# A Joint Neural Baseline for Concept, Assertion, and Relation Extraction from Clinical Text

arXiv: https://arxiv.org/abs/2603.07487 · HTML: https://mlsanity.com/paper/2603.07487/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 30 references that are in the map.
- First posted on arXiv 8 Mar 2026.

## Builds on (most cited first, 16 of 16)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [Joint Extraction of Entities and Relations Based on a Novel Tagging Scheme](https://mlsanity.com/paper/1706.05075/) (2017)
- [Joint entity recognition and relation extraction as a multi-head selection problem](https://mlsanity.com/paper/1804.07847/) (2018)
- [Adversarial training for multi-context joint entity and relation extraction](https://mlsanity.com/paper/1808.06876/) (2018)
- [Minimize Exposure Bias of Seq2Seq Models in Joint Entity and Relation Extraction](https://mlsanity.com/paper/2009.07503/) (2020)
- [Dependency Parsing as Head Selection](https://mlsanity.com/paper/1606.01280/) (2016)
- [Joint Entity Extraction and Assertion Detection for Clinical Text](https://mlsanity.com/paper/1812.05270/) (2018)
- [Dynamically Updating Event Representations for Temporal Relation Classification with Multi-category Learning](https://mlsanity.com/paper/2310.20236/) (2023)
- [JaMIE: A Pipeline Japanese Medical Information Extraction System](https://mlsanity.com/paper/2111.04261/) (2021)

## Abstract (arXiv)

Clinical information extraction (e.g., 2010 i2b2/VA challenge) usually presents tasks of concept recognition, assertion classification, and relation extraction. Jointly modeling the multi-stage tasks in the clinical domain is an underexplored topic. The existing independent task setting (reference inputs given in each stage) makes the joint models not directly comparable to the existing pipeline work. To address these issues, we define a joint task setting and propose a novel end-to-end system to jointly optimize three-stage tasks. We empirically investigate the joint evaluation of our proposal and the pipeline baseline with various embedding techniques: word, contextual, and in-domain contextual embeddings. The proposed joint system substantially outperforms the pipeline baseline by +0.3, +1.4, +3.1 for the concept, assertion, and relation F1. This work bridges joint approaches and clinical information extraction. The proposed approach could serve as a strong joint baseline for future research. The code is publicly available.