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README.md

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@@ -14,8 +14,12 @@ This work presents a systematic evaluation of tokenization approaches for clinic
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| -------------------- | ------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------ |
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| **Time Features** | Explicit time encodings showed no statistically significant benefit. | Sequence order in transformers may be sufficient for the tasks studied. |
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| **Value Features** | Importance is task-dependent (critical for mortality, less so for readmission). | Code sequences alone can carry significant predictive signal for some tasks. |
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| **Frozen Encoders** | Dramatically outperform trainable encoders with far fewer parameters. | Pretrained knowledge acts as a powerful, regularized feature extractor. |
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| **Code Information** | Emerges as the most critical predictive signal across all experiments. | The quality of code representations is paramount for model performance. |
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| **Frozen Encoders** | Tend to outperform trainable encoders with far fewer parameters. | Pretrained knowledge may serve as an effective regularized feature extractor. |
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| **Code Information** | Appears to be the strongest predictive signal across the experiments studied. | Code representation quality may be a key driver of model performance. |
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<p align="center">
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<img src="docs/waterfall_all_tasks_grouped.png" width="85%" alt="Waterfall plot of ablation results across all tasks" />
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</p>
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## Repository Structure
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- **Framework**: MEDS-Torch with transformer encoders
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- **Evaluation**: AUROC with 10 random seeds, statistical significance testing
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<p align="center">
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<img src="docs/efficiency_frontier_textcode.png" width="75%" alt="Efficiency frontier: performance vs. parameter count for TextCode variants" />
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</p>
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*This research demonstrates that simpler, more parameter-efficient tokenization approaches can achieve competitive performance in clinical time series modeling, challenging assumptions about the necessity of complex temporal encodings while clarifying the task-dependent role of value features.*
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*This research suggests that simpler, more parameter-efficient tokenization approaches may achieve competitive performance in clinical time series modeling, raising questions about the necessity of complex temporal encodings and highlighting the task-dependent role of value features.*
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---
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## Citation
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If you use this code or build on this work, please cite:
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```bibtex
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@misc{attrach2025ehrtokenization,
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title = {Rethinking Tokenization for Clinical Time Series: When Less is More},
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author = {Al Attrach, Rafi and Fani, Rajna and Restrepo, David and Jia, Yugang
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and Celi, Leo Anthony and Sch\"{u}ffler, Peter},
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year = {2025},
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note = {Machine Learning for Health (ML4H) 2025 - Findings Track}
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}
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```
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