arXiv subjects

Luke Daines

Publications and source records attributed to Luke Daines.

4 recordsLinked to original sources

arXiv2024

Edinburgh Clinical NLP at MEDIQA-CORR 2024: Guiding Large Language Models with Hints

The MEDIQA-CORR 2024 shared task aims to assess the ability of Large Language Models (LLMs) to identify and correct medical errors in clinical notes. In this study, we evaluate the capability of general LLMs, specifically GPT-3.5 and GPT-4, to identify and correct medical errors with multiple prompting strategies. Recognising the limitation of LLMs in generating accurate corrections only via prompting strategies, we propose incorporating error-span predictions from a smaller, fine-tuned model in two ways: 1) by presenting it as a hint in the prompt and 2) by framing it as multiple-choice questions from which the LLM can choose the best correction. We found that our proposed prompting strategies significantly improve the LLM's ability to generate corrections. Our best-performing solution with 8-shot + CoT + hints ranked sixth in the shared task leaderboard. Additionally, our comprehensive analyses show the impact of the location of the error sentence, the prompted role, and the position of the multiple-choice option on the accuracy of the LLM. This prompts further questions about the readiness of LLM to be implemented in real-world clinical settings.

cs.CL↗

arXiv2024

Edinburgh Clinical NLP at SemEval-2024 Task 2: Fine-tune your model unless you have access to GPT-4

The NLI4CT task assesses Natural Language Inference systems in predicting whether hypotheses entail or contradict evidence from Clinical Trial Reports. In this study, we evaluate various Large Language Models (LLMs) with multiple strategies, including Chain-of-Thought, In-Context Learning, and Parameter-Efficient Fine-Tuning (PEFT). We propose a PEFT method to improve the consistency of LLMs by merging adapters that were fine-tuned separately using triplet and language modelling objectives. We found that merging the two PEFT adapters improves the F1 score (+0.0346) and consistency (+0.152) of the LLMs. However, our novel methods did not produce more accurate results than GPT-4 in terms of faithfulness and consistency. Averaging the three metrics, GPT-4 ranks joint-first in the competition with 0.8328. Finally, our contamination analysis with GPT-4 indicates that there was no test data leakage.

cs.CL↗

arXiv2024

Can GPT-3.5 Generate and Code Discharge Summaries?

Objective: To investigate GPT-3.5 in generating and coding medical documents with ICD-10 codes for data augmentation on low-resources labels. Materials and Methods: Employing GPT-3.5 we generated and coded 9,606 discharge summaries based on lists of ICD-10 code descriptions of patients with infrequent (generation) codes within the MIMIC-IV dataset. Combined with the baseline training set, this formed an augmented training set. Neural coding models were trained on baseline and augmented data and evaluated on a MIMIC-IV test set. We report micro- and macro-F1 scores on the full codeset, generation codes, and their families. Weak Hierarchical Confusion Matrices were employed to determine within-family and outside-of-family coding errors in the latter codesets. The coding performance of GPT-3.5 was evaluated both on prompt-guided self-generated data and real MIMIC-IV data. Clinical professionals evaluated the clinical acceptability of the generated documents. Results: Augmentation slightly hinders the overall performance of the models but improves performance for the generation candidate codes and their families, including one unseen in the baseline training data. Augmented models display lower out-of-family error rates. GPT-3.5 can identify ICD-10 codes by the prompted descriptions, but performs poorly on real data. Evaluators note the correctness of generated concepts while suffering in variety, supporting information, and narrative. Discussion and Conclusion: GPT-3.5 alone is unsuitable for ICD-10 coding. Augmentation positively affects generation code families but mainly benefits codes with existing examples. Augmentation reduces out-of-family errors. Discharge summaries generated by GPT-3.5 state prompted concepts correctly but lack variety, and authenticity in narratives. They are unsuitable for clinical practice.

cs.CL↗

arXiv2023

Parameter-Efficient Fine-Tuning of LLaMA for the Clinical Domain

Adapting pretrained language models to novel domains, such as clinical applications, traditionally involves retraining their entire set of parameters. Parameter-Efficient Fine-Tuning (PEFT) techniques for fine-tuning language models significantly reduce computational requirements by selectively fine-tuning small subsets of parameters. In this study, we propose a two-step PEFT framework and evaluate it in the clinical domain. Our approach combines a specialised PEFT adapter layer designed for clinical domain adaptation with another adapter specialised for downstream tasks. We evaluate the framework on multiple clinical outcome prediction datasets, comparing it to clinically trained language models. Our framework achieves a better AUROC score averaged across all clinical downstream tasks compared to clinical language models. In particular, we observe large improvements of 4-5% AUROC in large-scale multilabel classification tasks, such as diagnoses and procedures classification. To our knowledge, this study is the first to provide an extensive empirical analysis of the interplay between PEFT techniques and domain adaptation in an important real-world domain of clinical applications.

cs.CL↗