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This paper describes the architecture and systems built towards solving the SemEval 2023 Task 2: MultiCoNER II (Multilingual Complex Named Entity Recognition) [1]. We evaluate two approaches (a) a traditional Conditional Random Fields model…

Diagnostic imaging relies on interpreting both images and radiology reports, but the growing data volumes place significant pressure on medical experts, yielding increased errors and workflow backlogs. Medical vision-language models…

Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base (KB), supporting clinical and biomedical NLP applications. However, expert-annotated training data for BEL are…

The clinical adoption of artificial intelligence (AI) in medical imaging requires models that are both diagnostically accurate and interpretable to clinicians. While current multimodal biomedical foundation models prioritize performance,…

We hypothesize that large language models (LLMs) based on the transformer architecture can enable automated detection of clinical phenotype terms, including terms not documented in the HPO. In this study, we developed two types of models:…

Vision-language pretraining has advanced image-text alignment, yet progress in radiology remains constrained by the heterogeneity of clinical reports, including abbreviations, impression-only notes, and stylistic variability. Unlike…

Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical…

We conduct investigations on clinical text machine translation by examining multilingual neural network models using deep learning such as Transformer based structures. Furthermore, to address the language resource imbalance issue, we also…

Transformers-based models, such as BERT, have dramatically improved the performance for various natural language processing tasks. The clinical knowledge enriched model, namely ClinicalBERT, also achieved state-of-the-art results when…

In this research, we explored the improvement in terms of multi-class disease classification via pre-trained language models over Medical-Abstracts-TC-Corpus that spans five medical conditions. We excluded non-cancer conditions and examined…

Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many feature extraction methods have been proposed to improve the…

Functional evidence is essential for clinical interpretation of genomic variants, but identifying relevant studies and translating experimental results into structured evidence remains labor intensive. We developed a benchmark based on…

When adapting an encoder to a new domain, the standard approach is to continue training with Masked Language Modeling (MLM). We show that temporarily switching to Causal Language Modeling (CLM) followed by a short MLM decay improves…

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for…

Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity…

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on…

The advent of transformer-based models such as BERT has led to the rise of neural ranking models. These models have improved the effectiveness of retrieval systems well beyond that of lexical term matching models such as BM25. While…

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a…

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129…

We present Clinical Camel, an open large language model (LLM) explicitly tailored for clinical research. Fine-tuned from LLaMA-2 using QLoRA, Clinical Camel achieves state-of-the-art performance across medical benchmarks among openly…