# LATTE: Label-efficient Incident Phenotyping from Longitudinal Electronic Health Records

arXiv: https://arxiv.org/abs/2305.11407 · HTML: https://mlsanity.com/paper/2305.11407/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 19 of its 59 references that are in the map.
- First posted on arXiv 19 May 2023.

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [ViViT: A Video Vision Transformer](https://mlsanity.com/paper/2103.15691/) (2021)
- [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)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism](https://mlsanity.com/paper/1608.05745/) (2016)
- [BEHRT: Transformer for Electronic Health Records](https://mlsanity.com/paper/1907.09538/) (2019)
- [Deep EHR: A Survey of Recent Advances in Deep Learning Techniques for Electronic Health Record (EHR) Analysis](https://mlsanity.com/paper/1706.03446/) (2017)
- [Learning the Graphical Structure of Electronic Health Records with Graph Convolutional Transformer](https://mlsanity.com/paper/1906.04716/) (2019)
- [CODER: Knowledge infused cross-lingual medical term embedding for term normalization](https://mlsanity.com/paper/2011.02947/) (2020)
- [Deep Representation Learning of Patient Data from Electronic Health Records (EHR): A Systematic Review](https://mlsanity.com/paper/2010.02809/) (2020)
- [Clinical Concept Embeddings Learned from Massive Sources of Multimodal Medical Data](https://mlsanity.com/paper/1804.01486/) (2018)
- [Temporal Phenotyping using Deep Predictive Clustering of Disease Progression](https://mlsanity.com/paper/2006.08600/) (2020)
- [SCEHR: Supervised Contrastive Learning for Clinical Risk Prediction using Electronic Health Records](https://mlsanity.com/paper/2110.04943/) (2021)
- [Risk Prediction with Imperfect Survival Outcome Information from Electronic Health Records](https://mlsanity.com/paper/2103.04409/) (2021)

## Abstract (arXiv)

Electronic health record (EHR) data are increasingly used to support real-world evidence (RWE) studies. Yet its ability to generate reliable RWE is limited by the lack of readily available precise information on the timing of clinical events such as the onset time of heart failure. We propose a LAbel-efficienT incidenT phEnotyping (LATTE) algorithm to accurately annotate the timing of clinical events from longitudinal EHR data. By leveraging the pre-trained semantic embedding vectors from large-scale EHR data as prior knowledge, LATTE selects predictive EHR features in a concept re-weighting module by mining their relationship to the target event and compresses their information into longitudinal visit embeddings through a visit attention learning network. LATTE employs a recurrent neural network to capture the sequential dependency between the target event and visit embeddings before/after it. To improve label efficiency, LATTE constructs highly informative longitudinal silver-standard labels from large-scale unlabeled patients to perform unsupervised pre-training and semi-supervised joint training. Finally, LATTE enhances cross-site portability via contrastive representation learning. LATTE is evaluated on three analyses: the onset of type-2 diabetes, heart failure, and the onset and relapses of multiple sclerosis. We use various evaluation metrics present in the literature including the ABCgain, the proportion of reduction in the area between the observed event indicator and the predicted cumulative incidences in reference to the prediction per incident prevalence. LATTE consistently achieves substantial improvement over benchmark methods such as SAMGEP and RETAIN in all settings.