Challenge: Large language models (LLMs) can generate natural language texts for various domains and tasks, but their potential for clinical text mining is under-explored.
Approach: They propose a pragmatic taxonomy for AD sign and symptom progression based on expert knowledge and train a system to detect AD-related signs and symptoms from EHRs.
Outcome: The proposed taxonomy outperforms existing methods using only the gold dataset and silver datasets.

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When Raw Data Prevails: Are Large Language Model Embeddings Effective in Numerical Data Representation for Medical Machine Learning Applications? (2024.findings-emnlp)

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Challenge: Numerical data is pivotal for medical questions and answers, but tabular data is not fully integrated into LLMs.
Approach: They examine the effectiveness of vector representations from last hidden states of LLMs for medical diagnostics and prognostics using electronic health record data.
Outcome: The proposed representations outperform those using raw numerical EHR data in medical diagnostics and prognostics.
An LLM-based Temporal-spatial Data Generation and Fusion Approach for Early Detection of Late Onset Alzheimer’s Disease (LOAD) Stagings Especially in Chinese and English-speaking Populations (2025.findings-emnlp)

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Challenge: Existing approaches struggle with temporal-spatial challenges in capturing subtle linguistic shifts across different disease stages.
Approach: They propose a large language model-driven T-S fusion framework that integrates multilingual LLMs, contrastive learning and interpretable marker discovery to revolutionize late onset AD detection.
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Improving Automatic Evaluation of Large Language Models (LLMs) in Biomedical Relation Extraction via LLMs-as-the-Judge (2025.acl-long)

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Challenge: Large Language Models generate human-like text, making them unreliable for biomedical relation extraction tasks.
Approach: They propose to use Large Language Models as judges to evaluate biomedical relation extraction . they propose structured output formatting for LLM-generated responses that helps LLMs improve their performance by 15%.
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Enrich, Aggregate, and Generate: Three-stage Biomedical Data-to-Text Generation Using Large Language Models in Low-resource Scenarios (2026.findings-acl)

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Challenge: Biomedical data-to-text generation is a branch of Natural Language Generation, aiming at generating textual natural language descriptions that can fluently and precisely describe the structured data.
Approach: They propose an LLM framework that can be used to generate textual natural language descriptions using in-context learning.
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Exploring LLM Annotation for Adaptation of Clinical Information Extraction Models under Data-sharing Restrictions (2025.findings-acl)

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Challenge: In-hospital text data often contains valuable clinical information, yet fine-tuned small language models (SLMs) for information extraction remain challenging due to differences in formatting and vocabulary across institutions.
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Large Language Models for Data Annotation and Synthesis: A Survey (2024.emnlp-main)

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Challenge: Existing surveys focus on LLMs' specific utility for data annotation and synthesis.
Approach: They propose to use large language models to generate annotations from raw data . they also propose to review learning strategies for models utilizing LLM-generated annotations .
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Making Large Language Models Better Data Creators (2023.emnlp-main)

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Challenge: Large language models (LLMs) have advanced the field of NLP significantly, but deploying them for downstream applications is still challenging due to cost, responsiveness, control, or concerns around privacy and security.
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Large Language Models with Temporal Reasoning for Longitudinal Clinical Summarization and Prediction (2025.findings-emnlp)

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Challenge: Recent advances in large language models have shown potential in clinical text summarization, but their ability to handle long patient trajectories with multi-modal data spread across time remains underexplored.
Approach: They evaluate open-source large language models, their Retrieval Augmented Generation variants and chain-of-thought prompting on long-context clinical summarization and prediction.
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Large Language Models Are Poor Clinical Decision-Makers: A Comprehensive Benchmark (2024.emnlp-main)

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Challenge: Existing studies focus on evaluating large language models in close-ended QA tasks, but many clinical decisions involve answering open-ended questions without pre-set options.
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RED-CT: A Systems Design Methodology for Using LLM-labeled Data to Train and Deploy Edge Linguistic Classifiers (2025.coling-industry)

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Challenge: Large language models have improved our ability to rapidly analyze and classify unstructured natural language data.
Approach: They propose a system approach to employing LLMs as imperfect data annotators for downstream supervised learning tasks.
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