Biomedical Information Retrieval Research Articles

Biomedical Information Retrieval with Positive-Unlabeled Learning and Knowledge Graphs

The rapid growth of biomedical publications has presented significant challenges in the field of information retrieval. Most existing work focuses on document retrieval given explicit queries. However, in real applications such as curated biomedical database maintenance, explicit queries are missing. In this paper, we propose a two-step model for biomedical information retrieval in the case that only a small set of example documents is available without explicit queries. Initially, we extract keywords from the observed documents using large pre-trained language models and biomedical knowledge graphs. These keywords are then enriched with domain-specific entities. Information retrieval techniques can subsequently use the collected entities to rank the documents. Following this, we introduce an iterative Positive-Unlabeled learning method to classify all unlabeled documents. Experiments conducted on the PubMed dataset demonstrate that the proposed technique outperforms the state-of-the-art positive-unlabeled learning methods. The results underscore the effectiveness of integrating large language models and biomedical knowledge graphs in improving zero-shot information retrieval performance in the biomedical domain.

Optimizing biomedical information retrieval with a keyword frequency-driven prompt enhancement strategy

BackgroundMining the vast pool of biomedical literature to extract accurate responses and relevant references is challenging due to the domain's interdisciplinary nature, specialized jargon, and continuous evolution. Early natural language processing (NLP) approaches often led to incorrect answers as they failed to comprehend the nuances of natural language. However, transformer models have significantly advanced the field by enabling the creation of large language models (LLMs), enhancing question-answering (QA) tasks. Despite these advances, current LLM-based solutions for specialized domains like biology and biomedicine still struggle to generate up-to-date responses while avoiding “hallucination” or generating plausible but factually incorrect responses.ResultsOur work focuses on enhancing prompts using a retrieval-augmented architecture to guide LLMs in generating meaningful responses for biomedical QA tasks. We evaluated two approaches: one relying on text embedding and vector similarity in a high-dimensional space, and our proposed method, which uses explicit signals in user queries to extract meaningful contexts. For robust evaluation, we tested these methods on 50 specific and challenging questions from diverse biomedical topics, comparing their performance against a baseline model, BM25. Retrieval performance of our method was significantly better than others, achieving a median Precision@10 of 0.95, which indicates the fraction of the top 10 retrieved chunks that are relevant. We used GPT-4, OpenAI's most advanced LLM to maximize the answer quality and manually accessed LLM-generated responses. Our method achieved a median answer quality score of 2.5, surpassing both the baseline model and the text embedding-based approach. We developed a QA bot, WeiseEule (https://github.com/wasimaftab/WeiseEule-LocalHost), which utilizes these methods for comparative analysis and also offers advanced features for review writing and identifying relevant articles for citation.ConclusionsOur findings highlight the importance of prompt enhancement methods that utilize explicit signals in user queries over traditional text embedding-based approaches to improve LLM-generated responses for specialized queries in specialized domains such as biology and biomedicine. By providing users complete control over the information fed into the LLM, our approach addresses some of the major drawbacks of existing web-based chatbots and LLM-based QA systems, including hallucinations and the generation of irrelevant or outdated responses.

Comparative Evaluation of Pre-Trained Language Models for Biomedical Information Retrieval.

Finding relevant information in the biomedical literature increasingly depends on efficient information retrieval (IR) algorithms. Cross-Encoders, SentenceBERT, and ColBERT are algorithms based on pre-trained language models that use nuanced but computable vector representations of search queries and documents for IR applications. Here we investigate how well these vectorization algorithms estimate relevance labels of biomedical documents for search queries using the OHSUMED dataset. For our evaluation, we compared computed scores to provided labels by using boxplots and Spearman's rank correlations. According to these metrics, we found that Sentence-BERT moderately outperformed the alternative vectorization algorithms and that additional fine-tuning based on a subset of OHSUMED labels yielded little additional benefit. Future research might aim to develop a larger dedicated dataset in order to optimize such methods more systematically, and to evaluate the corresponding functions in IR tools with end-users.

Deep Learning-Based Surgical Treatment Recommendation and Nonsurgical Prognosis Status Classification for Scaphoid Fractures by Automated X-ray Image Recognition.

Biomedical information retrieval for diagnosis, treatment and prognosis has been studied for a long time. In particular, image recognition using deep learning has been shown to be very effective for cancers and diseases. In these fields, scaphoid fracture recognition is a hot topic because the appearance of scaphoid fractures is not easy to detect. Although there have been a number of recent studies on this topic, no studies focused their attention on surgical treatment recommendations and nonsurgical prognosis status classification. Indeed, a successful treatment recommendation will assist the doctor in selecting an effective treatment, and the prognosis status classification will help a radiologist recognize the image more efficiently. For these purposes, in this paper, we propose potential solutions through a comprehensive empirical study assessing the effectiveness of recent deep learning techniques on surgical treatment recommendation and nonsurgical prognosis status classification. In the proposed system, the scaphoid is firstly segmented from an unknown X-ray image. Next, for surgical treatment recommendation, the fractures are further filtered and recognized. According to the recognition result, the surgical treatment recommendation is generated. Finally, even without sufficient fracture information, the doctor can still make an effective decision to opt for surgery or not. Moreover, for nonsurgical patients, the current prognosis status of avascular necrosis, non-union and union can be classified. The related experimental results made using a real dataset reveal that the surgical treatment recommendation reached 80% and 86% in accuracy and AUC (Area Under the Curve), respectively, while the nonsurgical prognosis status classification reached 91% and 96%, respectively. Further, the methods using transfer learning and data augmentation can bring out obvious improvements, which, on average, reached 21.9%, 28.9% and 5.6%, 7.8% for surgical treatment recommendations and nonsurgical prognosis image classification, respectively. Based on the experimental results, the recommended methods in this paper are DenseNet169 and ResNet50 for surgical treatment recommendation and nonsurgical prognosis status classification, respectively. We believe that this paper can provide an important reference for future research on surgical treatment recommendation and nonsurgical prognosis classification for scaphoid fractures.

Bridging the gap in biomedical information retrieval: Harnessing machine learning for enhanced search results and query semantics

The medical domain faces unique challenges in Information Retrieval (IR) due to the complexity of medical language and terminology discrepancies between user queries and documents. While traditional Keyword-Based Methods (KBM) have limitations, the integration of semantic knowledge bases and concept mapping techniques enhances data organization and retrieval. Addressing the growing demands in the biomedical field, a novel medical Information Retrieval System (IRS) is proposed that employs Deep Learning (DL) and KBM. This system comprises five core steps: pre-processing of texts, document indexing using DL (ELMo) and KBM, advanced query processing, a BiLSTM-based retrieval network for contextual representation, and a KR-R re-ranking algorithm to refine document relevance. The purpose of the system is to give users improved biomedical search results through the integration of all of these techniques into a method that takes into consideration the semantic problems of medical records. An in-depth examination of the TREC-PM track samples from 2017 to 2019 observed an impressive leading MRR score of 0.605 in 2017 and a best-in-class rPrec score of 0.350 in 2019, proving how well able the system is to detect and rank relevant medical records accurately.

Survey on Recommender Systems for Biomedical Items in Life and Health Sciences

The generation of biomedical data is of such magnitude that its retrieval and analysis have posed several challenges. A survey of recommender system (RS) approaches in biomedical fields is provided in this analysis, along with a discussion of existing challenges related to large-scale biomedical information retrieval systems. We collect original studies, identify entities and models, and discuss how knowledge graphs (KGs) can improve results. As a result, most of the papers used model-based collaborative filtering algorithms, most of the available datasets did not follow the standard format < user, item, rating >, and regarding qualitative evaluations of RSs use mainly classification metrics. Finally, we have assembled and coded a unique dataset of 60 papers — Sur-RS4BioT, available for download at DOI:10.34740/kaggle/ds/2346894

BIR: Biomedical Information Retrieval System for Cancer Treatment in Electronic Health Record Using Transformers

The rapid growth of electronic health records (EHRs) has led to unprecedented biomedical data. Clinician access to the latest patient information can improve the quality of healthcare. However, clinicians have difficulty finding information quickly and easily due to the sheer data mining volume. Biomedical information retrieval (BIR) systems can help clinicians find the information required by automatically searching EHRs and returning relevant results. However, traditional BIR systems cannot understand the complex relationships between EHR entities. Transformers are a new type of neural network that is very effective for natural language processing (NLP) tasks. As a result, transformers are well suited for tasks such as machine translation and text summarization. In this paper, we propose a new BIR system for EHRs that uses transformers for predicting cancer treatment from EHR. Our system can understand the complex relationships between the different entities in an EHR, which allows it to return more relevant results to clinicians. We evaluated our system on a dataset of EHRs and found that it outperformed state-of-the-art BIR systems on various tasks, including medical question answering and information extraction. Our results show that Transformers are a promising approach for BIR in EHRs, reaching an accuracy and an F1-score of 86.46%, and 0.8157, respectively. We believe that our system can help clinicians find the information they need more quickly and easily, leading to improved patient care.

Opportunities and challenges for ChatGPT and large language models in biomedicine and health.

ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and health. In this work, we examine the diverse applications of large language models (LLMs), such as ChatGPT, in biomedicine and health. Specifically, we explore the areas of biomedical information retrieval, question answering, medical text summarization, information extraction and medical education and investigate whether LLMs possess the transformative power to revolutionize these tasks or whether the distinct complexities of biomedical domain presents unique challenges. Following an extensive literature survey, we find that significant advances have been made in the field of text generation tasks, surpassing the previous state-of-the-art methods. For other applications, the advances have been modest. Overall, LLMs have not yet revolutionized biomedicine, but recent rapid progress indicates that such methods hold great potential to provide valuable means for accelerating discovery and improving health. We also find that the use of LLMs, like ChatGPT, in the fields of biomedicine and health entails various risks and challenges, including fabricated information in its generated responses, as well as legal and privacy concerns associated with sensitive patient data. We believe this survey can provide a comprehensive and timely overview to biomedical researchers and healthcare practitioners on the opportunities and challenges associated with using ChatGPT and other LLMs for transforming biomedicine and health.

MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval.

Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires abundant query-article annotations that are difficult to obtain in biomedicine. As a result, most biomedical IR systems only conduct lexical matching. In response, we introduce MedCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot semantic IR in biomedicine. To train MedCPT, we collected an unprecedented scale of 255 million user click logs from PubMed. With such data, we use contrastive learning to train a pair of closely integrated retriever and re-ranker. Experimental results show that MedCPT sets new state-of-the-art performance on six biomedical IR tasks, outperforming various baselines including much larger models, such as GPT-3-sized cpt-text-XL. In addition, MedCPT also generates better biomedical article and sentence representations for semantic evaluations. As such, MedCPT can be readily applied to various real-world biomedical IR tasks. The MedCPT code and model are available at https://github.com/ncbi/MedCPT.

Improving the robustness and stability of a machine learning model for breast cancer prognosis through the use of multi-modal classifiers

Breast cancer is a deadly disease with a high mortality rate among PAN cancers. The advancements in biomedical information retrieval techniques have been beneficial in developing early prognosis and diagnosis systems for cancer patients. These systems provide the oncologist with plenty of information from several modalities to make the correct and feasible treatment plan for breast cancer patients and protect them from unnecessary therapies and their toxic side effects. The cancer patient’s related information can be collected using various modalities like clinical, copy number variation, DNA-methylation, microRNA sequencing, gene expression, and histopathological whole slide images. High dimensionality and heterogeneity in these modalities demand the development of some intelligent systems to understand related features to the prognosis and diagnosis of diseases and make correct predictions. In this work, we have studied some end-to-end systems having two main components : (a) dimensionality reduction techniques applied to original features from different modalities and (b) classification techniques applied to the fusion of reduced feature vectors from different modalities for automatic predictions of breast cancer patients into two categories: short-time and long-time survivors. Principal component analysis (PCA) and variational auto-encoders (VAEs) are used as the dimensionality reduction techniques, followed by support vector machines (SVM) or random forest as the machine learning classifiers. The study utilizes raw, PCA, and VAE extracted features of the TCGA-BRCA dataset from six different modalities as input to the machine learning classifiers. We conclude this study by suggesting that adding more modalities to the classifiers provides complementary information to the classifier and increases the stability and robustness of the classifiers. In this study, the multimodal classifiers have not been validated on primary data prospectively.

MedGraph: A semantic biomedical information retrieval framework using knowledge graph embedding for PubMed.

Here we study the semantic search and retrieval problem in biomedical digital libraries. First, we introduce MedGraph, a knowledge graph embedding-based method that provides semantic relevance retrieval and ranking for the biomedical literature indexed in PubMed. Second, we evaluate our approach using PubMed's Best Match algorithm. Moreover, we compare our method MedGraph to a traditional TF-IDF-based algorithm. Third, we use a dataset extracted from PubMed, including 30 million articles' metadata such as abstracts, author information, citation information, and extracted biological entity mentions. We pull a subset of the dataset to evaluate MedGraph using predefined queries with ground truth ranked results. To our knowledge, this technique has not been explored before in biomedical information retrieval. In addition, our results provide some evidence that semantic approaches to search and relevance in biomedical digital libraries that rely on knowledge graph modeling offer better search relevance results when compared with traditional methods in terms of objective metrics.

An Efficient Method for Biomedical Entity Linking Based on Inter- and Intra-Entity Attention

Biomedical entity linking is an important research problem for many downstream tasks, such as biomedical intelligent question answering, information retrieval, and information extraction. Biomedical entity linking is the task of mapping mentions in medical texts to standard entities in a given knowledge base. Recently, BERT-based models have achieved state-of-the-art results on the biomedical entity linking task. Although this type of method is effective, it brings challenges for fine-tuning and online services in practical industries due to a large number of model parameters and long inference time. In addition, due to the numerous surface variants of biomedical mentions, it is difficult for a single matching module to achieve good results. To address the challenge, we propose an efficient biomedical entity linking method that integrates inter- and intra-entity attention to better capture the information between medical entity mentions and candidate entities themselves and each other, and the model in this paper is more lightweight. Experimental results show that our method achieves competitive performance on two biomedical benchmark datasets, NCBI and ADR, with an accuracy rate of 91.28% and 93.13%, respectively. Moreover, it also achieves comparable or even better results compared to the BERT-based entity linking method while having far fewer model parameters and very high inference speed.

Effective Natural Language Processing and Interpretable Machine Learning for Structuring CT Liver-Tumor Reports

In the past, the liver tumors were reported manually in an unstructured format. There actually exists much valuable knowledge in these reports for further disease risk assessment, disease recognition and treatment recommendation. Yet, it is not easy to read and mine knowledge from the unstructured reports. Hence, how to extract the knowledge from these biomedical reports effectively and efficiently has been a challenging issue in the past decades. Although a set of Natural Language Processing techniques were proposed for Bio-medical information retrieval, few related works were made on transforming the unstructured CT liver-tumor reports into structured ones. To aim at this issue, in this paper, we propose a two-stage report structuring method by integrating effective Natural Language Processing (NLP) and interpretable machine learning. For the first stage, the candidate keywords in unstructured reports are extracted. Next, the feature keywords are determined by the feature-selection technique. For the second stage, the well-known multi-classifiers are performed, and finally the reports are labeled in a refined structure format. Further, the factor keywords in the classification model are filtered to interpret the performance. In overall, the proposed report structuring method generates a hierarchical data structure, including the common features and refined features in the 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> and 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> levels/stages, respectively. To reveal the performance of proposed method, a set of evaluations were conducted and the results show that, the proposed method is more promising than the fashion neural networks such as Bert (Bidirectional Encoder Representations from Transformers) in terms of effectiveness and efficiency.

Examining the Effect of the Ratio of Biomedical Domain to General Domain Data in Corpus in Biomedical Literature Mining

Biomedical terms extracted using Word2vec, the most popular word embedding model in recent years, serve as the foundation for various natural language processing (NLP) applications, such as biomedical information retrieval, relation extraction, and recommendation systems. The objective of this study is to examine how changes in the ratio of the biomedical domain to general domain data in the corpus affect the extraction of similar biomedical terms using Word2vec. We downloaded abstracts of 214,892 articles from PubMed Central (PMC) and the 3.9 GB Billion Word (BW) benchmark corpus from the computer science community. The datasets were preprocessed and grouped into 11 corpora based on the ratio of BW to PMC, ranging from 0:10 to 10:0, and then Word2vec models were trained on these corpora. The cosine similarities between the biomedical terms obtained from the Word2vec models were then compared in each model. The results indicated that the models trained with both BW and PMC data outperformed the model trained only with medical data. The similarity between the biomedical terms extracted by the Word2vec model increased when the ratio of the biomedical domain to general domain data was 3:7 to 5:5. This study allows NLP researchers to apply Word2vec based on more information and increase the similarity of extracted biomedical terms to improve their effectiveness in NLP applications, such as biomedical information extraction.

Use of web-based health information portals in primary health care: Experience from a rural Primary Health Centre in Haryana.

Background:Health care informatics is the scientific field that deals with the data capture, storage, retrieval, and use of biomedical data, information, and knowledge for problem solving and decision-making. The objectives of the study were to describe the web-based portals used at the Primary Health Centre (PHC) and to appraise its utilization at the local level.Methods:Various methodologies included observation of portal use, record review, interview of stakeholders using the portals.Results:Health Workers workload increased because of physical record entry and time spent for entry in web-based health information portals. Web-based portals did not have options for utilization of the data generated at the PHC level. The options of feedback and helpline were not universally available.Conclusion:Web-based portals are integral part of health system at primary healthcare level. Adequate utilization of web-based health information portals may lead to efficient provision of health services at the primary health care level.

Efficacy and Safety of Endoscopic Resection and Open Surgery for Treating Thyroid Diseases: A Meta-Analysis

To explore the efficacy and safety of endoscopic resection and open surgery for treating thyroid diseases using meta-analysis. Related data in computer retrieval of Cochrane Library, American National Library of Medicine Biomedical Information Retrieval System (Pub Med), Dutch Medicine Abstracts (Embase), China Biomedical Literature Database (CBM), China Academic Journals Full-text Database (CNKI), Chinese Science and Technology Journal Database (VIP), and Western Language Biomedical Journal Literature Database (EMC) from December 2019 to April 2020 were retrieved. Relevant journals and included references were manually searched. Randomized controlled trials regarding the effects of endoscopic thyroid surgery and open thyroid surgery on the immune response of thyroid diseases were included. Two reviewers conducted independent data extraction, quality evaluation and cross-checking according to inclusion and exclusion criteria. RevMan 5.1.4 software was employed. Eight non-randomized controlled retrospective cohort studies were finally included. The curative rate (168/185, 90.81 % vs. 194/383, 50.65 %, p<0.01) was significantly higher in endoscopic resection group and the difference between local recurrence rates (2/366, 0.55 % vs. 83/603, 13.76 %, p<0.01) was significant. There was no significant difference between bleeding rate (1/325, 0.31 % vs. 4/407, 0.98 %, p=0.41). In terms of performing thyroid surgery under endoscopy, the efficacy of adjuvant treatment under endoscopy is significantly better than that of control group and the safety is similar to that of control group. Endoscopic treatment is suitable for treating thyroid diseases. However, the conclusions still need to be verified by multicenter randomized controlled trials with large sample sizes.

MeSHProbeNet-P

Indexing biomedical research articles with Medical Subject Headings (MeSH) can greatly facilitate biomedical research and information retrieval. Currently MeSH indexing is performed by human experts. To alleviate the time consumption and monetary cost caused by manual indexing, many automatic MeSH indexing models have been developed, such as MeSHProbeNet, DeepMeSH, and NLM’s official model Medical Text Indexer. In this article, we propose an end-to-end framework, MeSHProbeNet-P, which extends MeSHProbeNet with personalizable MeSH probes. In MeSHProbeNet-P, each MeSH probe carries certain aspects of biomedical knowledge and extracts related information from input articles. MeSHProbeNet-P is able to automatically personalize its MeSH probes for different input articles to ensure that the current MeSH probes best fit the current input article and the most informative features can be extracted from the article. We demonstrate the effectiveness of MeSHProbeNet-P in a real-world large-scale MeSH indexing challenge. MeSHProbeNet-P won the first place in the first batch of Task A in the 2019 BioASQ challenge. The result on the first test set of the challenge is reported in this article. We also provide ablation studies to show the advantages of personalizable MeSH probes.

A2A: a platform for research in biomedical literature search

BackgroundFinding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published literature, given a query. However, they are limited in how users can control the processing of queries and articles—or as we call them documents—by the search engine. To give this control to both biomedical researchers and computer scientists working in biomedical information retrieval, we introduce a public online tool for searching over biomedical literature. Our setup is guided by the NIST setup of the relevant TREC evaluation tasks in genomics, clinical decision support, and precision medicine.ResultsTo provide benchmark results for some of the most common biomedical information retrieval strategies, such as querying MeSH subject headings with a specific weight or querying over the title of the articles only, we present our evaluations on public datasets. Our experiments report well-known information retrieval metrics such as precision at a cutoff of ranked documents.ConclusionsWe introduce the A2A search and benchmarking tool which is publicly available for the researchers who want to explore different search strategies over published biomedical literature. We outline several query formulation strategies and present their evaluations with known human judgements for a large pool of topics, from genomics to precision medicine.

MeSH-Based Semantic Indexing Approach to Enhance Biomedical Information Retrieval

Abstract Owing to the tremendous size of electronic biomedical documents, users encounter difficulties in seeking useful biomedical information. An efficient and smart access to the relevant biomedical information has become a fundamental need. In this research paper, we set forward a novel biomedical MeSH-based semantic indexing approach to enhance biomedical information retrieval. The proposed semantic indexing approach attempts to strengthen the content representation of both documents and queries by incorporating unambiguous MeSH concepts as well as the adequate senses of ambiguous MeSH concepts. For this purpose, our proposed approach relies on a disambiguation method to identify the adequate senses of ambiguous MeSH concepts and introduces four representation enrichment strategies so as to identify the best appropriate representatives of the adequate sense in the textual entities representation. To prove its effectiveness, the proposed semantic indexing approach was evaluated by intensive experiments. These experiments were carried out on OHSUMED test collection. The results reveal that our proposal outperforms the state-of-the-art approaches and allow us to highlight the most effective strategy.

Identification of the Best Semantic Expansion to Query PubMed Through Automatic Performance Assessment of Four Search Strategies on All Medical Subject Heading Descriptors: Comparative Study.

BackgroundWith the continuous expansion of available biomedical data, efficient and effective information retrieval has become of utmost importance. Semantic expansion of queries using synonyms may improve information retrieval.ObjectiveThe aim of this study was to automatically construct and evaluate expanded PubMed queries of the form “preferred term”[MH] OR “preferred term”[TIAB] OR “synonym 1”[TIAB] OR “synonym 2”[TIAB] OR …, for each of the 28,313 Medical Subject Heading (MeSH) descriptors, by using different semantic expansion strategies. We sought to propose an innovative method that could automatically evaluate these strategies, based on the three main metrics used in information science (precision, recall, and F-measure).MethodsThree semantic expansion strategies were assessed. They differed by the synonyms used to build the queries as follows: MeSH synonyms, Unified Medical Language System (UMLS) mappings, and custom mappings (Catalogue et Index des Sites Médicaux de langue Française [CISMeF]). The precision, recall, and F-measure metrics were automatically computed for the three strategies and for the standard automatic term mapping (ATM) of PubMed. The method to automatically compute the metrics involved computing the number of all relevant citations (A), using National Library of Medicine indexing as the gold standard (“preferred term”[MH]), the number of citations retrieved by the added terms (”synonym 1“[TIAB] OR ”synonym 2“[TIAB] OR …) (B), and the number of relevant citations retrieved by the added terms (combining the previous two queries with an “AND” operator) (C). It was possible to programmatically compute the metrics for each strategy using each of the 28,313 MeSH descriptors as a “preferred term,” corresponding to 239,724 different queries built and sent to the PubMed application program interface. The four search strategies were ranked and compared for each metric.ResultsATM had the worst performance for all three metrics among the four strategies. The MeSH strategy had the best mean precision (51%, SD 23%). The UMLS strategy had the best recall and F-measure (41%, SD 31% and 36%, SD 24%, respectively). CISMeF had the second best recall and F-measure (40%, SD 31% and 35%, SD 24%, respectively). However, considering a cutoff of 5%, CISMeF had better precision than UMLS for 1180 descriptors, better recall for 793 descriptors, and better F-measure for 678 descriptors.ConclusionsThis study highlights the importance of using semantic expansion strategies to improve information retrieval. However, the performances of a given strategy, relatively to another, varied greatly depending on the MeSH descriptor. These results confirm there is no ideal search strategy for all descriptors. Different semantic expansions should be used depending on the descriptor and the user’s objectives. Thus, we developed an interface that allows users to input a descriptor and then proposes the best semantic expansion to maximize the three main metrics (precision, recall, and F-measure).