Huitong Pan

Huitong Pan, Qi Zhang, Cornelia Caragea et al.

Flowcharts are graphical tools for representing complex concepts in concise visual representations. This paper introduces the FlowLearn dataset, a resource tailored to enhance the understanding of flowcharts. FlowLearn contains complex scientific flowcharts and simulated flowcharts. The scientific subset contains 3,858 flowcharts sourced from scientific literature and the simulated subset contains 10,000 flowcharts created using a customizable script. The dataset is enriched with annotations for visual components, OCR, Mermaid code representation, and VQA question-answer pairs. Despite the proven capabilities of Large Vision-Language Models (LVLMs) in various visual understanding tasks, their effectiveness in decoding flowcharts - a crucial element of scientific communication - has yet to be thoroughly investigated. The FlowLearn test set is crafted to assess the performance of LVLMs in flowchart comprehension. Our study thoroughly evaluates state-of-the-art LVLMs, identifying existing limitations and establishing a foundation for future enhancements in this relatively underexplored domain. For instance, in tasks involving simulated flowcharts, GPT-4V achieved the highest accuracy (58%) in counting the number of nodes, while Claude recorded the highest accuracy (83%) in OCR tasks. Notably, no single model excels in all tasks within the FlowLearn framework, highlighting significant opportunities for further development.

Qi Zhang, Zhijia Chen, Huitong Pan et al.

Scientific information extraction (SciIE) is critical for converting unstructured knowledge from scholarly articles into structured data (entities and relations). Several datasets have been proposed for training and validating SciIE models. However, due to the high complexity and cost of annotating scientific texts, those datasets restrict their annotations to specific parts of paper, such as abstracts, resulting in the loss of diverse entity mentions and relations in context. In this paper, we release a new entity and relation extraction dataset for entities related to datasets, methods, and tasks in scientific articles. Our dataset contains 106 manually annotated full-text scientific publications with over 24k entities and 12k relations. To capture the intricate use and interactions among entities in full texts, our dataset contains a fine-grained tag set for relations. Additionally, we provide an out-of-distribution test set to offer a more realistic evaluation. We conduct comprehensive experiments, including state-of-the-art supervised models and our proposed LLM-based baselines, and highlight the challenges presented by our dataset, encouraging the development of innovative models to further the field of SciIE.

Qi Zhang, Huitong Pan, Zhijia Chen et al.

Distantly Supervised Named Entity Recognition (DS-NER) has attracted attention due to its scalability and ability to automatically generate labeled data. However, distant annotation introduces many mislabeled instances, limiting its performance. Most of the existing work attempt to solve this problem by developing intricate models to learn from the noisy labels. An alternative approach is to attempt to clean the labeled data, thus increasing the quality of distant labels. This approach has received little attention for NER. In this paper, we propose a training dynamics-based label cleaning approach, which leverages the behavior of a model as training progresses to characterize the distantly annotated samples. We also introduce an automatic threshold estimation strategy to locate the errors in distant labels. Extensive experimental results demonstrate that: (1) models trained on our cleaned DS-NER datasets, which were refined by directly removing identified erroneous annotations, achieve significant improvements in F1-score, ranging from 3.18% to 8.95%; and (2) our method outperforms numerous advanced DS-NER approaches across four datasets.

Mustapha Adamu, Qi Zhang, Huitong Pan et al.

The growing complexity and volume of climate science literature make it increasingly difficult for researchers to find relevant information across models, datasets, regions, and variables. This paper introduces a domain-specific Knowledge Graph (KG) built from climate publications and broader scientific texts, aimed at improving how climate knowledge is accessed and used. Unlike keyword based search, our KG supports structured, semantic queries that help researchers discover precise connections such as which models have been validated in specific regions or which datasets are commonly used with certain teleconnection patterns. We demonstrate how the KG answers such questions using Cypher queries, and outline its integration with large language models in RAG systems to improve transparency and reliability in climate-related question answering. This work moves beyond KG construction to show its real world value for climate researchers, model developers, and others who rely on accurate, contextual scientific information.

Huitong Pan, Qi Zhang, Cornelia Caragea et al.

We present SciDMT, an enhanced and expanded corpus for scientific mention detection, offering a significant advancement over existing related resources. SciDMT contains annotated scientific documents for datasets (D), methods (M), and tasks (T). The corpus consists of two components: 1) the SciDMT main corpus, which includes 48 thousand scientific articles with over 1.8 million weakly annotated mention annotations in the format of in-text span, and 2) an evaluation set, which comprises 100 scientific articles manually annotated for evaluation purposes. To the best of our knowledge, SciDMT is the largest corpus for scientific entity mention detection. The corpus's scale and diversity are instrumental in developing and refining models for tasks such as indexing scientific papers, enhancing information retrieval, and improving the accessibility of scientific knowledge. We demonstrate the corpus's utility through experiments with advanced deep learning architectures like SciBERT and GPT-3.5. Our findings establish performance baselines and highlight unresolved challenges in scientific mention detection. SciDMT serves as a robust benchmark for the research community, encouraging the development of innovative models to further the field of scientific information extraction.

Huitong Pan, Qi Zhang, Eduard Dragut et al.

The recognition of dataset names is a critical task for automatic information extraction in scientific literature, enabling researchers to understand and identify research opportunities. However, existing corpora for dataset mention detection are limited in size and naming diversity. In this paper, we introduce the Dataset Mentions Detection Dataset (DMDD), the largest publicly available corpus for this task. DMDD consists of the DMDD main corpus, comprising 31,219 scientific articles with over 449,000 dataset mentions weakly annotated in the format of in-text spans, and an evaluation set, which comprises of 450 scientific articles manually annotated for evaluation purposes. We use DMDD to establish baseline performance for dataset mention detection and linking. By analyzing the performance of various models on DMDD, we are able to identify open problems in dataset mention detection. We invite the community to use our dataset as a challenge to develop novel dataset mention detection models.