Biomedical Entity Linking (BEL) is a challenging task for low-resource languages, due to the lack of appropriate resources: datasets, knowledge bases (KBs), and pre-trained models. In this paper, we propose an approach to create a biomedical knowledge base for German BEL using UMLS information from Wikidata, that provides good coverage and can be easily extended to further languages. As a further contribution, we adapt several existing approaches for use in the German BEL setup, and report on their results. The chosen methods include a sparse model using character n-grams, a multilingual biomedical entity linker, and two general-purpose text retrieval models. Our results show that a language-specific KB that provides good coverage leads to most improvement in entity linking performance, irrespective of the used model. The finetuned German BEL model, newly created UMLSWikidata KB as well as the code to reproduce our results are publicly available1.
Extracting timeline information from clinical narratives is critical for cancer research and practice using electronic health records (EHRs). In this study, we apply MedTimeline, our endto-end hybrid NLP system combining large language model, deep learning with knowledge engineering, to the ChemoTimeLine challenge subtasks. Our experiment results in 0.83, 0.90, 0.84, and 0.53, 0.63, 0.39, respectively, for subtask1 and subtask2 in breast, melanoma and ovarian cancer.
In this paper, we present our work in the EHRSQL 2024 shared task which tackles reliable text-to-SQL modeling on Electronic Health Records. Our proposed system tackles the task with three modules - abstention module, text-to-SQL generation module, and reliability module. The abstention module identifies whether the question is answerable given the database schema. If the question is answerable, the text-to-SQL generation module generates the SQL query and associated confidence score. The reliability module has two key components - confidence score thresholding, which rejects generations with confidence below a predefined level, and error filtering, which identifies and excludes SQL queries that result in execution errors. In the official leaderboard for the task, our system ranks 6th. We have also made the source code public(1).
Remote patient care provides opportunities for expanding medical access, saving healthcare costs, and offering on-demand convenient services. In the MEDIQA-M3G 2024 Shared Task, researchers explored solutions for the specific task of dermatological consumer health visual question answering, where user generated queries and images are used as input and a freetext answer response is generated as output. In this novel challenge, eight teams with a total of 48 submissions were evaluated across three language test sets. In this work, we provide a summary of the dataset, as well as results and approaches. We hope that the insights learned here will inspire future research directions that can lead to technology that deburdens clinical workload and improves care.
This paper demonstrates CLD-MEC team submission to the MEDIQA-CORR 2024 shared task for identifying and correcting medical errors from clinical notes. We developed a framework to track two main types of medical errors: diagnostics and medical managementrelated errors. The tracking framework is implied utilizing a GPT-4 multi-stage promptingbased pipeline that ends with the three downstream tasks: classification of medical error existence (Task 1), identification of error location (Task 2), and correction error (Task 3). Throughout the pipeline, we employed clinical Chain of Thought (CoT) and Chain-ofVerification (CoVe) techniques to mitigate the hallucination and enforce the clinical context learning. The model performance is acceptable, given it is based on zero-shot learning. In addition, we developed a RAG system injected with clinical practice guidelines as an external knowledge datastore. Our RAG is based on the Bio_ClinicalBERT as a vector embedding model. However, our RAG system failed to get the desired results. We proposed recommendations to be investigated in future research work to overcome the limitations of our approach.
