arXiv subjects

Luke Solo

Publications and source records attributed to Luke Solo.

4 recordsLinked to original sources

arXiv2026

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

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. 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. 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.

cs.LG↗

arXiv2026

Federated generative event models for tokenized electronic health records

Electronic health record foundation models are limited by institutionally siloed data and substantial performance degradation under cross-site transfer. We evaluated federated training of tokenized generative event models (GEMs) across 122,251 intensive care hospitalizations from three independent health systems harmonized to the Common Longitudinal ICU Data Format. Models were assessed on 12 post-24-hour clinical prediction tasks using within-site, cross-site, centralized, and federated training configurations. GEMs achieved the highest mean within-site and cross-site ROC-AUC and were substantially more transportable than conventional supervised models: their average cross-site penalties were 0.025 ROC-AUC and 0.027 PR-AUC, compared with 0.079 and 0.089 for LightGBM. Federated Learning (FedAvg and FedAvgM) approached the performance of centralized GEM training, with most gains obtained within 5-10 communication rounds. However, centralized multi-site training provided only modest improvements over complete local training. Multi-site models were most useful when local training data were limited, with their advantage narrowing as institutional data accumulated. These findings show that federated GEM training is technically feasible and preserves most centralized performance, but that the main open challenge is learning transportable representations to translate larger, but heterogeneous data from multiple health systems into a reliable target-site benefit.

cs.LG↗

arXiv2026

Efficient Generative Prediction for EHR Foundation Models: The SCOPE and REACH Estimators

Generative foundation models trained on tokenized electronic health record (EHR) timelines show promise for clinical outcome prediction via Monte Carlo sampling of simulated future trajectories. However, this approach suffers from three coupled limitations: sparse estimate distributions that poorly differentiate patient risk levels, extreme computational cost, and high sampling variance. We propose two new estimators that leverage next-token probability distributions underutilized by standard Monte Carlo: the Sum of Conditional Outcome Probability Estimator (SCOPE) and Risk Estimation from Anticipated Conditional Hazards (REACH). We prove both are unbiased, that REACH guarantees variance reduction over Monte Carlo for any model and outcome, and that REACH is a Rao-Blackwellization of any naive importance sampling scheme that preserves the non-outcome token distribution. Empirically, across $11$ clinically important outcomes in MIMIC-IV and the UChicago health system, SCOPE and REACH match $100$-sample Monte Carlo accuracy with median token reductions of $2.5\times$ to $3.4\times$ and reductions exceeding $80\times$ for the rarest outcomes, with calibration preserved throughout. Because SCOPE reuses a single sampled pool across an arbitrary number of outcomes at no marginal generation cost while REACH provides a per-task variance guarantee, the two estimators are complementary in deployment and together meaningfully reduce the inference budget required for generative EHR foundation models, particularly for rare, high-impact outcomes in healthcare.

stat.ML↗

arXiv2025

Quantifying surprise in clinical care: Detecting highly informative events in electronic health records with foundation models

We present a foundation model-derived method to identify highly informative tokens and events in electronic health records. Our approach considers incoming data in the entire context of a patient's hospitalization and so can flag anomalous events that rule-based approaches would consider within a normal range. We demonstrate that the events our model flags are significant for predicting downstream patient outcomes and that a fraction of events identified as carrying little information can safely be dropped. Additionally, we show how informativeness can help interpret the predictions of prognostic models trained on foundation model-derived representations.

cs.LG↗