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}.
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.
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}
Coding of unstructured clinical free-text to produce interoperable structured data is essential to improve direct care, support clinical communication and to enable clinical research.However, manual clinical coding is difficult and time consuming, which motivates the development and use of natural language processing for automated coding. This work evaluates the quality and consistency of both manual and automated clinical coding of diagnoses from hospital outpatient letters. Using 100 randomly selected letters, two human clinicians performed coding of diagnosis lists to SNOMED CT. Automated coding was also performed using IMO's Concept Tagger. A gold standard was constructed by a panel of clinicians from a subset of the annotated diagnoses. This was used to evaluate the quality and consistency of both manual and automated coding via (1) a distance-based metric, treating SNOMED CT as a graph, and (2) a qualitative metric agreed upon by the panel of clinicians. Correlation between the two metrics was also evaluated. Comparing human and computer-generated codes to the gold standard, the results indicate that humans slightly out-performed automated coding, while both performed notably better when there was only a single diagnosis contained in the free-text description. Automated coding was considered acceptable by the panel of clinicians in approximately 90% of cases.
Access to real-world medical instructions is essential for medical research and healthcare quality improvement. However, access to real medical instructions 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 medical instructions based on provided labels, such as a vocabulary list of medications and their attributes. LT3 is trained on a vast corpus of medical instructions extracted from the MIMIC-III database, allowing the model to produce valuable synthetic medical instructions. 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}
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}
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}
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}
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.
Extracting meaningful drug-related information chunks, such as adverse drug events (ADE), is crucial for preventing morbidity and saving many lives. Most ADEs are reported via an unstructured conversation with the medical context, so applying a general entity recognition approach is not sufficient enough. In this paper, we propose a new multi-aspect cross-integration framework for drug entity/event detection by capturing and aligning different context/language/knowledge properties from drug-related documents. We first construct multi-aspect encoders to describe semantic, syntactic, and medical document contextual information by conducting those slot tagging tasks, main drug entity/event detection, part-of-speech tagging, and general medical named entity recognition. Then, each encoder conducts cross-integration with other contextual information in three ways: the key-value cross, attention cross, and feedforward cross, so the multi-encoders are integrated in depth. Our model outperforms all SOTA on two widely used tasks, flat entity detection and discontinuous event extraction.