ymoslem/acl-abstracts huggingface dataset:
Efficient Biomedical Entity Linking: Clinical Text Standardization with Low-Resource Techniques (2024)

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the Unified Medical Language System (UMLS) are developed and maintained to store millions of clinical entities including the definitions, relations and other corresponding information. These ontologies are used for standardization of clinical text by normalizing varying surface forms of a clinical term through Biomedical entity linking. With the introduction of transformer-based language models, there has been significant progress in Biomedical entity linking. In this work, we focus on learning through synonym pairs associated with the entities. As compared to the existing approaches, our approach significantly reduces the training data and resource consumption. Moreover, we propose a suite of context-based and context-less reranking techniques for performing the entity disambiguation. Overall, we achieve similar performance to the state-of-the-art zero-shot and distant supervised entity linking techniques on the Medmentions dataset, the largest annotated dataset on UMLS, without any domain-based training. Finally, we show that retrieval performance alone might not be sufficient as an evaluation metric and introduce an article level quantitative and qualitative analysis to reveal further insights on the performance of entity linking methods.
XAI for Better Exploitation of Text in Medical Decision Support (2024)

In electronic health records, text data is considered a valuable resource as it complements a medical history and may contain information that cannot be easily included in tables. But why does the inclusion of clinical texts as additional input into multimodal models, not always significantly improve the performance of medical decision-support systems? Explainable AI (XAI) might provide the answer. We examine which information in text and structured data influences the performance of models in the context of multimodal decision support for biomedical tasks. Using data from an intensive care unit and targeting a mortality prediction task, we compare information that has been considered relevant by XAI methods to the opinion of a physician.
Optimizing Multimodal Large Language Models for Detection of Alcohol Advertisements via Adaptive Prompting (2024)

Adolescents exposed to advertisements promoting addictive substances exhibit a higher likelihood of subsequent substance use. The predominant source for youth exposure to such advertisements is through online content accessed via smartphones. Detecting these advertisements is crucial for establishing and maintaining a safer online environment for young people. In our study, we utilized Multimodal Large Language Models (MLLMs) to identify addictive substance advertisements in digital media. The performance of MLLMs depends on the quality of the prompt used to instruct the model. To optimize our prompts, an adaptive prompt engineering approach was implemented, leveraging a genetic algorithm to refine and enhance the prompts. To evaluate the model`s performance, we augmented the RICO dataset, consisting of Android user interface screenshots, by superimposing alcohol ads onto them. Our results indicate that the MLLM can detect advertisements promoting alcohol with a 0.94 accuracy and a 0.94 F1 score.
Extracting Epilepsy Patient Data with Llama 2 (2024)

We fill a gap in scholarship by applying a generative Large Language Model (LLM) to extract information from clinical free text about the frequency of seizures experienced by people with epilepsy. Seizure frequency is difficult to determine across time from unstructured doctors' and nurses' reports of outpatients' visits that are stored in Electronic Health Records (EHRs) in the United Kingdom`s National Health Service (NHS). We employ Meta`s Llama 2 to mine the EHRs of people with epilepsy and determine, where possible, a person`s seizure frequency at a given point in time. The results demonstrate that the new, powerful generative LLMs may improve outcomes for clinical NLP research in epilepsy and other areas.
How do you know that? Teaching Generative Language Models to Reference Answers to Biomedical Questions (2024)

Large language models (LLMs) have recently become the leading source of answers for users' questions online. Despite their ability to offer eloquent answers, their accuracy and reliability can pose a significant challenge. This is especially true for sensitive domains such as biomedicine, where there is a higher need for factually correct answers. This paper introduces a biomedical retrieval-augmented generation (RAG) system designed to enhance the reliability of generated responses. The system is based on a fine-tuned LLM for the referenced question-answering, where retrieved relevant abstracts from PubMed are passed to LLM`s context as input through a prompt. Its output is an answer based on PubMed abstracts, where each statement is referenced accordingly, allowing the users to verify the answer. Our retrieval system achieves an absolute improvement of 23{\%} compared to the PubMed search engine. Based on the manual evaluation on a small sample, our fine-tuned LLM component achieves comparable results to GPT-4 Turbo in referencing relevant abstracts. We make the dataset used to fine-tune the models and the fine-tuned models based on Mistral-7B-instruct-v0.1 and v0.2 publicly available.
Low Resource ICD Coding of Hospital Discharge Summaries (2024)

Medical coding is the process by which standardized medical codes are assigned to patient health records. This is a complex and challenging task that typically requires an expert human coder to review health records and assign codes from a classification system based on a standard set of rules. Since health records typically consist of a large proportion of free-text documents, this problem has traditionally been approached as a natural language processing (NLP) task. While machine learning-based methods have seen recent popularity on this task, they tend to struggle with codes that are assigned less frequently, for which little or no training data exists. In this work we utilize the open-source NLP programming language, NLP++, to design and build an automated system to assign International Classification of Diseases (ICD) codes to discharge summaries that functions in the absence of labeled training data. We evaluate our system using the MIMIC-III dataset and find that for codes with little training data, our approach achieves competitive performance compared to state-of-the-art machine learning approaches.
Towards ML-supported Triage Prediction in Real-World Emergency Room Scenarios (2024)

In emergency wards, patients are prioritized by clinical staff according to the urgency of their medical condition. This can be achieved by categorizing patients into different labels of urgency ranging from immediate to not urgent. However, in order to train machine learning models offering support in this regard, there is more than approaching this as a multi-class problem. This work explores the challenges and obstacles of automatic triage using anonymized real-world multi-modal ambulance data in Germany.
Creating Ontology-annotated Corpora from Wikipedia for Medical Named-entity Recognition (2024)

Acquiring annotated corpora for medical NLP is challenging due to legal and privacy constraints and costly annotation efforts, and using annotated public datasets may do not align well to the desired target application in terms of annotation style or language. We investigate the approach of utilizing Wikipedia and WikiData jointly to acquire an unsupervised annotated corpus for named-entity recognition (NER). By controlling the annotation ruleset through WikiData`s ontology, we extract custom-defined annotations and dynamically impute weak annotations by an adaptive loss scaling. Our validation on German medication detection datasets yields competitive results. The entire pipeline only relies on open models and data resources, enabling reproducibility and open sharing of models and corpora. All relevant assets are shared on GitHub.
Paragraph Retrieval for Enhanced Question Answering in Clinical Documents (2024)

Healthcare professionals often manually extract information from large clinical documents to address patient-related questions. The use of Natural Language Processing (NLP) techniques, particularly Question Answering (QA) models, is a promising direction for improving the efficiency of this process. However, document-level QA from large documents is often impractical or even infeasible (for model training and inference). In this work, we solve the document-level QA from clinical reports in a two-step approach: first, the entire report is split into segments and for a given question the most relevant segment is predicted by a NLP model; second, a QA model is applied to the question and the retrieved segment as context. We investigate the effectiveness of heading-based and naive paragraph segmentation approaches for various paragraph lengths on two subsets of the emrQA dataset. Our experiments reveal that an average paragraph length used as a parameter for the segmentation has no significant effect on performance during the whole document-level QA process. That means experiments focusing on segmentation into shorter paragraphs perform similarly to those focusing on entire unsegmented reports. Surprisingly, naive uniform segmentation is sufficient even though it is not based on prior knowledge of the clinical document`s characteristics.
CID at RRG24: Attempting in a Conditionally Initiated Decoding of Radiology Report Generation with Clinical Entities (2024)

Radiology Report Generation (RRG) seeks to leverage deep learning techniques to automate the reporting process of radiologists. Current methods are typically modelling RRG as an image-to-text generation task that takes X-ray images as input and generates textual reports describing the corresponding clinical observations. However, the wording of the same clinical observation could have been influenced by the expression preference of radiologists. Nevertheless, such variability can be mitigated by normalizing textual reports into structured representations such as a graph structure. In this study, we attempt a novel paradigm for incorporating graph structural data into the RRG model. Our approach involves predicting graph labels based on visual features and subsequently initiating the decoding process through a template injection conditioned on the predicted labels. We trained and evaluated our model on the BioNLP 2024 Shared Task on Large-Scale Radiology Report Generation and submitted our results to the ViLMedic RRG leaderboard. Although our model showed a moderate ranking on the leaderboard, the results provide preliminary evidence for the feasibility of this new paradigm, warranting further exploration and refinement.
MAIRA at RRG24: A specialised large multimodal model for radiology report generation (2024)

This paper discusses the participation of the MSR MAIRA team in the Large-Scale Radiology Report Generation Shared Task Challenge, as part of the BioNLP workshop at ACL 2024. We present a radiology-specific multimodal model designed to generate radiological reports from chest X-Rays (CXRs). Our proposed model combines a CXR-specific image encoder RAD-DINO with a Large Language Model (LLM) based on Vicuna-7B, via a multi-layer perceptron (MLP) adapter. Both the adapter and the LLM have been fine-tuned in a single-stage training setup to generate radiology reports. Experimental results indicate that a joint training setup with findings and impression sections improves findings prediction. Additionally, incorporating lateral images alongside frontal images when available further enhances all metrics. More information and resources about MAIRA can be found on the project website: http://aka.ms/maira.
AIRI at RRG24: LLaVa with specialised encoder and decoder (2024)

We present a new approach to generating the {\textquoteleft}Findings' and {\textquoteleft}Impression' sections in the chest X-rays radiology reports, developed as part of the shared radiology task at BioNLP 2024. By integrating a DINOv2 vision encoder trained on medical data with specialized biomedical large language model using the LLaVA framework, our method addresses complex medical semantics and diverse findings in imaging. We use datasets from PadChest, BIMCV-COVID19, CheXpert, OpenI, and MIMIC-CXR. The evaluation metrics demonstrate our method`s effectiveness and the potential for automating the generation of radiology reports.
iHealth-Chile-1 at RRG24: In-context Learning and Finetuning of a Large Multimodal Model for Radiology Report Generation (2024)

This paper presents the approach of the iHealth-Chile-1 team for the shared task of Large-Scale Radiology Report Generation at the BioNLP workshop, inspired by progress in large multimodal models for processing images and text. In this work, we leverage LLaVA, a Visual-Language Model (VLM), composed of a vision-encoder, a vision-language connector or adapter, and a large language model able to process text and visual embeddings. We achieve our best result by enriching the input prompt of LLaVA with the text output of a simpler report generation model. With this enriched-prompt technique, we improve our results in 4 of 5 metrics (BLEU-4, Rouge-L, BertScore and F1-RadGraph,), only doing in-context learning. Moreover, we provide details about different architecture settings, fine-tuning strategies, and dataset configurations.
iHealth-Chile-3\&2 at RRG24: Template Based Report Generation (2024)

This paper presents the approaches of the iHealth-Chile-3 and iHealth-Chile-2 teams for the shared task of Large-Scale Radiology Report Generation at the BioNLP workshop. Inspired by prior work on template-based report generation, both teams focused on exploring various template-based strategies, using predictions from multi-label image classifiers as input. Our best approach achieved a modest F1-RadGraph score of 19.42 on the findings hidden test set, ranking 7th on the leaderboard. Notably, we consistently observed a discrepancy between our classification metrics and the F1-CheXbert metric reported on the leaderboard, which always showed lower scores. This suggests that the F1-CheXbert metric may be missing some of the labels mentioned by the templates.
Gla-AI4BioMed at RRG24: Visual Instruction-tuned Adaptation for Radiology Report Generation (2024)

This paper introduces a radiology-focused visual language model designed to generate radiology reports from chest X-rays. Building on previous findings that large language models can acquire multimodal capabilities when aligned with pretrained vision encoders, we demonstrate similar potential with chest X-ray images. The model combines an image encoder (CLIP) with a fine-tuned large language model (LLM) based on the Vicuna-7B architecture. The training process involves a two-stage approach: initial alignment of chest X-ray features with the LLM, followed by fine-tuning for radiology report generation. The study highlights the importance of generating both FINDINGS and IMPRESSIONS sections in radiology reports and evaluates the model`s performance using various metrics, achieving notable accuracy in generating high-quality medical reports. The research also addresses the need for domain-specific fine-tuning to capture the intricate details necessary for accurate medical interpretations and reports.
SICAR at RRG2024: GPU Poor`s Guide to Radiology Report Generation (2024)

Radiology report generation (RRG) aims to create free-text radiology reports from clinical imaging. Our solution employs a lightweight multimodal language model (MLLM) enhanced with a two-stage post-processing strategy, utilizing a Large Language Model (LLM) to boost diagnostic accuracy and ensure patient safety. We introduce the {\textquotedblleft}First, Do No Harm{\textquotedblright} SafetyNet, which incorporates Xraydar, an advanced X-ray classification model, to cross-verify the model outputs and specifically address false negatives from the MLLM. This comprehensive approach combines the efficiency of lightweight models with the robustness of thorough post-processing techniques, offering a reliable solution for radiology report generation. Our system achieved fourth place on the F1-Radgraph metric for findings generation in the Radiology Report Generation Shared Task (RRG24).
Shimo Lab at \textquotedblleftDischarge Me!\textquotedblright: Discharge Summarization by Prompt-Driven Concatenation of Electronic Health Record Sections (2024)

In this paper, we present our approach to the shared task {\textquotedblleft}Discharge Me!{\textquotedblright} at the BioNLP Workshop 2024. The primary goal of this task is to reduce the time and effort clinicians spend on writing detailed notes in the electronic health record (EHR). Participants develop a pipeline to generate the {\textquotedblleft}Brief Hospital Course{\textquotedblright} and {\textquotedblleft}Discharge Instructions{\textquotedblright} sections from the EHR. Our approach involves a first step of extracting the relevant sections from the EHR. We then add explanatory prompts to these sections and concatenate them with separate tokens to create the input text. To train a text generation model, we perform LoRA fine-tuning on the ClinicalT5-large model. On the final test data, our approach achieved a ROUGE-1 of 0.394, which is comparable to the top solutions.
Ixa-Med at Discharge Me! Retrieval-Assisted Generation for Streamlining Discharge Documentation (2024)

In this paper we present our system for the BioNLP ACL`24 {\textquotedblleft}Discharge Me!{\textquotedblright} task on automating discharge summary section generation. Using Retrieval-Augmented Generation, we combine a Large Language Model (LLM) with external knowledge to guide the generation of the target sections. Our approach generates structured patient summaries from discharge notes using an instructed LLM, retrieves relevant {\textquotedblleft}Brief Hospital Course{\textquotedblright} and {\textquotedblleft}Discharge Instructions{\textquotedblright} examples via BM25 and SentenceBERT, and provides this context to a frozen LLM for generation. Our top system using SentenceBERT retrieval achieves an overall score of 0.183, outperforming zero-shot baselines. We analyze performance across different aspects, discussing limitations and future research directions.
QUB-Cirdan at \textquotedblleftDischarge Me!\textquotedblright: Zero shot discharge letter generation by open-source LLM (2024)

The BioNLP ACL`24 Shared Task on Streamlining Discharge Documentation aims to reduce the administrative burden on clinicians by automating the creation of critical sections of patient discharge letters. This paper presents our approach using the Llama3 8B quantized model to generate the {\textquotedblleft}Brief Hospital Course{\textquotedblright} and {\textquotedblleft}Discharge Instructions{\textquotedblright} sections. We employ a zero-shot method combined with Retrieval-Augmented Generation (RAG) to produce concise, contextually accurate summaries. Our contributions include the development of a curated template-based approach to ensure reliability and consistency, as well as the integration of RAG for word count prediction. We also describe several unsuccessful experiments to provide insights into our pathway for the competition. Our results demonstrate the effectiveness and efficiency of our approach, achieving high scores across multiple evaluation metrics.
e-Health CSIRO at \textquotedblleftDischarge Me!\textquotedblright 2024: Generating Discharge Summary Sections with Fine-tuned Language Models (2024)

Clinical documentation is an important aspect of clinicians' daily work and often demands a significant amount of time. The BioNLP 2024 Shared Task on Streamlining Discharge Documentation (Discharge Me!) aims to alleviate this documentation burden by automatically generating discharge summary sections, including brief hospital course and discharge instruction, which are often time-consuming to synthesize and write manually. We approach the generation task by fine-tuning multiple open-sourced language models (LMs), including both decoder-only and encoder-decoder LMs, with various configurations on input context. We also examine different setups for decoding algorithms, model ensembling or merging, and model specialization. Our results show that conditioning on the content of discharge summary prior to the target sections is effective for the generation task. Furthermore, we find that smaller encoder-decoder LMs can work as well or even slightly better than larger decoder-based LMs fine-tuned through LoRA. The model checkpoints from our team (aehrc) are openly available.
UF-HOBI at \textquotedblleftDischarge Me!\textquotedblright: A Hybrid Solution for Discharge Summary Generation Through Prompt-based Tuning of GatorTronGPT Models (2024)

Automatic generation of discharge summaries presents significant challenges due to the length of clinical documentation, the dispersed nature of patient information, and the diverse terminology used in healthcare. This paper presents a hybrid solution for generating discharge summary sections as part of our participation in the {\textquotedblleft}Discharge Me!{\textquotedblright} Challenge at the BioNLP 2024 Shared Task. We developed a two-stage generation method using both extractive and abstractive techniques, in which we first apply name entity recognition (NER) to extract key clinical concepts, which are then used as input for a prompt-tuning based GatorTronGPT model to generate coherent text for two important sections including {\textquotedblleft}Brief Hospital Course{\textquotedblright} and {\textquotedblleft}Discharge Instructions{\textquotedblright}. Our system was ranked 5th in this challenge, achieving an overall score of 0.284. The results demonstrate the effectiveness of our hybrid solution in improving the quality of automated discharge section generation.
EPFL-MAKE at \textquotedblleftDischarge Me!\textquotedblright: An LLM System for Automatically Generating Discharge Summaries of Clinical Electronic Health Record (2024)

This paper presents our contribution to the Streamlining Discharge Documentation shared task organized as part of the ACL`24 workshop. We propose MEDISCHARGE (Meditron-7B Based Medical Summary Generation System for Discharge Me), an LLM-based system to generate Brief Hospital Course and Discharge Instruction summaries based on a patient`s Electronic Health Record. Our system is build on a Meditron-7B with context window extension, ensuring the system can handle cases of variable lengths with high quality. When the length of the input exceeds the system input limitation, we use a dynamic information selection framework to automatically extract important sections from the full discharge text. Then, extracted sections are removed in increasing order of importance until the input length requirement is met. We demonstrate our approach outperforms tripling the size of the context window of the model. Our system obtains a 0.289 overall score in the leaderboard, an improvement of 183{\%} compared to the baseline, and a ROUGE-1 score of 0.444, achieving a second place performance in the shared task.