GenAI4ELab/papercli-papers huggingface dataset:
Extracting Drug-Drug and Protein-Protein Interactions from Text using a Continuous Update of Tree-Transformers
Authors: Sudipta Singha Roy; Robert E. Mercer
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Understanding biological mechanisms requires determining mutual protein-protein interactions (PPI). Obtaining drug-drug interactions (DDI) from scientific articles provides important information about drugs. Extracting such medical entity interactions from biomedical articles is challenging due to complex sentence structures. To address this issue, our proposed model utilizes tree-transformers to generate the sentence representation first, and then a sentence-to-word update step to fine-tune the word embeddings which are again used by the tree-transformers to generate enriched sentence representations. Using the tree-transformers helps the model preserve syntactical information and provide semantic information. The fine-tuning provided by the continuous update step adds improved semantics to the representation of each sentence. Our model outperforms other prominent models with a significant performance boost on the five standard PPI corpora and a performance boost on the one benchmark DDI corpus that are used in our experiments.
Resolving Elliptical Compounds in German Medical Text
Authors: Niklas Kammer; Florian Borchert; Silvia Winkler; Gerard de Melo; Matthieu-P. Schapranow
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Elliptical coordinated compound noun phrases (ECCNPs), a special kind of coordination ellipsis, are a common phenomenon in German medical texts. As their presence is known to affect the performance in downstream tasks such as entity extraction and disambiguation, their resolution can be a useful preprocessing step in information extraction pipelines. In this work, we present a new comprehensive dataset of more than 4,000 manually annotated ECCNPs in German medical text, along with the respective ground truth resolutions. Based on this data, we propose a generative encoder-decoder Transformer model, allowing for a simple end-to-end resolution of ECCNPs from raw input strings with very high accuracy (90.5% exact match score). We compare our approach to an elaborate rule-based baseline, which the generative model outperforms by a large margin. We further investigate different scenarios for prompting large language models (LLM) to resolve ECCNPs. In a zero-shot setting, performance is remarkably poor (21.6% exact matches), as the LLM tends to apply complex changes to the inputs unrelated to our specific task. We also find no improvement over the generative model when using the LLM for post-filtering of generated candidate resolutions.
Augmenting Reddit Posts to Determine Wellness Dimensions impacting Mental Health
Authors: Chandreen Liyanage; Muskan Garg; Vijay Mago; Sunghwan Sohn
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Amid ongoing health crisis, there is a growing necessity to discern possible signs of Wellness Dimensions (WD) manifested in self-narrated text. As the distribution of WD on social media data is intrinsically imbalanced, we experiment the generative AI techniques for data augmentation to enable further improvement in the pre-screening task of classifying WD. To this end, we propose a simple yet effective data augmentation approach through prompt-based Generative AI models, and evaluate the ROUGE scores and syntactic/ semantic similarity among existing interpretations and augmented data. Our approach with ChatGPT model surpasses all the other methods and achieves improvement over baselines such as Easy-Data Augmentation (EDA) and Backtranslation (BT).
End-to-end clinical temporal information extraction with multi-head attention
Authors: Timothy Miller; Steven Bethard; Dmitriy Dligach; Guergana Savova
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Understanding temporal relationships in text from electronic health records can be valuable for many important downstream clinical applications. Since Clinical TempEval 2017, there has been little work on end-to-end systems for temporal relation extraction, with most work focused on the setting where gold standard events and time expressions are given. In this work, we make use of a novel multi-headed attention mechanism on top of a pre-trained transformer encoder to allow the learning process to attend to multiple aspects of the contextualized embeddings. Our system achieves state of the art results on the THYME corpus by a wide margin, in both the in-domain and cross-domain settings.
Intermediate Domain Finetuning for Weakly Supervised Domain-adaptive Clinical NER
Authors: Shilpa Suresh; Nazgol Tavabi; Shahriar Golchin; Leah Gilreath; Rafael Garcia-Andujar; Alexander Kim; Joseph Murray; Blake Bacevich; Ata Kiapour
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Accurate human-annotated data for real-worlduse cases can be scarce and expensive to obtain. In the clinical domain, obtaining such data is evenmore difficult due to privacy concerns which notonly restrict open access to quality data but also require that the annotation be done by domain experts. In this paper, we propose a novel framework - InterDAPT - that leverages Intermediate Domain Finetuning to allow language models to adapt to narrow domains with small, noisy datasets. By making use of peripherally-related, unlabeled datasets,this framework circumvents domain-specific datascarcity issues. Our results show that this weaklysupervised framework provides performance improvements in downstream clinical named entityrecognition tasks.
Evaluation of ChatGPT on Biomedical Tasks: A Zero-Shot Comparison with Fine-Tuned Generative Transformers
Authors: Israt Jahan; Md Tahmid Rahman Laskar; Chun Peng; Jimmy Huang
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: ChatGPT is a large language model developed by OpenAI. Despite its impressive performance across various tasks, no prior work has investigated its capability in the biomedical domain yet. To this end, this paper aims to evaluate the performance of ChatGPT on various benchmark biomedical tasks, such as relation extraction, document classification, question answering, and summarization. To the best of our knowledge, this is the first work that conducts an extensive evaluation of ChatGPT in the biomedical domain. Interestingly, we find based on our evaluation that in biomedical datasets that have smaller training sets, zero-shot ChatGPT even outperforms the state-of-the-art fine-tuned generative transformer models, such as BioGPT and BioBART. This suggests that ChatGPT’s pre-training on large text corpora makes it quite specialized even in the biomedical domain. Our findings demonstrate that ChatGPT has the potential to be a valuable tool for various tasks in the biomedical domain that lack large annotated data.
BIOptimus: Pre-training an Optimal Biomedical Language Model with Curriculum Learning for Named Entity Recognition
Authors: Vera Pavlova; Mohammed Makhlouf
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity Recognition (NER). Recent research in biomedical language processing has offered a number of biomedical LMs pre-trained using different methods and techniques that advance results on many BioNLP tasks, including NER. However, there is still a lack of a comprehensive comparison of pre-training approaches that would work more optimally in the biomedical domain. This paper aims to investigate different pre-training methods, such as pre-training the biomedical LM from scratch and pre-training it in a continued fashion. We compare existing methods with our proposed pre-training method of initializing weights for new tokens by distilling existing weights from the BERT model inside the context where the tokens were found. The method helps to speed up the pre-training stage and improve performance on NER. In addition, we compare how masking rate, corruption strategy, and masking strategies impact the performance of the biomedical LM. Finally, using the insights from our experiments, we introduce a new biomedical LM (BIOptimus), which is pre-trained using Curriculum Learning (CL) and contextualized weight distillation method. Our model sets new states of the art on several biomedical Named Entity Recognition (NER) tasks. We release our code and all pre-trained models.
Biomedical Language Models are Robust to Sub-optimal Tokenization
Authors: Bernal Jimenez Gutierrez; Huan Sun; Yu Su
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.
Distantly Supervised Document-Level Biomedical Relation Extraction with Neighborhood Knowledge Graphs
Authors: Takuma Matsubara; Makoto Miwa; Yutaka Sasaki
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: We propose a novel distantly supervised document-level biomedical relation extraction model that uses partial knowledge graphs that include the graph neighborhood of the entities appearing in each input document. Most conventional distantly supervised relation extraction methods use only the entity relations automatically annotated by using knowledge base entries. They do not fully utilize the rich information in the knowledge base, such as entities other than the target entities and the network of heterogeneous entities defined in the knowledge base. To address this issue, our model integrates the representations of the entities acquired from the neighborhood knowledge graphs with the representations of the input document. We conducted experiments on the ChemDisGene dataset using Comparative Toxicogenomics Database (CTD) for document-level relation extraction with respect to interactions between drugs, diseases, and genes. Experimental results confirmed the performance improvement by integrating entities and their neighborhood biochemical information from the knowledge base.
BioNART: A Biomedical Non-AutoRegressive Transformer for Natural Language Generation
Authors: Masaki Asada; Makoto Miwa
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: We propose a novel Biomedical domain-specific Non-AutoRegressive Transformer model for natural language generation: BioNART. Our BioNART is based on an encoder-decoder model, and both encoder and decoder are compatible with widely used BERT architecture, which allows benefiting from publicly available pre-trained biomedical language model checkpoints. We performed additional pre-training and fine-tuned BioNART on biomedical summarization and doctor-patient dialogue tasks. Experimental results show that our BioNART achieves about 94% of the ROUGE score to the pre-trained autoregressive model while realizing an 18 times faster inference speed on the iCliniq dataset.
Biomedical Relation Extraction with Entity Type Markers and Relation-specific Question Answering
Authors: Koshi Yamada; Makoto Miwa; Yutaka Sasaki
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Recently, several methods have tackled the relation extraction task with QA and have shown successful results. However, the effectiveness of existing methods in specific domains, such as the biomedical domain, is yet to be verified. When there are multiple entity pairs that share an entity in a sentence, a QA-based relation extraction model that outputs only one single answer to a given question may not extract desired relations. In addition, these methods employ QA models that are not tuned for relation extraction. To address these issues, we first extend and apply a span QA-based relation extraction method to the drug-protein relation extraction by creating question templates and incorporating entity type markers. We further propose a binary QA-based method that directly uses the entity information available in the relation extraction task. The experimental results on the DrugProt dataset show that our QA-based methods, especially the proposed binary QA method, are effective for drug-protein relation extraction.
Biomedical Document Classification with Literature Graph Representations of Bibliographies and Entities
Authors: Ryuki Ida; Makoto Miwa; Yutaka Sasaki
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: This paper proposes a new document classification method that incorporates the representations of a literature graph created from bibliographic and entity information. Recently, document classification performance has been significantly improved with large pre-trained language models; however, there still remain documents that are difficult to classify. External information, such as bibliographic information, citation links, descriptions of entities, and medical taxonomies, has been considered one of the keys to dealing with such documents in document classification. Although several document classification methods using external information have been proposed, they only consider limited relationships, e.g., word co-occurrence and citation relationships. However, there are multiple types of external information. To overcome the limitation of the conventional use of external information, we propose a document classification model that simultaneously considers bibliographic and entity information to deeply model the relationships among documents using the representations of the literature graph. The experimental results show that our proposed method outperforms existing methods on two document classification datasets in the biomedical domain with the help of the literature graph.
Zero-Shot Information Extraction for Clinical Meta-Analysis using Large Language Models
Authors: David Kartchner; Selvi Ramalingam; Irfan Al-Hussaini; Olivia Kronick; Cassie Mitchell
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Meta-analysis of randomized clinical trials (RCTs) plays a crucial role in evidence-based medicine but can be labor-intensive and error-prone. This study explores the use of large language models to enhance the efficiency of aggregating results from randomized clinical trials (RCTs) at scale. We perform a detailed comparison of the performance of these models in zero-shot prompt-based information extraction from a diverse set of RCTs to traditional manual annotation methods. We analyze the results for two different meta-analyses aimed at drug repurposing in cancer therapy pharmacovigilience in chronic myeloid leukemia. Our findings reveal that the best model for the two demonstrated tasks, ChatGPT can generally extract correct information and identify when the desired information is missing from an article. We additionally conduct a systematic error analysis, documenting the prevalence of diverse error types encountered during the process of prompt-based information extraction.
Can Social Media Inform Dietary Approaches for Health Management? A Dataset and Benchmark for Low-Carb Diet
Authors: Skyler Zou; Xiang Dai; Grant Brinkworth; Pennie Taylor; Sarvnaz Karimi
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Social media offers an accessible avenue for individuals of diverse backgrounds and circumstances to share their unique perspectives and experiences. Our study focuses on the experience of low carbohydrate diets, motivated by recent research and clinical trials that elucidates the diet’s promising health benefits. Given the lack of any suitable annotated dataset in this domain, we first define an annotation schema that reflects the interests of healthcare professionals and then manually annotate data from the Reddit social network. Finally, we benchmark the effectiveness of several classification approaches that are based on statistical Support Vector Machines (SVM) classifier, pre-train-then-finetune RoBERTa classifier, and, off-the-shelf ChatGPT API, on our annotated dataset. Our annotations and scripts that are used to download the Reddit posts are publicly available at https://data.csiro.au/collection/csiro:59208.
Promoting Fairness in Classification of Quality of Medical Evidence
Authors: Simon Suster; Timothy Baldwin; Karin Verspoor
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Automatically rating the quality of published research is a critical step in medical evidence synthesis. While several methods have been proposed, their algorithmic fairness has been overlooked even though significant risks may follow when such systems are deployed in biomedical contexts. In this work, we study fairness on two systems along two sensitive attributes, participant sex and medical area. In some cases, we find important inequalities, leading us to apply various debiasing methods. Upon examining an interplay of systems’ predictive performance, fairness, as well as medically critical selective classification capabilities and calibration performance, we find that fairness can sometimes improve through debiasing, but at a cost in other performance measures.
WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with Cost-sensitive Learning
Authors: Ghadeer Mobasher; Wolfgang Müller; Olga Krebs; Michael Gertz
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Fine-tuning biomedical pre-trained language models (BioPLMs) such as BioBERT has become a common practice dominating leaderboards across various natural language processing tasks. Despite their success and wide adoption, prevailing fine-tuning approaches for named entity recognition (NER) naively train BioPLMs on targeted datasets without considering class distributions. This is problematic especially when dealing with imbalanced biomedical gold-standard datasets for NER in which most biomedical entities are underrepresented. In this paper, we address the class imbalance problem and propose WeLT, a cost-sensitive fine-tuning approach based on new re-scaled class weights for the task of biomedical NER. We evaluate WeLT’s fine-tuning performance on mixed-domain and domain-specific BioPLMs using eight biomedical gold-standard datasets. We compare our approach against vanilla fine-tuning and three other existing re-weighting schemes. Our results show the positive impact of handling the class imbalance problem. WeLT outperforms all the vanilla fine-tuned models. Furthermore, our method demonstrates advantages over other existing weighting schemes in most experiments.
Hospital Discharge Summarization Data Provenance
Authors: Paul Landes; Aaron Chaise; Kunal Patel; Sean Huang; Barbara Di Eugenio
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: Summarization of medical notes has been studied for decades with hospital discharge summaries garnering recent interest in the research community. While methods for summarizing these notes have been the focus, there has been little work in understanding the feasibility of this task. We believe this effort is warranted given the notes’ length and complexity, and that they are often riddled with poorly formatted structured data and redundancy in copy and pasted text. In this work, we investigate the feasibility of the summarization task by finding the origin, or data provenance, of the discharge summary’s source text. As a motivation to understanding the data challenges of the summarization task, we present DSProv, a new dataset of 51 hospital admissions annotated by clinical informatics physicians. The dataset is analyzed for semantics and the extent of copied text from human authored electronic health record (EHR) notes. We also present a novel unsupervised method of matching notes used in discharge summaries, and release our annotation dataset1 and source code to the community.
RadAdapt: Radiology Report Summarization via Lightweight Domain Adaptation of Large Language Models
Authors: Dave Van Veen; Cara Van Uden; Maayane Attias; Anuj Pareek; Christian Bluethgen; Malgorzata Polacin; Wah Chiu; Jean-Benoit Delbrouck; Juan Manuel Zambrano Chaves; Curtis P. Langlotz; Akshay S. Chaudhari; John Pauly
Venue: ACL 2023 (Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks)

Abstract: We systematically investigate lightweight strategies to adapt large language models (LLMs) for the task of radiology report summarization (RRS). Specifically, we focus on domain adaptation via pretraining (on natural language, biomedical text, or clinical text) and via discrete prompting or parameter-efficient fine-tuning. Our results consistently achieve best performance by maximally adapting to the task via pretraining on clinical text and fine-tuning on RRS examples. Importantly, this method fine-tunes a mere 0.32% of parameters throughout the model, in contrast to end-to-end fine-tuning (100% of parameters). Additionally, we study the effect of in-context examples and out-of-distribution (OOD) training before concluding with a radiologist reader study and qualitative analysis. Our findings highlight the importance of domain adaptation in RRS and provide valuable insights toward developing effective natural language processing solutions for clinical tasks.