ArticleJournal of biomedical informatics2025
Scalable scientific interest profiling using large language models.
Article in Journal of biomedical informatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- A data-driven method for research trend analysis in a scientific discipline: Application to the journal of biomedical informatics.Journal of biomedical informatics · 2026Article
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9 authors.
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Abstract
objectiveResearch profiles highlight scientists' research focus, enabling talent discovery and fostering collaborations, but they are often outdated. Automated, scalable methods are urgently needed to keep these profiles current.
methodsIn this study, we design and evaluate two Large Language Models (LLMs)-based methods to generate scientific interest profiles-one summarizing researchers' PubMed abstracts and the other generating a summary using their publications' Medical Subject Headings (MeSH) terms-and compare these machine-generated profiles with researchers' self-summarized interests. We collected the titles, MeSH terms, and abstracts of PubMed publications for 595 faculty members affiliated with Columbia University Irving Medical Center (CUIMC), for 167 of whom we obtained human-written online research profiles. Subsequently, GPT-4o-mini, a state-of-the-art LLM, was prompted to summarize each researcher's interests. Both manual and automated evaluations were conducted to characterize the similarities and differences between the machine-generated and self-written research profiles.
resultsThe similarity study showed low ROUGE-L, BLEU, and METEOR scores, reflecting little overlap between terminologies used in machine-generated and self-written profiles. BERTScore analysis revealed moderate semantic similarity between machine-generated and reference summaries (F1: 0.542 for MeSH-based, 0.555 for abstract-based), despite low lexical overlap. In validation, paraphrased summaries achieved a higher F1 of 0.851. A further comparison between the original and paraphrased manually written summaries indicates the limitations of such metrics. Kullback-Leibler (KL) Divergence of term frequency-inverse document frequency (TF-IDF) values (8.56 and 8.58 for profiles derived from MeSH terms and abstracts, respectively) suggests that machine-generated summaries employ different keywords than human-written summaries. Manual reviews further showed that 77.78% rated the overall impression of MeSH-based profiling as "good" or "excellent," with readability receiving favorable ratings in 93.44% of cases, though granularity and factual accuracy varied. Overall, panel reviews favored 67.86% of machine-generated profiles derived from MeSH terms over those derived from abstracts.
conclusionLLMs promise to automate scientific interest profiling at scale. Profiles derived from MeSH terms have better readability than profiles derived from abstracts. Overall, machine-generated summaries differ from human-written ones in their choice of concepts, with the latter initiating more novel ideas.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.