Representation Before Training: A Practical Benchmark for Generative Medical Event Model

Fused tokens pairing codes with value deciles increased performance across all eight outcome families relative to the equivalent unfused tokenized input with area under the receiver operating characteristic curve (AUROC) gains of $+0.002$ to $+0.033$ and Spearman correlation gains of $+0.025$ to $+0.114$. It comes from a paper posted to arXiv on 21 September 2026. Generative medical event models use tokenized sequences of patient timelines as input, but practical guidance on the many decisions around tokenization is limited. We benchmark quantization granularity, reference-range anchoring, code--value fusion, numeric and temporal encodings, and native versus harmonized event representations from an expert-mapped common data model. Using both Llama and Qwen architectures, 156 models were trained on full hospitalizations from three initialization seeds, with each configuration following a shared training recipe for up to five epochs. We evaluated learned representations from the first 24 hours of hospitalization with linear probes to predict binary and continuous outcomes during hours 24-48. Neither anchoring value bins to reference ranges nor increasing quantization granularity consistently improved performance, while xVal variants underperformed both discrete and soft encodings. Alternatives to explicit time tokens, such as event-order and admission-relative rotary position embeddings (RoPE), yielded higher family-mean point estimates across all eight families while reducing input length. When evaluating native input against input mapped to the Common Longitudinal Intensive Care Unit Data Format (CLIF), the CLIF full-hospitalization training sequences contained 28.6% as many tokens as the native sequences and improved performance across six of eight outcome families. These findings show that tokenization and event encoding are consequential design choices when learning patient representations for downstream classification and regression tasks.

Why it counts

Fused tokens pairing codes with value deciles increased performance across all eight outcome families relative to the equivalent unfused tokenized input with area under the receiver operating characteristic curve (AUROC) gains of $+0.002$ to $+0.033$ and Spearman correlation gains of $+0.025$ to $+0.114$. Neither anchoring value bins to reference ranges nor increasing quantization granularity consistently improved performance, while xVal variants underperformed both discrete and soft encodings. Alternatives to explicit time tokens, such as event-order and admission-relative rotary position embeddings (RoPE), yielded higher family-mean point estimates across all eight families while reducing input length.

Sources

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What is not known

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