# Entity-driven Fact-aware Abstractive Summarization of Biomedical Literature

arXiv: https://arxiv.org/abs/2203.15959 · HTML: https://mlsanity.com/paper/2203.15959/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 47 of its 72 references that are in the map.
- First posted on arXiv 30 Mar 2022.

## Builds on (most cited first, 30 of 47)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [BERTScore: Evaluating Text Generation with BERT](https://mlsanity.com/paper/1904.09675/) (2019)
- [Dense Passage Retrieval for Open-Domain Question Answering](https://mlsanity.com/paper/2004.04906/) (2020)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [REALM: Retrieval-Augmented Language Model Pre-Training](https://mlsanity.com/paper/2002.08909/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [Get To The Point: Summarization with Pointer-Generator Networks](https://mlsanity.com/paper/1704.04368/) (2017)
- [Leveraging Passage Retrieval with Generative Models for Open Domain Question Answering](https://mlsanity.com/paper/2007.01282/) (2020)
- [PEGASUS: Pre-training with Extracted Gap-sentences for Abstractive Summarization](https://mlsanity.com/paper/1912.08777/) (2019)
- [Evaluating the Factual Consistency of Abstractive Text Summarization](https://mlsanity.com/paper/1910.12840/) (2019)
- [KILT: a Benchmark for Knowledge Intensive Language Tasks](https://mlsanity.com/paper/2009.02252/) (2020)
- [Text Summarization with Pretrained Encoders](https://mlsanity.com/paper/1908.08345/) (2019)
- [ERNIE: Enhanced Language Representation with Informative Entities](https://mlsanity.com/paper/1905.07129/) (2019)
- [A Discourse-Aware Attention Model for Abstractive Summarization of Long Documents](https://mlsanity.com/paper/1804.05685/) (2018)
- [Multi-News: a Large-Scale Multi-Document Summarization Dataset and Abstractive Hierarchical Model](https://mlsanity.com/paper/1906.01749/) (2019)
- [A Neural Attention Model for Abstractive Sentence Summarization](https://mlsanity.com/paper/1509.00685/) (2015)
- [A Deep Reinforced Model for Abstractive Summarization](https://mlsanity.com/paper/1705.04304/) (2017)
- [AllenNLP: A Deep Semantic Natural Language Processing Platform](https://mlsanity.com/paper/1803.07640/) (2018)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [End-to-end Neural Coreference Resolution](https://mlsanity.com/paper/1707.07045/) (2017)
- [Extractive Summarization as Text Matching](https://mlsanity.com/paper/2004.08795/) (2020)
- [BIGPATENT: A Large-Scale Dataset for Abstractive and Coherent Summarization](https://mlsanity.com/paper/1906.03741/) (2019)
- [Question and Answer Test-Train Overlap in Open-Domain Question Answering Datasets](https://mlsanity.com/paper/2008.02637/) (2020)
- [TLDR: Extreme Summarization of Scientific Documents](https://mlsanity.com/paper/2004.15011/) (2020)

## Built on by (most cited first, 3 of 3)

- [Retrieval augmentation of large language models for lay language generation](https://mlsanity.com/paper/2211.03818/) (2022)
- [README: Bridging Medical Jargon and Lay Understanding for Patient Education through Data-Centric NLP](https://mlsanity.com/paper/2312.15561/) (2023)
- [Compositional Zero-Shot Domain Transfer with Text-to-Text Models](https://mlsanity.com/paper/2303.13386/) (2023)

## Abstract (arXiv)

As part of the large number of scientific articles being published every year, the publication rate of biomedical literature has been increasing. Consequently, there has been considerable effort to harness and summarize the massive amount of biomedical research articles. While transformer-based encoder-decoder models in a vanilla source document-to-summary setting have been extensively studied for abstractive summarization in different domains, their major limitations continue to be entity hallucination (a phenomenon where generated summaries constitute entities not related to or present in source article(s)) and factual inconsistency. This problem is exacerbated in a biomedical setting where named entities and their semantics (which can be captured through a knowledge base) constitute the essence of an article. The use of named entities and facts mined from background knowledge bases pertaining to the named entities to guide abstractive summarization has not been studied in biomedical article summarization literature. In this paper, we propose an entity-driven fact-aware framework for training end-to-end transformer-based encoder-decoder models for abstractive summarization of biomedical articles. We call the proposed approach, whose building block is a transformer-based model, EFAS, Entity-driven Fact-aware Abstractive Summarization. We conduct experiments using five state-of-the-art transformer-based models (two of which are specifically designed for long document summarization) and demonstrate that injecting knowledge into the training/inference phase of these models enables the models to achieve significantly better performance than the standard source document-to-summary setting in terms of entity-level factual accuracy, N-gram novelty, and semantic equivalence while performing comparably on ROUGE metrics. The proposed approach is evaluated on ICD-11-Summ-1000, and PubMed-50k.