# FlatASCEND: Autoregressive Clinical Sequence Generation with Continuous Time Prediction and Association-Based Pharmacological Testing

arXiv: https://arxiv.org/abs/2605.04071 · HTML: https://mlsanity.com/paper/2605.04071/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 7 of its 20 references that are in the map.
- First posted on arXiv 13 Apr 2026.

## Builds on (most cited first, 7 of 7)

- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [Med-BERT: pre-trained contextualized embeddings on large-scale structured electronic health records for disease prediction](https://mlsanity.com/paper/2005.12833/) (2020)
- [BEHRT: Transformer for Electronic Health Records](https://mlsanity.com/paper/1907.09538/) (2019)
- [MOTOR: A Time-To-Event Foundation Model For Structured Medical Records](https://mlsanity.com/paper/2301.03150/) (2023)
- [Building the EHR Foundation Model via Next Event Prediction](https://mlsanity.com/paper/2509.25591/) (2025)
- [Scaling Recurrence-aware Foundation Models for Clinical Records via Next-Visit Prediction](https://mlsanity.com/paper/2603.24562/) (2026)

## Abstract (arXiv)

Autoregressive models can predict clinical events, but generating patient-conditioned multi-step trajectories that respond to intervention tokens and testing whether those responses preserve known pharmacological associations has received limited attention. We present FlatASCEND, a 14.5M-parameter autoregressive clinical sequence model using flat composite tokens and a zero-inflated log-normal time head. Standard distributional metrics (Jaccard 0.889-0.954) do not distinguish FlatASCEND from trivial baselines; the model's value lies in conditional generation from patient-specific prefixes. A prompt-shuffle ablation shows patient-specific conditioning amplifies mechanistic pharmacological effects (2.0-2.2x for steroid to glucose, diuretic to potassium) while leaving confounding-driven associations unchanged (0.9x for insulin to glucose). An incident-user framework assesses directional consistency against prior pharmacological knowledge on MIMIC-IV (N=500 per comparison): 4/10 recover correct mechanistic directions, 2 reproduce treatment-context associations, 4 are incorrect (9/10 significant, Wilcoxon p<0.05). This pattern - partial recovery under residual confounding - is consistent with learned observational associations without causal distinction. Direct preference optimisation with surrogate reward destroys all correct associations (3/3 to 0/3), illustrating reward exploitation when reward and evaluation share an outcome domain. Generative evidence is strongest for short-horizon ICU data; outpatient temporal fidelity is weaker (median 10 vs 154 days on INSPECT), and zero-shot cross-site transfer degrades without adaptation.