ClinicalBench

TLDR: Can LLMs Beat Traditional ML Models in Clinical Prediction? Not yet. We discover that both general-purpose and medical LLMs, even with different model scales and temperatures, diverse prompting or fine-tuning strategies, still cannot beat traditional ML models in clinical prediction yet, shedding light on their potential deficiency in clinical reasoning and decision-making.

Canyu Chen*, Jian Yu*, Shan Chen, Che Liu, Zhongwei Wan, Shuang Zhou, Yuan Luo, Rui Zhang, Danielle S. Bitterman, Fei Wang, Kai Shu†
_{*equal contribution  ·  †corresponding author}

Updates

• 2026-08. v1.0 restructures the repository into an installable clinicalbench package: one config per paper table and figure, 99.1% of the paper's runs re-scorable from the shipped results without a GPU, 104 regression tests, and the reproducibility fixes listed in docs/reproduction.md.
• 2026. ClinicalBench is accepted at KDD 2026.
• 2024-11. Paper on arXiv, with the first release of code and results.

Overview

ClinicalBench benchmarks 22 LLMs (14 general-purpose, 8 medical) against 11 traditional ML models on three clinical prediction tasks across two databases, under matched cohorts, features and evaluation.

Databases: MIMIC-III and MIMIC-IV (both credentialed).

The gap is not small. On MIMIC-III mortality prediction, scored from the released result files:

Key features

• Any HuggingFace causal LM, in one command: clinicalbench-llm --base_model <hf-id> --task mortality_pred --dataset mimic3. The paper's 22 checkpoints are a roster in configs/models.yaml, not a hard-coded list, so evaluating a model we never ran is one id away. 0.5B to 70B tested, --device_map auto shards across GPUs, --lora_path merges an adapter.
• 11 traditional ML baselines on matched inputs: XGBoost, LogisticRegression, DecisionTree, RandomForest, AdaBoost, SVM, NaiveBayes, KNN, NeuralNetwork, Transformer and RNN, fit on bag-of-codes features (2,000 each for conditions, procedures and drugs, plus age band and gender) built from the same index visit the LLM prompt describes. 20-seed sweep, best validation F1 scored. CPU, minutes per cohort.
• Six prompting strategies, two scoring paths: --mode ORI | ICL | COT | RP | SR | LORA. --scoring logits takes one forward pass and records a softmax over the answer tokens, which is what AUROC needs; --scoring generate decodes up to 512 tokens and backward-scans for the answer, which COT and SR need because the answer is buried in prose. Unparseable answers are scored as wrong rather than dropped, and every table carries an inv% column.
• Raw MIMIC to prompts in one pass: scripts/prepare_data.sh reads the credentialed PhysioNet tables and writes samples, prompts and cohort splits for 3 tasks × 2 databases. Training splits are class-balanced while val and test preserve natural prevalence, and the seeded index files ship in data/, so your split is the published split.
• Config-driven experiment matrix: one YAML per paper table and figure expands into the exact runs behind it, with three verbs: list them, --check which ones you have already run, and --run --skip-existing to fill the gaps. 2,505 runs, all re-scorable without a GPU from a gated Hub dataset, canyuchen/clinicalbench-results.

Repository layout

clinicalbench/
├── config.py              task wording, database schemas, cohort split spec
├── naming.py              result-file naming (shared by runner and evaluator)
├── answers.py             answer extraction and the invalid-output penalty
├── experiments.py         expands a paper config into runs
├── data/                  cohort building, prompt rendering, splits, fine-tune export
│   └── templates/icl/     few-shot exemplars, one file per task x database
├── inference/             LLM runner and the prompt-engineering modes
├── baselines/             the 11 traditional ML models and their features
├── eval/                  scoring one result file; aggregating a whole table
└── _vendor/pyhealth/      reduced PyHealth, for reading MIMIC (see NOTICE)

configs/models.yaml        checkpoint ids and the roster each table uses
configs/paper/             one config per table and figure
data/{task}/{dataset}/     cohort index files (.npy), 108 of them
results/                   released model outputs, fetched from the Hub
docs/                      install, data, running, reproduction, methodology
scripts/                   data-preparation shell entry point
tests/                     104 tests, no GPU or MIMIC access required

Installation

conda create -n clinicalbench python=3.10 && conda activate clinicalbench
pip install -e ".[llm]"     # omit [llm] to only score released results
pytest tests/ -q

Details in docs/installation.md.

Data

Three pieces, with different access rules:

Raw MIMIC cannot be redistributed, so the prompts are not here. Both databases are free but credentialed: complete CITI training and sign the DUA at MIMIC-III v1.4 and MIMIC-IV v2.2, decompress the tables, then build everything in one pass:

scripts/prepare_data.sh --mimic3 /path/to/mimic-iii/1.4 --mimic4 /path/to/mimic-iv/2.2/hosp

The 108 split-index files do ship, so your cohorts are the published ones rather than a fresh shuffle. Regenerating them is a no-op that overwrites them with identical bytes. This only holds on the versions above: another MIMIC release produces a different sample list, and the shipped indices would then point at different patients.

Our 3,015 released result files are hosted separately so cloning stays cheap. They are patient-level model outputs derived from MIMIC, so the dataset is gated; accept the terms once and approval is automatic:

clinicalbench-fetch-results     # 295 MB into results/

Full walkthrough in docs/data_preparation.md; file naming and columns in results/README.md.

Models

14 general-purpose LLMs (Llama3 8B/70B, Mistral-v0.3-7B, Gemma2-9B, Qwen2 0.5B/1.5B/7B, Yi-v1.5 6B/9B/34B, Vicuna-v1.5-7B, Phi3.5-mini-3.8B, InternLM2.5-7B, MiniCPM3-4B), 8 medical LLMs (Meditron 7B/70B, Medllama3-8B, BioMistral-7B, Med42 8B/70B, BioMedGPT-7B, Internist-7B), and 11 traditional models (XGBoost, LogisticRegression, DecisionTree, RandomForest, AdaBoost, SVM, NaiveBayes, KNN, NeuralNetwork, Transformer, RNN).

Checkpoint ids and the roster each table uses are in configs/models.yaml. That file is a convenience list, not a restriction: --base_model takes any HuggingFace id or local path.

Quick start

# 1) Evaluate an LLM on one task and cohort
clinicalbench-llm --base_model meta-llama/Meta-Llama-3-8B-Instruct \
    --task mortality_pred --dataset mimic3 --mode ORI --scoring logits --random_index 0

# 2) The 11 traditional baselines on the same cohort, on CPU
clinicalbench-baselines --task mortality_pred --dataset mimic3 --random_index 0

# 3) Score a run, with AUROC
clinicalbench-score --base_model meta-llama/Meta-Llama-3-8B-Instruct \
    --task mortality_pred --dataset mimic3 --random_index 0 --auroc

# 4) Average several splits into a table with confidence intervals
clinicalbench-table configs/paper/table_1.yaml --task mortality_pred --dataset mimic3

# 5) Chain-of-thought, which needs the generative scoring path
clinicalbench-llm --base_model meta-llama/Meta-Llama-3-8B-Instruct \
    --task mortality_pred --dataset mimic3 --mode COT --scoring generate

Steps 3 and 4 need no GPU and no MIMIC access once clinicalbench-fetch-results has run. Flag-by-flag reference in docs/running.md.

Reading our metrics without downloading anything:

import pandas as pd
df = pd.read_csv("hf://datasets/canyuchen/clinicalbench-results/summary.csv")

Reproducing the paper

Every run behind these tables is re-scorable from the released files. Figure 4 is the exception: it needs fine-tuned adapters, which were not released, so docs/fine_tuning.md covers training them yourself.

Full commands in docs/reproduction.md.

Documentation

Read methodology.md before quoting a number. Two things there change how results should be read: unparseable LLM answers are scored as wrong rather than dropped, and the two scoring paths extract answers differently.

Acknowledgments

Built on PyHealth; a reduced copy is vendored under clinicalbench/_vendor/pyhealth/. See NOTICE for attribution and the list of modifications.

License

MIT. See LICENSE. We do not own any of the datasets used.

Citation

@inproceedings{chen2026clinicalbench,
  title     = {ClinicalBench: Can LLMs Beat Traditional ML Models in Clinical Prediction?},
  author    = {Chen, Canyu and Yu, Jian and Chen, Shan and Liu, Che and Wan, Zhongwei
               and Zhou, Shuang and Luo, Yuan and Zhang, Rui and Bitterman, Danielle S.
               and Wang, Fei and Shu, Kai},
  booktitle = {Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery
               and Data Mining (KDD '26)},
  year      = {2026}
}