Overview of MWE history, challenges, and horizons: standing at the 20th anniversary of the MWE workshop series via MWE-UD2024

Starting in 2003 when the first MWE workshop was held with ACL in Sapporo, Japan, this year, the joint workshop of MWE-UD co-located with the LREC-COLING 2024 conference marked the 20th anniversary of MWE workshop events over the past nearly two decades. Standing at this milestone, we look back to this workshop series and summarise the research topics and methodologies researchers have carried out over the years. We also discuss the current challenges that we are facing and the broader impacts/synergies of MWE research within the CL and NLP fields. Finally, we give future research perspectives. We hope this position paper can help researchers, students, and industrial practitioners interested in MWE get a brief but easy understanding of its history, current, and possible future.

BeeManc at the PLABA Track of TAC-2024: RoBERTa for task 1 and LLaMA3.1 and GPT-4o for task 2

This report is the system description of the BeeManc team for shared task Plain Language Adaptation of Biomedical Abstracts (PLABA) 2024. This report contains two sections corresponding to the two sub-tasks in PLABA 2024. In task one, we applied fine-tuned ReBERTa-Base models to identify and classify the difficult terms, jargon and acronyms in the biomedical abstracts and reported the F1 score. Due to time constraints, we didn't finish the replacement task. In task two, we leveraged Llamma3.1-70B-Instruct and GPT-4o with the one-shot prompts to complete the abstract adaptation and reported the scores in BLEU, SARI, BERTScore, LENS, and SALSA. From the official Evaluation from PLABA-2024 on Task 1A and 1B, our \textbf{much smaller fine-tuned RoBERTa-Base} model ranked 3rd and 2nd respectively on the two sub-task, and the \textbf{1st on averaged F1 scores across the two tasks} from 9 evaluated systems. Our share our fine-tuned models and related resources at \url{https://github.com/HECTA-UoM/PLABA2024}

DeIDClinic: A Multi-Layered Framework for De-identification of Clinical Free-text Data

De-identification is important in protecting patients' privacy for healthcare text analytics. The MASK framework is one of the best on the de-identification shared task organised by n2c2/i2b2 challenges. This work enhances the MASK framework by integrating ClinicalBERT, a deep learning model specifically fine-tuned on clinical texts, alongside traditional de-identification methods like dictionary lookup and rule-based approaches. The system effectively identifies and either redacts or replaces sensitive identifiable entities within clinical documents, while also allowing users to customise the masked documents according to their specific needs. The integration of ClinicalBERT significantly improves the performance of entity recognition, achieving 0.9732 F1-score, especially for common entities such as names, dates, and locations. A risk assessment feature has also been developed, which analyses the uniqueness of context within documents to classify them into risk levels, guiding further de-identification efforts. While the system demonstrates strong overall performance, this work highlights areas for future improvement, including handling more complex entity occurrences and enhancing the system's adaptability to different clinical settings.

INSIGHTBUDDY-AI: Medication Extraction and Entity Linking using Large Language Models and Ensemble Learning

Medication Extraction and Mining play an important role in healthcare NLP research due to its practical applications in hospital settings, such as their mapping into standard clinical knowledge bases (SNOMED-CT, BNF, etc.). In this work, we investigate state-of-the-art LLMs in text mining tasks on medications and their related attributes such as dosage, route, strength, and adverse effects. In addition, we explore different ensemble learning methods (\textsc{Stack-Ensemble} and \textsc{Voting-Ensemble}) to augment the model performances from individual LLMs. Our ensemble learning result demonstrated better performances than individually fine-tuned base models BERT, RoBERTa, RoBERTa-L, BioBERT, BioClinicalBERT, BioMedRoBERTa, ClinicalBERT, and PubMedBERT across general and specific domains. Finally, we build up an entity linking function to map extracted medical terminologies into the SNOMED-CT codes and the British National Formulary (BNF) codes, which are further mapped to the Dictionary of Medicines and Devices (dm+d), and ICD. Our model's toolkit and desktop applications are publicly available at \url{https://github.com/HECTA-UoM/ensemble-NER}.

LLM-CARD: Towards a Description and Landscape of Large Language Models

With the rapid growth of the Natural Language Processing (NLP) field, a vast variety of Large Language Models (LLMs) continue to emerge for diverse NLP tasks. As an increasing number of papers are presented, researchers and developers face the challenge of information overload. Thus, it is particularly important to develop a system that can automatically extract and organise key information about LLMs from academic papers (\textbf{LLM model card}). This work is to develop such a pioneer system by using Named Entity Recognition (\textbf{NER}) and Relation Extraction (\textbf{RE}) methods that automatically extract key information about large language models from the papers, helping researchers to efficiently access information about LLMs. These features include model \textit{licence}, model \textit{name}, and model \textit{application}. With these features, we can form a model card for each paper. \textbf{Data-contribution} wise, 106 academic papers were processed by defining three dictionaries - LLMs name, licence, and application. 11,051 sentences were extracted through dictionary lookup, and the dataset was constructed through manual review of the final selection of 129 sentences that have a link between the name and the licence, and 106 sentences that have a link between the model name and the application.

Generating Synthetic Free-text Medical Records with Low Re-identification Risk using Masked Language Modeling

In this paper, we present a system that generates synthetic free-text medical records, such as discharge summaries, admission notes and doctor correspondences, using Masked Language Modeling (MLM). Our system is designed to preserve the critical information of the records while introducing significant diversity and minimizing re-identification risk. The system incorporates a de-identification component that uses Philter to mask Protected Health Information (PHI), followed by a Medical Entity Recognition (NER) model to retain key medical information. We explore various masking ratios and mask-filling techniques to balance the trade-off between diversity and fidelity in the synthetic outputs without affecting overall readability. Our results demonstrate that the system can produce high-quality synthetic data with significant diversity while achieving a HIPAA-compliant PHI recall rate of 0.96 and a low re-identification risk of 0.035. Furthermore, downstream evaluations using a NER task reveal that the synthetic data can be effectively used to train models with performance comparable to those trained on real data. The flexibility of the system allows it to be adapted for specific use cases, making it a valuable tool for privacy-preserving data generation in medical research and healthcare applications.

Synthetic4Health: Generating Annotated Synthetic Clinical Letters

Since clinical letters contain sensitive information, clinical-related datasets can not be widely applied in model training, medical research, and teaching. This work aims to generate reliable, various, and de-identified synthetic clinical letters. To achieve this goal, we explored different pre-trained language models (PLMs) for masking and generating text. After that, we worked on Bio\_ClinicalBERT, a high-performing model, and experimented with different masking strategies. Both qualitative and quantitative methods were used for evaluation. Additionally, a downstream task, Named Entity Recognition (NER), was also implemented to assess the usability of these synthetic letters. The results indicate that 1) encoder-only models outperform encoder-decoder models. 2) Among encoder-only models, those trained on general corpora perform comparably to those trained on clinical data when clinical information is preserved. 3) Additionally, preserving clinical entities and document structure better aligns with our objectives than simply fine-tuning the model. 4) Furthermore, different masking strategies can impact the quality of synthetic clinical letters. Masking stopwords has a positive impact, while masking nouns or verbs has a negative effect. 5) For evaluation, BERTScore should be the primary quantitative evaluation metric, with other metrics serving as supplementary references. 6) Contextual information does not significantly impact the models' understanding, so the synthetic clinical letters have the potential to replace the original ones in downstream tasks.

BeeManc at the PLABA Track of TAC-2023: Investigating LLMs and Controllable Attributes for Improving Biomedical Text Readability

In this system report, we describe the models and methods we used for our participation in the PLABA2023 task on biomedical abstract simplification, part of the TAC 2023 tracks. The system outputs we submitted come from the following three categories: 1) domain fine-tuned T5-like models including Biomedical-T5 and Lay-SciFive; 2) fine-tuned BARTLarge model with controllable attributes (via tokens) BART-w-CTs; 3) ChatGPTprompting. We also present the work we carried out for this task on BioGPT finetuning. In the official automatic evaluation using SARI scores, BeeManc ranks 2nd among all teams and our model LaySciFive ranks 3rd among all 13 evaluated systems. In the official human evaluation, our model BART-w-CTs ranks 2nd on Sentence-Simplicity (score 92.84), 3rd on Term-Simplicity (score 82.33) among all 7 evaluated systems; It also produced a high score 91.57 on Fluency in comparison to the highest score 93.53. In the second round of submissions, our team using ChatGPT-prompting ranks the 2nd in several categories including simplified term accuracy score 92.26 and completeness score 96.58, and a very similar score on faithfulness score 95.3 to re-evaluated PLABA-base-1 (95.73) via human evaluations. Our codes, fine-tuned models, prompts, and data splits from the system development stage will be available at https://github.com/ HECTA-UoM/PLABA-MU

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.