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Causal Discovery: Part 2: Formal Definitions

2. Formal Definitions

Formal Definitions develops the part of causal discovery specified by the approved Chapter 22 table of contents. The treatment is causal, not merely predictive: the central objects are mechanisms, interventions, assumptions, and counterfactuals.

2.1 DAG and adjacency matrix $A$

Dag and adjacency matrix $a$ belongs to the canonical scope of Causal Discovery. The central move in causal inference is to distinguish a statistical relation from a claim about what would happen under an intervention.

For this subsection, the working scope is constraint-based, score-based, functional, invariant, and optimization-based causal graph discovery with clear assumptions and evaluation metrics. The mathematical objects are variables, mechanisms, graphs, interventions, and assumptions. A causal claim is incomplete until all five are visible.

$$h(W)=\operatorname{tr}(e^{W\odot W})-d=0.$$

The formula gives a compact handle on dag and adjacency matrix $a$. It should not be read as a purely algebraic identity. In causal inference, equations encode assumptions about mechanisms, missing variables, and which parts of the world remain stable under intervention.

Three examples of dag and adjacency matrix $a$:

1. A recommender team wants the causal effect of ranking a document higher, not merely the correlation between rank and clicks.
2. An LLM platform changes a safety policy and wants to estimate whether refusals changed because of the policy or because user prompts shifted.
3. A fairness auditor asks whether a proxy feature transmits an impermissible causal path into a model decision.

Two non-examples expose the boundary:

1. A high predictive coefficient is not a causal effect unless the graph and intervention assumptions justify it.
2. A plausible narrative produced by a language model is not a counterfactual unless it is grounded in a causal model.

The proof habit for dag and adjacency matrix $a$ is to name the graph operation. Conditioning restricts a distribution. Intervention replaces a mechanism. Counterfactual reasoning updates exogenous uncertainty from evidence, changes a mechanism, then predicts.

observed association:      P(Y | X=x)
intervention question:     P(Y | do(X=x))
counterfactual question:   P(Y_x | E=e)
discovery question:        which G could have generated P(V)?

In machine learning, dag and adjacency matrix $a$ is valuable because models are often deployed under interventions: ranking changes, policy changes, safety filters, tool-use gates, data collection changes, and human feedback loops. Prediction alone does not tell us which change caused which downstream behavior.

Notebook implementation will use synthetic SCMs and small graphs. This keeps the examples executable while preserving the conceptual split between identification and estimation.

Checklist for using dag and adjacency matrix $a$ responsibly:

• State the causal question before choosing a method.
• Draw or describe the assumed causal graph.
• Mark observed, latent, treatment, outcome, and adjustment variables.
• Separate intervention notation from conditioning notation.
• Decide whether the query is identifiable before estimating it.
• Report assumptions that cannot be tested from the observed data alone.
• Use ML as an estimation aid, not as a substitute for causal design.

This chapter follows the boundary set by Chapter 21. Statistical learning theory controls prediction error under distributional assumptions. Causal inference asks what happens when the distribution changes because something is done.

Modern AI systems make this distinction unavoidable. A foundation model can predict which action historically followed a context, but a decision system needs to know what would happen if it took a different action in that context.

Thus, dag and adjacency matrix $a$ is not an abstract philosophical add-on. It is a production and research tool for deciding which model, prompt, policy, feature, or intervention actually changed an outcome.

A final diagnostic question is whether the claim would survive a policy change. If the answer depends only on a historical correlation, it belongs in predictive modeling. If the answer depends on what mechanism is replaced and which paths remain active, it belongs in causal inference.

2.2 conditional independence oracle

Conditional independence oracle belongs to the canonical scope of Causal Discovery. The central move in causal inference is to distinguish a statistical relation from a claim about what would happen under an intervention.

For this subsection, the working scope is constraint-based, score-based, functional, invariant, and optimization-based causal graph discovery with clear assumptions and evaluation metrics. The mathematical objects are variables, mechanisms, graphs, interventions, and assumptions. A causal claim is incomplete until all five are visible.

$$\operatorname{SHD}(G,\widehat{G})=\#\{\text{edge additions, deletions, reversals}\}.$$

The formula gives a compact handle on conditional independence oracle. It should not be read as a purely algebraic identity. In causal inference, equations encode assumptions about mechanisms, missing variables, and which parts of the world remain stable under intervention.

Three examples of conditional independence oracle:

1. A recommender team wants the causal effect of ranking a document higher, not merely the correlation between rank and clicks.
2. An LLM platform changes a safety policy and wants to estimate whether refusals changed because of the policy or because user prompts shifted.
3. A fairness auditor asks whether a proxy feature transmits an impermissible causal path into a model decision.

Two non-examples expose the boundary:

1. A high predictive coefficient is not a causal effect unless the graph and intervention assumptions justify it.
2. A plausible narrative produced by a language model is not a counterfactual unless it is grounded in a causal model.

The proof habit for conditional independence oracle is to name the graph operation. Conditioning restricts a distribution. Intervention replaces a mechanism. Counterfactual reasoning updates exogenous uncertainty from evidence, changes a mechanism, then predicts.

observed association:      P(Y | X=x)
intervention question:     P(Y | do(X=x))
counterfactual question:   P(Y_x | E=e)
discovery question:        which G could have generated P(V)?

In machine learning, conditional independence oracle is valuable because models are often deployed under interventions: ranking changes, policy changes, safety filters, tool-use gates, data collection changes, and human feedback loops. Prediction alone does not tell us which change caused which downstream behavior.

Notebook implementation will use synthetic SCMs and small graphs. This keeps the examples executable while preserving the conceptual split between identification and estimation.

Checklist for using conditional independence oracle responsibly:

• State the causal question before choosing a method.
• Draw or describe the assumed causal graph.
• Mark observed, latent, treatment, outcome, and adjustment variables.
• Separate intervention notation from conditioning notation.
• Decide whether the query is identifiable before estimating it.
• Report assumptions that cannot be tested from the observed data alone.
• Use ML as an estimation aid, not as a substitute for causal design.

This chapter follows the boundary set by Chapter 21. Statistical learning theory controls prediction error under distributional assumptions. Causal inference asks what happens when the distribution changes because something is done.

Modern AI systems make this distinction unavoidable. A foundation model can predict which action historically followed a context, but a decision system needs to know what would happen if it took a different action in that context.

Thus, conditional independence oracle is not an abstract philosophical add-on. It is a production and research tool for deciding which model, prompt, policy, feature, or intervention actually changed an outcome.

A final diagnostic question is whether the claim would survive a policy change. If the answer depends only on a historical correlation, it belongs in predictive modeling. If the answer depends on what mechanism is replaced and which paths remain active, it belongs in causal inference.

2.3 Markov equivalence class

Markov equivalence class belongs to the canonical scope of Causal Discovery. The central move in causal inference is to distinguish a statistical relation from a claim about what would happen under an intervention.

For this subsection, the working scope is constraint-based, score-based, functional, invariant, and optimization-based causal graph discovery with clear assumptions and evaluation metrics. The mathematical objects are variables, mechanisms, graphs, interventions, and assumptions. A causal claim is incomplete until all five are visible.

$$X_j=f_j(\operatorname{pa}_j)+N_j,\qquad N_j \perp\!\!\!\perp \operatorname{pa}_j.$$

The formula gives a compact handle on markov equivalence class. It should not be read as a purely algebraic identity. In causal inference, equations encode assumptions about mechanisms, missing variables, and which parts of the world remain stable under intervention.

Three examples of markov equivalence class:

1. A recommender team wants the causal effect of ranking a document higher, not merely the correlation between rank and clicks.
2. An LLM platform changes a safety policy and wants to estimate whether refusals changed because of the policy or because user prompts shifted.
3. A fairness auditor asks whether a proxy feature transmits an impermissible causal path into a model decision.

Two non-examples expose the boundary:

1. A high predictive coefficient is not a causal effect unless the graph and intervention assumptions justify it.
2. A plausible narrative produced by a language model is not a counterfactual unless it is grounded in a causal model.

The proof habit for markov equivalence class is to name the graph operation. Conditioning restricts a distribution. Intervention replaces a mechanism. Counterfactual reasoning updates exogenous uncertainty from evidence, changes a mechanism, then predicts.

observed association:      P(Y | X=x)
intervention question:     P(Y | do(X=x))
counterfactual question:   P(Y_x | E=e)
discovery question:        which G could have generated P(V)?

In machine learning, markov equivalence class is valuable because models are often deployed under interventions: ranking changes, policy changes, safety filters, tool-use gates, data collection changes, and human feedback loops. Prediction alone does not tell us which change caused which downstream behavior.

Notebook implementation will use synthetic SCMs and small graphs. This keeps the examples executable while preserving the conceptual split between identification and estimation.

Checklist for using markov equivalence class responsibly:

• State the causal question before choosing a method.
• Draw or describe the assumed causal graph.
• Mark observed, latent, treatment, outcome, and adjustment variables.
• Separate intervention notation from conditioning notation.
• Decide whether the query is identifiable before estimating it.
• Report assumptions that cannot be tested from the observed data alone.
• Use ML as an estimation aid, not as a substitute for causal design.

This chapter follows the boundary set by Chapter 21. Statistical learning theory controls prediction error under distributional assumptions. Causal inference asks what happens when the distribution changes because something is done.

Modern AI systems make this distinction unavoidable. A foundation model can predict which action historically followed a context, but a decision system needs to know what would happen if it took a different action in that context.

Thus, markov equivalence class is not an abstract philosophical add-on. It is a production and research tool for deciding which model, prompt, policy, feature, or intervention actually changed an outcome.

A final diagnostic question is whether the claim would survive a policy change. If the answer depends only on a historical correlation, it belongs in predictive modeling. If the answer depends on what mechanism is replaced and which paths remain active, it belongs in causal inference.

2.4 CPDAG

Cpdag belongs to the canonical scope of Causal Discovery. The central move in causal inference is to distinguish a statistical relation from a claim about what would happen under an intervention.

For this subsection, the working scope is constraint-based, score-based, functional, invariant, and optimization-based causal graph discovery with clear assumptions and evaluation metrics. The mathematical objects are variables, mechanisms, graphs, interventions, and assumptions. A causal claim is incomplete until all five are visible.

$$A_{ij}=1 \iff X_i \to X_j.$$

The formula gives a compact handle on cpdag. It should not be read as a purely algebraic identity. In causal inference, equations encode assumptions about mechanisms, missing variables, and which parts of the world remain stable under intervention.

Three examples of cpdag:

1. A recommender team wants the causal effect of ranking a document higher, not merely the correlation between rank and clicks.
2. An LLM platform changes a safety policy and wants to estimate whether refusals changed because of the policy or because user prompts shifted.
3. A fairness auditor asks whether a proxy feature transmits an impermissible causal path into a model decision.

Two non-examples expose the boundary:

1. A high predictive coefficient is not a causal effect unless the graph and intervention assumptions justify it.
2. A plausible narrative produced by a language model is not a counterfactual unless it is grounded in a causal model.

The proof habit for cpdag is to name the graph operation. Conditioning restricts a distribution. Intervention replaces a mechanism. Counterfactual reasoning updates exogenous uncertainty from evidence, changes a mechanism, then predicts.

observed association:      P(Y | X=x)
intervention question:     P(Y | do(X=x))
counterfactual question:   P(Y_x | E=e)
discovery question:        which G could have generated P(V)?

In machine learning, cpdag is valuable because models are often deployed under interventions: ranking changes, policy changes, safety filters, tool-use gates, data collection changes, and human feedback loops. Prediction alone does not tell us which change caused which downstream behavior.

Notebook implementation will use synthetic SCMs and small graphs. This keeps the examples executable while preserving the conceptual split between identification and estimation.

Checklist for using cpdag responsibly:

• State the causal question before choosing a method.
• Draw or describe the assumed causal graph.
• Mark observed, latent, treatment, outcome, and adjustment variables.
• Separate intervention notation from conditioning notation.
• Decide whether the query is identifiable before estimating it.
• Report assumptions that cannot be tested from the observed data alone.
• Use ML as an estimation aid, not as a substitute for causal design.

This chapter follows the boundary set by Chapter 21. Statistical learning theory controls prediction error under distributional assumptions. Causal inference asks what happens when the distribution changes because something is done.

Modern AI systems make this distinction unavoidable. A foundation model can predict which action historically followed a context, but a decision system needs to know what would happen if it took a different action in that context.

Thus, cpdag is not an abstract philosophical add-on. It is a production and research tool for deciding which model, prompt, policy, feature, or intervention actually changed an outcome.

A final diagnostic question is whether the claim would survive a policy change. If the answer depends only on a historical correlation, it belongs in predictive modeling. If the answer depends on what mechanism is replaced and which paths remain active, it belongs in causal inference.

2.5 acyclicity constraint

Acyclicity constraint belongs to the canonical scope of Causal Discovery. The central move in causal inference is to distinguish a statistical relation from a claim about what would happen under an intervention.

For this subsection, the working scope is constraint-based, score-based, functional, invariant, and optimization-based causal graph discovery with clear assumptions and evaluation metrics. The mathematical objects are variables, mechanisms, graphs, interventions, and assumptions. A causal claim is incomplete until all five are visible.

$$h(W)=\operatorname{tr}(e^{W\odot W})-d=0.$$

The formula gives a compact handle on acyclicity constraint. It should not be read as a purely algebraic identity. In causal inference, equations encode assumptions about mechanisms, missing variables, and which parts of the world remain stable under intervention.

Three examples of acyclicity constraint:

1. A recommender team wants the causal effect of ranking a document higher, not merely the correlation between rank and clicks.
2. An LLM platform changes a safety policy and wants to estimate whether refusals changed because of the policy or because user prompts shifted.
3. A fairness auditor asks whether a proxy feature transmits an impermissible causal path into a model decision.

Two non-examples expose the boundary:

1. A high predictive coefficient is not a causal effect unless the graph and intervention assumptions justify it.
2. A plausible narrative produced by a language model is not a counterfactual unless it is grounded in a causal model.

The proof habit for acyclicity constraint is to name the graph operation. Conditioning restricts a distribution. Intervention replaces a mechanism. Counterfactual reasoning updates exogenous uncertainty from evidence, changes a mechanism, then predicts.

observed association:      P(Y | X=x)
intervention question:     P(Y | do(X=x))
counterfactual question:   P(Y_x | E=e)
discovery question:        which G could have generated P(V)?

In machine learning, acyclicity constraint is valuable because models are often deployed under interventions: ranking changes, policy changes, safety filters, tool-use gates, data collection changes, and human feedback loops. Prediction alone does not tell us which change caused which downstream behavior.

Notebook implementation will use synthetic SCMs and small graphs. This keeps the examples executable while preserving the conceptual split between identification and estimation.

Checklist for using acyclicity constraint responsibly:

• State the causal question before choosing a method.
• Draw or describe the assumed causal graph.
• Mark observed, latent, treatment, outcome, and adjustment variables.
• Separate intervention notation from conditioning notation.
• Decide whether the query is identifiable before estimating it.
• Report assumptions that cannot be tested from the observed data alone.
• Use ML as an estimation aid, not as a substitute for causal design.

This chapter follows the boundary set by Chapter 21. Statistical learning theory controls prediction error under distributional assumptions. Causal inference asks what happens when the distribution changes because something is done.

Modern AI systems make this distinction unavoidable. A foundation model can predict which action historically followed a context, but a decision system needs to know what would happen if it took a different action in that context.

Thus, acyclicity constraint is not an abstract philosophical add-on. It is a production and research tool for deciding which model, prompt, policy, feature, or intervention actually changed an outcome.

A final diagnostic question is whether the claim would survive a policy change. If the answer depends only on a historical correlation, it belongs in predictive modeling. If the answer depends on what mechanism is replaced and which paths remain active, it belongs in causal inference.