ymoslem/acl-abstracts huggingface dataset:
UoG Siephers at \textquotedblleftDischarge Me!\textquotedblright: Exploring Ways to Generate Synthetic Patient Notes From Multi-Part Electronic Health Records (2024)

This paper presents the UoG Siephers team participation at the Discharge Me! Shared Task on Streamlining Discharge Documentation. For our participation, we investigate appropriately selecting and encoding specific sections of Electronic Health Records (EHR) as input data for sequence-to-sequence models, to generate the discharge instructions and brief hospital course sections of a patient`s EHR. We found that, despite the large volume of disparate information that is often available in EHRs, selectively choosing an appropriate EHR section for training and prompting sequence-to-sequence models resulted in improved generative quality. In particular, we found that using only the history of present illness section of an EHR as input often led to better performance than using multiple EHR sections.
Roux-lette at \textquotedblleftDischarge Me!\textquotedblright: Reducing EHR Chart Burden with a Simple, Scalable, Clinician-Driven AI Approach (2024)

Healthcare providers spend a significant amount of time reading and synthesizing electronic health records (EHRs), negatively impacting patient outcomes and causing provider burnout. Traditional supervised machine learning approaches using large language models (LLMs) to summarize clinical text have struggled due to hallucinations and lack of relevant training data. Here, we present a novel, simplified solution for the {\textquotedblleft}Discharge Me!{\textquotedblright} shared task. Our approach mimics human clinical workflow, using pre-trained LLMs to answer specific questions and summarize the answers obtained from discharge summaries and other EHR sections. This method (i) avoids hallucinations through hybrid-RAG/zero-shot contextualized prompting; (ii) requires no extensive training or fine-tuning; and (iii) is adaptable to various clinical tasks.
Yale at \textquotedblleftDischarge Me!\textquotedblright: Evaluating Constrained Generation of Discharge Summaries with Unstructured and Structured Information (2024)

In this work, we propose our top-ranking (2nd place) pipeline for the generation of discharge summary subsections as a part of the BioNLP 2024 Shared Task 2: {\textquotedblleft}Discharge Me!{\textquotedblright}. We evaluate both encoder-decoder and state-of-the-art decoder-only language models on the generation of two key sections of the discharge summary. To evaluate the ability of NLP methods to further alleviate the documentation burden on physicians, we also design a novel pipeline to generate the brief hospital course directly from structured information found in the EHR. Finally, we evaluate a constrained beam search approach to inject external knowledge about relevant patient problems into the text generation process. We find that a BioBART model fine-tuned on a larger fraction of the data without constrained beam search outperforms all other models.
IgnitionInnovators at \textquotedblleftDischarge Me!\textquotedblright: Chain-of-Thought Instruction Finetuning Large Language Models for Discharge Summaries (2024)

This paper presents our proposed approach to the Discharge Me! shared task, collocated with the 23th Workshop on Biomedical Natural Language Processing (BioNLP). In this work, we develop an LLM-based framework for solving the Discharge Summary Documentation (DSD) task, i.e., generating the two critical target sections {\textquoteleft}Brief Hospital Course' and {\textquoteleft}Discharge Instructions' in the discharge summary. By streamlining the recent instruction-finetuning process on LLMs, we explore several prompting strategies for optimally adapting LLMs to specific generation task of DSD. Experimental results show that providing a clear output structure, complimented by a set of comprehensive Chain-of-Thoughts (CoT) questions, effectively improves the model`s reasoning capability, and thereby, enhancing the structural correctness and faithfulness of clinical information in the generated text. Source code is available at: https://anonymous.4open.science/r/Discharge{\_}LLM-A233
MLBMIKABR at \textquotedblleftDischarge Me!\textquotedblright: Concept Based Clinical Text Description Generation (2024)

This paper presents a method called Concept Based Description Generation, aimed at creating summaries (Brief Hospital Course and Discharge Instructions) using source (Discharge and Radiology) texts. We propose a rule-based approach for segmenting both the source and target texts. In the target text, we not only segment the content but also identify the concept of each segment based on text patterns. Our methodology involves creating a combined summarized version of each text segment, extracting important information, and then fine-tuning a Large Language Model (LLM) to generate aspects. Subsequently, we fine-tune a new LLM using a specific aspect, the combined summary, and a list of all aspects to generate detailed descriptions for each task. This approach integrates segmentation, concept identification, summarization, and language modeling to achieve accurate and informative descriptions for medical documentation tasks. Due to lack to time, We could only train on 10000 training data.
DeakinNLP at BioLaySumm: Evaluating Fine-tuning Longformer and GPT-4 Prompting for Biomedical Lay Summarization (2024)

This paper presents our approaches for the BioLaySumm 2024 Shared Task. We evaluate two methods for generating lay summaries based on biomedical articles: (1) fine-tuning the Longformer-Encoder-Decoder (LED) model, and (2) zero-shot and few-shot prompting on GPT-4. In the fine-tuning approach, we individually fine-tune the LED model using two datasets: PLOS and eLife. This process is conducted under two different settings: one utilizing 50{\%} of the training dataset, and the other utilizing the entire 100{\%} of the training dataset. We compare the results of both methods with GPT-4 in zero-shot and few-shot prompting. The experiment results demonstrate that fine-tuning with 100{\%} of the training data achieves better performance than prompting with GPT-4. However, under data scarcity circumstances, prompting GPT-4 seems to be a better solution.
ELiRF-VRAIN at BioLaySumm: Boosting Lay Summarization Systems Performance with Ranking Models (2024)

This paper presents our contribution to the BioLaySumm 2024 shared task of the 23rd BioNLP Workshop. The task is to create a lay summary, given a biomedical research article and its technical summary. As the input to the system could be large, a Longformer Encoder-Decoder (LED) has been used. We continuously pre-trained a general domain LED model with biomedical data to adapt it to this specific domain. In the pre-training phase, several pre-training tasks were aggregated to inject linguistic knowledge and increase the abstractivity of the generated summaries. Since the distribution of samples between the two datasets, eLife and PLOS, is unbalanced, we fine-tuned two models: one for eLife and another for PLOS. To increase the quality of the lay summaries of the system, we developed a regression model that helps us rank the summaries generated by the summarization models. This regression model predicts the quality of the summary in three different aspects: Relevance, Readability, and Factuality. We present the results of our models and a study to measure the ranking capabilities of the regression model.
BioLay\_AK\_SS at BioLaySumm: Domain Adaptation by Two-Stage Fine-Tuning of Large Language Models used for Biomedical Lay Summary Generation (2024)

Lay summarization is essential but challenging, as it simplifies scientific information for non-experts and keeps them updated with the latest scientific knowledge. In our participation in the Shared Task: Lay Summarization of Biomedical Research Articles @ BioNLP Workshop (Goldsack et al., 2024), ACL 2024, we conducted a comprehensive evaluation on abstractive summarization of biomedical literature using Large Language Models (LLMs) and assessed the performance using ten metrics across three categories: relevance, readability, and factuality, using eLife and PLOS datasets provided by the organizers. We developed a two-stage framework for lay summarization of biomedical scientific articles. In the first stage, we generated summaries using BART and PEGASUS LLMs by fine-tuning them on the given datasets. In the second stage, we combined the generated summaries and input them to BioBART, and then fine-tuned it on the same datasets. Our findings show that combining general and domain-specific LLMs enhances performance.
WisPerMed at BioLaySumm: Adapting Autoregressive Large Language Models for Lay Summarization of Scientific Articles (2024)

This paper details the efforts of the WisPerMed team in the BioLaySumm2024 Shared Task on automatic lay summarization in the biomedical domain, aimed at making scientific publications accessible to non-specialists. Large language models (LLMs), specifically the BioMistral and Llama3 models, were fine-tuned and employed to create lay summaries from complex scientific texts. The summarization performance was enhanced through various approaches, including instruction tuning, few-shot learning, and prompt variations tailored to incorporate specific context information. The experiments demonstrated that fine-tuning generally led to the best performance across most evaluated metrics. Few-shot learning notably improved the models' ability to generate relevant and factually accurate texts, particularly when using a well-crafted prompt. Additionally, a Dynamic Expert Selection (DES) mechanism to optimize the selection of text outputs based on readability and factuality metrics was developed. Out of 54 participants, the WisPerMed team reached the 4th place, measured by readability, factuality, and relevance. Determined by the overall score, our approach improved upon the baseline by approx. 5.5 percentage points and was only approx. 1.5 percentage points behind the first place.
HULAT-UC3M at BiolaySumm: Adaptation of BioBART and Longformer models to summarizing biomedical documents (2024)

This article presents our submission to the Bio- LaySumm 2024 shared task: Lay Summarization of Biomedical Research Articles. The objective of this task is to generate summaries that are simplified in a concise and less technical way, in order to facilitate comprehension by non-experts users. A pre-trained BioBART model was employed to fine-tune the articles from the two journals, thereby generating two models, one for each journal. The submission achieved the 12th best ranking in the task, attaining a meritorious first place in the Relevance ROUGE-1 metric.
Saama Technologies at BioLaySumm: Abstract based fine-tuned models with LoRA (2024)

Lay summarization of biomedical research articles is a challenging problem due to their use of technical terms and background knowledge requirements, despite the potential benefits of these research articles to the public. We worked on this problem as participating in BioLaySumm 2024. We experimented with various fine-tuning approaches to generate better lay summaries for biomedical research articles. After several experiments, we built a LoRA model with unsupervised fine-tuning based on the abstracts of the given articles, followed by a post-processing unit to take off repeated sentences. Our model was ranked 3rd overall in the BioLaySumm 2024 leaderboard. We analyzed the different approaches we experimented with and suggested several ideas to improve our model further.
AUTH at BioLaySumm 2024: Bringing Scientific Content to Kids (2024)

The BioLaySumm 2024 shared task at the ACL 2024 BioNLP workshop aims to transform biomedical research articles into lay summaries suitable for a broad audience, including children. We utilize the BioBART model, designed for the biomedical sector, to convert complex scientific data into clear, concise summaries. Our dataset, which includes a range of scientific abstracts, enables us to address the diverse information needs of our audience. This focus ensures that our summaries are accessible to both general and younger lay audience. Additionally, we employ specialized tokens and augmentation techniques to optimize the model`s performance. Our methodology proved effective, earning us the 7th rank on the final leaderboard out of 57 participants.
SINAI at BioLaySumm: Self-Play Fine-Tuning of Large Language Models for Biomedical Lay Summarisation (2024)

An effective disclosure of scientific knowledge and advancements to the general public is often hindered by the complexity of the technical language used in research which often results very difficult, if not impossible, for non-experts to understand. In this paper we present the approach developed by the SINAI team as the result of our participation in BioLaySumm shared task hosted by the BioNLP workshop at ACL 2024. Our approach stems from the experimentation we performed in order to test the ability of state-of-the-art pre-trained large language models, namely GPT 3.5, GPT 4 and Llama-3, to tackle this task in a few-shot manner. In order to improve this baseline, we opted for fine-tuning Llama-3 by applying parameter-efficient methodologies. The best performing system which resulted from applying self-play fine tuning method which allows the model to improve while learning to distinguish between its own generations from the previous step from the gold standard summaries. This approach achieved 0.4205 ROUGE-1 score and 0.8583 BERTScore.
RAG-RLRC-LaySum at BioLaySumm: Integrating Retrieval-Augmented Generation and Readability Control for Layman Summarization of Biomedical Texts (2024)

This paper introduces the RAG-RLRC-LaySum framework, designed to make complex biomedical research accessible to laymen through advanced Natural Language Processing (NLP) techniques. Our innovative Retrieval Augmentation Generation (RAG) solution, enhanced by a reranking method, utilizes multiple knowledge sources to ensure the precision and pertinence of lay summaries. Additionally, our Reinforcement Learning for Readability Control (RLRC) strategy improves readability, making scientific content comprehensible to non-specialists. Evaluations using the publicly accessible PLOS and eLife datasets show that our methods surpass Plain Gemini model, demonstrating a 20{\%} increase in readability scores, a 15{\%} improvement in ROUGE-2 relevance scores, and a 10{\%} enhancement in factual accuracy. The RAG-RLRC-LaySum framework effectively democratizes scientific knowledge, enhancing public engagement with biomedical discoveries.
Team YXZ at BioLaySumm: Adapting Large Language Models for Biomedical Lay Summarization (2024)

Biomedical literature are crucial for disseminating new scientific findings. However, the complexity of these research articles often leads to misinterpretations by the public. To address this urgent issue, we participated in the BioLaySumm task at the 2024 ACL BioNLP workshop, which focuses on automatically simplifying technical biomedical articles for non-technical audiences. We conduct a systematic evaluation of the SOTA large language models (LLMs) in 2024 and found that LLMs can generally achieve better readability scores than smaller models like Bart. Then we iteratively developed techniques of title infusing, K-shot prompting , LLM rewriting and instruction finetuning to further boost readability while balancing factuality and relevance. Notably, our submission achieved the first place in readability at the workshop, and among the top-3 teams with the highest readability scores, we have the best overall rank. Here, we present our experiments and findings on how to effectively adapt LLMs for automatic lay summarization. Our code is available at https://github.com/zhoujieli/biolaysumm.
Eulerian at BioLaySumm: Preprocessing Over Abstract is All You Need (2024)

In this paper, we present our approach to the BioLaySumm 2024 Shared Task on Lay Sum- marization of Biomedical Research Articles at BioNLP workshop 2024. The task aims to generate lay summaries from the abstract and main texts of biomedical research articles, making them understandable to lay audiences. We used some preprocessing techniques and finetuned FLAN-T5 models for the summarization task. Our method achieved an AlignScore of 0.9914 and a SummaC metric score of 0.944.
HGP-NLP at BioLaySumm: Leveraging LoRA for Lay Summarization of Biomedical Research Articles using Seq2Seq Transformers (2024)

Lay summarization aims to generate summaries of technical articles for non-experts, enabling easy comprehension for a general audience. The technical language used in research often hinders effective communication of scientific knowledge, making it difficult for non-experts to understand. Automatic lay summarization can enhance access to scientific literature, promoting interdisciplinary knowledge sharing and public understanding. This has become especially important for biomedical articles, given the current global need for clear medical information. Large Language Models (LLMs), with their remarkable language understanding capabilities, are ideal for abstractive summarization, helping to make complex information accessible to the public. This paper details our submissions to the BioLaySumm 2024 Shared Task: Lay Summarization of Biomedical Research Articles. We fine-tune and evaluate sequence-to-sequence models like T5 across various training dataset settings and optimization methods such as LoRA for lay summarization. Our submission achieved the 53rd position overall.
Ctyun AI at BioLaySumm: Enhancing Lay Summaries of Biomedical Articles Through Large Language Models and Data Augmentation (2024)

Lay summaries play a crucial role in making scientific research accessible to a wider audience. However, generating lay summaries from lengthy articles poses significant challenges. We consider two approaches to address this issue: Hard Truncation, which preserves the most informative initial portion of the article, and Text Chunking, which segments articles into smaller, manageable chunks. Our workflow encompasses data preprocessing, augmentation, prompt engineering, and fine-tuning large language models. We explore the influence of pretrained model selection, inference prompt design, and hyperparameter tuning on summarization performance. Our methods demonstrate effectiveness in generating high-quality, informative lay summaries, achieving the second-best performance in the BioLaySumm shared task at BioNLP 2024.
How Good are Modern LLMs in Generating Relevant and High-Quality Questions at Different Bloom`s Skill Levels for Indian High School Social Science Curriculum? (2024)

The creation of pedagogically effective questions is a challenge for teachers and requires significant time and meticulous planning, especially in resource-constrained economies. For example, in India, assessments for social science in high schools are characterized by rote memorization without regard to higher-order skill levels. Automated educational question generation (AEQG) using large language models (LLMs) has the potential to help teachers develop assessments at scale. However, it is important to evaluate the quality and relevance of these questions. In this study, we examine the ability of different LLMs (Falcon 40B, Llama2 70B, Palm 2, GPT 3.5, and GPT 4) to generate relevant and high-quality questions of different cognitive levels, as defined by Bloom`s taxonomy. We prompt each model with the same instructions and different contexts to generate 510 questions in the social science curriculum of a state educational board in India. Two human experts used a nine-item rubric to assess linguistic correctness, pedagogical relevance and quality, and adherence to Bloom`s skill levels. Our results showed that 91.56{\%} of the LLM-generated questions were relevant and of high quality. This suggests that LLMs can generate relevant and high-quality questions at different cognitive levels, making them useful for creating assessments for scaling education in resource-constrained economies.
Synthetic Data Generation for Low-resource Grammatical Error Correction with Tagged Corruption Models (2024)

Tagged corruption models provide precise control over the introduction of grammatical errors into clean text. This capability has made them a powerful tool for generating pre-training data for grammatical error correction (GEC) in English. In this work, we demonstrate their application to four languages with substantially fewer GEC resources than English: German, Romanian, Russian, and Spanish. We release a new tagged-corruption dataset consisting of 2.5M examples per language that was generated by a fine-tuned PaLM 2 foundation model. Pre-training on tagged corruptions yields consistent gains across all four languages, especially for small model sizes and languages with limited human-labelled data.
Pillars of Grammatical Error Correction: Comprehensive Inspection Of Contemporary Approaches In The Era of Large Language Models (2024)

In this paper, we carry out experimental research on Grammatical Error Correction, delving into the nuances of single-model systems, comparing the efficiency of ensembling and ranking methods, and exploring the application of large language models to GEC as single-model systems, as parts of ensembles, and as ranking methods. We set new state-of-the-art records with F{\_}0.5 scores of 72.8 on CoNLL-2014-test and 81.4 on BEA-test, respectively. To support further advancements in GEC and ensure the reproducibility of our research, we make our code, trained models, and systems' outputs publicly available, facilitating future findings.
Using Adaptive Empathetic Responses for Teaching English (2024)

Existing English-teaching chatbots rarely incorporate empathy explicitly in their feedback, but empathetic feedback could help keep students engaged and reduce learner anxiety. Toward this end, we propose the task of negative emotion detection via audio, for recognizing empathetic feedback opportunities in language learning. We then build the first spoken English-teaching chatbot with adaptive, empathetic feedback. This feedback is synthesized through automatic prompt optimization of ChatGPT and is evaluated with English learners. We demonstrate the effectiveness of our system through a preliminary user study.
Beyond Flesch-Kincaid: Prompt-based Metrics Improve Difficulty Classification of Educational Texts (2024)

Using large language models (LLMs) for educational applications like dialogue-based teaching is a hot topic. Effective teaching, however, requires teachers to adapt the difficulty of content and explanations to the education level of their students. Even the best LLMs today struggle to do this well. If we want to improve LLMs on this adaptation task, we need to be able to measure adaptation success reliably. However, current Static metrics for text difficulty, like the Flesch-Kincaid Reading Ease score, are known to be crude and brittle. We, therefore, introduce and evaluate a new set of Prompt-based metrics for text difficulty. Based on a user study, we create Prompt-based metrics as inputs for LLMs. They leverage LLM`s general language understanding capabilities to capture more abstract and complex features than Static metrics. Regression experiments show that adding our Prompt-based metrics significantly improves text difficulty classification over Static metrics alone. Our results demonstrate the promise of using LLMs to evaluate text adaptation to different education levels.