Stefan Winkler


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A Two-Stage Decoder for Efficient ICD Coding
Thanh-Tung Nguyen | Viktor Schlegel | Abhinav Ramesh Kashyap | Stefan Winkler
Findings of the Association for Computational Linguistics: ACL 2023

Clinical notes in healthcare facilities are tagged with the International Classification of Diseases (ICD) code; a list of classification codes for medical diagnoses and procedures. ICD coding is a challenging multilabel text classification problem due to noisy clinical document inputs and long-tailed label distribution. Recent automated ICD coding efforts improve performance by encoding medical notes and codes with additional data and knowledge bases. However, most of them do not reflect how human coders generate the code: first, the coders select general code categories and then look for specific subcategories that are relevant to a patient’s condition. Inspired by this, we propose a two-stage decoding mechanism to predict ICD codes. Our model uses the hierarchical properties of the codes to split the prediction into two steps: At first, we predict the parent code and then predict the child code based on the previous prediction. Experiments on the public MIMIC-III data set have shown that our model performs well in single-model settings without external data or knowledge.

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Team:PULSAR at ProbSum 2023:PULSAR: Pre-training with Extracted Healthcare Terms for Summarising Patients’ Problems and Data Augmentation with Black-box Large Language Models
Hao Li | Yuping Wu | Viktor Schlegel | Riza Batista-Navarro | Thanh-Tung Nguyen | Abhinav Ramesh Kashyap | Xiao-Jun Zeng | Daniel Beck | Stefan Winkler | Goran Nenadic
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks

Medical progress notes play a crucial role in documenting a patient’s hospital journey, including his or her condition, treatment plan, and any updates for healthcare providers. Automatic summarisation of a patient’s problems in the form of a “problem list” can aid stakeholders in understanding a patient’s condition, reducing workload and cognitive bias. BioNLP 2023 Shared Task 1A focusses on generating a list of diagnoses and problems from the provider’s progress notes during hospitalisation. In this paper, we introduce our proposed approach to this task, which integrates two complementary components. One component employs large language models (LLMs) for data augmentation; the other is an abstractive summarisation LLM with a novel pre-training objective for generating the patients’ problems summarised as a list. Our approach was ranked second among all submissions to the shared task. The performance of our model on the development and test datasets shows that our approach is more robust on unknown data, with an improvement of up to 3.1 points over the same size of the larger model.