causal-mm 0.3.1

Time-series Double Machine Learning for Fuzzy Cognitive Maps

causal_mm

Time-series Double Machine Learning for Fuzzy Cognitive Maps (FCMs). Estimates directed edge strengths, bounds them to [-1, +1] for visualization, and writes everything back into a single fcm_project.json bundle.

Why this exists

• Small, time-dependent datasets: forward-chaining DML handles temporal dependence and avoids look-ahead bias.
• Prior knowledge first: uses your drawn FCM as structural prior; estimates "how strong" each edge is instead of discovering a spaghetti graph.
• Stakeholder-friendly outputs: scaled weights in [-1, +1], optional uncertainty, and an adjacency matrix block ready for downstream tools.

What it does

• Load one fcm_project.json that holds meta, model, timeseries, settings, estimates, and optional results.
• Per edge: build lagged controls, run forward-fold DML, compute tau_raw, then scale with tanh(alpha_scale * tau_raw) to [-1, +1].
• Optional block bootstrap: confidence intervals (ci_low, ci_high), standard errors, and sign-stability.
• Persist results back into the JSON (estimates + results.adjacency_matrix) and stamp meta.weights_computed_at / meta.weights_method.
• Refresh-only helper: recompute_adjacency rewrites just the stored adjacency matrix from existing estimates.
• Compare models: scripts/compare_mental_models.py reads the stored adjacency matrices and reports similarity + Generalized Distance Ratio (GDR).

Single-file project format (input/output)

Top-level keys in fcm_project.json:

• meta: project metadata; will be updated with computation timestamp/method.
• model: concepts (integer IDs) and edges (source, target, optional stakeholder_weight).
• timeseries: index array; data keyed by stringified concept IDs; arrays aligned to index.
• settings: passthrough config (currently optional, preserved).
• estimates: filled after estimation; keys like "src->tgt".
• results (optional): adjacency_matrix with concept_ids, matrix, weight_type. Rules: concept IDs are integers everywhere; JSON keys use their string form; all timeseries arrays share length; results.adjacency_matrix order must match concept_ids so comparison scripts align correctly.

Installation

From PyPI (recommended)

pip install causal-mm

With optional econml backends:

pip install causal-mm[econml]

From GitHub

pip install git+https://github.com/skp703/causal-mm.git

From source (development)

git clone https://github.com/skp703/causal-mm.git
cd causal-mm
pip install -e .

GUI

Launch the interactive visualizer (part of the deployed package):

causal-mm-gui

Or from the source repository:

streamlit run gui/app.py

Using conda

conda env create -f environment.yml
conda activate causal-mm
pip install -e .

CLI

causal-mm-run --input path/to/model.fcm_project.json --output path/to/output.fcm_project.json \
  --max-lag 3 --n-folds 3 --min-train-size 10 --alpha-scale 1.0 \
  --outcome-model ridge --treatment-model ridge \
  [--controls-selection all|connected] \
  [--bootstrap --n-bootstrap 200 --block-size 5 --bs-n-jobs 1 --random-state 123] \
  [--use-econml --econml-estimator linear_dml|causal_forest|ortho_forest]

Common variants:

• Smaller data, fewer controls: --controls-selection connected
• Uncertainty: add --bootstrap --n-bootstrap 500 --block-size 5
• Nonlinear nuisances: --outcome-model random_forest --treatment-model random_forest
• EconML backend: --use-econml --econml-estimator causal_forest

Defaults and how changing them affects results

• max_lag (default 3): higher captures longer memory but increases features and variance; lower is safer for very short series. Must keep min_train_size > max_lag.
• include_self_lags (default True, Python-only): turning off removes autoregressive terms for the target; speeds up and reduces variance but risks omitting genuine inertia.
• drop_initial_na (default True, Python-only): keeps only rows with full lag history; set False to retain earliest rows at the cost of introducing NaNs you must handle downstream.
• controls_selection (default all): all guards against omitted confounders; connected keeps only parents + self lags, reducing variance for tiny samples but assumes your graph is correct.
• outcome_model / treatment_model (default ridge): ridge is fast and stable. random_forest/gbm capture nonlinearity but can overfit small data. lasso yields sparse linear models; linear is plain OLS.
• n_folds (default 3): more folds reduce bias but shrink train windows; with short series prefer 3. If n_folds too high relative to length you will drop too much data.
• min_train_size (default 10): enforce enough history before the first fold. Increase for more stable nuisance models; decrease only if data are extremely short.
• alpha_scale (default 1.0): larger values push tanh toward +/-1 faster (good for visualization saturation); smaller keeps weights more linear and comparable across runs.
• random_state (default 123): controls fold splits and bootstrap resampling; change for robustness checks or unset in Python to allow full randomness.
• bootstrap (default off): enable to get tau_se, ci_low/high, sign_stability. Adds ~n_bootstrap times compute cost.
• n_bootstrap (default 200): more draws tighten CI at higher cost; for quick smoke tests use 50-100, for final reports 500+ if time allows.
• block_size (default 5): should match dependence length (e.g., 5 for annual data with medium persistence). Too small underestimates uncertainty; too large inflates variance.
• bs_n_jobs (default 1): increase for parallel bootstrap on multicore machines; beware memory use.
• use_econml (default False) and econml_estimator (default linear_dml): switch to leverage econml backends (causal_forest, ortho_forest) when you need built-in heterogeneity handling or alternative orthogonalization; compute cost rises notably for forests.

Changing options via CLI: pass the flag shown above. Changing Python-only options (include_self_lags, drop_initial_na, custom hyperparameters) requires constructing the config objects directly:

from causal_mm.config import LagConfig, MLModelConfig, DMLConfig

lag_cfg = LagConfig(max_lag=2, include_self_lags=False, drop_initial_na=True)
dml_cfg = DMLConfig(
    lag_config=lag_cfg,
    outcome_model=MLModelConfig("random_forest", {"n_estimators": 300, "random_state": 42}),
    treatment_model=MLModelConfig("random_forest", {"n_estimators": 300, "random_state": 42}),
    n_folds=4,
    min_train_size=20,
    alpha_scale=0.8,
    controls_selection="connected",
)

Python API

from pathlib import Path
from causal_mm.config import LagConfig, MLModelConfig, DMLConfig, BootstrapConfig
from causal_mm.pipeline import run_estimation

input_path = Path("data/models/my_model.fcm_project.json")
output_path = Path("data/models/my_model_with_estimates.fcm_project.json")

lag_cfg = LagConfig(max_lag=3)
dml_cfg = DMLConfig(
    lag_config=lag_cfg,
    outcome_model=MLModelConfig("ridge", {"alpha": 1.0}),
    treatment_model=MLModelConfig("ridge", {"alpha": 1.0}),
    n_folds=3,
    min_train_size=10,
    alpha_scale=1.0,
)
bs_cfg = BootstrapConfig(n_bootstrap=200, block_size=5, random_state=123, n_jobs=1)

run_estimation(
    input_path=input_path,
    output_path=output_path,
    dml_config=dml_cfg,
    bootstrap_config=bs_cfg,
)

How the estimator works (and why)

1. Lag all concepts up to max_lag; drop initial rows if requested to avoid NA leakage.
2. Select controls:
   • all (default) keeps lags of every concept (more robust to omitted variables).
   • connected keeps only parent + self lags (lower variance on tiny datasets).
3. Forward-chaining cross-fitting (n_folds, min_train_size) prevents peeking into the future.
4. Fit outcome and treatment models per fold; residualize; accumulate tau_raw = sum(Y_tilde * T_tilde) / sum(T_tilde^2).
5. Scale with tanh(alpha_scale * tau_raw) so weights stay in [-1, +1] for FCM visualization.
6. Uncertainty (optional): block bootstrap resamples contiguous blocks to preserve time dependence; reports tau_se, percentile ci_low/high, and sign_stability.
7. Metadata stamped: lag_used, n_obs, computed_at, method (dml or bootstrap-dml).

Outputs written to the project file

• estimates["src->tgt"]: tau_raw, tau_se, ci_low, ci_high, sign_stability, scaled_weight, n_obs, lag_used, status, error_message, computed_at, method.
• meta.weights_computed_at (UTC ISO8601) and meta.weights_method.
• results.adjacency_matrix: concept_ids (order) + matrix of scaled_weight values (weight_type set to scaled_weight).

Comparing multiple mental models

python scripts/compare_mental_models.py data/models/a.json data/models/b.json
python scripts/compare_mental_models.py data/models/*.json --format csv --output temp/compare.csv
python scripts/compare_mental_models.py data/models/*.json --format json --precision 6

Reads each file's results.adjacency_matrix, aligns by concept ID, and reports similarity and GDR. Use CSV/JSON for dashboards.

Metrics and diagnostics available in code

• generalized_distance_ratio (modified GDR) with tunable penalties.
• graph_complexity_metrics: N, edge count, density, hierarchy index.
• concept_centrality_metrics: in-degree, out-degree, total centrality.
• score_models / best_model: time-series CV for trying multiple ML models.
• compare_weights, weight_distance: adjacency-level comparisons.

Simulation

simulation.py builds an adjacency matrix from scaled_weight and simulates FCM dynamics using tanh, logistic, or identity activations.

Data requirements and pitfalls

• Timeseries arrays must align; concept IDs must match between model.edges and timeseries.data (stringified).
• min_train_size must exceed max_lag so folds have usable history.
• Block bootstrap is recommended whenever you care about uncertainty in time-dependent data.
• Cycles are fine: time lags break simultaneity (A_t depends on B_{t-1}, B_t on A_{t-1}).

Interactive GUI

The gui/ directory contains a Streamlit-based visualizer for inspecting, analyzing, and creating fcm_project.json files in the browser.

Install GUI dependencies

pip install causal-mm[gui]
# or
pip install -r gui/requirements.txt

Launch

streamlit run gui/app.py

Opens at http://localhost:8501 with pages for:

Page	What it shows
🕸️ Network	Interactive directed graph (colored nodes, weighted edges, adjacency heatmap)
⚖️ Weights	Edge-weight table, forest plot with 95% CI, sign-stability bars
📈 Time Series	Multi-line Plotly charts, z-score toggle, correlation matrix
📊 Metrics	Graph complexity KPIs, concept centrality, node-role distribution
✏️ Editor	Create/edit concepts, edges, import CSV time series, export JSON

See gui/README.md for full documentation.

Repository layout

• src/causal_mm/: core package (config, data, fcm, dml, bootstrap, metrics, io, pipeline, simulation).
• gui/: Streamlit interactive visualizer (network graph, weights, time series, metrics, editor).
• scripts/: utilities (e.g., compare_mental_models.py).
• tests/: unit tests.
• Packaging: pyproject.toml; console entry point causal-mm-run.

FAQ -- Why FCM instead of full causal discovery?

• Data efficiency: testing every possible edge on short time-series yields noise; using the FCM as prior constrains the search.
• Regularization through expertise: arrows you drew act as structural prior; estimator asks "how strong," not "does it exist."
• Trust: outputs stay interpretable and aligned with stakeholder mental models.

Tests

pip install -e .
pytest