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Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a…

In this work, we revisit the problem of semi-supervised named entity recognition (NER) focusing on extremely light supervision, consisting of a lexicon containing only 10 examples per class. We introduce ELLEN, a simple, fully modular,…

Accurate classification and anatomical localization are essential for effective medical diagnostics and research, which may be efficiently performed using deep learning techniques. However, availability of limited labeled data poses a…

Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…

We study the named entity recognition (NER) problem under the extremely weak supervision (XWS) setting, where only one example entity per type is given in a context-free way. While one can see that XWS is lighter than one-shot in terms of…

Named entity recognition (NER) aims to identify mentions of named entities in an unstructured text and classify them into predefined named entity classes. While deep learning-based pre-trained language models help to achieve good predictive…

Few-shot node classification aims at classifying nodes with limited labeled nodes as references. Recent few-shot node classification methods typically learn from classes with abundant labeled nodes (i.e., meta-training classes) and then…

Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity…

Large language models (LLMs) have become the preferred solution for many natural language processing tasks. In low-resource environments such as specialized domains, their few-shot capabilities are expected to deliver high performance.…

The scale and quality of datasets are crucial for training robust perception models. However, obtaining large-scale annotated data is both costly and time-consuming. Generative models have emerged as a powerful tool for data augmentation by…

Although Large Language Models (LLMs) exhibit remarkable adaptability across domains, these models often fall short in structured knowledge extraction tasks such as named entity recognition (NER). This paper explores an innovative,…

When combined with In-Context Learning, a technique that enables models to adapt to new tasks by incorporating task-specific examples or demonstrations directly within the input prompt, autoregressive language models have achieved good…

Quantitative disease severity scoring in medical imaging is costly, time-consuming, and subject to inter-reader variability. At the same time, clinical archives contain far more longitudinal imaging data than expert-annotated severity…

Grounded Multimodal Named Entity Recognition (GMNER) extends traditional NER by jointly detecting textual mentions and grounding them to visual regions. While existing supervised methods achieve strong performance, they rely on costly…

In cross-lingual named entity recognition (NER), self-training is commonly used to bridge the linguistic gap by training on pseudo-labeled target-language data. However, due to sub-optimal performance on target languages, the pseudo labels…

In recent years, with the growing amount of biomedical documents, coupled with advancement in natural language processing algorithms, the research on biomedical named entity recognition (BioNER) has increased exponentially. However, BioNER…

Recurrent Neural Network models are the state-of-the-art for Named Entity Recognition (NER). We present two innovations to improve the performance of these models. The first innovation is the introduction of residual connections between the…

Named entity recognition (NER) identifies typed entity mentions in raw text. While the task is well-established, there is no universally used tagset: often, datasets are annotated for use in downstream applications and accordingly only…

Precision is of utmost importance in the realm of clinical entity extraction from clinical notes and reports. Encoder Models fine-tuned for Named Entity Recognition (NER) are an efficient choice for this purpose, as they don't hallucinate.…

Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network…