Mexico

This paper presents our LLM-based system designed for the MEDIQA-CORR @ NAACL-ClinicalNLP 2024 Shared Task 3, focusing on medical error detection and correction in medical records. Our approach consists of three key components: entity extraction, prompt engineering, and ensemble. First, we automatically extract biomedical entities such as therapies, diagnoses, and biological species. Next, we explore few-shot learning techniques and incorporate graph information from the MeSH database for the identified entities. Finally, we investigate two methods for ensembling: (i) combining the predictions of three previous LLMs using an AND strategy within a prompt and (ii) integrating the previous predictions into the prompt as separate &#39;expert&#39; solutions, accompanied by trust scores representing their performance. The latter system ranked second with a BERTScore score of 0.8059 and third with an aggregated score of 0.7806 out of the 15 teams&#39; solutions in the shared task.

NAACL 2024

HSE NLP Team at MEDIQA-CORR 2024 Task: In-Prompt Ensemble with Entities and Knowledge Graph for Medical Error Correction

in-context learning

large language models

natural language processing

few-shot learning

knowledge graph

## Welcome to 2024 Annual Conference of the North American Chapter of the Association for Computational Linguistics!
This year, the conference is in Mexico City. NAACL was actually already planned for Mexico City in 2021, but due to the pandemic the entire conference was moved online. This year, finally, we get to go! So it is my sincere pleasure to welcome you to Mexico City, whether in person or virtually. Having the conference in Mexico City is a good opportunity to emphasize that NAACL is our flagship conference for ACL members not only in North America but also in Central and South America, even though NAACL has been bearing “North” in its name. At this year’s conference, we have a theme to match, with a theme track on the Languages of Latin America to showcase the linguistic diversity of the region.
 
The opportunity to present at NAACL should not depend on a researcher’s travel budget, or their family status. This is why it is so important to make virtual participation at NAACL as good an experience as possible – but we want to also provide a good experience for in-person participants. As a community, we are still working out the best way to do that. This year at NAACL, we are trying out a big virtual poster session ahead of the conference, with the hope that this will make make for a lively and interactive experience. At the same time, we are reducing virtual oral presentations, which seem to be particularly tricky to make to work well. A big thanks to the NAACL program chairs and to Luciana Benotti for all their ideas and work to improve the virtual experience. And participants, virtual as well as in-person: Please let us know what worked for you and what didn’t, so we can continue to improve hybrid conferences. 
 
I have been lucky to work with many amazing people. Without their insight, dedication and patience, and without the many hours of work they put in, NAACL would not have been possible. A huge thank you to the program chairs Helena Gomez, Kevin Duh, and Steve Bethard – you are the best! 
 
Finally, I would like to thank all authors, invited speakers and panelists, area chairs and reviewers, the volunteers organizing and chairing sessions, and all attendees, in-person and virtual. Thank you for helping us make NAACL 2024 come to life. 
 
Welcome and hope you all enjoy the conference! 
Katrin Erk 
The University of Texas at Austin 
NAACL-2024 General Chair 
*You can read the full Welcome message in the [Conference Handbook (downloadable)](https://drive.google.com/file/d/1H1NvW0VASQjkSCYgw3mr-3l4yYDSxz6B/view?usp=sharing)*

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2024 Annual Conference of the North American Chapter of the Association for Computational Linguistics

This paper presents our LLM-based system designed for the MEDIQA-CORR @ NAACL-ClinicalNLP 2024 Shared Task 3, focusing on medical error detection and correction in medical records. Our approach consists of three key components: entity extraction, prompt engineering, and ensemble. First, we automatically extract biomedical entities such as therapies, diagnoses, and biological species. Next, we explore few-shot learning techniques and incorporate graph information from the MeSH database for the identified entities. Finally, we investigate two methods for ensembling: (i) combining the predictions of three previous LLMs using an AND strategy within a prompt and (ii) integrating the previous predictions into the prompt as separate 'expert' solutions, accompanied by trust scores representing their performance. The latter system ranked second with a BERTScore score of 0.8059 and third with an aggregated score of 0.7806 out of the 15 teams' solutions in the shared task.

workshop paper

This paper presents our team's participation in the MEDIQA-ClinicalNLP 2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85\% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show it’s superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

UMass-BioNLP at MEDIQA-M3G 2024: DermPrompt - A Systematic Exploration of Prompt Engineering with GPT-4V for Dermatological Diagnosis

This paper describes our submission to MEDIQA-CORR 2024 shared task for automatic identification and correction of medical errors in a given clinical text. We report results from two approaches: the first uses a few-shot in-context learning (ICL) with a Large Language Model (LLM) and the second approach extends the idea by using a knowledge-enhanced few-shot ICL approach. We used Azure OpenAI GPT-4 API as the LLM and Wikipedia as the external knowledge source. We report evaluation metrics (accuracy, ROUGE, BERTScore, BLEURT) across both approaches for validation and test datasets. Of the two approaches implemented, our experimental results show that the knowledge-enhanced few-shot ICL approach with GPT-4 performed better with error flag (subtask A) and error sentence detection (subtask B) with accuracies of 68% and 64%, respectively on the test dataset. These results positioned us fourth in subtask A and second in subtask B, respectively in the shared task.

EM_Mixers at MEDIQA-CORR 2024: Knowledge-Enhanced Few-Shot In-Context Learning for Medical Error Detection and Correction

Medical errors in clinical text pose significant risks to patient safety. The MEDIQA-CORR 2024 shared task focuses on detecting and correcting these errors across three subtasks: identifying the presence of an error, extracting the erroneous sentence, and generating a corrected sentence. In this paper, we present our approach that achieved top performance in all three subtasks. For the MS dataset, which contains subtle errors, we developed a retrieval-based system leveraging external medical question-answering datasets. For the UW dataset, reflecting more realistic clinical notes, we created a pipeline of modules to detect, localize, and correct errors. Both approaches utilized the DSPy framework for optimizing prompts and few-shot examples in large language model (LLM) based programs. Our results demonstrate the effectiveness of LLM based programs for medical error correction. However, our approach has limitations in addressing the full diversity of potential errors in medical documentation. We discuss the implications of our work and highlight future research directions to advance the robustness and applicability of medical error detection and correction systems.

WangLab at MEDIQA-CORR 2024: Optimized LLM-based Programs for Medical Error Detection and Correction

Transforming natural language questions into SQL queries is crucial for precise data retrieval from electronic health record (EHR) databases. A significant challenge in this process is detecting and rejecting unanswerable questions that request information outside the database's scope or exceed the system's capabilities. In this paper, we introduce a novel text-to-SQL framework that focuses on standardizing the structure of questions into a templated format. Our framework begins by fine-tuning GPT-3.5-turbo, a powerful large language model (LLM), with detailed prompts involving the table schemas of the EHR database system. Our approach shows promising results on the EHRSQL-2024 benchmark dataset, part of the ClinicalNLP shared task. Although fine-tuning GPT achieves third place on the development set, it struggled with the diverse questions in the test set. With our framework, we improve our system's adaptability and achieve fourth position in the official leaderboard of the EHRSQL-2024 challenge.

KU-DMIS at EHRSQL 2024 : Generating SQL query via question templatization in EHR

In this paper, we present our work in the EHRSQL 2024 shared task which tackles reliable text-to-SQL modeling on Electronic Health Records. Our proposed system tackles the task with three modules - abstention module, text-to-SQL generation module, and reliability module. The abstention module identifies whether the question is answerable given the database schema. If the question is answerable, the text-to-SQL generation module generates the SQL query and associated confidence score. The reliability module has two key components - confidence score thresholding, which rejects generations with confidence below a pre-defined level, and error filtering, which identifies and excludes SQL queries that result in execution errors. In the official leaderboard for the task, our system ranks 6th. We have also made the source code public.

LTRC-IIITH at EHRSQL 2024: Enhancing Reliability of Text-to-SQL Systems through Abstention and Confidence Thresholding

In this paper, we present our work to the MEDIQA-M3G 2024 shared task, which tackles multilingual and multimodal medical answer generation. Our system consists of a lightweight Vision-and-Language Transformer (ViLT) model which is fine-tuned for the clinical dermatology visual question-answering task. In the official leaderboard for the task, our system ranks 6th. After the challenge, we experiment with training the ViLT model on more data. We also explore the capabilities of large Vision-Language Models (VLMs) such as Gemini and LLaVA.

LTRC-IIITH at MEDIQA-M3G 2024: Medical Visual Question Answering with Vision-Language Models

The introduction of conversational systems have made synthesized speech technologies common tools for daily activities. However, not all synthetic speech systems are designed with the needs of people with disabilities in mind. This paper describes a study in which 198 people -- 80 participants with self-reported disabilities and 118 participants without -- were recruited to listen to navigation instructions from a spoken dialogue system with different prosodic features. Results showed that slowing down speech rate aids in participants' number recall, but not in noun recall. From our results, we provide suggestions for developers for building accessible synthetic speech systems.

Examining Prosody in Spoken Navigation Instructions for People with Disabilities

The self-rationalising capabilities of large language models (LLMs) have been explored in restricted settings, using task-specific data sets. However, current LLMs do not (only) rely on specifically annotated data; nonetheless, they frequently explain their outputs. The properties of the generated explanations are influenced by the pre-training corpus and by the target data used for instruction fine-tuning. As the pre-training corpus includes a large amount of human-written explanations ``in the wild'', we hypothesise that LLMs adopt common properties of human explanations. By analysing the outputs for a multi-domain instruction fine-tuning data set, we find that generated explanations show selectivity and contain illustrative elements, but less frequently are subjective or misleading. We discuss reasons and consequences of the properties' presence or absence. In particular, we outline positive and negative implications depending on the goals and user groups of the self-rationalising system.

Properties and Challenges of LLM-Generated Explanations

When users want to write a story with a language model (LM) assistant, it is often very difficult to provide a prompt that clearly specifies all their interests. For the developers of LM assistants, it is also difficult to ensure their output stories come from a dataset without copyright concerns. Motivated by these limitations, we propose a coarse-to-fine (C2F) tree-based story generation framework, which is called C2F-StoryTree, where the LM iteratively generates more and more specific story prompts based on a user's input prompt and the desired plot selected by the user. To realize our C2F-StoryTree framework, we propose an entailment hierarchy (EH) text structure, in which a more specific response entails more general prompt (e.g., a story entails a summary). We also propose novel annotation tasks, decoding methods, and a human-and-machine-in-the-loop procedure to minimize the annotation cost of building the text structure. We build an entailment hierarchy dataset on top of the story datasets with desired licenses and styles, on which the developers can fine-tune or evaluate their LMs. In our experiments, we demonstrate that our C2F-StoryTree system not only allows users to collaborate with a LM in a new paradigm, but also generates the short stories with human-level quality. Furthermore, our entailment hierarchy and C2F generation substantially make the generated stories more diverse, coherent, engaging, and creative.

Fine-to-Coarse Entailment Hierarchy Construction for Coarse-to-Fine Story Generation

In the realm of research support tools, there exists a notable void in resources tailored specifically for aiding researchers during the crucial ideation phase of the research life-cycle. We address this gap by introducing 'Acceleron', a `Co-Pilot' for researchers, designed specifically to accelerate the ideation phase of the research life-cycle. Leveraging the reasoning and domain-specific skills of Large Language Models (LLMs) within an agent-based architecture with distinct personas, Acceleron aids researchers through the formulation of a comprehensive research proposals. It emulates the ideation process, engaging researchers in an interactive fashion to validate the novelty of the proposal and generate plausible set-of hypotheses. Notably, it addresses challenges inherent in LLMs, such as hallucinations, implements a two-stage aspect-based retrieval to manage precision-recall trade-offs, and tackles issues of unanswerability. Our observations and end-user evaluations illustrate the efficacy of Acceleron as an enhancer of researcher's productivity.

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