GenAI4ELab/papercli-papers huggingface dataset:
Harnessing the Power of BERT in the Turkish Clinical Domain: Pretraining Approaches for Limited Data Scenarios
Authors: Hazal Türkmen; Oguz Dikenelli; Cenk Eraslan; Mehmet Calli; Suha Ozbek
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Recent advancements in natural language processing (NLP) have been driven by large language models (LLMs), thereby revolutionizing the field. Our study investigates the impact of diverse pre-training strategies on the performance of Turkish clinical language models in a multi-label classification task involving radiology reports, with a focus on overcoming language resource limitations. Additionally, for the first time, we evaluated the simultaneous pre-training approach by utilizing limited clinical task data. We developed four models: TurkRadBERT-task v1, TurkRadBERT-task v2, TurkRadBERT-sim v1, and TurkRadBERT-sim v2. Our results revealed superior performance from BERTurk and TurkRadBERT-task v1, both of which leverage a broad general-domain corpus. Although task-adaptive pre-training is capable of identifying domain-specific patterns, it may be prone to overfitting because of the constraints of the task-specific corpus. Our findings highlight the importance of domain-specific vocabulary during pre-training to improve performance. They also affirmed that a combination of general domain knowledge and task-specific fine-tuning is crucial for optimal performance across various categories. This study offers key insights for future research on pre-training techniques in the clinical domain, particularly for low-resource languages.
A Meta-dataset of German Medical Corpora: Harmonization of Annotations and Cross-corpus NER Evaluation
Authors: Ignacio Llorca; Florian Borchert; Matthieu-P. Schapranow
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Over the last years, an increasing number of publicly available, semantically annotated medical corpora have been released for the German language. While their annotations cover comparable semantic classes, the synergies of such efforts have not been explored, yet. This is due to substantial differences in the data schemas (syntax) and annotated entities (semantics), which hinder the creation of common meta-datasets. For instance, it is unclear whether named entity recognition (NER) taggers trained on one or more of such datasets are useful to detect entities in any of the other datasets. In this work, we create harmonized versions of German medical corpora using the BigBIO framework, and make them available to the community. Using these as a meta-dataset, we perform a series of cross-corpus evaluation experiments on two settings of aligned labels. These consist in fine-tuning various pre-trained Transformers on different combinations of training sets, and testing them against each dataset separately. We find that a) trained NER models generalize poorly, with F1 scores dropping approx. 20 pp. on unseen test data, and b) current pre-trained Transformer models for the German language do not systematically alleviate this issue. However, our results suggest that models benefit from additional training corpora in most cases, even if these belong to different medical fields or text genres.
Uncovering the Potential for a Weakly Supervised End-to-End Model in Recognising Speech from Patient with Post-Stroke Aphasia
Authors: Giulia Sanguedolce; Patrick A. Naylor; Fatemeh Geranmayeh
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Post-stroke speech and language deficits (aphasia) significantly impact patients’ quality of life. Many with mild symptoms remain undiagnosed, and the majority do not receive the intensive doses of therapy recommended, due to healthcare costs and/or inadequate services. Automatic Speech Recognition (ASR) may help overcome these difficulties by improving diagnostic rates and providing feedback during tailored therapy. However, its performance is often unsatisfactory due to the high variability in speech errors and scarcity of training datasets. This study assessed the performance of Whisper, a recently released end-to-end model, in patients with post-stroke aphasia (PWA). We tuned its hyperparameters to achieve the lowest word error rate (WER) on aphasic speech. WER was significantly higher in PWA compared to age-matched controls (10.3% vs 38.5%, p<0.001). We demonstrated that worse WER was related to the more severe aphasia as measured by expressive (overt naming, and spontaneous speech production) and receptive (written and spoken comprehension) language assessments. Stroke lesion size did not affect the performance of Whisper. Linear mixed models accounting for demographic factors, therapy duration, and time since stroke, confirmed worse Whisper performance with left hemispheric frontal lesions.We discuss the implications of these findings for how future ASR can be improved in PWA.
Textual Entailment for Temporal Dependency Graph Parsing
Authors: Jiarui Yao; Steven Bethard; Kristin Wright-Bettner; Eli Goldner; David Harris; Guergana Savova
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: We explore temporal dependency graph (TDG) parsing in the clinical domain. We leverage existing annotations on the THYME dataset to semi-automatically construct a TDG corpus. Then we propose a new natural language inference (NLI) approach to TDG parsing, and evaluate it both on general domain TDGs from wikinews and the newly constructed clinical TDG corpus. We achieve competitive performance on general domain TDGs with a much simpler model than prior work. On the clinical TDGs, our method establishes the first result of TDG parsing on clinical data with 0.79/0.88 micro/macro F1.
Generating medically-accurate summaries of patient-provider dialogue: A multi-stage approach using large language models
Authors: Varun Nair; Elliot Schumacher; Anitha Kannan
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: A medical provider’s summary of a patient visit serves several critical purposes, including clinical decision-making, facilitating hand-offs between providers, and as a reference for the patient. An effective summary is required to be coherent and accurately capture all the medically relevant information in the dialogue, despite the complexity of patient-generated language. Even minor inaccuracies in visit summaries (for example, summarizing “patient does not have a fever” when a fever is present) can be detrimental to the outcome of care for the patient. This paper tackles the problem of medical conversation summarization by discretizing the task into several smaller dialogue-understanding tasks that are sequentially built upon. First, we identify medical entities and their affirmations within the conversation to serve as building blocks. We study dynamically constructing few-shot prompts for tasks by conditioning on relevant patient information and use GPT-3 as the backbone for our experiments. We also develop GPT-derived summarization metrics to measure performance against reference summaries quantitatively. Both our human evaluation study and metrics for medical correctness show that summaries generated using this approach are clinically accurate and outperform the baseline approach of summarizing the dialog in a zero-shot, single-prompt setting.
Factors Affecting the Performance of Automated Speaker Verification in Alzheimer’s Disease Clinical Trials
Authors: Malikeh Ehghaghi; Marija Stanojevic; Ali Akram; Jekaterina Novikova
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Detecting duplicate patient participation in clinical trials is a major challenge because repeated patients can undermine the credibility and accuracy of the trial’s findings and result in significant health and financial risks. Developing accurate automated speaker verification (ASV) models is crucial to verify the identity of enrolled individuals and remove duplicates, but the size and quality of data influence ASV performance. However, there has been limited investigation into the factors that can affect ASV capabilities in clinical environments. In this paper, we bridge the gap by conducting analysis of how participant demographic characteristics, audio quality criteria, and severity level of Alzheimer’s disease (AD) impact the performance of ASV utilizing a dataset of speech recordings from 659 participants with varying levels of AD, obtained through multiple speech tasks. Our results indicate that ASV performance: 1) is slightly better on male speakers than on female speakers; 2) degrades for individuals who are above 70 years old; 3) is comparatively better for non-native English speakers than for native English speakers; 4) is negatively affected by clinician interference, noisy background, and unclear participant speech; 5) tends to decrease with an increase in the severity level of AD. Our study finds that voice biometrics raise fairness concerns as certain subgroups exhibit different ASV performances owing to their inherent voice characteristics. Moreover, the performance of ASV is influenced by the quality of speech recordings, which underscores the importance of improving the data collection settings in clinical trials.
Team Cadence at MEDIQA-Chat 2023: Generating, augmenting and summarizing clinical dialogue with large language models
Authors: Ashwyn Sharma; David Feldman; Aneesh Jain
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: This paper describes Team Cadence’s winning submission to Task C of the MEDIQA-Chat 2023 shared tasks. We also present the set of methods, including a novel N-pass strategy to summarize a mix of clinical dialogue and an incomplete summarized note, used to complete Task A and Task B, ranking highly on the leaderboard amongst stable and reproducible code submissions. The shared tasks invited participants to summarize, classify and generate patient-doctor conversations. Considering the small volume of training data available, we took a data-augmentation-first approach to the three tasks by focusing on the dialogue generation task, i.e., Task C. It proved effective in improving our models’ performance on Task A and Task B. We also found the BART architecture to be highly versatile, as it formed the base for all our submissions. Finally, based on the results shared by the organizers, we note that Team Cadence was the only team to submit stable and reproducible runs to all three tasks.
Method for Designing Semantic Annotation of Sepsis Signs in Clinical Text
Authors: Melissa Yan; Lise Gustad; Lise Høvik; Øystein Nytrø
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Annotated clinical text corpora are essential for machine learning studies that model and predict care processes and disease progression. However, few studies describe the necessary experimental design of the annotation guideline and annotation phases. This makes replication, reuse, and adoption challenging. Using clinical questions about sepsis, we designed a semantic annotation guideline to capture sepsis signs from clinical text. The clinical questions aid guideline design, application, and evaluation. Our method incrementally evaluates each change in the guideline by testing the resulting annotated corpus using clinical questions. Additionally, our method uses inter-annotator agreement to judge the annotator compliance and quality of the guideline. We show that the method, combined with controlled design increments, is simple and allows the development and measurable improvement of a purpose-built semantic annotation guideline. We believe that our approach is useful for incremental design of semantic annotation guidelines in general.
Prompt Discriminative Language Models for Domain Adaptation
Authors: Keming Lu; Peter Potash; Xihui Lin; Yuwen Sun; Zihan Qian; Zheng Yuan; Tristan Naumann; Tianxi Cai; Junwei Lu
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Prompt tuning offers an efficient approach to domain adaptation for pretrained language models, which predominantly focus on masked language modeling or generative objectives. However, the potential of discriminative language models in biomedical tasks remains underexplored.To bridge this gap, we develop BioDLM, a method tailored for biomedical domain adaptation of discriminative language models that incorporates prompt-based continual pretraining and prompt tuning for downstream tasks. BioDLM aims to maximize the potential of discriminative language models in low-resource scenarios by reformulating these tasks as span-level corruption detection, thereby enhancing performance on domain-specific tasks and improving the efficiency of continual pertaining. In this way, BioDLM provides a data-efficient domain adaptation method for discriminative language models, effectively enhancing performance on discriminative tasks within the biomedical domain.
Cross-domain German Medical Named Entity Recognition using a Pre-Trained Language Model and Unified Medical Semantic Types
Authors: Siting Liang; Mareike Hartmann; Daniel Sonntag
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Information extraction from clinical text has the potential to facilitate clinical research and personalized clinical care, but annotating large amounts of data for each set of target tasks is prohibitive. We present a German medical Named Entity Recognition (NER) system capable of cross-domain knowledge transferring. The system builds on a pre-trained German language model and a token-level binary classifier, employing semantic types sourced from the Unified Medical Language System (UMLS) as entity labels to identify corresponding entity spans within the input text. To enhance the system’s performance and robustness, we pre-train it using a medical literature corpus that incorporates UMLS semantic term annotations. We evaluate the system’s effectiveness on two German annotated datasets obtained from different clinics in zero- and few-shot settings. The results show that our approach outperforms task-specific Condition Random Fields (CRF) classifiers in terms of accuracy. Our work contributes to developing robust and transparent German medical NER models that can support the extraction of information from various clinical texts.
Reducing Knowledge Noise for Improved Semantic Analysis in Biomedical Natural Language Processing Applications
Authors: Usman Naseem; Surendrabikram Thapa; Qi Zhang; Liang Hu; Anum Masood; Mehwish Nasim
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Graph-based techniques have gained traction for representing and analyzing data in various natural language processing (NLP) tasks. Knowledge graph-based language representation models have shown promising results in leveraging domain-specific knowledge for NLP tasks, particularly in the biomedical NLP field. However, such models have limitations, including knowledge noise and neglect of contextual relationships, leading to potential semantic errors and reduced accuracy. To address these issues, this paper proposes two novel methods. The first method combines knowledge graph-based language model with nearest-neighbor models to incorporate semantic and category information from neighboring instances. The second method involves integrating knowledge graph-based language model with graph neural networks (GNNs) to leverage feature information from neighboring nodes in the graph. Experiments on relation extraction (RE) and classification tasks in English and Chinese language datasets demonstrate significant performance improvements with both methods, highlighting their potential for enhancing the performance of language models and improving NLP applications in the biomedical domain.
Medical knowledge-enhanced prompt learning for diagnosis classification from clinical text
Authors: Yuxing Lu; Xukai Zhao; Jinzhuo Wang
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Artificial intelligence based diagnosis systems have emerged as powerful tools to reform traditional medical care. Each clinician now wants to have his own intelligent diagnostic partner to expand the range of services he can provide. When reading a clinical note, experts make inferences with relevant knowledge. However, medical knowledge appears to be heterogeneous, including structured and unstructured knowledge. Existing approaches are incapable of uniforming them well. Besides, the descriptions of clinical findings in clinical notes, which are reasoned to diagnosis, vary a lot for different diseases or patients. To address these problems, we propose a Medical Knowledge-enhanced Prompt Learning (MedKPL) model for diagnosis classification. First, to overcome the heterogeneity of knowledge, given the knowledge relevant to diagnosis, MedKPL extracts and normalizes the relevant knowledge into a prompt sequence. Then, MedKPL integrates the knowledge prompt with the clinical note into a designed prompt for representation. Therefore, MedKPL can integrate medical knowledge into the models to enhance diagnosis and effectively transfer learned diagnosis capacity to unseen diseases using alternating relevant disease knowledge. The experimental results on two medical datasets show that our method can obtain better medical text classification results and can perform better in transfer and few-shot settings among datasets of different diseases.
Multilingual Clinical NER: Translation or Cross-lingual Transfer?
Authors: Félix Gaschi; Xavier Fontaine; Parisa Rastin; Yannick Toussaint
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Natural language tasks like Named Entity Recognition (NER) in the clinical domain on non-English texts can be very time-consuming and expensive due to the lack of annotated data. Cross-lingual transfer (CLT) is a way to circumvent this issue thanks to the ability of multilingual large language models to be fine-tuned on a specific task in one language and to provide high accuracy for the same task in another language. However, other methods leveraging translation models can be used to perform NER without annotated data in the target language, by either translating the training set or test set. This paper compares cross-lingual transfer with these two alternative methods, to perform clinical NER in French and in German without any training data in those languages. To this end, we release MedNERF a medical NER test set extracted from French drug prescriptions and annotated with the same guidelines as an English dataset. Through extensive experiments on this dataset and on a German medical dataset (Frei and Kramer, 2021), we show that translation-based methods can achieve similar performance to CLT but require more care in their design. And while they can take advantage of monolingual clinical language models, those do not guarantee better results than large general-purpose multilingual models, whether with cross-lingual transfer or translation.
UMLS-KGI-BERT: Data-Centric Knowledge Integration in Transformers for Biomedical Entity Recognition
Authors: Aidan Mannion; Didier Schwab; Lorraine Goeuriot
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment analysis, document classification and many others. In the biomedical domain, significant progress has been made in adapting this paradigm to NLP tasks that require the integration of domain-specific knowledge as well as statistical modelling of language. In particular, research in this area has focused on the question of how best to construct LMs that take into account not only the patterns of token distribution in medical text, but also the wealth of structured information contained in terminology resources such as the UMLS. This work contributes a data-centric paradigm for enriching the language representations of biomedical transformer-encoder LMs by extracting text sequences from the UMLS.This allows for graph-based learning objectives to be combined with masked-language pre-training. Preliminary results from experiments in the extension of pre-trained LMs as well as training from scratch show that this framework improves downstream performance on multiple biomedical and clinical Named Entity Recognition (NER) tasks. All pre-trained models, data processing pipelines and evaluation scripts will be made publicly available.
WangLab at MEDIQA-Chat 2023: Clinical Note Generation from Doctor-Patient Conversations using Large Language Models
Authors: John Giorgi; Augustin Toma; Ronald Xie; Sondra Chen; Kevin An; Grace Zheng; Bo Wang
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: 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.
Automatic Coding at Scale: Design and Deployment of a Nationwide System for Normalizing Referrals in the Chilean Public Healthcare System
Authors: Fabián Villena; Matías Rojas; Felipe Arias; Jorge Pacheco; Paulina Vera; Jocelyn Dunstan
Venue: ACL 2023 (Proceedings of the 5th Clinical Natural Language Processing Workshop)

Abstract: The disease coding task involves assigning a unique identifier from a controlled vocabulary to each disease mentioned in a clinical document. This task is relevant since it allows information extraction from unstructured data to perform, for example, epidemiological studies about the incidence and prevalence of diseases in a determined context. However, the manual coding process is subject to errors as it requires medical personnel to be competent in coding rules and terminology. In addition, this process consumes a lot of time and energy, which could be allocated to more clinically relevant tasks. These difficulties can be addressed by developing computational systems that automatically assign codes to diseases. In this way, we propose a two-step system for automatically coding diseases in referrals from the Chilean public healthcare system. Specifically, our model uses a state-of-the-art NER model for recognizing disease mentions and a search engine system based on Elasticsearch for assigning the most relevant codes associated with these disease mentions. The system’s performance was evaluated on referrals manually coded by clinical experts. Our system obtained a MAP score of 0.63 for the subcategory level and 0.83 for the category level, close to the best-performing models in the literature. This system could be a support tool for health professionals, optimizing the coding and management process. Finally, to guarantee reproducibility, we publicly release the code of our models and experiments.