A Comparative Study on Automatic Coding of Medical Letters with Explainability

This study aims to explore the implementation of Natural Language Processing (NLP) and machine learning (ML) techniques to automate the coding of medical letters with visualised explainability and light-weighted local computer settings. Currently in clinical settings, coding is a manual process that involves assigning codes to each condition, procedure, and medication in a patient's paperwork (e.g., 56265001 heart disease using SNOMED CT code). There are preliminary research on automatic coding in this field using state-of-the-art ML models; however, due to the complexity and size of the models, the real-world deployment is not achieved. To further facilitate the possibility of automatic coding practice, we explore some solutions in a local computer setting; in addition, we explore the function of explainability for transparency of AI models. We used the publicly available MIMIC-III database and the HAN/HLAN network models for ICD code prediction purposes. We also experimented with the mapping between ICD and SNOMED CT knowledge bases. In our experiments, the models provided useful information for 97.98\% of codes. The result of this investigation can shed some light on implementing automatic clinical coding in practice, such as in hospital settings, on the local computers used by clinicians , project page \url{https://github.com/Glenj01/Medical-Coding}.

The Multi-Range Theory of Translation Quality Measurement: MQM scoring models and Statistical Quality Control

The year 2024 marks the 10th anniversary of the Multidimensional Quality Metrics (MQM) framework for analytic translation quality evaluation. The MQM error typology has been widely used by practitioners in the translation and localization industry and has served as the basis for many derivative projects. The annual Conference on Machine Translation (WMT) shared tasks on both human and automatic translation quality evaluations used the MQM error typology. The metric stands on two pillars: error typology and the scoring model. The scoring model calculates the quality score from annotation data, detailing how to convert error type and severity counts into numeric scores to determine if the content meets specifications. Previously, only the raw scoring model had been published. This April, the MQM Council published the Linear Calibrated Scoring Model, officially presented herein, along with the Non-Linear Scoring Model, which had not been published before. This paper details the latest MQM developments and presents a universal approach to translation quality measurement across three sample size ranges. It also explains why Statistical Quality Control should be used for very small sample sizes, starting from a single sentence.

Exploration of Masked and Causal Language Modelling for Text Generation

Large Language Models (LLMs) have revolutionised the field of Natural Language Processing (NLP) and have achieved state-of-the-art performance in practically every task in this field. However, the prevalent approach used in text generation, Causal Language Modelling (CLM), which generates text sequentially from left to right, inherently limits the freedom of the model, which does not decide when and where each token is generated. In contrast, Masked Language Modelling (MLM), primarily used for language understanding tasks, can generate tokens anywhere in the text and any order. This paper conducts an extensive comparison of MLM and CLM approaches for text generation tasks. To do so, we pre-train several language models of comparable sizes on three different datasets, namely 1) medical discharge summaries, 2) movie plot synopses, and 3) authorship verification datasets. To assess the quality of the generations, we first employ quantitative metrics and then perform a qualitative human evaluation to analyse coherence and grammatical correctness. In addition, we evaluate the usefulness of the generated texts by using them in three different downstream tasks: 1) Entity Recognition, 2) Text Classification, and 3) Authorship Verification. The results show that MLM consistently outperforms CLM in text generation across all datasets, with higher quantitative scores and better coherence in the generated text. The study also finds \textit{no strong correlation} between the quality of the generated text and the performance of the models in the downstream tasks. With this study, we show that MLM for text generation has great potential for future research and provides direction for future studies in this area.

CANTONMT: Investigating Back-Translation and Model-Switch Mechanisms for Cantonese-English Neural Machine Translation

This paper investigates the development and evaluation of machine translation models from Cantonese to English, where we propose a novel approach to tackle low-resource language translations. The main objectives of the study are to develop a model that can effectively translate Cantonese to English and evaluate it against state-of-the-art commercial models. To achieve this, a new parallel corpus has been created by combining different available corpora online with preprocessing and cleaning. In addition, a monolingual Cantonese dataset has been created through web scraping to aid the synthetic parallel corpus generation. Following the data collection process, several approaches, including fine-tuning models, back-translation, and model switch, have been used. The translation quality of models has been evaluated with multiple quality metrics, including lexicon-based metrics (SacreBLEU and hLEPOR) and embedding-space metrics (COMET and BERTscore). Based on the automatic metrics, the best model is selected and compared against the 2 best commercial translators using the human evaluation framework HOPES. The best model proposed in this investigation (NLLB-mBART) with model switch mechanisms has reached comparable and even better automatic evaluation scores against State-of-the-art commercial models (Bing and Baidu Translators), with a SacreBLEU score of 16.8 on our test set. Furthermore, an open-source web application has been developed to allow users to translate between Cantonese and English, with the different trained models available for effective comparisons between models from this investigation and users. CANTONMT is available at https://github.com/kenrickkung/CantoneseTranslation

CantonMT: Cantonese to English NMT Platform with Fine-Tuned Models Using Synthetic Back-Translation Data

Neural Machine Translation (NMT) for low-resource languages is still a challenging task in front of NLP researchers. In this work, we deploy a standard data augmentation methodology by back-translation to a new language translation direction Cantonese-to-English. We present the models we fine-tuned using the limited amount of real data and the synthetic data we generated using back-translation including OpusMT, NLLB, and mBART. We carried out automatic evaluation using a range of different metrics including lexical-based and embedding-based. Furthermore. we create a user-friendly interface for the models we included in this\textsc{ CantonMT} research project and make it available to facilitate Cantonese-to-English MT research. Researchers can add more models into this platform via our open-source\textsc{ CantonMT} toolkit \url{https://github.com/kenrickkung/CantoneseTranslation}.

Neural Machine Translation of Clinical Text: An Empirical Investigation into Multilingual Pre-Trained Language Models and Transfer-Learning

We conduct investigations on clinical text machine translation by examining multilingual neural network models using deep learning such as Transformer based structures. Furthermore, to address the language resource imbalance issue, we also carry out experiments using a transfer learning methodology based on massive multilingual pre-trained language models (MMPLMs). The experimental results on three subtasks including 1) clinical case (CC), 2) clinical terminology (CT), and 3) ontological concept (OC) show that our models achieved top-level performances in the ClinSpEn-2022 shared task on English-Spanish clinical domain data. Furthermore, our expert-based human evaluations demonstrate that the small-sized pre-trained language model (PLM) won over the other two extra-large language models by a large margin, in the clinical domain fine-tuning, which finding was never reported in the field. Finally, the transfer learning method works well in our experimental setting using the WMT21fb model to accommodate a new language space Spanish that was not seen at the pre-training stage within WMT21fb itself, which deserves more exploitation for clinical knowledge transformation, e.g. to investigate into more languages. These research findings can shed some light on domain-specific machine translation development, especially in clinical and healthcare fields. Further research projects can be carried out based on our work to improve healthcare text analytics and knowledge transformation.

Generating Medical Prescriptions with Conditional Transformer

Access to real-world medication prescriptions is essential for medical research and healthcare quality improvement. However, access to real medication prescriptions is often limited due to the sensitive nature of the information expressed. Additionally, manually labelling these instructions for training and fine-tuning Natural Language Processing (NLP) models can be tedious and expensive. We introduce a novel task-specific model architecture, Label-To-Text-Transformer (\textbf{LT3}), tailored to generate synthetic medication prescriptions based on provided labels, such as a vocabulary list of medications and their attributes. LT3 is trained on a set of around 2K lines of medication prescriptions extracted from the MIMIC-III database, allowing the model to produce valuable synthetic medication prescriptions. We evaluate LT3's performance by contrasting it with a state-of-the-art Pre-trained Language Model (PLM), T5, analysing the quality and diversity of generated texts. We deploy the generated synthetic data to train the SpacyNER model for the Named Entity Recognition (NER) task over the n2c2-2018 dataset. The experiments show that the model trained on synthetic data can achieve a 96-98\% F1 score at Label Recognition on Drug, Frequency, Route, Strength, and Form. LT3 codes and data will be shared at \url{https://github.com/HECTA-UoM/Label-To-Text-Transformer}

Extraction of Medication and Temporal Relation from Clinical Text using Neural Language Models

Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of \textbf{MedTem} project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at \url{https://github.com/HECTA-UoM/MedTem}

Large Language Models and Control Mechanisms Improve Text Readability of Biomedical Abstracts

Biomedical literature often uses complex language and inaccessible professional terminologies. That is why simplification plays an important role in improving public health literacy. Applying Natural Language Processing (NLP) models to automate such tasks allows for quick and direct accessibility for lay readers. In this work, we investigate the ability of state-of-the-art large language models (LLMs) on the task of biomedical abstract simplification, using the publicly available dataset for plain language adaptation of biomedical abstracts (\textbf{PLABA}). The methods applied include domain fine-tuning and prompt-based learning (PBL) on: 1) Encoder-decoder models (T5, SciFive, and BART), 2) Decoder-only GPT models (GPT-3.5 and GPT-4) from OpenAI and BioGPT, and 3) Control-token mechanisms on BART-based models. We used a range of automatic evaluation metrics, including BLEU, ROUGE, SARI, and BERTscore, and also conducted human evaluations. BART-Large with Control Token (BART-L-w-CT) mechanisms reported the highest SARI score of 46.54 and T5-base reported the highest BERTscore 72.62. In human evaluation, BART-L-w-CTs achieved a better simplicity score over T5-Base (2.9 vs. 2.2), while T5-Base achieved a better meaning preservation score over BART-L-w-CTs (3.1 vs. 2.6). We also categorised the system outputs with examples, hoping this will shed some light for future research on this task. Our code, fine-tuned models, and data splits are available at \url{https://github.com/HECTA-UoM/PLABA-MU}

Predicting Perfect Quality Segments in MT Output with Fine-Tuned OpenAI LLM: Is it possible to capture editing distance patterns from historical data?

Translation Quality Estimation (TQE) is an essential step before deploying the output translation into usage. TQE is also critical in assessing machine translation (MT) and human translation (HT) quality without seeing the reference translations. This work examines whether the state-of-the-art large language models (LLMs) can be fine-tuned for the TQE task and their capability. We take ChatGPT as one example and approach TQE as a binary classification task. Using \textbf{eight language pairs} including English to Italian, German, French, Japanese, Dutch, Portuguese, Turkish, and Chinese training corpora, our experimental results show that fine-tuned ChatGPT via its API can achieve a relatively high score on predicting translation quality, i.e. \textit{if the translation needs to be edited}. However, there is definitely much space to improve the model accuracy, e.g. they are 82.42\% and 83.69\% for English-Italian and English-German respectively using our experimental settings. English-Italiano bilingual Abstract is available in the paper.