Nina Smirnova

Xu Tong, Nina Smirnova, Sharmila Upadhyaya et al.

Objective: To explore and compare the performance of ChatGPT and other state-of-the-art LLMs on domain-specific NER tasks covering different entity types and domains in TCM against COVID-19 literature. Methods: We established a dataset of 389 articles on TCM against COVID-19, and manually annotated 48 of them with 6 types of entities belonging to 3 domains as the ground truth, against which the NER performance of LLMs can be assessed. We then performed NER tasks for the 6 entity types using ChatGPT (GPT-3.5 and GPT-4) and 4 state-of-the-art BERT-based question-answering (QA) models (RoBERTa, MiniLM, PubMedBERT and SciBERT) without prior training on the specific task. A domain fine-tuned model (GSAP-NER) was also applied for a comprehensive comparison. Results: The overall performance of LLMs varied significantly in exact match and fuzzy match. In the fuzzy match, ChatGPT surpassed BERT-based QA models in 5 out of 6 tasks, while in exact match, BERT-based QA models outperformed ChatGPT in 5 out of 6 tasks but with a smaller F-1 difference. GPT-4 showed a significant advantage over other models in fuzzy match, especially on the entity type of TCM formula and the Chinese patent drug (TFD) and ingredient (IG). Although GPT-4 outperformed BERT-based models on entity type of herb, target, and research method, none of the F-1 scores exceeded 0.5. GSAP-NER, outperformed GPT-4 in terms of F-1 by a slight margin on RM. ChatGPT achieved considerably higher recalls than precisions, particularly in the fuzzy match. Conclusions: The NER performance of LLMs is highly dependent on the entity type, and their performance varies across application scenarios. ChatGPT could be a good choice for scenarios where high recall is favored. However, for knowledge acquisition in rigorous scenarios, neither ChatGPT nor BERT-based QA models are off-the-shelf tools for professional practitioners.

Panggih Kusuma Ningrum, Philipp Mayr, Nina Smirnova et al.

UnScientify, a system designed to detect scientific uncertainty in scholarly full text. The system utilizes a weakly supervised technique to identify verbally expressed uncertainty in scientific texts and their authorial references. The core methodology of UnScientify is based on a multi-faceted pipeline that integrates span pattern matching, complex sentence analysis and author reference checking. This approach streamlines the labeling and annotation processes essential for identifying scientific uncertainty, covering a variety of uncertainty expression types to support diverse applications including information retrieval, text mining and scientific document processing. The evaluation results highlight the trade-offs between modern large language models (LLMs) and the UnScientify system. UnScientify, which employs more traditional techniques, achieved superior performance in the scientific uncertainty detection task, attaining an accuracy score of 0.808. This finding underscores the continued relevance and efficiency of UnScientify's simple rule-based and pattern matching strategy for this specific application. The results demonstrate that in scenarios where resource efficiency, interpretability, and domain-specific adaptability are critical, traditional methods can still offer significant advantages.