Oscar Perez-Concha

Bokang Bi, Leibo Liu, Sanja Lujic et al.

The increasing volume and complexity of clinical documentation in Electronic Medical Records systems pose significant challenges for clinical coders, who must mentally process and summarise vast amounts of clinical text to extract essential information needed for coding tasks. While large language models have been successfully applied to shorter summarisation tasks in recent years, the challenge of summarising a hospital course remains an open area for further research and development. In this study, we adapted three pre trained LLMs, Llama 3, BioMistral, Mistral Instruct v0.1 for the hospital course summarisation task, using Quantized Low Rank Adaptation fine tuning. We created a free text clinical dataset from MIMIC III data by concatenating various clinical notes as the input clinical text, paired with ground truth Brief Hospital Course sections extracted from the discharge summaries for model training. The fine tuned models were evaluated using BERTScore and ROUGE metrics to assess the effectiveness of clinical domain fine tuning. Additionally, we validated their practical utility using a novel hospital course summary assessment metric specifically tailored for clinical coding. Our findings indicate that fine tuning pre trained LLMs for the clinical domain can significantly enhance their performance in hospital course summarisation and suggest their potential as assistive tools for clinical coding. Future work should focus on refining data curation methods to create higher quality clinical datasets tailored for hospital course summary tasks and adapting more advanced open source LLMs comparable to proprietary models to further advance this research.

Leibo Liu, Oscar Perez-Concha, Anthony Nguyen et al.

International Classification of Diseases (ICD) coding plays an important role in systematically classifying morbidity and mortality data. In this study, we propose a hierarchical label-wise attention Transformer model (HiLAT) for the explainable prediction of ICD codes from clinical documents. HiLAT firstly fine-tunes a pretrained Transformer model to represent the tokens of clinical documents. We subsequently employ a two-level hierarchical label-wise attention mechanism that creates label-specific document representations. These representations are in turn used by a feed-forward neural network to predict whether a specific ICD code is assigned to the input clinical document of interest. We evaluate HiLAT using hospital discharge summaries and their corresponding ICD-9 codes from the MIMIC-III database. To investigate the performance of different types of Transformer models, we develop ClinicalplusXLNet, which conducts continual pretraining from XLNet-Base using all the MIMIC-III clinical notes. The experiment results show that the F1 scores of the HiLAT+ClinicalplusXLNet outperform the previous state-of-the-art models for the top-50 most frequent ICD-9 codes from MIMIC-III. Visualisations of attention weights present a potential explainability tool for checking the face validity of ICD code predictions.

Leibo Liu, Oscar Perez-Concha, Anthony Nguyen et al.

Background: Encouraged by the success of pretrained Transformer models in many natural language processing tasks, their use for International Classification of Diseases (ICD) coding tasks is now actively being explored. In this study, we investigate three types of Transformer-based models, aiming to address the extreme label set and long text classification challenges that are posed by automated ICD coding tasks. Methods: The Transformer-based model PLM-ICD achieved the current state-of-the-art (SOTA) performance on the ICD coding benchmark dataset MIMIC-III. It was chosen as our baseline model to be further optimised. XR-Transformer, the new SOTA model in the general extreme multi-label text classification domain, and XR-LAT, a novel adaptation of the XR-Transformer model, were also trained on the MIMIC-III dataset. XR-LAT is a recursively trained model chain on a predefined hierarchical code tree with label-wise attention, knowledge transferring and dynamic negative sampling mechanisms. Results: Our optimised PLM-ICD model, which was trained with longer total and chunk sequence lengths, significantly outperformed the current SOTA PLM-ICD model, and achieved the highest micro-F1 score of 60.8%. The XR-Transformer model, although SOTA in the general domain, did not perform well across all metrics. The best XR-LAT based model obtained results that were competitive with the current SOTA PLM-ICD model, including improving the macro-AUC by 2.1%. Conclusion: Our optimised PLM-ICD model is the new SOTA model for automated ICD coding on the MIMIC-III dataset, while our novel XR-LAT model performs competitively with the previous SOTA PLM-ICD model.

Oisin Fitzgerald, Oscar Perez-Concha, Blanca Gallego-Luxan et al.

Irregularly measured time series are common in many of the applied settings in which time series modelling is a key statistical tool, including medicine. This provides challenges in model choice, often necessitating imputation or similar strategies. Continuous time autoregressive recurrent neural networks (CTRNNs) are a deep learning model that account for irregular observations through incorporating continuous evolution of the hidden states between observations. This is achieved using a neural ordinary differential equation (ODE) or neural flow layer. In this manuscript, we give an overview of these models, including the varying architectures that have been proposed to account for issues such as ongoing medical interventions. Further, we demonstrate the application of these models to probabilistic forecasting of blood glucose in a critical care setting using electronic medical record and simulated data. The experiments confirm that addition of a neural ODE or neural flow layer generally improves the performance of autoregressive recurrent neural networks in the irregular measurement setting. However, several CTRNN architecture are outperformed by an autoregressive gradient boosted tree model (Catboost), with only a long short-term memory (LSTM) and neural ODE based architecture (ODE-LSTM) achieving comparable performance on probabilistic forecasting metrics such as the continuous ranked probability score (ODE-LSTM: 0.118$\pm$0.001; Catboost: 0.118$\pm$0.001), ignorance score (0.152$\pm$0.008; 0.149$\pm$0.002) and interval score (175$\pm$1; 176$\pm$1).

Leibo Liu, Oscar Perez-Concha, Anthony Nguyen et al.

Electronic Medical Records (EMRs) contain clinical narrative text that is of great potential value to medical researchers. However, this information is mixed with Personally Identifiable Information (PII) that presents risks to patient and clinician confidentiality. This paper presents an end-to-end deidentification framework to automatically remove PII from Australian hospital discharge summaries. Our corpus included 600 hospital discharge summaries which were extracted from the EMRs of two principal referral hospitals in Sydney, Australia. Our end-to-end de-identification framework consists of three components: 1) Annotation: labelling of PII in the 600 hospital discharge summaries using five pre-defined categories: person, address, date of birth, individual identification number, phone/fax number; 2) Modelling: training six named entity recognition (NER) deep learning base-models on balanced and imbalanced datasets; and evaluating ensembles that combine all six base-models, the three base-models with the best F1 scores and the three base-models with the best recall scores respectively, using token-level majority voting and stacking methods; and 3) De-identification: removing PII from the hospital discharge summaries. Our results showed that the ensemble model combined using the stacking Support Vector Machine (SVM) method on the three base-models with the best F1 scores achieved excellent results with a F1 score of 99.16% on the test set of our corpus. We also evaluated the robustness of our modelling component on the 2014 i2b2 de-identification dataset. Our ensemble model, which uses the token-level majority voting method on all six basemodels, achieved the highest F1 score of 96.24% at strict entity matching and the highest F1 score of 98.64% at binary token-level matching compared to two state-of-the-art methods.

Sebastiano Barbieri, James Kemp, Oscar Perez-Concha et al.

Objective: To compare different deep learning architectures for predicting the risk of readmission within 30 days of discharge from the intensive care unit (ICU). The interpretability of attention-based models is leveraged to describe patients-at-risk. Methods: Several deep learning architectures making use of attention mechanisms, recurrent layers, neural ordinary differential equations (ODEs), and medical concept embeddings with time-aware attention were trained using publicly available electronic medical record data (MIMIC-III) associated with 45,298 ICU stays for 33,150 patients. Bayesian inference was used to compute the posterior over weights of an attention-based model. Odds ratios associated with an increased risk of readmission were computed for static variables. Diagnoses, procedures, medications, and vital signs were ranked according to the associated risk of readmission. Results: A recurrent neural network, with time dynamics of code embeddings computed by neural ODEs, achieved the highest average precision of 0.331 (AUROC: 0.739, F1-Score: 0.372). Predictive accuracy was comparable across neural network architectures. Groups of patients at risk included those suffering from infectious complications, with chronic or progressive conditions, and for whom standard medical care was not suitable. Conclusions: Attention-based networks may be preferable to recurrent networks if an interpretable model is required, at only marginal cost in predictive accuracy.