research and discovery, the rate at which the field of materials science and engineering capitalizes on these advances hinges on collaboration between numerous stakeholders. Here, we provide a contemporary extension to the classic materials tetrahedron with a dual framework—adapted from the concept of a “digital twin”—which offers a nexus joining materials science and information science. We believe this high-level framework, the materials–information twin tetrahedra (MITT), will provide stakeholders with a platform to contextualize, translate, and direct efforts in the pursuit of propelling materials science and technology forward.

     Impact statement

    This article provides a contemporary reimagination of the classic materials tetrahedron by augmenting it with parallel notions from information science. Since the materials tetrahedron (processing, structure, properties, performance) made its first debut, advances in computational and informational tools have transformed the landscape and outlook of materials research and development. Drawing inspiration from the notion of a digital twin, the materials–information twin tetrahedra (MITT) framework captures a holistic perspective of materials science and engineering in the presence of modern digital tools and infrastructures. This high-level framework incorporates sustainability and FAIR data principles (Findable, Accessible, Interoperable, Reusable)—factors that recognize how systems impact and interact with other systems—in addition to the data and information flows that play a pivotal role in knowledge generation. The goal of the MITT framework is to give stakeholders from academia, industry, and government a communication tool for focusing efforts around the design, development, and deployment of materials in the years ahead.

     Graphic abstract 
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  6. ; ; ; ; ; ( , Macromolecules)
  7. ; ; ; ; ; ; ; ; ; ; et al ( , ACS Central Science)