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Abstract

MEDLINE is the National Library of Medicine's (NLM) journal citation database. It contains over 28 million references to biomedical and life science journal articles, and a key feature of the database is that all articles are indexed with NLM Medical Subject Headings (MeSH). The library employs a team of MeSH indexers, and in recent years they have been asked to index close to 1 million articles per year in order to keep MEDLINE up to date. An important part of the MEDLINE indexing process is the assignment of articles to indexers. High quality and timely indexing is only possible when articles are assigned to indexers with suitable expertise. This article introduces the NLM indexer assignment dataset: a large dataset of 4.2 million indexer article assignments for articles indexed between 2011 and 2019. The dataset is shown to be a valuable testbed for expert matching and assignment algorithms, and indexer article assignment is also found to be useful domain-adaptive pre-training for the closely related task of reviewer assignment.

Date

22. 1.2023 18:49:49

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Abstract

Images contained in scientific publications are widely considered useful for educational and research purposes, and their accurate indexing is critical for efficient and effective retrieval. Such image retrieval is complicated by the fact that figures in the scientific literature often combine multiple individual subfigures (panels). Multipanel figures are in fact the predominant pattern in certain types of scientific publications. The goal of this work is to automatically segment multipanel figures-a necessary step for automatic semantic indexing and in the development of image retrieval systems targeting the scientific literature. We have developed a method that uses the image content as well as the associated figure caption to: (1) automatically detect panel boundaries; (2) detect panel labels in the images and convert them to text; and (3) detect the labels and textual descriptions of each panel within the captions. Our approach combines the output of image-content and text-based processing steps to split the multipanel figures into individual subfigures and assign to each subfigure its corresponding section of the caption. The developed system achieved precision of 81% and recall of 73% on the task of automatic segmentation of multipanel figures.

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Abstract

An experiment was performed at the National Library of Medicine® (NLM®) in word sense disambiguation (WSD) using the Journal Descriptor Indexing (JDI) methodology. The motivation is the need to solve the ambiguity problem confronting NLM's MetaMap system, which maps free text to terms corresponding to concepts in NLM's Unified Medical Language System® (UMLS®) Metathesaurus®. If the text maps to more than one Metathesaurus concept at the same high confidence score, MetaMap has no way of knowing which concept is the correct mapping. We describe the JDI methodology, which is ultimately based an statistical associations between words in a training set of MEDLINE® citations and a small set of journal descriptors (assigned by humans to journals per se) assumed to be inherited by the citations. JDI is the basis for selecting the best meaning that is correlated to UMLS semantic types (STs) assigned to ambiguous concepts in the Metathesaurus. For example, the ambiguity transport has two meanings: "Biological Transport" assigned the ST Cell Function and "Patient transport" assigned the ST Health Care Activity. A JDI-based methodology can analyze text containing transport and determine which ST receives a higher score for that text, which then returns the associated meaning, presumed to apply to the ambiguity itself. We then present an experiment in which a baseline disambiguation method was compared to four versions of JDI in disambiguating 45 ambiguous strings from NLM's WSD Test Collection. Overall average precision for the highest-scoring JDI version was 0.7873 compared to 0.2492 for the baseline method, and average precision for individual ambiguities was greater than 0.90 for 23 of them (51%), greater than 0.85 for 24 (53%), and greater than 0.65 for 35 (79%). On the basis of these results, we hope to improve performance of JDI and test its use in applications.