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Creators/Authors contains: "Shomer, Harry"

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  1. Mills, Caitlin; Alexandron, Giora; Taibi, Davide; Lo_Bosco, Giosuè; Paquette, Luc (Ed.)
    Open-text responses provide researchers and educators with rich, nuanced insights that multiple-choice questions cannot capture. When reliably assessed, such responses have the potential to enhance teaching and learning. However, scaling and consistently capturing these nuances remain significant challenges, limiting the widespread use of open-text questions in educational research and assessments. In this paper, we introduce and evaluate GradeOpt, a unified multiagent automatic short-answer grading (ASAG) framework that leverages large language models (LLMs) as graders for short-answer responses. More importantly, GradeOpt incorporates two additional LLM-based agents—the reflector and the refiner—into the multi-agent system. This enables GradeOpt to automatically optimize the original grading guidelines by performing self-reflection on its errors. To assess GradeOpt's effectiveness, we conducted experiments on two representative ASAG datasets, which include items designed to capture key aspects of teachers' pedagogical knowledge and students' learning progress. Our results demonstrate that GradeOpt consistently outperforms representative baselines in both grading accuracy and alignment with human evaluators across different knowledge domains. Finally, comprehensive ablation studies validate the contributions of GradeOpt's individual components, confirming their impact on overall performance. 
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    Free, publicly-accessible full text available July 12, 2026
  2. Knowledge graphs (KGs) facilitate a wide variety of applications. Despite great efforts in creation and maintenance, even the largest KGs are far from complete. Hence, KG completion (KGC) has become one of the most crucial tasks for KG research. Recently, considerable literature in this space has centered around the use of Message Passing (Graph) Neural Networks (MPNNs), to learn powerful embeddings. The success of these methods is naturally attributed to the use of MPNNs over simpler multi-layer perceptron (MLP) models, given their additional message passing (MP) component. In this work, we find that surprisingly, simple MLP models are able to achieve comparable performance to MPNNs, suggesting that MP may not be as crucial as previously believed. With further exploration, we show careful scoring function and loss function design has a much stronger influence on KGC model performance. This suggests a conflation of scoring function design, loss function design, and MP in prior work, with promising insights regarding the scalability of state-of-the-art KGC methods today, as well as careful attention to more suitable MP designs for KGC tasks tomorrow. Our codes are publicly available at: https://github.com/Juanhui28/Are_MPNNs_helpful. 
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  3. Abstract PremiseThe selection ofArabidopsisas a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural‐ or ecological‐based model species were rejected, in favor of building knowledge in a species that would facilitate genome‐enabled research. MethodsHere, we examine the ability of models based onArabidopsisgene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested onArabidopsisdata achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained onArabidopsisdata, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64. ResultsThe identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance fromArabidopsis.k‐nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants. DiscussionOur data‐driven results highlight that the assertion that knowledge fromArabidopsisis translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis onArabidopsisand prioritize plant diversity. 
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    Free, publicly-accessible full text available January 1, 2026