Yuan An

Yuan An, Jane Greenberg, Alex Kalinowski et al.

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.

Yuan An, Jane Greenberg, Xintong Zhao et al.

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.

Alexander Kalinowski, Yuan An

The majority of knowledge graph embedding techniques treat entities and predicates as separate embedding matrices, using aggregation functions to build a representation of the input triple. However, these aggregations are lossy, i.e. they do not capture the semantics of the original triples, such as information contained in the predicates. To combat these shortcomings, current methods learn triple embeddings from scratch without utilizing entity and predicate embeddings from pre-trained models. In this paper, we design a novel fine-tuning approach for learning triple embeddings by creating weak supervision signals from pre-trained knowledge graph embeddings. We develop a method for automatically sampling triples from a knowledge graph and estimating their pairwise similarities from pre-trained embedding models. These pairwise similarity scores are then fed to a Siamese-like neural architecture to fine-tune triple representations. We evaluate the proposed method on two widely studied knowledge graphs and show consistent improvement over other state-of-the-art triple embedding methods on triple classification and triple clustering tasks.

Yuan An, Alex Kalinowski, Jane Greenberg

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.

Yuan An, Samarth Kolanupaka, Jacob An et al.

This paper introduces an intelligent lecturing assistant (ILA) system that utilizes a knowledge graph to represent course content and optimal pedagogical strategies. The system is designed to support instructors in enhancing student learning through real-time analysis of voice, content, and teaching methods. As an initial investigation, we present a case study on lecture voice sentiment analysis, in which we developed a training set comprising over 3,000 one-minute lecture voice clips. Each clip was manually labeled as either engaging or non-engaging. Utilizing this dataset, we constructed and evaluated several classification models based on a variety of features extracted from the voice clips. The results demonstrate promising performance, achieving an F1-score of 90% for boring lectures on an independent set of over 800 test voice clips. This case study lays the groundwork for the development of a more sophisticated model that will integrate content analysis and pedagogical practices. Our ultimate goal is to aid instructors in teaching more engagingly and effectively by leveraging modern artificial intelligence techniques.

Jane Greenberg, Scott McClellan, Addy Ireland et al.

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.

Alexander Kalinowski, Yuan An

Sentence embeddings encode natural language sentences as low-dimensional dense vectors. A great deal of effort has been put into using sentence embeddings to improve several important natural language processing tasks. Relation extraction is such an NLP task that aims at identifying structured relations defined in a knowledge base from unstructured text. A promising and more efficient approach would be to embed both the text and structured knowledge in low-dimensional spaces and discover semantic alignments or mappings between them. Although a number of techniques have been proposed in the literature for embedding both sentences and knowledge graphs, little is known about the structural and semantic properties of these embedding spaces in terms of relation extraction. In this paper, we investigate the aforementioned properties by evaluating the extent to which sentences carrying similar senses are embedded in close proximity sub-spaces, and if we can exploit that structure to align sentences to a knowledge graph. We propose a set of experiments using a widely-used large-scale data set for relation extraction and focusing on a set of key sentence embedding methods. We additionally provide the code for reproducing these experiments at https://github.com/akalino/semantic-structural-sentences. These embedding methods cover a wide variety of techniques ranging from simple word embedding combination to transformer-based BERT-style model. Our experimental results show that different embedding spaces have different degrees of strength for the structural and semantic properties. These results provide useful information for developing embedding-based relation extraction methods.

Yuan An, John Liu, Niyam Acharya et al.

Retrieval practice is a well-established pedagogical technique known to significantly enhance student learning and knowledge retention. However, generating high-quality retrieval practice questions is often time-consuming and labor intensive for instructors, especially in rapidly evolving technical subjects. Large Language Models (LLMs) offer the potential to automate this process by generating questions in response to prompts, yet the effectiveness of LLM-generated retrieval practice on student learning remains to be established. In this study, we conducted an empirical study involving two college-level data science courses, with approximately 60 students. We compared learning outcomes during one week in which students received LLM-generated multiple-choice retrieval practice questions to those from a week in which no such questions were provided. Results indicate that students exposed to LLM-generated retrieval practice achieved significantly higher knowledge retention, with an average accuracy of 89%, compared to 73% in the week without such practice. These findings suggest that LLM-generated retrieval questions can effectively support student learning and may provide a scalable solution for integrating retrieval practice into real-time teaching. However, despite these encouraging outcomes and the potential time-saving benefits, cautions must be taken, as the quality of LLM-generated questions can vary. Instructors must still manually verify and revise the generated questions before releasing them to students.

Yuan An

Advances in large language models (LLMs) are rapidly transforming scientific work, yet empirical evidence on how these systems reshape research activities remains limited. We report a mixed-methods pilot evaluation of an AI-orchestrated research workflow in which a human researcher coordinated multiple LLM-based agents to perform data extraction, corpus construction, artifact generation, and artifact evaluation. Using the generation and assessment of multiple-choice questions (MCQs) as a testbed, we collected 1,071 SAT Math MCQs and employed LLM agents to extract questions from PDFs, retrieve and convert open textbooks into structured representations, align each MCQ with relevant textbook content, generate new MCQs under specified difficulty and cognitive levels, and evaluate both original and generated MCQs using a 24-criterion quality framework. Across all evaluations, average MCQ quality was high. However, criterion-level analysis and equivalence testing show that generated MCQs are not fully comparable to expert-vetted baseline questions. Strict similarity (24/24 criteria equivalent) was never achieved. Persistent gaps concentrated in skill\ depth, cognitive engagement, difficulty calibration, and metadata alignment, while surface-level qualities, such as {grammar fluency}, {clarity options}, {no duplicates}, were consistently strong. Beyond MCQ outcomes, the study documents a labor shift. The researcher's work moved from ``authoring items'' toward {specification, orchestration, verification}, and {governance}. Formalizing constraints, designing rubrics, building validation loops, recovering from tool failures, and auditing provenance constituted the primary activities. We discuss implications for the future of scientific work, including emerging ``AI research operations'' skills required for AI-empowered research pipelines.

Yuan An, Ruhma Hashmi, Michelle Rogers et al.

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.

Yuan An, Alexander Kalinowski, Jane Greenberg

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.

Alexander Kalinowski, Yuan An

Neural embedding approaches have become a staple in the fields of computer vision, natural language processing, and more recently, graph analytics. Given the pervasive nature of these algorithms, the natural question becomes how to exploit the embedding spaces to map, or align, embeddings of different data sources. To this end, we survey the current research landscape on word, sentence and knowledge graph embedding algorithms. We provide a classification of the relevant alignment techniques and discuss benchmark datasets used in this field of research. By gathering these diverse approaches into a singular survey, we hope to further motivate research into alignment of embedding spaces of varied data types and sources.