ICD Codes are Insufficient to Create Datasets for Machine Learning: An Evaluation Using All of Us Data for Coccidioidomycosis and Myocardial Infarction

In medicine, machine learning (ML) datasets are often built using the International Classification of Diseases (ICD) codes. As new models are being developed, there is a need for larger datasets. However, ICD codes are intended for billing. We aim to determine how suitable ICD codes are for creating datasets to train ML models. We focused on a rare and common disease using the All of Us database. First, we compared the patient cohort created using ICD codes for Valley fever (coccidioidomycosis, CM) with that identified via serological confirmation. Second, we compared two similarly created patient cohorts for myocardial infarction (MI) patients. We identified significant discrepancies between these two groups, and the patient overlap was small. The CM cohort had 811 patients in the ICD-10 group, 619 patients in the positive-serology group, and 24 with both. The MI cohort had 14,875 patients in the ICD-10 group, 23,598 in the MI laboratory-confirmed group, and 6,531 in both. Demographics, rates of disease symptoms, and other clinical data varied across our case study cohorts.

Utilizing Large Language Models to Generate Synthetic Data to Increase the Performance of BERT-Based Neural Networks

An important issue impacting healthcare is a lack of available experts. Machine learning (ML) models could resolve this by aiding in diagnosing patients. However, creating datasets large enough to train these models is expensive. We evaluated large language models (LLMs) for data creation. Using Autism Spectrum Disorders (ASD), we prompted ChatGPT and GPT-Premium to generate 4,200 synthetic observations to augment existing medical data. Our goal is to label behaviors corresponding to autism criteria and improve model accuracy with synthetic training data. We used a BERT classifier pre-trained on biomedical literature to assess differences in performance between models. A random sample (N=140) from the LLM-generated data was evaluated by a clinician and found to contain 83% correct example-label pairs. Augmenting data increased recall by 13% but decreased precision by 16%, correlating with higher quality and lower accuracy across pairs. Future work will analyze how different synthetic data traits affect ML outcomes.

Effects of Added Emphasis and Pause in Audio Delivery of Health Information

Health literacy is crucial to supporting good health and is a major national goal. Audio delivery of information is becoming more popular for informing oneself. In this study, we evaluate the effect of audio enhancements in the form of information emphasis and pauses with health texts of varying difficulty and we measure health information comprehension and retention. We produced audio snippets from difficult and easy text and conducted the study on Amazon Mechanical Turk (AMT). Our findings suggest that emphasis matters for both information comprehension and retention. When there is no added pause, emphasizing significant information can lower the perceived difficulty for difficult and easy texts. Comprehension is higher (54%) with correctly placed emphasis for the difficult texts compared to not adding emphasis (50%). Adding a pause lowers perceived difficulty and can improve retention but adversely affects information comprehension.

Text and Audio Simplification: Human vs. ChatGPT

Text and audio simplification to increase information comprehension are important in healthcare. With the introduction of ChatGPT, an evaluation of its simplification performance is needed. We provide a systematic comparison of human and ChatGPT simplified texts using fourteen metrics indicative of text difficulty. We briefly introduce our online editor where these simplification tools, including ChatGPT, are available. We scored twelve corpora using our metrics: six text, one audio, and five ChatGPT simplified corpora. We then compare these corpora with texts simplified and verified in a prior user study. Finally, a medical domain expert evaluated these texts and five, new ChatGPT simplified versions. We found that simple corpora show higher similarity with the human simplified texts. ChatGPT simplification moves metrics in the right direction. The medical domain expert evaluation showed a preference for the ChatGPT style, but the text itself was rated lower for content retention.

APPLS: A Meta-evaluation Testbed for Plain Language Summarization

While there has been significant development of models for Plain Language Summarization (PLS), evaluation remains a challenge. This is in part because PLS involves multiple, interrelated language transformations (e.g., adding background explanations, removing specialized terminology). No metrics are explicitly engineered for PLS, and the suitability of other text generation evaluation metrics remains unclear. To address these concerns, our study presents a granular meta-evaluation testbed, APPLS, designed to evaluate existing metrics for PLS. Drawing on insights from previous research, we define controlled perturbations for our testbed along four criteria that a metric of plain language should capture: informativeness, simplification, coherence, and faithfulness. Our analysis of metrics using this testbed reveals that current metrics fail to capture simplification, signaling a crucial gap. In response, we introduce POMME, a novel metric designed to assess text simplification in PLS. We demonstrate its correlation with simplification perturbations and validate across a variety of datasets. Our research contributes the first meta-evaluation testbed for PLS and a comprehensive evaluation of existing metrics, offering insights with relevance to other text generation tasks.

CELLS: A Parallel Corpus for Biomedical Lay Language Generation

Recent lay language generation systems have used Transformer models trained on a parallel corpus to increase health information accessibility. However, the applicability of these models is constrained by the limited size and topical breadth of available corpora. We introduce CELLS, the largest (63k pairs) and broadest-ranging (12 journals) parallel corpus for lay language generation. The abstract and the corresponding lay language summary are written by domain experts, assuring the quality of our dataset. Furthermore, qualitative evaluation of expert-authored plain language summaries has revealed background explanation as a key strategy to increase accessibility. Such explanation is challenging for neural models to generate because it goes beyond simplification by adding content absent from the source. We derive two specialized paired corpora from CELLS to address key challenges in lay language generation: generating background explanations and simplifying the original abstract. We adopt retrieval-augmented models as an intuitive fit for the task of background explanation generation, and show improvements in summary quality and simplicity while maintaining factual correctness. Taken together, this work presents the first comprehensive study of background explanation for lay language generation, paving the path for disseminating scientific knowledge to a broader audience. CELLS is publicly available at: https://github.com/LinguisticAnomalies/pls_retrieval.

AutoMeTS: The Autocomplete for Medical Text Simplification

The goal of text simplification (TS) is to transform difficult text into a version that is easier to understand and more broadly accessible to a wide variety of readers. In some domains, such as healthcare, fully automated approaches cannot be used since information must be accurately preserved. Instead, semi-automated approaches can be used that assist a human writer in simplifying text faster and at a higher quality. In this paper, we examine the application of autocomplete to text simplification in the medical domain. We introduce a new parallel medical data set consisting of aligned English Wikipedia with Simple English Wikipedia sentences and examine the application of pretrained neural language models (PNLMs) on this dataset. We compare four PNLMs(BERT, RoBERTa, XLNet, and GPT-2), and show how the additional context of the sentence to be simplified can be incorporated to achieve better results (6.17% absolute improvement over the best individual model). We also introduce an ensemble model that combines the four PNLMs and outperforms the best individual model by 2.1%, resulting in an overall word prediction accuracy of 64.52%.