cadence-core 1.0.6

Neural model for next clinical event prediction from EHR sequences using the Narrative Velocity framework

cadence-core

cadence-core is a pretrained neural model for next clinical event prediction from electronic health record (EHR) sequences. Given a patient's longitudinal clinical history, it predicts which of 48 clinical event categories will occur next and how many days until that event.

Documentation & Paper →

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Key Features

• 5.86M parameter residual MLP — lightweight, fast inference, no GPU required
• Trained on MIMIC-IV v3.1 — 100k patient sequences from a large academic medical center
• Joint prediction — simultaneous 48-class event classification and time-to-event regression
• 34.18% top-1 accuracy, 36.95 days MAE — outperforms XGBoost and all evaluated baselines
• Self-knowledge distillation — improved generalization without external teacher models
• Auto-downloads checkpoint — model weights fetched from GitHub Releases on first use
• Drop-in inference — three lines of code from install to prediction

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Installation

pip install cadence-core

Requires Python 3.10+. No GPU needed for inference.

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Quick Start

import torch
from cadence import CadenceModel, load_checkpoint

# Load model and pretrained weights (checkpoint auto-downloads on first run)
model = CadenceModel()
load_checkpoint(model)
model.eval()

# Input: 2420-dimensional feature vector per patient visit
# [0:884]    — 884 Narrative Velocity (NV) clinical features
# [884:1652] — 768-dim PubMedBERT mean-pooled cluster-semantic embedding
# [1652:2420] — 768-dim PubMedBERT last-token cluster-semantic embedding
x = torch.randn(1, 2420)  # batch_size=1, feature_dim=2420

with torch.no_grad():
    logits, time_bins = model(x)

# logits    : (batch, 48)  — classification logits over 48 event categories
# time_bins : (batch, 19)  — regression logits over 19 discretized time bins
event_probs = torch.softmax(logits, dim=-1)
top1_event  = event_probs.argmax(dim=-1).item()
print(f"Predicted next event class : {top1_event}")
print(f"Top-1 probability          : {event_probs.max().item():.3f}")

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Model Architecture

cadence-core implements the Narrative Velocity Composite (NV-C) framework — a residual MLP that fuses structured clinical features with contextual language embeddings.

Component	Details
Input dimension	2420 (884 NV features + 768 PubMedBERT mean + 768 PubMedBERT last)
Backbone	3-block MLP with residual skip connections and LayerNorm
Classification head	Linear → 48 event-class logits
Regression head	Linear → 19-bin discretized time-to-event logits
Parameters	5.86M
Training objective	Cross-entropy (classification) + ordinal regression loss (time), with self-KD

The 884 NV features capture structured clinical signals (labs, vitals, medications, procedures) encoded as narrative velocity trajectories. PubMedBERT embeddings are cluster-semantic embeddings — microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext encodings of event-category labels (not raw clinical note text) — frozen at inference. Self-knowledge distillation applied after PubMedBERT cluster-semantic fusion yields a disproportionately large top-1 gain (+0.81 pp), substantially exceeding the gain from self-KD on structured features alone.

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Performance

100k Training Tier — Male Cohort (MIMIC-IV v3.1)

Results are 3-seed means with bootstrap 95% CIs. XGBoost falls outside Cadence's CI on both metrics.

Model	Top-1 Accuracy	MAE (days)
cadence-core (NV-C)	34.18% [33.84%, 34.42%]	36.95 [36.10, 37.68]
XGBoost	32.35%	38.58
Random Forest	24.1%	53.2
Logistic Regression	21.3%	58.7
RETAIN (baseline)	22.8%	54.1
Majority-class baseline	9.25%	—
Random baseline	2.08%	—

Full-Cohort Results (MIMIC-IV v3.1)

At full cohort, cadence-core leads all models on top-1 accuracy. FT-Transformer achieves the best MAE.

Cohort	Model	Top-1 Accuracy	MAE (days)
Male	cadence-core (NV-C)	38.04%	29.39
Male	FT-Transformer	—	27.82
Female	cadence-core (NV-C)	35.66%	39.88
Female	FT-Transformer	—	37.08

External Validation — BWH Dataset (1,120 patients)

External validation on de-identified records from Brigham and Women's Hospital (BWH) — a geographically and demographically distinct population with missing structured features and population shift. BWH events were LLM-extracted and mapped to the MIMIC-IV 48-cluster event schema.

Model	Top-1 Accuracy
RETAIN	20.98% (best overall)
cadence-core (NV-C)	11.88% (leads structured-feature models)

Under domain shift with missing structured features, RETAIN achieves the best overall top-1 on BWH. Cadence leads among structured-feature models.

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Paper & Citation

Cadence: A Benchmark Evaluation of the Narrative Velocity Framework for Next Clinical Event Prediction in MIMIC-IV Rouhollahi A. and Nezami F.R. — bioRxiv, 2026. doi.org/10.64898/2026.05.06.722409

If you use cadence-core in your research, please cite:

@article{rouhollahi2026cadence,
  title   = {Cadence: A Benchmark Evaluation of the Narrative Velocity Framework for Next Clinical Event Prediction in {MIMIC-IV}},
  author  = {Rouhollahi, Amir and Nezami, Farhad R.},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.05.06.722409},
  url     = {https://doi.org/10.64898/2026.05.06.722409}
}

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Reproducibility

Data access requires a signed PhysioNet credentialed account for MIMIC-IV:

https://physionet.org/content/mimiciv/3.1/

Once access is granted, follow the preprocessing instructions in src/ to generate the NV feature sequences and PubMedBERT embeddings used for training.

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License

This project is released under the MIT License. The pretrained model checkpoint is provided for research use only. MIMIC-IV data is subject to its own PhysioNet Credentialed Health Data License.

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Contact

Amir Rouhollahi Brigham and Women's Hospital / Harvard Medical School [e-mail] GitHub · PyPI