arXiv subjects

Jane Greenberg

Publications and source records attributed to Jane Greenberg.

At least 19 recordsLinked to original sources

arXiv2025

Human-in-the-Loop and AI: Crowdsourcing Metadata Vocabulary for Materials Science

Metadata vocabularies are essential for advancing FAIR and FARR data principles, but their development constrained by limited human resources and inconsistent standardization practices. This paper introduces MatSci-YAMZ, a platform that integrates artificial intelligence (AI) and human-in-the-loop (HILT), including crowdsourcing, to support metadata vocabulary development. The paper reports on a proof-of-concept use case evaluating the AI-HILT model in materials science, a highly interdisciplinary domain Six (6) participants affiliated with the NSF Institute for Data-Driven Dynamical Design (ID4) engaged with the MatSci-YAMZ plaform over several weeks, contributing term definitions and providing examples to prompt the AI-definitions refinement. Nineteen (19) AI-generated definitions were successfully created, with iterative feedback loops demonstrating the feasibility of AI-HILT refinement. Findings confirm the feasibility AI-HILT model highlighting 1) a successful proof of concept, 2) alignment with FAIR and open-science principles, 3) a research protocol to guide future studies, and 4) the potential for scalability across domains. Overall, MatSci-YAMZ's underlying model has the capacity to enhance semantic transparency and reduce time required for consensus building and metadata vocabulary development.

cs.AI↗

arXiv2025

Rate-Distortion Guided Knowledge Graph Construction from Lecture Notes Using Gromov-Wasserstein Optimal Transport

Task-oriented knowledge graphs (KGs) enable AI-powered learning assistant systems to automatically generate high-quality multiple-choice questions (MCQs). Yet converting unstructured educational materials, such as lecture notes and slides, into KGs that capture key pedagogical content remains difficult. We propose a framework for knowledge graph construction and refinement grounded in rate-distortion (RD) theory and optimal transport geometry. In the framework, lecture content is modeled as a metric-measure space, capturing semantic and relational structure, while candidate KGs are aligned using Fused Gromov-Wasserstein (FGW) couplings to quantify semantic distortion. The rate term, expressed via the size of KG, reflects complexity and compactness. Refinement operators (add, merge, split, remove, rewire) minimize the rate-distortion Lagrangian, yielding compact, information-preserving KGs. Our prototype applied to data science lectures yields interpretable RD curves and shows that MCQs generated from refined KGs consistently surpass those from raw notes on fifteen quality criteria. This study establishes a principled foundation for information-theoretic KG optimization in personalized and AI-assisted education.

cs.AI↗

arXiv2025

Towards MatCore: A Unified Metadata Standard for Materials Science

The materials science community seeks to support the FAIR principles for computational simulation research. The MatCore Project was recently launched to address this need, with the goal of developing an overall metadata framework and accompanying guidelines. This paper reports on the MatCore goals and overall progress. Historical background context is provided, including a review of the principles underlying successful core metadata standards. The paper also presents selected MatCore examples and discusses future plans.

cond-mat.mtrl-sci↗

arXiv2024

Enhancing Semantic Interoperability Across Materials Science With HIVE4MAT

HIVE4MAT is a linked data interactive application for navigating ontologies of value to materials science. HIVE enables automatic indexing of textual resources with standardized terminology. This article presents the motivation underlying HIVE4MAT, explains the system architecture, reports on two evaluations, and discusses future plans.

cs.IR↗

arXiv2024

Making Sense of Metadata Mess: Alignment & Risk Assessment for Diatom Data Use Case

Biologists study Diatoms, a fundamental algae, to assess the health of aquatic systems. Diatom specimens have traditionally been preserved on analog slides, where a single slide can contain thousands of these microscopic organisms. Digitization of these collections presents both metadata challenges and opportunities. This paper reports on metadata research aimed at providing access to a digital portion of the Academy of Natural Sciences' Diatom Herbarium, Drexel University. We report results of a 3-part study covering 1) a review of relevant metadata standards and a microscopy metadata framework shared by Hammer et al., 2) a baseline metadata alignment mapping current diatom metadata properties to standard metadata types, and 3) a metadata risk analysis associated with the course of standard data curation practices. This research is part of an effort involving the transfer of these digital slides to an new system, DataFed, to support global accessible. The final section of this paper includes a conclusion and discusses next steps.

cs.IR↗

arXiv2024

Research evolution of metal organic frameworks: A scientometric approach with human-in-the-loop

This paper reports on a scientometric analysis bolstered by human in the loop, domain experts, to examine the field of metal organic frameworks (MOFs) research. Scientometric analyses reveal the intellectual landscape of a field. The study engaged MOF scientists in the design and review of our research workflow. MOF materials are an essential component in next generation renewable energy storage and biomedical technologies. The research approach demonstrates how engaging experts, via human in the loop processes, can help develop a comprehensive view of a field research trends, influential works, and specialized topics.

cs.DL↗

arXiv2024

Knowledge Graph Question Answering for Materials Science (KGQA4MAT): Developing Natural Language Interface for Metal-Organic Frameworks Knowledge Graph (MOF-KG) Using LLM

We present a comprehensive benchmark dataset for Knowledge Graph Question Answering in Materials Science (KGQA4MAT), with a focus on metal-organic frameworks (MOFs). A knowledge graph for metal-organic frameworks (MOF-KG) has been constructed by integrating structured databases and knowledge extracted from the literature. To enhance MOF-KG accessibility for domain experts, we aim to develop a natural language interface for querying the knowledge graph. We have developed a benchmark comprised of 161 complex questions involving comparison, aggregation, and complicated graph structures. Each question is rephrased in three additional variations, resulting in 644 questions and 161 KG queries. To evaluate the benchmark, we have developed a systematic approach for utilizing the LLM, ChatGPT, to translate natural language questions into formal KG queries. We also apply the approach to the well-known QALD-9 dataset, demonstrating ChatGPT's potential in addressing KGQA issues for different platforms and query languages. The benchmark and the proposed approach aim to stimulate further research and development of user-friendly and efficient interfaces for querying domain-specific materials science knowledge graphs, thereby accelerating the discovery of novel materials.

cs.AI↗

arXiv2024

Characterizing Semantic Ambiguity of the Materials Science Ontologies

Growth in computational materials science and initiatives such as the Materials Genome Initiative (MGI) and the European Materials Modelling Council (EMMC) has motivated the development and application of ontologies. A key factor has been increased adoption of the FAIR principles, making research data findable, accessible, interoperable, and reusable (Wilkinson et al. 2016). This paper characterizes semantic interoperability among a subset of materials science ontologies in the MatPortal repository. Background context covers semantic interoperability, ontological commitment, and the materials science ontology landscape. The research focused on MatPortal's two interoperability protocols: LOOM term matching and URI matching. Results report the degree of overlap and demonstrate the different types of ambiguity among ontologies. The discussion considers implications for FAIR and AI, and the conclusion highlight key findings and next steps.

cs.DL↗

arXiv2023

Building Open Knowledge Graph for Metal-Organic Frameworks (MOF-KG): Challenges and Case Studies

Metal-Organic Frameworks (MOFs) are a class of modular, porous crystalline materials that have great potential to revolutionize applications such as gas storage, molecular separations, chemical sensing, catalysis, and drug delivery. The Cambridge Structural Database (CSD) reports 10,636 synthesized MOF crystals which in addition contains ca. 114,373 MOF-like structures. The sheer number of synthesized (plus potentially synthesizable) MOF structures requires researchers pursue computational techniques to screen and isolate MOF candidates. In this demo paper, we describe our effort on leveraging knowledge graph methods to facilitate MOF prediction, discovery, and synthesis. We present challenges and case studies about (1) construction of a MOF knowledge graph (MOF-KG) from structured and unstructured sources and (2) leveraging the MOF-KG for discovery of new or missing knowledge.

cs.AI↗

arXiv2023

Metadata for Scientific Experiment Reporting: A Case Study in Metal-Organic Frameworks

Research methods and procedures are core aspects of the research process. Metadata focused on these components is critical to supporting the FAIR principles, particularly reproducibility. The research reported on in this paper presents a methodological framework for metadata documentation supporting the reproducibility of research producing Metal Organic Frameworks (MOFs). The MOF case study involved natural language processing to extract key synthesis experiment information from a corpus of research literature. Following, a classification activity was performed by domain experts to identify entity-relation pairs. Results include: 1) a research framework for metadata design, 2) a metadata schema that includes nine entities and two relationships for reporting MOF synthesis experiments, and 3) a growing database of MOF synthesis reports structured by our metadata scheme. The metadata schema is intended to support discovery and reproducibility of metal-organic framework research and the FAIR principles. The paper provides background information, identifies the research goals and objectives, research design, results, a discussion, and the conclusion.

cs.DL↗

arXiv2022

Materials Science Ontology Design with an Analytico-Synthetic Facet Analysis Framework

Researchers across nearly every discipline seek to leverage ontologies for knowledge discovery and computational tasks; yet, the number of machine readable materials science ontologies is limited. The work presented in this paper explores the Processing, Structure, Properties and Performance (PSPP) framework for accelerating the development of materials science ontologies. We pursue a case study framed by the creation of an Aerogel ontology and a Battery Cathode ontology and demonstrate the Helping Interdisciplinary Vocabulary Engineer for Materials Science (HIVE4MAT) as a proof of concept showing PSPP relationships. The paper includes background context covering materials science, the PSPP framework, and faceted analysis for ontologies. We report our research objectives, methods, research procedures, and results. The findings indicate that the PSPP framework offers a rubric that may help guide and potentially accelerate ontology development.

cs.DL↗

arXiv2022

Toward a Flexible Metadata Pipeline for Fish Specimen Images

Flexible metadata pipelines are crucial for supporting the FAIR data principles. Despite this need, researchers seldom report their approaches for identifying metadata standards and protocols that support optimal flexibility. This paper reports on an initiative targeting the development of a flexible metadata pipeline for a collection containing over 300,000 digital fish specimen images, harvested from multiple data repositories and fish collections. The images and their associated metadata are being used for AI-related scientific research involving automated species identification, segmentation and trait extraction. The paper provides contextual background, followed by the presentation of a four-phased approach involving: 1. Assessment of the Problem, 2. Investigation of Solutions, 3. Implementation, and 4. Refinement. The work is part of the NSF Harnessing the Data Revolution, Biology Guided Neural Networks (NSF/HDR-BGNN) project and the HDR Imageomics Institute. An RDF graph prototype pipeline is presented, followed by a discussion of research implications and conclusion summarizing the results.

cs.CV↗

arXiv2022

Exploring Wasserstein Distance across Concept Embeddings for Ontology Matching

Measuring the distance between ontological elements is fundamental for ontology matching. String-based distance metrics are notorious for shallow syntactic matching. In this exploratory study, we investigate Wasserstein distance targeting continuous space that can incorporate various types of information. We use a pre-trained word embeddings system to embed ontology element labels. We examine the effectiveness of Wasserstein distance for measuring similarity between ontologies, and discovering and refining matchings between individual elements. Our experiments with the OAEI conference track and MSE benchmarks achieved competitive results compared to the leading systems.

cs.AI↗

arXiv2022

Temporal Concept Drift and Alignment: An empirical approach to comparing Knowledge Organization Systems over time

This research explores temporal concept drift and temporal alignment in knowledge organization systems (KOS). A comparative analysis is pursued using the 1910 Library of Congress Subject Headings, 2020 FAST Topical, and automatic indexing. The use case involves a sample of 90 nineteenth-century Encyclopedia Britannica entries. The entries were indexed using two approaches: 1) full-text indexing; 2) Named Entity Recognition was performed upon the entries with Stanza, Stanford's NLP toolkit, and entities were automatically indexed with the Helping Interdisciplinary Vocabulary application (HIVE), using both 1910 LCSH and FAST Topical. The analysis focused on three goals: 1) identifying results that were exclusive to the 1910 LCSH output; 2) identifying terms in the exclusive set that have been deprecated from the contemporary LCSH, demonstrating temporal concept drift; and 3) exploring the historical significance of these deprecated terms. Results confirm that historical vocabularies can be used to generate anachronistic subject headings representing conceptual drift across time in KOS and historical resources. A methodological contribution is made demonstrating how to study changes in KOS over time and improve the contextualization of historical humanities resources.

cs.CL↗

arXiv2022

MEDFORD: A human and machine readable metadata markup language

Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle, or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space to store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEDFORD, in which scientists can record all details relevant to their research. Human-readable, easily-editable, and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections.

cs.DL↗

arXiv2021

FAIR Metadata: A Community-driven Vocabulary Application

FAIR metadata is critical to supporting FAIR data overall. Transparency, community engagement, and flexibility are key aspects of FAIR that apply to metadata. This paper presents YAMZ (Yet Another Metadata Zoo), a community-driven vocabulary application that supports FAIR. The history ofYAMZ and its original features are reviewed, followed by a presentation of recent innovations and a discussion of how YAMZ supports FAIR principles. The conclusion identifies next steps and key outputs.

cs.DL↗

arXiv2021

Clustering and Network Analysis for the Embedding Spaces of Sentences and Sub-Sentences

Sentence embedding methods offer a powerful approach for working with short textual constructs or sequences of words. By representing sentences as dense numerical vectors, many natural language processing (NLP) applications have improved their performance. However, relatively little is understood about the latent structure of sentence embeddings. Specifically, research has not addressed whether the length and structure of sentences impact the sentence embedding space and topology. This paper reports research on a set of comprehensive clustering and network analyses targeting sentence and sub-sentence embedding spaces. Results show that one method generates the most clusterable embeddings. In general, the embeddings of span sub-sentences have better clustering properties than the original sentences. The results have implications for future sentence embedding models and applications.

cs.CL↗

arXiv2021

Modeling Ephraim Chambers' Knowledge Structure from a Naive Standpoint

In the preface to his Cyclopaedia published in 1728 Ephraim Chambers offers readers a systematized structure of his attempt to produce a universal repository of human knowledge. Divided into an interconnected taxonomic tree and domain vocabulary, this structure forms the basis of one effort from the Metadata Research Center to study historical ontologies. The knowledge structure is being encoded into a Simple Knowledge Organization System (SKOS) form as well as a Web Ontology Language (OWL) version. This paper explores the expressive and functional differences between these SKOS and OWL versions of Chambers' knowledge structure. As part of this goal, the paper research focused on the construction and application of rules in each system to produce a more computationally ready representation of Chambers' structure in SKOS, which is more thesaurus-like, and OWL, which represents additional ontological nuances. First, studying the various textual aspects at the semantic, syntactic, and typographic levels allowed for the relationships between terms to manifest from which rules governing expression of the connections between elements developed. Second, because each language, SKOS and OWL, functionally expresses different logical relationships, their possibilities and limitations offer a ground for further analyzing the resultant knowledge structures; although, each stemmed from the same basic source of Chambers' text. Lastly this paper will examine rule making and expression in light of Paul Grice's theory of conversational implicature to understand how a naive agent formulates and applies these rules to a knowledge structure.

cs.DL↗