Mexico

The advancement of natural language processing (NLP) systems in healthcare hinges on language models&#39; ability to interpret the intricate information contained within clinical notes. 
This process often requires integrating information from various time points in a patient&#39;s medical history. 
However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. 
In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. 
ClinicalMamba models, with 130 million and 2.8 billion parameters, demonstrate superior performance in modeling clinical language across extended text lengths compared to Mamba and other clinical models based on longformer and Llama. 
With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and performance, outperforming existing clinical language models and large language models like GPT-4 in longitudinal clinical tasks.

NAACL 2024

ClinicalMamba: A Generative Clinical Language Model on Longitudinal Clinical Notes

mamba

generative ai

large language model

prompt

The advancement of natural language processing (NLP) systems in healthcare hinges on language models' ability to interpret the intricate information contained within clinical notes. 
This process often requires integrating information from various time points in a patient's medical history. 
However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. 
In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. 
ClinicalMamba models, with 130 million and 2.8 billion parameters, demonstrate superior performance in modeling clinical language across extended text lengths compared to Mamba and other clinical models based on longformer and Llama. 
With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and performance, outperforming existing clinical language models and large language models like GPT-4 in longitudinal clinical tasks.

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. 
 
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)*

To access the event page you need to register [**here.**](http://acl.swoogo.com/naacl2024) 
Your access to the event page is limited based on your registration type. If you registered for workshops only, you will gain access to full workshops content on the day of the workshops program.

Please register!

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

Automatic depression detection from conversational data has gained significant interest in recent years.
The DAIC-WOZ dataset, interviews conducted by a human-controlled virtual agent, has been widely used for this task.
Recent studies have reported enhanced performance when incorporating interviewer's prompts into the model.
In this work, we hypothesize that this improvement might be mainly due to a bias present in these prompts, rather than the proposed architectures and methods.
Through ablation experiments and qualitative analysis, we discover that models using interviewer's prompts learn to focus on a specific region of the interviews, where questions about past experiences with mental health issues are asked, and use them as discriminative shortcuts to detect depressed participants. 
In contrast, models using participant responses gather evidence from across the entire interview.
Finally, to highlight the magnitude of this bias, we achieve a 0.90 F1 score by intentionally exploiting it, the highest result reported to date on this dataset using only textual information.
Our findings underline the need for caution when incorporating interviewers' prompts into models, as they may inadvertently learn to exploit targeted prompts, rather than learning to characterize the language and behavior that are genuinely indicative of the patient's mental health condition.

DAIC-WOZ: On the Validity of Using the Therapist's prompts in Automatic Depression Detection from Clinical Interviews

Information extraction from Electronic Health Records (EHRs) is a crucial task in healthcare, and the lack of resources and language specificity pose significant challenges. This study addresses the limited availability of Italian Natural Language Processing (NLP) tools for clinical applications and the computational demand of large language models (LLMs) for training. We present LlamaMTS, an instruction-tuned Llama for the Italian language, leveraging the LoRA technique. It is ensembled with a BERT-based model to classify EHRs based on the presence or absence of metastasis in patients affected by Breast cancer. Through our evaluation analysis, we discovered that LlamaMTS exhibits superior performance compared to both zero-shot LLMs and other Italian BERT-based models specifically fine-tuned on the same metastatic task. LlamaMTS demonstrates promising results in resource-constrained environments, offering a practical solution for information extraction from Italian EHRs in oncology, potentially improving patient care and outcomes.

LlamaMTS: Optimizing Metastasis Detection with Llama Instruction Tuning and BERT-Based Ensemble in Italian Clinical Reports

This study evaluates the proficiency of Large Language Models (LLMs) in accurately labeling clinical document excerpts. Our focus is on the assignment of potential or confirmed diagnoses and medical procedures to snippets of medical text sourced from unstructured clinical patient records. We explore how the performance of LLMs compare against human annotators in classifying these excerpts. Employing a few-shot, chain-of-thought prompting approach with the MIMIC-III dataset, Med-PaLM 2 showcases annotation accuracy comparable to human annotators, achieving a notable precision rate of approximately 92\% relative to the gold standard labels established by human experts.

Large Language Models Provide Human-Level Medical Text Snippet Labeling

Given the increasing demand for mental health assistance, artificial intelligence (AI), particularly large language models (LLMs), may be valuable for integration into automated clinical support systems. In this work, we leverage a decision transformer architecture for topic recommendation in counseling conversations between patients and mental health professionals. The architecture is utilized for offline reinforcement learning, and we extract states (dialogue turn embeddings), actions (conversation topics), and rewards (scores measuring the alignment between patient and therapist) from previous turns within a conversation to train a decision transformer model. We demonstrate an improvement over baseline reinforcement learning methods, and propose a novel system of utilizing our model's output as synthetic labels for fine-tuning a large language model for the same task. Although our implementation based on LLaMA-2 7B has mixed results, future work can undoubtedly build on the design.

Conversational Topic Recommendation in Counseling and Psychotherapy with Decision Transformer and Large Language Models

Improving the accessibility of psychotherapy with the aid of Large Language Models (LLMs) is garnering a significant attention in recent years. Recognizing cognitive distortions from the interviewee's utterances can be an essential part of psychotherapy, especially for cognitive behavioral therapy. In this paper, we propose ERD, which improves LLM-based cognitive distortion classification performance with the aid of additional modules of (1) extracting the parts related to cognitive distortion, and (2) debating the reasoning steps by multiple agents. Our experimental results on a public dataset show that ERD improves the multi-class F1 score as well as binary specificity score. Regarding the latter score, it turns out that our method is effective in debiasing the baseline method which has high false positive rate, especially when the summary of multi-agent debate is provided to LLMs.

ERD: A Framework for Improving LLM Reasoning for Cognitive Distortion Classification

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.

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

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

Premium content

ClinicalMamba: A Generative Clinical Language Model on Longitudinal Clinical Notes

Downloads

Next from NAACL 2024

DAIC-WOZ: On the Validity of Using the Therapist's prompts in Automatic Depression Detection from Clinical Interviews

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES