Related papers: An evaluation of DeepSeek Models in Biomedical Nat…

This research investigates the application of Large Language Models (LLMs) to augment conversational agents in process mining, aiming to tackle its inherent complexity and diverse skill requirements. While LLM advancements present novel…

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful…

Recognizing spans of biomedical concepts and their types (e.g., drug or gene) in free text, often called biomedical named entity recognition (NER), is a basic component of information extraction (IE) pipelines. Without a strong NER…

Lately, instruction-based techniques have made significant strides in improving performance in few-shot learning scenarios. They achieve this by bridging the gap between pre-trained language models and fine-tuning for specific downstream…

Open-weight versions of large language models (LLMs) are rapidly advancing, with state-of-the-art models like DeepSeek-V3 now performing comparably to proprietary LLMs. This progression raises the question of whether small open-weight LLMs…

Objective: To optimize in-context learning in biomedical natural language processing by improving example selection. Methods: We introduce a novel multi-mode retrieval-augmented generation (MMRAG) framework, which integrates four retrieval…

The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…

Cutting edge techniques developed in the general NLP domain are often subsequently applied to the high-value, data-rich biomedical domain. The past few years have seen generative language models (LMs), instruction finetuning, and few-shot…

Generative Large Language Models (LLMs) hold significant promise in healthcare, demonstrating capabilities such as passing medical licensing exams and providing clinical knowledge. However, their current use as information retrieval tools…

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of…

With the rapid rise of large language models (LLMs) in medicine, a key question is whether they can function as competent pediatricians in real-world clinical settings. We developed PEDIASBench, a systematic evaluation framework centered on…

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial…

Large Language Models (LLMs) consistently excel in diverse medical Natural Language Processing (NLP) tasks, yet their substantial computational requirements often limit deployment in real-world healthcare settings. In this work, we…

Large language models (LLMs) have demonstrated remarkable versatility across a wide range of natural language processing tasks and domains. One such task is Named Entity Recognition (NER), which involves identifying and classifying proper…

We investigate the effectiveness of fine-tuning large language models (LLMs) on small medical datasets for text classification and named entity recognition tasks. Using a German cardiology report dataset and the i2b2 Smoking Challenge…

Language models have steadily increased in size over the past few years. They achieve a high level of performance on various natural language processing (NLP) tasks such as question answering and summarization. Large language models (LLMs)…

Background: The potential of large language models (LLMs) to automate and support pharmacoepidemiologic study design is an emerging area of interest, yet their reliability remains insufficiently characterized. General-purpose LLMs often…

Entity matching (EM) is a critical step in entity resolution (ER). Recently, entity matching based on large language models (LLMs) has shown great promise. However, current LLM-based entity matching approaches typically follow a binary…

Biomedical text mining and question-answering are essential yet highly demanding tasks, particularly in the face of the exponential growth of biomedical literature. In this work, we present our participation in the 13th edition of the…

Deep learning has significantly advanced molecular modeling and design, enabling efficient understanding and discovery of novel molecules. In particular, large language models (LLMs) introduce a fresh research paradigm to tackle scientific…