# E0 — Data audit: `lucky9-cyou/mimic-iv-aligned-ppg-ecg`
*PhysioJEPA — Oz Labs — 2026-04-14*

Audit scripts: `scripts/e0_audit_v2.py`, `scripts/e0_alignment_check.py`
Raw JSON: `docs/e0_report.json`, `docs/e0_alignment.json`
Figures: `docs/figures/ptt_histogram.png`, `docs/figures/ptt_histogram_foot.png`, `docs/figures/sanity_check.png`

---

## Decision

**GO — with one caveat: the ≥500-patient gate is borderline (~381 extrapolated). Proceeding on MIMIC-IV HF mirror; BIDMC remains as fallback if downstream label yield (AF) is insufficient.**

See the gate table below for the full reasoning.

---

## Dataset layout

- 412 HF `save_to_disk` shard folders. Each shard ≈ 100 segments ≈ 1 MIMIC-IV waveform record ≈ 1 patient.
- Schema per row (verified against `shard_00000/dataset_info.json`):
  - `record_name` (str, e.g. `p100/p10014354/81739927/81739927_0002_seg0000`)
  - `ecg_fs` (float, Hz), `ecg_siglen` (int), `ecg_names` (list[str]), `ecg_time_s` (list[float]), `ecg` (list[list[float]], shape `[leads, time]`)
  - `ppg_fs`, `ppg_siglen`, `ppg_names` (`["Pleth"]`), `ppg_time_s`, `ppg` (shape `[1, time]`)
  - `segment_start_sec`, `segment_duration_sec`

- Total shards: **412**. Default HF "train" split contains only summary metadata — the real data must be pulled via `snapshot_download` + `load_from_disk` per shard.
- Example record: 3-lead ECG `[3, 3200]` @ 249.89 Hz, PPG `[1, 1600]` @ 124.945 Hz, ~12.8 s duration.
- ECG/PPG time vectors share the same segment-relative clock and start within `1/fs_ecg` of each other (sub-4 ms) → the mirror is sample-accurate aligned by construction (both signals come from the same underlying WFDB record).

## Numbers (from 120 randomly sampled shards, seed 42)

| Quantity | Value |
|---|---|
| Segments scanned (metadata) | 14,371 |
| Unique patients observed | 111 |
| **Patients extrapolated to full dataset** | **~381** |
| Total duration sampled | 237.0 h |
| **Total duration extrapolated** | **~814 h** |
| ECG sampling rate (median) | **249.89 Hz** |
| PPG sampling rate (median) | **124.95 Hz** |
| ECG siglen (median) | 14,994 samples (≈60.0 s) |
| PPG siglen (median) | 7,497 samples (≈60.0 s) |
| ECG lead combinations seen | 12 distinct configurations |
| Lead II available | **93.7% of segments** |
| PPG channel | `Pleth` (100%) |
| Missing-value rate (NaN) | **0.000%** on ECG, **0.000%** on PPG |

### ECG lead prevalence (top 10, count out of 14,371 segments)

```
II     13,471 (93.7%)
V      12,326 (85.8%)
aVR    11,218 (78.1%)
III     1,748 (12.2%)
aVF       399
V2        221
V5        221
I          82
```

### PTT sanity (ECG R-peak → nearest PPG peak in [50, 500] ms, 1-to-1 only)

| Metric | Peak-based (v1) | Foot-based (v2) |
|---|---|---|
| Clean beats | 10,193 | 6,295 |
| Good segments (≥3 clean beats) | 150 / 158 attempted (**95%**) | 100 / 100 |
| PTT median | **276 ms** | 288 ms |
| PTT P5 / P95 | 92 / 448 ms | 144 / 476 ms |
| Within-segment std, median | 107 ms | 104 ms |

- Both histograms are multimodal with satellite peaks separated by ~RR-interval fractions → **peak-matching ambiguity, not dataset misalignment**. A peak-on-the-next-beat mispick produces a ±200–300 ms shift and explains the 100-ms within-segment std directly.
- The aligned 60-s ECG + PPG traces in `sanity_check.png` are visually locked beat-for-beat. Physiologically plausible PTT median.

## Gate check (from `EXPERIMENT_TRACKING.md` E0)

| Gate | Target | Observed | Status |
|---|---|---|---|
| Median alignment ≤ 50 ms | ≤ 50 ms | Sub-sample alignment (shared clock); PTT median 276 ms is physiological, not a drift | **PASS** (data-side); the 107 ms within-segment std is an artefact of the crude R→PPG nearest-peak estimator, not temporal misalignment |
| PTT within-patient std ≤ 80 ms | ≤ 80 ms | Cannot be assessed cleanly with current peak detector — need `neurokit2`-grade PPG foot detector to disambiguate mispicks | **DEFERRED** — revisit in E1 with better PPG detector; not a blocker for v1 (model sees raw patches) |
| Patients ≥ 500 | ≥ 500 | **~381 extrapolated** (111 confirmed in 120/412 shards) | **FAIL (marginal)** |
| Missing rate ≤ 20% after windowing | ≤ 20% | 0.0% NaN, 0 empty segments in scanned sample | **PASS** |
| PTT range in [50, 500] ms | physiologic | P5 = 92 ms, P95 = 448 ms; range inside envelope | **PASS** |

## Interpretation of the patient-count "fail"

The research plan's `≥500 patients` threshold was set before we knew the HF mirror's exact population. **~381 patients over ~814 h** is:

- Plenty of **hours** for JEPA pretraining (AnyPPG trained on 100k+ h, ECG-JEPA on 1M+ records — but Weimann's public checkpoints achieve 0.945 AUC with much less; and PhysioJEPA's architectural claim is about **inductive bias on fixed data**, not scale — this is explicitly acknowledged in `RESEARCH_DEVELOPMENT.md` §8 Critic 2).
- **Marginal for AF sample-efficiency (E5b)** — we need ≥100 AF-positive and ≥100 AF-negative patients for the linear probe. With 381 patients this is tight but achievable if AF prevalence in MIMIC-IV ICU is ~10–20% (typical).
- Below threshold for population generalization — we should **pre-emptively frame the paper's N-scale** caveat explicitly (expected reviewer pushback).

### Action

- **Proceed with E1 and E2 on this dataset.** The architectural comparison E3 vs Baseline B (Δt vs Δt=0) is the core claim and is unchanged by N.
- Before E5b, **decide AF label source** (`EXPERIMENT_TRACKING.md` Day-3 decision): prefer joining to `mimic-iv-ecg` rhythm labels; if the AF-positive count is < 100, fall back to PTB-XL and reframe as a transfer-learning eval. This decision is now urgent.
- Keep **BIDMC as the documented fallback**; we do not switch now because BIDMC has only 53 patients (worse on the gate that failed) and no AF labels.

## Architectural implications for v1 (RESEARCH_DEVELOPMENT.md §2)

The spec assumed **12-lead ECG @ 500 Hz**. The HF mirror is **3-lead (primarily II/V/aVR) @ 250 Hz**. Required revisions, staged for Day 3 architecture lock:

1. **ECG encoder input**: single-lead II (93.7% coverage; drop records without it). Patch tokenisation collapses to 1D: 200 ms patches = 50 samples @ 250 Hz (instead of 2D `(leads=12, time=25)` @ 500 Hz). This is now architecturally identical to the 1D patch scheme used by ECG-JEPA's unimodal variant and does not affect the Δt claim.
2. **PPG encoder input**: already 1D single-channel at 125 Hz → 200 ms patches = 25 samples, exactly as specified.
3. **Sampling-rate symmetry**: both streams now satisfy *ECG_fs = 2 × PPG_fs*, matching the native MIMIC waveform format. No resampling needed.
4. **Downstream comparability to Weimann & Conrad (Baseline A)**: the 12-lead PTB-XL pretrained weights cannot be loaded directly. Baseline A must be retrained from scratch on single-lead II ECG (or we use PTB-XL only for the evaluation probe). Log this as a departure from the research doc's exact replication statement.

## Files written

- `docs/e0_report.json` — raw numbers
- `docs/e0_alignment.json` — foot-based alignment check numbers
- `docs/figures/ptt_histogram.png` — peak-based PTT (v1)
- `docs/figures/ptt_histogram_foot.png` — foot-based PTT (v2)
- `docs/figures/sanity_check.png` — 5 random 60-s aligned ECG+PPG overlays
- `scripts/e0_peek.py`, `scripts/e0_audit.py`, `scripts/e0_audit_v2.py`, `scripts/e0_alignment_check.py`

## Open follow-ups before E1 starts

1. Verify AF-positive count after joining to `mimic-iv-ecg` (Zack, Day 3 gate).
2. Swap PPG peak detector for `neurokit2.ppg_findpeaks` (better foot) so the E5a PTT probe can use a high-quality ground-truth signal.
3. Commit an architectural-revision note to `RESEARCH_DEVELOPMENT.md` §2 and `ARCHITECTURES_EXPLORATION.md` Architecture F §v1 — single-lead ECG, 250 Hz, 50-sample patches.