# On Preserving the Knowledge of Long Clinical Texts

arXiv: https://arxiv.org/abs/2311.01571 · HTML: https://mlsanity.com/paper/2311.01571/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 35 of its 62 references that are in the map.
- First posted on arXiv 2 Nov 2023.

## Builds on (most cited first, 30 of 35)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter](https://mlsanity.com/paper/1910.01108/) (2019)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context](https://mlsanity.com/paper/1901.02860/) (2019)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Reformer: The Efficient Transformer](https://mlsanity.com/paper/2001.04451/) (2020)
- [Quantization and Training of Neural Networks for Efficient Integer-Arithmetic-Only Inference](https://mlsanity.com/paper/1712.05877/) (2017)
- [PEGASUS: Pre-training with Extracted Gap-sentences for Abstractive Summarization](https://mlsanity.com/paper/1912.08777/) (2019)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Compressive Transformers for Long-Range Sequence Modelling](https://mlsanity.com/paper/1911.05507/) (2019)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [How to Fine-Tune BERT for Text Classification?](https://mlsanity.com/paper/1905.05583/) (2019)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [The Lottery Ticket Hypothesis for Pre-trained BERT Networks](https://mlsanity.com/paper/2007.12223/) (2020)
- [I-BERT: Integer-only BERT Quantization](https://mlsanity.com/paper/2101.01321/) (2021)
- [Extractive Summarization as Text Matching](https://mlsanity.com/paper/2004.08795/) (2020)
- [Blockwise Self-Attention for Long Document Understanding](https://mlsanity.com/paper/1911.02972/) (2019)
- [Adaptive Attention Span in Transformers](https://mlsanity.com/paper/1905.07799/) (2019)
- [Hierarchical Transformers for Long Document Classification](https://mlsanity.com/paper/1910.10781/) (2019)
- [Multi-passage BERT: A Globally Normalized BERT Model for Open-domain Question Answering](https://mlsanity.com/paper/1908.08167/) (2019)
- [CharacterBERT: Reconciling ELMo and BERT for Word-Level Open-Vocabulary Representations From Characters](https://mlsanity.com/paper/2010.10392/) (2020)
- [Show, Attend and Distill:Knowledge Distillation via Attention-based Feature Matching](https://mlsanity.com/paper/2102.02973/) (2021)
- [Integrated multimodal artificial intelligence framework for healthcare applications](https://mlsanity.com/paper/2202.12998/) (2022)
- [Clinical-Longformer and Clinical-BigBird: Transformers for long clinical sequences](https://mlsanity.com/paper/2201.11838/) (2022)
- [Class Attention Transfer Based Knowledge Distillation](https://mlsanity.com/paper/2304.12777/) (2023)

## Abstract (arXiv)

Clinical texts, such as admission notes, discharge summaries, and progress notes, contain rich and valuable information that can be used for clinical decision making. However, a severe bottleneck in using transformer encoders for processing clinical texts comes from the input length limit of these models: transformer-based encoders use fixed-length inputs. Therefore, these models discard part of the inputs while processing medical text. There is a risk of losing vital knowledge from clinical text if only part of it is processed. This paper proposes a novel method to preserve the knowledge of long clinical texts in the models using aggregated ensembles of transformer encoders. Previous studies used either ensemble or aggregation, but we studied the effects of fusing these methods. We trained several pre-trained BERT-like transformer encoders on two clinical outcome tasks: mortality prediction and length of stay prediction. Our method achieved better results than all baseline models for prediction tasks on long clinical notes. We conducted extensive experiments on the MIMIC-III clinical database's admission notes by combining multiple unstructured and high-dimensional datasets, demonstrating our method's effectiveness and superiority over existing approaches. This study shows that fusing ensemble and aggregation improves the model performance for clinical prediction tasks, particularly the mortality and the length of hospital stay.