# Clinical Utility of the Automatic Phenotype Annotation in Unstructured Clinical Notes: ICU Use Cases

arXiv: https://arxiv.org/abs/2107.11665 · HTML: https://mlsanity.com/paper/2107.11665/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 66 references that are in the map.
- First posted on arXiv 24 Jul 2021.

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Multitask learning and benchmarking with clinical time series data](https://mlsanity.com/paper/1703.07771/) (2017)
- [Identifying Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks](https://mlsanity.com/paper/1904.04990/) (2019)
- [MedCAT -- Medical Concept Annotation Tool](https://mlsanity.com/paper/1912.10166/) (2019)
- [Neural Document Embeddings for Intensive Care Patient Mortality Prediction](https://mlsanity.com/paper/1612.00467/) (2016)
- [Dynamic Prediction of ICU Mortality Risk Using Domain Adaptation](https://mlsanity.com/paper/1912.10080/) (2019)

## Built on by (most cited first, 2 of 2)

- [Unsupervised Numerical Reasoning to Extract Phenotypes from Clinical Text by Leveraging External Knowledge](https://mlsanity.com/paper/2204.10202/) (2022)
- [A Scalable Workflow to Build Machine Learning Classifiers with Clinician-in-the-Loop to Identify Patients in Specific Diseases](https://mlsanity.com/paper/2205.08891/) (2022)

## Abstract (arXiv)

Objective: Clinical notes contain information not present elsewhere, including drug response and symptoms, all of which are highly important when predicting key outcomes in acute care patients. We propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information, which is complementary to typically used vital signs and laboratory test results, to predict outcomes in the Intensive Care Unit (ICU). Methods: We develop a novel phenotype annotation model to annotate phenotypic features of patients which are then used as input features of predictive models to predict ICU patient outcomes. We demonstrate and validate our approach conducting experiments on three ICU prediction tasks including in-hospital mortality, physiological decompensation and length of stay for over 24,000 patients by using MIMIC-III dataset. Results: The predictive models incorporating phenotypic information achieve 0.845 (AUC-ROC) to predict in-hospital mortality, 0.839 (AUC-ROC) for physiological decompensation and 0.430 (Kappa) for length of stay, all of which consistently outperform the baseline models leveraging only vital signs and laboratory test results. Moreover, we conduct a thorough interpretability study, showing that phenotypes provide valuable insights at the patient and cohort levels. Conclusion: The proposed approach demonstrates phenotypic information complements traditionally used vital signs and laboratory test results, improving significantly forecast of outcomes in the ICU.