Mexico

Automatic conversion of free-text radiology reports into structured data using Natural Language Processing (NLP) techniques is crucial for analyzing diseases on a large scale. While effective for tasks in widely spoken languages like English, generative large language models (LLMs) typically underperform with less common languages and can pose potential risks to patient privacy. Fine-tuning local NLP models is hindered by the skewed nature of real-world medical datasets, where rare findings represent a significant data imbalance. We introduce SMP-BERT, a novel prompt learning method that leverages the structured nature of reports to overcome these challenges. In our studies involving a substantial collection of Crohn&#39;s disease radiology reports in Hebrew (over 8,000 patients and 10,000 reports), SMP-BERT greatly surpassed traditional fine-tuning methods in performance, notably in detecting infrequent conditions (AUC: 0.99 vs 0.94, F1: 0.84 vs 0.34). SMP-BERT empowers more accurate AI diagnostics available for low-resource languages.

NAACL 2024

Leveraging Prompt-Learning for Structured Information Extraction from Crohn’s Disease Radiology Reports in a Low-Resource Language

structured information extraction

radiology reports

prompt learning

low-resource language

### Welcome to the 17th Conference of the European Chapter of the Association for Computational Linguistics (EACL) 
Continuing its mission of expanding and involving the science community of all European countries, EACL had selected the Ukrainian community for the 16th EACL, which took place online due to the COVID pandemic. Unfortunately, the ongoing war made the organisation in Kyiv impossible. Considering the importance of physical interaction among researchers, especially after the restrictions imposed by the COVID pandemic, in addition to an online mode, the conference will be held in Dubrovnik, Croatia, from 2 to 6 of May, 2023. The original aim of strengthening the connection with the Ukrainian community will not change as our program will feature a dedicated session and a workshop to highlight work on Ukrainian language technologies. As the flagship European conference in the field of computational linguistics, EACL welcomes European and international researchers covering a broad spectrum of research areas that are concerned with computational approaches to natural language.

You need to register for the conference in order to access this site. Please visit https://2023.eacl.org/registration for more information.

EACL 2023

As the flagship European conference in the field of computational linguistics, EACL welcomes European and international researchers covering a broad spectrum of research areas that are concerned with computational approaches to natural language.

Automatic conversion of free-text radiology reports into structured data using Natural Language Processing (NLP) techniques is crucial for analyzing diseases on a large scale. While effective for tasks in widely spoken languages like English, generative large language models (LLMs) typically underperform with less common languages and can pose potential risks to patient privacy. Fine-tuning local NLP models is hindered by the skewed nature of real-world medical datasets, where rare findings represent a significant data imbalance. We introduce SMP-BERT, a novel prompt learning method that leverages the structured nature of reports to overcome these challenges. In our studies involving a substantial collection of Crohn's disease radiology reports in Hebrew (over 8,000 patients and 10,000 reports), SMP-BERT greatly surpassed traditional fine-tuning methods in performance, notably in detecting infrequent conditions (AUC: 0.99 vs 0.94, F1: 0.84 vs 0.34). SMP-BERT empowers more accurate AI diagnostics available for low-resource languages.

workshop paper

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

In the realm of dialogue systems, generated responses often lack personalization. This is particularly true in the medical domain, where research is limited by scarce available domain-specific data and the complexities of modeling medical context and persona information. In this work, we investigate the potential of harnessing large language models for personalized medical dialogue generation. In particular, to better aggregate the long conversational context, we adopt topic-focused summarization to distill core information from the dialogue history, and use such information to guide the conversation flow and generated content. Drawing inspiration from real-world telehealth conversations, we outline a comprehensive pipeline encompassing data processing, profile construction, and domain adaptation. This work not only highlights our technical approach but also shares distilled insights from the data preparation and model construction phases.

Context Aggregation with Topic-focused Summarization for Personalized Medical Dialogue Generation

We construct a word complexity lexicon for medical terms in Japanese.
To facilitate communication between medical practitioners and patients, medical text simplification is being studied.
Medical text simplification is a natural language processing task that paraphrases complex technical terms into expressions that patients can understand.
However, in contrast to English, where this task is being actively studied, there are insufficient language resources in Japanese.
As a first step in advancing research on medical text simplification in Japanese, we annotate the 370,000 words from a large-scale medical terminology lexicon with a five-point scale of complexity for patients.

Semi-automatic Construction of a Word Complexity Lexicon for Japanese Medical Terminology

This paper presents our approach to the EHRSQL-2024 shared task, which aims to develop a reliable Text-to-SQL system for electronic health records. We propose two approaches that leverage large language models (LLMs) for prompting and fine-tuning to generate EHRSQL queries. In both techniques, we concentrate on bridging the gap between the real-world knowledge on which LLMs are trained and the domain-specific knowledge required for the task. The paper provides the results of each approach individually, demonstrating that they achieve high execution accuracy. Additionally, we show that an ensemble approach further enhances generation reliability by reducing errors. This approach secured us 2nd place in the shared task competition. The methodologies outlined in this paper are designed to be transferable to domain-specific Text-to-SQL problems that emphasize both accuracy and reliability.

PromptMind Team at EHRSQL-2024: Improving Reliability of SQL Generation using Ensemble LLMs

Automatic generation of chemotherapy treatment timelines from electronic health records (EHRs) notes not only streamlines clinical workflows but also promotes better coordination and improvements in cancer treatment and quality of care. This paper describes the submission to the Chemotimelines 2024 shared task that aims to automatically build a chemotherapy treatment timeline for each patient using their complete set of EHR notes, spanning various sources such as primary care provider, oncology, discharge summaries, emergency department, pathology, radiology, and more. We report results from two large language models (LLMs), namely Llama 2 and Mistral 7B, applied to the shared task data using zero-shot prompting.

Lexicans at Chemotimelines 2024: Chemotimeline Chronicles - Leveraging Large Language Models (LLMs) for Temporal Relations Extraction in Oncological Electronic Health Records

This paper presents our participation in the Chemotimelines 2024 subtask2, focusing on the development of an end-to-end system for chemotherapy timeline extraction. We initially adopt a basic framework from subtask2, utilizing Apache cTAKES for entity recognition and a BERT-based model for classifying the temporal relationship between chemotherapy events and associated times. Subsequently, we enhance this pipeline through two key directions: first, by expanding the exploration of the system, achieved by extending the search dictionary of cTAKES with the UMLS database; second, by reducing false positives through preprocessing of clinical notes and implementing filters to reduce the potential errors from the BERT-based model. To validate the effectiveness of our framework, we conduct extensive experiments using clinical notes from breast, ovarian, and melanoma cancer cases. Our results demonstrate improvements over the previous approach.

KCLab at Chemotimelines 2024: End-to-end system for chemotherapy timeline extraction – Subtask2

This paper explores the application of the sqlcoders model, a pre-trained
neural network, for automatic SQL query generation from natural language
questions. We focus on the model’s internal functionality and demon
strate its effectiveness on a domain-specific validation dataset provided
by EHRSQL. The sqlcoders model, based on transformers with attention
mechanisms, has been trained on paired examples of natural language ques
tions and corresponding SQL queries. It takes advantage of a carefully
crafted prompt that incorporates the database schema alongside the question to guide the model towards the desired output format.

Team_Optimist at EHRSQL 2024 : Text-to-SQL Generation using Large Language Model for EHR Analysis

The extraction of chemotherapy treatment timelines from clinical narratives poses significant challenges due to the complexity of medical language and patient-specific treatment regimens. This paper describes the NYULangone team's approach to Subtask 2 of the Chemotimelines 2024 shared task, focusing on leveraging a locally hosted Large Language Model (LLM), Mixtral 8x7B (Mistral AI, France), to interpret and extract relevant events from clinical notes without relying on domain-specific training data. Despite facing challenges due to the task's complexity and the current capacity of open-source AI, our methodology highlights the future potential of local foundational LLMs in specialized domains like biomedical data processing.

NYULangone at Chemotimelines 2024: Utilizing Open-Weights Large Language Models for Chemotherapy Event Extraction

This paper presents our solution to the MEDIQA-M3G Challenge at NAACL-ClinicalNLP 2024. We participated in all three languages, ranking first in Chinese and Spanish and third in English. Our approach utilizes LLaVA-med, an open-source, medical vision-language model (VLM) for visual question-answering in Chinese, and Mixtral-8x7B-instruct, a Large Language Model (LLM) for a subsequent translation into English and Spanish. In addition to our final method, we experiment with alternative approaches: Training three different models for each language instead of translating the results from one model, using different combinations and numbers of input images, and additional training on publicly available data that was not part of the original challenge training set.

IKIM at MEDIQA-M3G 2024: Multilingual Visual Question-Answering for Dermatology through VLM Fine-tuning and LLM Translations

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.

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

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.

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Next from NAACL 2024

Context Aggregation with Topic-focused Summarization for Personalized Medical Dialogue Generation

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Information Extraction from Polish Radiology Reports using Language Models

Stay up to date with the latest Underline news!

PRESENTATIONS

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