| --- |
| license: other |
| tags: |
| - missing-data |
| - imputation |
| - benchmark |
| - healthcare |
| --- |
| |
| # Missing-Data Prediction Benchmark — results |
|
|
| Two experiments on 5 classification + 5 regression medical datasets under simulated |
| missingness (MCAR/MAR/MNAR, rates 0.1–0.5, seeds 42/1/7), reported as **mean [95% CI]**. |
|
|
| ## Headline |
|
|
| A **cheap Active-Feature-Acquisition arm matches or beats a strong LLM baseline |
| (gpt-5.6-terra) on accuracy while using 97.3–99.5% fewer tokens** (cached; 76.2–95.3% |
| under conservative per-step accounting). |
|
|
| ### Experiment 2 — LLM baseline vs AFA (headline) |
|
|
| | dataset | mech | LLM acc | AFA acc | best AFA | LLM tokens | S2 cached | S2 uncached | ↓ cached | ↓ uncached | |
| |---|---|--:|--:|---|--:|--:|--:|--:|--:| |
| | breast_cancer | MAR | 0.915 | 0.965 | smart | 463,109 | 4,835 | 110,018 | **99.0%** | 76.2% | |
| | breast_cancer | MCAR | 0.924 | 0.98 | mim_smim | 414,789 | 4,515 | 19,485 | **98.9%** | 95.3% | |
| | breast_cancer | MNAR | 0.933 | 0.962 | xgboost | 480,151 | 4,835 | 110,615 | **99.0%** | 77.0% | |
| | gallstone | MAR | 0.49 | 0.771 | random_forest | 1,103,203 | 6,043 | 60,795 | **99.5%** | 94.5% | |
| | gallstone | MCAR | 0.495 | 0.755 | mim_smim | 830,642 | 6,043 | 43,630 | **99.3%** | 94.7% | |
| | gallstone | MNAR | 0.49 | 0.76 | random_forest | 1,289,357 | 6,043 | 76,806 | **99.5%** | 94.0% | |
| | heart_disease | MAR | 0.7 | 0.839 | smart | 258,031 | 2,068 | 25,029 | **99.2%** | 90.3% | |
| | heart_disease | MCAR | 0.694 | 0.856 | mim_smim | 208,505 | 2,068 | 11,775 | **99.0%** | 94.4% | |
| | heart_disease | MNAR | 0.694 | 0.833 | smart | 198,665 | 2,068 | 18,187 | **99.0%** | 90.8% | |
| | parkinsons | MAR | 0.761 | 0.897 | hist_gb | 159,996 | 3,368 | 19,475 | **97.9%** | 87.8% | |
| | parkinsons | MCAR | 0.744 | 0.872 | hist_gb | 234,958 | 3,211 | 22,513 | **98.6%** | 90.4% | |
| | parkinsons | MNAR | 0.752 | 0.897 | lightgbm | 113,330 | 3,097 | 9,260 | **97.3%** | 91.8% | |
| |
| |
| |
| ## How to read (no download needed) |
| |
| Every CSV opens in HuggingFace's Dataset Viewer (sortable, in-browser): |
| |
| - `experiment2_acquisition/acquisition_ab_report.csv` — the table above. |
| - `experiment1_prediction/prediction_classification_long.csv` / `prediction_regression_long.csv` — **one tidy row per (method, dataset, mechanism, rate, seed)** with all metrics + status. This is the clean, flat view of every run (no folder-diving). |
| - `experiment1_prediction/classification_mean_ci.csv` / `regression_mean_ci.csv` — the same, collapsed to mean [95% CI] over seeds (blank cells carry a `Status`). |
| - `experiment2_acquisition/curves_long.csv` — per-budget line-plot data. |
| - `DATA_DICTIONARY.md` — column definitions and status meanings. |
| - `raw_prediction/` — per-cell raw Exp-1 metric JSON (in-scope datasets, canonical layout, see raw_prediction/README_LATEST.md). |
| - `raw_acquisition/` — per-cell raw Exp-2 AFA traces + LLM-baseline outputs (no model weights). |
|
|
| ## Data-use / MIMIC-III notice |
|
|
| One regression dataset (`mimic_lengthofstay`) is derived from **MIMIC-III**, credentialed |
| under the PhysioNet Data Use Agreement. This repository contains only **aggregate derived |
| metrics** — no patient-level records, no raw MIMIC data, and no models trained on MIMIC. |
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| Generated 2026-08-11 by `scripts/reporting/prepare_hf_upload.py`. |
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