MedLexSp - a medical lexicon for Spanish medical natural language processing

Hybrid natural language processing tool for semantic annotation of medical texts in Spanish

BACKGROUND

Natural language processing (NLP) enables the extraction of information embedded within unstructured texts, such as clinical case reports and trial eligibility criteria. By identifying relevant medical concepts, NLP facilitates the generation of structured and actionable data, supporting complex tasks like cohort identification and the analysis of clinical records. To accomplish those tasks, we introduce a deep learning-based and lexicon-based named entity recognition (NER) tool for texts in Spanish. It performs medical NER and normalization, medication information extraction and detection of temporal entities, negation and speculation, and temporality or experiencer attributes (Age, Contraindicated, Negated, Speculated, Hypothetical, Future, Family_member, Patient and Other). We built the tool with a dedicated lexicon and rules adapted from NegEx and HeidelTime. Using these resources, we annotated a corpus of 1200 texts, with high inter-annotator agreement (average F1 = 0.841% ± 0.045 for entities, and average F1 = 0.881% ± 0.032 for attributes). We used this corpus to train Transformer-based models (RoBERTa-based models, mBERT and mDeBERTa). We integrated them with the dictionary-based system in a hybrid tool, and distribute the models via the Hugging Face hub. For an internal validation, we used a held-out test set and conducted an error analysis. For an external validation, eight medical professionals evaluated the system by revising the annotation of 200 new texts not used in development.

RESULTS

In the internal validation, the models yielded F1 values up to 0.915. In the external validation with 100 clinical trials, the tool achieved an average F1 score of 0.858 (± 0.032); and in 100 anonymized clinical cases, it achieved an average F1 score of 0.910 (± 0.019).

CONCLUSIONS

The tool is available at https://claramed.csic.es/medspaner . We also release the code ( https://github.com/lcampillos/medspaner ) and the annotated corpus to train the models.

Year 2023 in Biomedical Natural Language Processing: a Tribute to Large Language Models and Generative AI

OBJECTIVES

This synopsis gives insights into scientific publications from 2023 in Natural Language Processing for the biomedical domain. We present the process we followed to identify candidates for NLP's best papers and the two best papers of this year. We also analyze the current trends in the 2023 publications.

METHODS

We queried two bibliographic databases (Medline and the ACL anthology) and refined the outputs through automatic scoring. We then manually shortlisted publications to review and selected candidate papers through an adjudication process. External reviewers assessed the interest of the 13 selected candidates. At last, the section editors chose the best NLP papers.

RESULTS

We collected 2,148 papers published in 2023, of which two were the best and selected as part of this NLP synopsis. Both address language models and propose solutions for data augmenta-tion, domain-specific model adaptation, and model distillation. Work is done on social media con-tent and electronic health records, using deep learning approaches such as ChatGPT and large lan-guage models.

CONCLUSION

Trends from 2023 cover classical NLP tasks (information extraction, text categoriza-tion, sentiment analysis), existing topics from several years (medical education), mainstream applications (Chatbots, generative approaches), and specific issues (cancer, COVID-19, mental health). Specifically for COVID-19, current researches deal with post-COVID-19 conditions, and they explore the understanding of how this pandemic has been managed and welcomed by populations. In addition, due to language models, a few works have been done to process languages other than English, especially using language portability approaches.

Topic prediction for tobacco control based on COP9 tweets using machine learning techniques

The prediction of tweets associated with specific topics offers the potential to automatically focus on and understand online discussions surrounding these issues. This paper introduces a comprehensive approach that centers on the topic of "harm reduction" within the broader context of tobacco control. The study leveraged tweets from the period surrounding the ninth Conference of the Parties to review the Framework Convention on Tobacco Control (COP9) as a case study to pilot this approach. By using Latent Dirichlet Allocation (LDA)-based topic modeling, the study successfully categorized tweets related to harm reduction. Subsequently, various machine learning techniques were employed to predict these topics, achieving a prediction accuracy of 91.87% using the Random Forest algorithm. Additionally, the study explored correlations between retweets and sentiment scores. It also conducted a toxicity analysis to understand the extent to which online conversations lacked neutrality. Understanding the topics, sentiment, and toxicity of Twitter data is crucial for identifying public opinion and its formation. By specifically focusing on the topic of "harm reduction" in tweets related to COP9, the findings offer valuable insights into online discussions surrounding tobacco control. This understanding can aid policymakers in effectively informing the public and garnering public support, ultimately contributing to the successful implementation of tobacco control policies.