Mexico

Biomedical Entity Linking (BEL) is a challenging task for low-resource languages, due to the lack of appropriate resources: datasets, knowledge bases (KBs), and pre-trained models. In this paper, we propose an approach to create a biomedical knowledge base for German BEL using UMLS information from Wikidata, that provides good coverage and can be easily extended to further languages. As a further contribution, we adapt several existing approaches for use in the German BEL setup, and report on their results. The chosen methods include a sparse model using character n-grams, a multilingual biomedical entity linker, and two general-purpose text retrieval models. Our results show that a language-specific KB that provides good coverage leads to most improvement in entity linking performance, irrespective of the used model. The finetuned German BEL model, newly created UMLS$_{Wikidata}$ KB as well as the code to reproduce our results are publicly available.

NAACL 2024

Leveraging Wikidata for Biomedical Entity Linking in a Low-Resource Setting: A Case Study for German

biomedical entity linking

umls

wikidata

german

low-resource

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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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

Clinical Decision Support Systems assist medical professionals in providing optimal care for patients.
A prominent data source used for creating tasks for such systems is the Medical Information Mart for Intensive Care (MIMIC).
MIMIC contains electronic health records (EHR) gathered in a tertiary hospital in the United States.
The majority of past work is based on the third version of MIMIC, although the fourth is the most recent version.
This new version, not only introduces more data into MIMIC, but also increases the variety of patients.
While MIMIC-III is limited to intensive care units, MIMIC-IV also offers EHRs from the emergency department.
In this work, we investigate how to adapt previous work to update clinical outcome prediction for MIMIC-IV.
We revisit several established tasks, including prediction of diagnoses, procedures, length-of-stay, and also introduce a novel task: patient routing prediction.
Furthermore, we quantitatively and qualitatively evaluate all tasks on several bio-medical transformer encoder models.
Finally, we provide narratives for future research directions in the clinical outcome prediction domain.
We make our source code publicly available to reproduce our experiments, data, and tasks.

Revisiting Clinical Outcome Prediction for MIMIC-IV

We explore the potential of Large Language Models (LLMs) to assist and potentially correct physicians in medical decision-making tasks. We evaluate several LLMs, including Meditron, Llama2, and Mistral, to analyze the ability of these models to interact effectively with physicians across different scenarios. We consider questions from PubMedQA and several tasks, ranging from binary (yes/no) responses to long answer generation, where the answer of the model is produced after an interaction with a physician. Our findings suggest that prompt design significantly influences the downstream accuracy of LLMs and that LLMs can provide valuable feedback to physicians, challenging incorrect diagnoses and contributing to more accurate decision-making. For example, when the physician is accurate 38% of the time, Mistral can produce the correct answer, improving accuracy up to 74% depending on the prompt being used, while Llama2 and Meditron models exhibit greater sensitivity to prompt choice. Our analysis also uncovers the challenges of ensuring that LLM-generated suggestions are pertinent and useful, emphasizing the need for further research in this area.

Can LLMs Correct Physicians, Yet? Investigating Effective Interaction Methods in the Medical Domain

We explore the utility of pre-trained Large Language Models (LLMs) in detecting the presence, subtypes, and severity of aphasia across English and Mandarin Chinese speakers. Our investigation suggests that even without fine-tuning or domain-specific training, pre-trained LLMs can offer some insights on language disorders, regardless of speakers' first language. Our analysis also reveals noticeable differences between English and Chinese LLMs. While the English LLMs exhibit near-chance level accuracy in subtyping aphasia, the Chinese counterparts demonstrate less than satisfactory performance in distinguishing between individuals with and without aphasia. This research advocates for the importance of linguistically tailored and specified approaches in leveraging LLMs for clinical applications, especially in the context of multilingual populations.

Leveraging pre-trained large language models for aphasia detection in English and Chinese speakers

Vision-language models, while effective in general domains and showing strong performance in diverse multi-modal applications like visual question-answering (VQA), struggle to maintain the same level of effectiveness in more specialized domains, e.g., medical. We propose a medical vision-language model that integrates large vision and language models adapted for the medical domain. This model goes through three stages of parameter-efficient training using three separate biomedical and radiology multi-modal visual and text datasets. The proposed model achieves state-of-the-art performance on the SLAKE 1.0 medical VQA (MedVQA) dataset with an overall accuracy of 87.5% and demonstrates strong performance on another MedVQA dataset, VQA-RAD, achieving an overall accuracy of 73.2%.

Fusion of Domain-Adapted Vision and Language Models for Medical Visual Question Answering

This paper is dedicated to the design and evaluation of the first AMR parser tailored for clinical notes. Our objective was to facilitate the precise transformation of the clinical notes into structured AMR expressions, thereby enhancing the interpretability and usability of clinical text data at scale. Leveraging the colon cancer dataset from the Temporal Histories of Your Medical Events (THYME) corpus, we adapted a state-of-the-art AMR parser utilizing continuous training. Our approach incorporates data augmentation techniques to enhance the accuracy of AMR structure predictions. Notably, through this learning strategy, our parser achieved an impressive F1 score of 88\% on the THYME corpus's colon cancer dataset. Moreover, our research delved into the efficacy of data required for domain adaptation within the realm of clinical notes, presenting domain adaptation data requirements for AMR parsing. This exploration not only underscores the parser's robust performance but also highlights its potential in facilitating a deeper understanding of clinical narratives through structured semantic representations.

Adapting Abstract Meaning Representation Parsing to the Clinical Narrative – the SPRING THYME parser

Radiology Report Generation (R2Gen) demonstrates how Multi-modal Large Language Models (MLLMs) can automate the creation of accurate and coherent radiological reports. Existing methods often hallucinate details in text-based reports that don’t accurately reflect the image content. To mitigate this, we introduce a novel strategy, SERPENT-VLM (SElf Refining Radiology RePort GENeraTion using Vision Language Models), which improves the R2Gen task by integrating a self-refining mechanism into the MLLM framework. We employ a unique self-supervised loss that leverages similarity between pooled image representations and the contextual representations of the generated radiological text, alongside the standard Causal Language Modeling objective, to refine image-text representations. This allows the model to scrutinize and align the generated text through dynamic interaction between a given image and the generated text, therefore reducing hallucination and continuously enhancing nuanced report generation. SERPENT-VLM outperforms existing baselines such as LlaVA-Med, BiomedGPT, etc., achieving SoTA performance on the IU X-ray and Radiology Objects in COntext (ROCO) datasets, and also proves to be robust against noisy images. A qualitative case study emphasizes the significant advancements towards more sophisticated MLLM frameworks for R2Gen, opening paths for further research into self-supervised refinement in the medical imaging domain.

SERPENT-VLM : Self-Refining Radiology Report Generation Using Vision Language Models

This paper explores the impact of incorporating sentiment, emotion, and domain-specific lexicons into a transformer-based model for depression symptom estimation. Lexicon information is added by marking the words in the input transcripts of patient-therapist conversations as well as in social media posts. Overall results show that the introduction of external knowledge within pre-trained language models can be beneficial for prediction performance, while different lexicons show distinct behaviours depending on the targeted task. Additionally, new state-of-the-art results are obtained for the estimation of depression level over patient-therapist interviews.

Evaluating Lexicon Incorporation for Depression Symptom Estimation

With the widespread adoption of large language models (LLMs) in numerous applications, the challenge of factuality and the propensity for hallucinations has emerged as a significant concern. To address this issue, particularly in retrieval-augmented in-context learning, we introduce the hierarchical graph of thoughts (HGOT), a structured, multi-layered graph approach designed to enhance the retrieval of pertinent passages during in-context learning. The framework utilizes the emergent planning capabilities of LLMs, employing the divide-and-conquer strategy to break down complex queries into manageable sub-queries. It refines self-consistency majority voting for answer selection, which incorporates the recently proposed citation recall and precision metrics to assess the quality of thoughts, linking an answer's credibility intrinsically to the thought's quality. This methodology introduces a weighted system in majority voting, prioritizing answers based on the citation quality of their thoughts. Additionally, we propose a scoring mechanism for evaluating retrieved passages, considering factors such as citation frequency and quality, self-consistency confidence, and the retrieval module's ranking. Experiments indicate that HGOT excels as a versatile approach, outperforming competing models in FEVER by up to 7% and matching leading models such as Retrieve-then-Read in Open-SQuAD, and DSP in HotPotQA, demonstrating its efficacy in enhancing LLMs' factuality.

HGOT: Hierarchical Graph of Thoughts for Retrieval-Augmented In-Context Learning in Factuality Evaluation

As generative dialog models become ubiquitous in real-world applications, it is paramount to ensure a harmless generation. There are two major challenges when enforcing safety to open-domain chatbots (ODC). Firstly, it is impractical to provide training data reflecting the desired response to all emerging forms of toxicity (generalisation challenge). Secondly, implementing safety features may compromise the quality of the conversation (trade-off challenge). To tackle the challenges, this paper introduces a regularized fine-tuning approach called safeGD. By employing a safety-tailored loss, we translate better optimization to more safety. To ensure better convergence, safeGD penalizes sharp minima. Experimental results on datasets of "BAD" and "prosocial dialog" demonstrate that our model outperforms the current baselines \ignore{state-of-the-art methods} in reducing toxicity while preserving the conversation quality. Moreover, compared to other baselines, safeGD can better generalize to unseen toxicity.

Flatness-Aware Gradient Descent for Safe Conversational AI

GPT-4V has attracted considerable attention due to its extraordinary capacity for integrating and processing multimodal information. At the same time, its ability of face recognition raises new safety concerns of privacy leakage. Despite researchers' efforts in safety alignment through RLHF or preprocessing filters, vulnerabilities might still be exploited. In our study, we introduce \textbf{AutoRec}, an innovative automatic jailbreak technique inspired by prompt optimization. We leverage Large Language Models (LLMs) for red-teaming to refine the jailbreak prompt and employ weak-to-strong in-context learning prompts to boost efficiency. Furthermore, we present an effective search method that incorporates early stopping to minimize optimization time and token expenditure. Our experiments demonstrate that \textbf{AutoRec} significantly surpasses conventional methods, achieving an Attack Success Rate (ASR) exceeding 95.3\%. This research sheds light on strengthening GPT-4V security, underscoring the potential for LLMs to be exploited in compromising GPT-4V integrity.

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Leveraging Wikidata for Biomedical Entity Linking in a Low-Resource Setting: A Case Study for German

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