Exp Lens Pipeline Integrity

Pipeline Integrity Experimental Design Lens

Philosophical Mode: Integrity Primary Question: "Could data handling create optimistic bias?" Focus: Data Splits, Leakage Points, Preprocessing Order, Label Contamination, Pipeline Invariants

Arguments

/autoskillit:exp-lens-pipeline-integrity [context_path] [experiment_plan_path]

• context_path (optional positional arg 1) — Absolute path to a lens context file containing IV/DV tables, H0/H1 hypotheses, controlled variables, and success criteria. If provided, read this file before beginning analysis to obtain structured context. If omitted, discover context by exploring the CWD.
• experiment_plan_path (optional positional arg 2) — Absolute path to the full experiment plan. If provided, read for complete experimental methodology and design. If omitted, locate the experiment plan by exploring the CWD.

When to Use

• ML pipeline with train/test splits
• Preprocessing before or after splitting is ambiguous
• Feature engineering touching labels
• User invokes /autoskillit:exp-lens-pipeline-integrity or /autoskillit:make-experiment-diag pipeline

Critical Constraints

NEVER:

• Modify any source code files
• Do not litter the codebase with useless comments, TODO markers, or explanatory annotations — the skill output and diagram speak for themselves
• Create files outside {{AUTOSKILLIT_TEMP}}/exp-lens-pipeline-integrity/
• Run subagents in the background (run_in_background: true is prohibited)

ALWAYS:

• Classify every pipeline stage as pre-split or post-split

• Trace whether transforms are fitted on full data or train-only

• Flag all label-touching feature engineering steps

• Document pipeline invariants that guard against leakage

• BEFORE creating any diagram, LOAD the /autoskillit:mermaid skill using the Skill tool - this is MANDATORY

• If the Skill tool cannot be used (disable-model-invocation) or refuses this invocation, do NOT proceed with diagram creation. Abort this step and omit the diagram from output.

• Write output to {{AUTOSKILLIT_TEMP}}/exp-lens-pipeline-integrity/exp_diag_pipeline_integrity_{YYYY-MM-DD_HHMMSS}.md

• After writing the file, emit the structured output token as literal plain text with no markdown formatting on the token name (the adjudicator performs a regex match):

  diagram_path = /absolute/path/to/{{AUTOSKILLIT_TEMP}}/exp-lens-pipeline-integrity/exp_diag_pipeline_integrity_{...}.md
  

Analysis Workflow

Step 0: Parse optional arguments

If positional arg 1 (context_path) is provided and the file exists, read it to obtain IV/DV tables, H0/H1 hypotheses, controlled variables, and success criteria. If positional arg 2 (experiment_plan_path) is provided and exists, read the experiment plan for full methodology. Use this structured context as the foundation for Steps 1-5; skip the CWD exploration for these fields if the context file supplies them.

Step 1: Launch Parallel Exploration Subagents

Spawn Explore subagents to investigate:

Data Loading & Sources

• Find data ingestion code, raw data paths
• Look for: load, read, fetch, dataset, csv, parquet, download

Preprocessing & Transforms

• Find normalization, encoding, imputation steps
• Look for: transform, normalize, scale, encode, impute, clean, preprocess

Split Logic

• Find train/test/validation split code
• Look for: split, train_test, fold, cross_val, stratify, group

Feature Engineering

• Find feature creation, selection, extraction
• Look for: feature, extract, select, engineer, embed, vectorize

Model Training & Evaluation

• Find training loops and evaluation metrics
• Look for: fit, train, predict, evaluate, score, metric, loss

Step 2: Map the Complete Pipeline

Map the full pipeline from raw data to reported metrics. For each stage, determine:

• What information flows in?
• What information flows out?
• Could any downstream information leak upstream?
• Classify each stage as pre-split or post-split.

Step 3: Identify Leakage Risks

CRITICAL — Analyze Leakage Direction: For every data transformation:

• Does it use information from the full dataset (leakage risk) or only from the training partition?
• Is normalization fitted on train-only or all data?
• Are features derived from labels?

Assign a severity level (High/Medium/Low) to each leakage risk based on whether it would invalidate reported metrics.

Step 4: Create the Diagram

Use flowchart with:

Direction: LR (data flows left to right)

Subgraphs:

• RAW DATA
• PREPROCESSING
• SPLIT POINT
• TRAIN PATH
• TEST PATH
• EVALUATION

Node Styling:

• cli class: Data sources
• handler class: Transforms
• detector class: Split point and validation gates
• stateNode class: Data stores
• gap class: Leakage risks
• output class: Metrics and results
• phase class: Model training

Edge Labels: full data, train only, test only, LEAKAGE RISK

Step 5: Write Output

Write the diagram to: {{AUTOSKILLIT_TEMP}}/exp-lens-pipeline-integrity/exp_diag_pipeline_integrity_{YYYY-MM-DD_HHMMSS}.md (relative to the current working directory)

Output Template

# Pipeline Integrity Diagram: {Experiment Name}

**Lens:** Pipeline Integrity (Integrity)
**Question:** Could data handling create optimistic bias?
**Date:** {YYYY-MM-DD}
**Scope:** {What was analyzed}

## Pipeline Stages

| Stage | Input | Output | Pre/Post Split | Leakage Risk? |
|-------|-------|--------|----------------|---------------|
| {stage} | {input} | {output} | {Pre/Post} | {Yes/No} |

## Pipeline Diagram

```mermaid
%%{init: {'flowchart': {'nodeSpacing': 50, 'rankSpacing': 60, 'curve': 'basis'}}}%%
flowchart LR
    %% CLASS DEFINITIONS %%
    classDef cli fill:#1a237e,stroke:#7986cb,stroke-width:2px,color:#fff;
    classDef stateNode fill:#004d40,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef handler fill:#e65100,stroke:#ffb74d,stroke-width:2px,color:#fff;
    classDef phase fill:#6a1b9a,stroke:#ba68c8,stroke-width:2px,color:#fff;
    classDef newComponent fill:#2e7d32,stroke:#81c784,stroke-width:2px,color:#fff;
    classDef output fill:#00695c,stroke:#4db6ac,stroke-width:2px,color:#fff;
    classDef detector fill:#b71c1c,stroke:#ef5350,stroke-width:2px,color:#fff;
    classDef gap fill:#ff6f00,stroke:#ffa726,stroke-width:2px,color:#000;
    classDef integration fill:#c62828,stroke:#ef9a9a,stroke-width:2px,color:#fff;

    subgraph Raw ["RAW DATA"]
        SRC["Raw Dataset<br/>━━━━━━━━━━<br/>Source path<br/>N samples"]
    end

    subgraph Preprocessing ["PREPROCESSING"]
        PREP["Normalization / Encoding<br/>━━━━━━━━━━<br/>Fitted on: full/train?"]
        LEAK["Leaky Transform<br/>━━━━━━━━━━<br/>Uses full dataset"]
    end

    subgraph SplitPoint ["SPLIT POINT"]
        SPLIT["Train/Test Split<br/>━━━━━━━━━━<br/>Stratified? Ratio?"]
    end

    subgraph TrainPath ["TRAIN PATH"]
        TRAIN_DATA["Train Set<br/>━━━━━━━━━━<br/>N_train samples"]
        MODEL["Model Training<br/>━━━━━━━━━━<br/>fit()"]
    end

    subgraph TestPath ["TEST PATH"]
        TEST_DATA["Test Set<br/>━━━━━━━━━━<br/>N_test samples"]
    end

    subgraph Evaluation ["EVALUATION"]
        METRIC["Reported Metric<br/>━━━━━━━━━━<br/>score / loss"]
    end

    %% PIPELINE FLOWS %%
    SRC -->|"full data"| PREP
    PREP -->|"full data"| LEAK
    LEAK -.->|"LEAKAGE RISK"| METRIC
    PREP -->|"full data"| SPLIT
    SPLIT -->|"train only"| TRAIN_DATA
    SPLIT -->|"test only"| TEST_DATA
    TRAIN_DATA -->|"fit"| MODEL
    MODEL -->|"predict"| TEST_DATA
    TEST_DATA -->|"evaluate"| METRIC

    %% CLASS ASSIGNMENTS %%
    class SRC cli;
    class PREP handler;
    class LEAK gap;
    class SPLIT detector;
    class TRAIN_DATA,TEST_DATA stateNode;
    class MODEL phase;
    class METRIC output;

Color Legend:

Leakage Assessment

Pipeline Invariants

• All scalers/encoders fitted on train partition only
• Feature selection criteria computed from train partition only
• No label information used in feature construction
• Test set never seen by any fitting step

---

## Pre-Diagram Checklist

Before creating the diagram, verify:

- [ ] LOADED `/autoskillit:mermaid` skill using the Skill tool
- [ ] Using ONLY classDef styles from the mermaid skill (no invented colors)
- [ ] Diagram will include a color legend table

---

## Related Skills

- `/autoskillit:make-experiment-diag` - Parent skill for lens selection
- `/autoskillit:mermaid` - MUST BE LOADED before creating diagram
- `/autoskillit:exp-lens-reproducibility-artifacts` - For artifact completeness audit
- `/autoskillit:exp-lens-measurement-validity` - For outcome measurement validity