# From Generative Modeling to Clinical Classification: A GPT-Based Architecture for EHR Notes

arXiv: https://arxiv.org/abs/2601.21955 · HTML: https://mlsanity.com/paper/2601.21955/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 43 of its 63 references that are in the map.
- First posted on arXiv 29 Jan 2026.

## Builds on (most cited first, 30 of 43)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [The Power of Scale for Parameter-Efficient Prompt Tuning](https://mlsanity.com/paper/2104.08691/) (2021)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [Longformer: The Long-Document Transformer](https://mlsanity.com/paper/2004.05150/) (2020)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [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)
- [Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context](https://mlsanity.com/paper/1901.02860/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Reformer: The Efficient Transformer](https://mlsanity.com/paper/2001.04451/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison](https://mlsanity.com/paper/1901.07031/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [BitFit: Simple Parameter-efficient Fine-tuning for Transformer-based Masked Language-models](https://mlsanity.com/paper/2106.10199/) (2021)

## Built on by (most cited first, 1 of 1)

- [A Hybrid Retrieval and Reranking Framework for Evidence-Grounded Retrieval-Augmented Generation](https://mlsanity.com/paper/2605.01664/) (2026)

## Abstract (arXiv)

The increasing availability of unstructured clinical narratives in electronic health records (EHRs) has created new opportunities for automated disease characterization, cohort identification, and clinical decision support. However, modeling long, domain-specific clinical text remains challenging due to limited labeled data, severe class imbalance, and the high computational cost of adapting large pretrained language models. This study presents a GPT-based architecture for clinical text classification that adapts a pretrained decoder-only Transformer using a selective fine-tuning strategy. Rather than updating all model parameters, the majority of the GPT-2 backbone is frozen, and training is restricted to the final Transformer block, the final layer normalization, and a lightweight classification head. This approach substantially reduces the number of trainable parameters while preserving the representational capacity required to model complex clinical language. The proposed method is evaluated on radiology reports from the MIMIC-IV-Note dataset using uncertainty-aware CheXpert-style labels derived directly from report text. Experiments cover multiple problem formulations, including multi-label classification of radiographic findings, binary per-label classification under different uncertainty assumptions, and aggregate disease outcome prediction. Across varying dataset sizes, the model exhibits stable convergence behavior and strong classification performance, particularly in settings dominated by non-mention and negated findings. Overall, the results indicate that selective fine-tuning of pretrained generative language models provides an efficient and effective pathway for clinical text classification, enabling scalable adaptation to real-world EHR data while significantly reducing computational complexity.