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A Dataset for Pharmacovigilance in German, French, and Japanese: Annotating Adverse Drug Reactions across Languages
Mar 27, 2024
User-generated data sources have gained significance in uncovering Adverse Drug Reactions (ADRs), with an increasing number of discussions occurring in the digital world. However, the existing clinical corpora predominantly revolve around scientific articles in English. This work presents a multilingual corpus of texts concerning ADRs gathered from diverse sources, including patient fora, social media, and clinical reports in German, French, and Japanese. Our corpus contains annotations covering 12 entity types, four attribute types, and 13 relation types. It contributes to the development of real-world multilingual language models for healthcare. We provide statistics to highlight certain challenges associated with the corpus and conduct preliminary experiments resulting in strong baselines for extracting entities and relations between these entities, both within and across languages.
xMEN: A Modular Toolkit for Cross-Lingual Medical Entity Normalization
Oct 17, 2023
Objective: To improve performance of medical entity normalization across many languages, especially when fewer language resources are available compared to English. Materials and Methods: We introduce xMEN, a modular system for cross-lingual medical entity normalization, which performs well in both low- and high-resource scenarios. When synonyms in the target language are scarce for a given terminology, we leverage English aliases via cross-lingual candidate generation. For candidate ranking, we incorporate a trainable cross-encoder model if annotations for the target task are available. We also evaluate cross-encoders trained in a weakly supervised manner based on machine-translated datasets from a high resource domain. Our system is publicly available as an extensible Python toolkit. Results: xMEN improves the state-of-the-art performance across a wide range of multilingual benchmark datasets. Weakly supervised cross-encoders are effective when no training data is available for the target task. Through the compatibility of xMEN with the BigBIO framework, it can be easily used with existing and prospective datasets. Discussion: Our experiments show the importance of balancing the output of general-purpose candidate generators with subsequent trainable re-rankers, which we achieve through a rank regularization term in the loss function of the cross-encoder. However, error analysis reveals that multi-word expressions and other complex entities are still challenging. Conclusion: xMEN exhibits strong performance for medical entity normalization in multiple languages, even when no labeled data and few terminology aliases for the target language are available. Its configuration system and evaluation modules enable reproducible benchmarks. Models and code are available online at the following URL: https://github.com/hpi-dhc/xmen
Factuality Detection using Machine Translation -- a Use Case for German Clinical Text
Aug 17, 2023
Factuality can play an important role when automatically processing clinical text, as it makes a difference if particular symptoms are explicitly not present, possibly present, not mentioned, or affirmed. In most cases, a sufficient number of examples is necessary to handle such phenomena in a supervised machine learning setting. However, as clinical text might contain sensitive information, data cannot be easily shared. In the context of factuality detection, this work presents a simple solution using machine translation to translate English data to German to train a transformer-based factuality detection model.
Cross-lingual Approaches for the Detection of Adverse Drug Reactions in German from a Patient's Perspective
Aug 03, 2022
In this work, we present the first corpus for German Adverse Drug Reaction (ADR) detection in patient-generated content. The data consists of 4,169 binary annotated documents from a German patient forum, where users talk about health issues and get advice from medical doctors. As is common in social media data in this domain, the class labels of the corpus are very imbalanced. This and a high topic imbalance make it a very challenging dataset, since often, the same symptom can have several causes and is not always related to a medication intake. We aim to encourage further multi-lingual efforts in the domain of ADR detection and provide preliminary experiments for binary classification using different methods of zero- and few-shot learning based on a multi-lingual model. When fine-tuning XLM-RoBERTa first on English patient forum data and then on the new German data, we achieve an F1-score of 37.52 for the positive class. We make the dataset and models publicly available for the community.
A Medical Information Extraction Workbench to Process German Clinical Text
Jul 08, 2022
Background: In the information extraction and natural language processing domain, accessible datasets are crucial to reproduce and compare results. Publicly available implementations and tools can serve as benchmark and facilitate the development of more complex applications. However, in the context of clinical text processing the number of accessible datasets is scarce -- and so is the number of existing tools. One of the main reasons is the sensitivity of the data. This problem is even more evident for non-English languages. Approach: In order to address this situation, we introduce a workbench: a collection of German clinical text processing models. The models are trained on a de-identified corpus of German nephrology reports. Result: The presented models provide promising results on in-domain data. Moreover, we show that our models can be also successfully applied to other biomedical text in German. Our workbench is made publicly available so it can be used out of the box, as a benchmark or transferred to related problems.
When Performance is not Enough -- A Multidisciplinary View on Clinical Decision Support
Apr 27, 2022
Scientific publications about machine learning in healthcare are often about implementing novel methods and boosting the performance - at least from a computer science perspective. However, beyond such often short-lived improvements, much more needs to be taken into consideration if we want to arrive at a sustainable progress in healthcare. What does it take to actually implement such a system, make it usable for the domain expert, and possibly bring it into practical usage? Targeted at Computer Scientists, this work presents a multidisciplinary view on machine learning in medical decision support systems and covers information technology, medical, as well as ethical aspects. Along with an implemented risk prediction system in nephrology, challenges and lessons learned in a pilot project are presented.
From Witch's Shot to Music Making Bones -- Resources for Medical Laymen to Technical Language and Vice Versa
May 23, 2020
Many people share information in social media or forums, like food they eat, sports activities they do or events which have been visited. This also applies to information about a person's health status. Information we share online unveils directly or indirectly information about our lifestyle and health situation and thus provides a valuable data resource. If we can make advantage of that data, applications can be created that enable e.g. the detection of possible risk factors of diseases or adverse drug reactions of medications. However, as most people are not medical experts, language used might be more descriptive rather than the precise medical expression as medics do. To detect and use those relevant information, laymen language has to be translated and/or linked to the corresponding medical concept. This work presents baseline data sources in order to address this challenge for German. We introduce a new data set which annotates medical laymen and technical expressions in a patient forum, along with a set of medical synonyms and definitions, and present first baseline results on the data.
SIA: A Scalable Interoperable Annotation Server for Biomedical Named Entities
Apr 08, 2020
Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools. However, the integration of freely available tools into customized workflows is often cumbersome and difficult. We describe SIA (Scalable Interoperable Annotation Server), our contribution to the BeCalm-Technical interoperability and performance of annotation servers (BeCalm-TIPS) task, a scalable, extensible, and robust annotation service. The system currently covers six named entity types (i.e., Chemicals, Diseases, Genes, miRNA, Mutations, and Organisms) and is freely available under Apache 2.0 license at https://github.com/Erechtheus/sia.
* 11 pages, 2 figures, published in Journal of Cheminformatics
Cross-lingual Candidate Search for Biomedical Concept Normalization
May 04, 2018
Biomedical concept normalization links concept mentions in texts to a semantically equivalent concept in a biomedical knowledge base. This task is challenging as concepts can have different expressions in natural languages, e.g. paraphrases, which are not necessarily all present in the knowledge base. Concept normalization of non-English biomedical text is even more challenging as non-English resources tend to be much smaller and contain less synonyms. To overcome the limitations of non-English terminologies we propose a cross-lingual candidate search for concept normalization using a character-based neural translation model trained on a multilingual biomedical terminology. Our model is trained with Spanish, French, Dutch and German versions of UMLS. The evaluation of our model is carried out on the French Quaero corpus, showing that it outperforms most teams of CLEF eHealth 2015 and 2016. Additionally, we compare performance to commercial translators on Spanish, French, Dutch and German versions of Mantra. Our model performs similarly well, but is free of charge and can be run locally. This is particularly important for clinical NLP applications as medical documents underlay strict privacy restrictions.
Creation of an Annotated Corpus of Spanish Radiology Reports
Oct 30, 2017
This paper presents a new annotated corpus of 513 anonymized radiology reports written in Spanish. Reports were manually annotated with entities, negation and uncertainty terms and relations. The corpus was conceived as an evaluation resource for named entity recognition and relation extraction algorithms, and as input for the use of supervised methods. Biomedical annotated resources are scarce due to confidentiality issues and associated costs. This work provides some guidelines that could help other researchers to undertake similar tasks.