Canada

This paper describes our submission to the MEDIQA-Chat 2023 shared task for automatic clinical note generation from doctor-patient conversations. We report results for two approaches: the first fine-tunes a pre-trained language model (PLM) on the shared task data, and the second uses few-shot in-context learning (ICL) with a large language model (LLM). Both achieve high performance as measured by automatic metrics (e.g. ROUGE, BERTScore) and ranked second and first, respectively, of all submissions to the shared task. Expert human scrutiny indicates that notes generated via the ICL-based approach with GPT-4 are preferred about as often as human-written notes, making it a promising path toward automated note generation from doctor-patient conversations.

ACL 2023

WangLab at MEDIQA-Chat 2023: Clinical Note Generation from Doctor-Patient Conversations using Large Language Models

clinicalnlp

clinical note generation

large language models

### Welcome to the 17th Conference of the European Chapter of the Association for Computational Linguistics (EACL) 
Continuing its mission of expanding and involving the science community of all European countries, EACL had selected the Ukrainian community for the 16th EACL, which took place online due to the COVID pandemic. Unfortunately, the ongoing war made the organisation in Kyiv impossible. Considering the importance of physical interaction among researchers, especially after the restrictions imposed by the COVID pandemic, in addition to an online mode, the conference will be held in Dubrovnik, Croatia, from 2 to 6 of May, 2023. The original aim of strengthening the connection with the Ukrainian community will not change as our program will feature a dedicated session and a workshop to highlight work on Ukrainian language technologies. As the flagship European conference in the field of computational linguistics, EACL welcomes European and international researchers covering a broad spectrum of research areas that are concerned with computational approaches to natural language.

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EACL 2023

As the flagship European conference in the field of computational linguistics, EACL welcomes European and international researchers covering a broad spectrum of research areas that are concerned with computational approaches to natural language.

workshop paper

### Welcome to ACL 2023, the 61st Annual Meeting of the Association for Computational Linguistics! 
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The Association for Computational Linguistics (ACL) is the premier international scientific and professional society for people working on computational problems involving human language, a field often referred to as either computational linguistics or natural language processing.

Detecting testimonial injustice is an essential element of addressing inequities and promoting inclusive healthcare practices, many of which are life-critical. However, using a single demographic factor to detect testimonial injustice does not fully encompass the nuanced identities that contribute to a patient's experience. Further, some injustices may only be evident when examining the nuances that arise through the lens of intersectionality. Ignoring such injustices can result in poor quality of care or life-endangering events. Thus, considering intersectionality could result in more accurate classifications and just decisions. To illustrate this, we use real-world medical data to determine whether medical records exhibit words that could lead to testimonial injustice, employ fairness metrics (e.g. demographic parity, differential intersectional fairness, and subgroup fairness) to assess the severity to which subgroups are experiencing testimonial injustice, and analyze how the intersectionality of demographic features (e.g. gender and race) make a difference in uncovering testimonial injustice. From our analysis, we found that with intersectionality we can better see disparities in how subgroups are treated and there are differences in how someone is treated based on the intersection of their demographic attributes. This has not been previously studied in clinical records, nor has it been proven through empirical study.

Intersectionality and Testimonial Injustice in Medical Records

In this paper, we introduce the design and various attempts for Task B of MEDIQA-Chat 2023. The goal of Task B in MEDIQA-Chat 2023 is to generate full clinical note from doctor-patient consultation dialogues. This task has several challenging issues, such as lack of training data, handling long dialogue inputs, and generating semi-structured clinical note which have section heads. To address these issues, we conducted various experiments and analyzed their results. We utilized the DialogLED model pre-trained on long dialogue data to handle long inputs, and we pre-trained on other dialogue datasets to address the lack of training data. We also attempted methods such as using prompts and contrastive learning for handling sections. This paper provides insights into clinical note generation through analyzing experimental methods and results, and it suggests future research directions.

Teddysum at MEDIQA-Chat 2023: an analysis of fine-tuning strategy for long dialog summarization

Multi-label clinical text classification, such as automatic ICD coding, has always been a challenging subject in Natural Language Processing, due to its long, domain-specific documents and long-tail distribution over a large label set. Existing methods adopt different model architectures to encode the clinical notes. Whereas without digging out the useful connections between labels, the model presents a huge gap in predicting performances between rare and frequent codes. In this work, we propose a novel method for further mining the helpful relations between different codes via a relation-enhanced code encoder to improve the rare code performance. Starting from the simple code descriptions, the model reaches comparable, even better performances than models with heavy external knowledge. Our proposed method is evaluated on MIMIC-III, a common dataset in the medical domain. It outperforms the previous state-of-art models on both overall metrics and rare code performances. Moreover, the interpretation results further prove the effectiveness of our methods.

Rare Codes Count: Mining Inter-code Relations for Long-tail Clinical Text Classification

The field of clinical natural language processing (NLP) can extract useful information from clinical text. Since 2017, the NLP field has shifted towards using pre-trained language models (PLMs), improving performance in several tasks. Most of the research in this field has focused on English text, but there are some available PLMs in Spanish. In this work, we use clinical PLMs to analyze text from admission and medical reports in Spanish for an insurance and health provider to give a probability of no coverage in a labor insurance process. Our results show that fine-tuning a PLM pre-trained with the provider's data leads to better results, but this process is time-consuming and computationally expensive. At least for this task, fine-tuning publicly available clinical PLM leads to comparable results to a custom PLM, but in less time and with fewer resources. Analyzing large volumes of insurance requests is burdensome for employers, and models can ease this task by pre-classifying reports that are likely not to have coverage. Our approach of entirely using clinical-related text improves the current models while reinforcing the idea of clinical support systems that simplify human labor but do not replace it. To our knowledge, the clinical corpus collected for this study is the largest one reported for the Spanish language.

Pre-trained language models in Spanish for health insurance coverage

In response to the global challenge of mental health problems, we proposes a Logical Neural Network (LNN) based Neuro-Symbolic AI method for the diagnosis of mental disorders. Due to the lack of effective therapy coverage for mental disorders, there is a need for an AI solution that can assist therapists with the diagnosis. However, current Neural Network models lack explainability and may not be trusted by therapists. The LNN is a Recurrent Neural Network architecture that combines the learning capabilities of neural networks with the reasoning capabilities of classical logic-based AI. The proposed system uses input predicates from clinical interviews to output a mental disorder class, and different predicate pruning techniques are used to achieve scalability and higher scores. In addition, we provide an insight extraction method to aid therapists with their diagnosis. The proposed system addresses the lack of explainability of current Neural Network models and provides a more trustworthy solution for mental disorder diagnosis.

Utterance Classification with Logical Neural Network: Explainable AI for Mental Disorder Diagnosis

Medical Report Generation (MRG) is a sub-task of Natural Language Generation (NLG) and aims to present information from various sources in textual form and synthesize salient information, with the goal of reducing the time spent by domain experts in writing medical reports and providing support information for decision-making. Given the specificity of the medical domain, the evaluation of automatically generated medical reports is of paramount importance to the validity of these systems. Therefore, in this paper, we focus on the evaluation of automatically generated medical reports from the perspective of automatic and human evaluation. We present evaluation methods for general NLG evaluation and how they have been applied to domain-specific medical tasks. The study shows that MRG evaluation methods are very diverse, and that further work is needed to build shared evaluation methods. The state of the art also emphasizes that such an evaluation must be task specific and include human assessments, requesting the participation of experts in the field.

A Survey of Evaluation Methods of Generated Medical Textual Reports

In recent years, we have seen many Transformer based models being created to address Dialog Summarization problem. While there has been a lot of work on understanding how these models stack against each other in summarizing regular conversations such as the ones found in DialogSum dataset, there haven't been many analysis of these models on Clinical Dialog Summarization. In this article, we describe our solution to MEDIQA-Chat 2023 Shared Tasks as part of ACL-ClinicalNLP 2023 workshop which benchmarks some of the popular Transformer Architectures such as BioBart, Flan-T5, DialogLED, and OpenAI GPT3 on the problem of Clinical Dialog Summarization. We analyse their performance on two tasks - summarizing short conversations and long conversations. In addition to this, we also benchmark two popular summarization ensemble methods and report their performance.

HealthMavericks@MEDIQA-Chat 2023: Benchmarking different Transformer based models for Clinical Dialogue Summarization

To gain a better understanding of the linguistic information encoded in character-based language models, we probe the multilingual contextual CANINE model. We design a range of phonetic probing tasks in six Nordic languages, including Faroese as an additional zero-shot instance. We observe that some phonetic information is indeed encoded in the character representations, as consonants and vowels can be well distinguished using a linear classifier. Furthermore, results for the Danish and Norwegian language seem to be worse for the consonant/vowel distinction in comparison to other languages. The information encoded in these representations can also be learned in a zero-shot scenario, as Faroese shows a reasonably good performance in the same vowel/consonant distinction task.

The hidden folk: linguistic properties encoded in multilingual contextual character representations

Multilingual models such as mBERT have been demonstrated to exhibit impressive 
cross-lingual transfer for a number of languages. Despite this, the performance drops for lower-resourced languages, especially when they are not part of the pre-training setup and when there are script differences.
In this work we consider Maltese, a low-resource language of Arabic and Romance origins written in Latin script. Specifically, we investigate the impact of transliterating Maltese into Arabic scipt on a number of downstream tasks: Part-of-Speech Tagging, Dependency Parsing, and Sentiment Analysis. We compare multiple transliteration pipelines ranging from deterministic character maps to more sophisticated alternatives, including manually annotated word mappings and non-deterministic character mappings. For the latter, we show that selection techniques using n-gram language models of Tunisian Arabic, the dialect with the highest degree of mutual intelligibility to Maltese, yield better results on downstream tasks. Moreover, our experiments highlight that the use of an Arabic pre-trained model paired with transliteration outperforms mBERT. Overall, our results show that transliterating Maltese can be considered an option to improve the cross-lingual transfer capabilities.

Exploring the impact of transliteration on NLP performance for low-resource languages: the case of Malese and Arabic

We propose methods for transliterating English loanwords in Japanese from their Japanese written form (katakana/romaji) to their original English written form. Our data is a Japanese-English loanwords dictionary that we have created ourselves. We employ two approaches: direct transliteration, which directly converts words from katakana to English, and indirect transliteration, which utilizes the English pronunciation as a means to convert katakana words into their corresponding English sound representations, which are subsequently converted into English words. Additionally, we compare the effectiveness of using katakana versus romaji as input characters. We develop 6 models of 2 types for our experiments: one with an English lexicon-filter, and the other without. For each type, we built 3 models, including a pair n-gram based on WFSTs and two sequence-to-sequence models leveraging LSTM and transformer. Our best performing model was the pair n-gram model with a lexicon- filter, directly transliterating from katakana to English.

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Intersectionality and Testimonial Injustice in Medical Records

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An Empirical Study of Clinical Note Generation from Doctor-Patient Encounters

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Intersectionality and Testimonial Injustice in Medical Records

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An Empirical Study of Clinical Note Generation from Doctor-Patient Encounters

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