Causal Identifiability

Protein-molecule virtual screening is increasingly cast as a problem of representation learning in a shared embedding space. Existing methods rely on dense holistic alignment, entangling invariant binding determinants with nuisance correlations and limiting transfer to new targets. It has been noted that binding in protein-molecule systems involves sparse cross-modality interactions: binding is governed by a small contact interface and a few decisive local interactions (e.g., hydrogen bonds, hydrophobic contacts, and salt bridges) rather than the global structures of the protein and molecule. We hypothesize that uncovering and leveraging sparse interaction patterns is critical for generalization beyond the training data, as these patterns are reusable and expected to improve performance across different scenarios. In this paper, we aim to identify and leverage sparse interaction patterns, and verify our hypothesis. Since the training data contain only observed binding pairs, we formalize this prior via a V-structure causal model under Heckman-style selection, and establish three theoretical results: (i) the latent concepts of interacting proteins and molecules are not identifiable without appropriate sparsity constraints; (ii) these concepts and their sparse interactions are component-wise identifiable under structural sparsity conditions; and (iii) a low-rank relaxation of these conditions yields subspace identifiability of the concepts and interactions. Inspired by these principles, we propose CausalBind with three implementation variants. Extensive experiments on DUD-E and LIT-PCBA benchmarks show that all variants consistently outperform strong retrieval baselines, with the largest gains on LIT-PCBA early enrichment, and further generalize to target- and scaffold-level out-of-distribution splits. Code is available at https://github.com/lokali/CausalBind.

Causal representation learning (CRL) is the process of recovering causally-related latent variables from high-dimensional observations. As a label-free inference method, CRL is particularly attractive for applications where data labels are unavailable or impractical to obtain. While there has been significant progress in understanding the identifiability guarantees of CRL, such guarantees often hold under highly stylized assumptions, which temper the direct application to real-world problems. This paper has a two-fold objective for interventional CRL. First, it establishes identifiability guarantees for substantially weaker interventional assumptions, resulting in block disentanglement of the causal variables, where the block structure depends on the realistically available intervention mechanisms. Secondly, the block disentanglement framework is used for embodied visual state estimation, in which the objective is to recover the latent physical variables of a robotic system directly from visual data (images and videos) without labeled data. These two components are critically complementary. The block disentanglement theory delineates identifiability guarantees under weakened assumptions, and the application demonstrates that the resulting objective remains effective in a controlled embodied setting despite further assumption violations, providing a theory-to-practice bridge needed to translate the promise of label-free CRL into practical problems.

Causal representation learning aims to discover robust features by exploiting the causal structure underlying data generation. Existing methods require specifying the causal structure a priori, yet different structures demand fundamentally incompatible invariance constraints, and misspecification leads to representations that discard predictive information. We introduce SaCRL, a framework that jointly identifies the causal structure and learns the corresponding invariant representation without prior structural knowledge. Our approach formulates structure selection as a soft optimization over candidate invariances using HSIC-based violation metrics, with adaptive weights that automatically concentrate on the achievable structure. We provide theoretical guarantees for structure identification, including under random-feature approximation, invariance satisfaction, and out-of-distribution generalization. Empirically, SaCRL recovers the true structure on synthetic and semi-synthetic Bayesian-network benchmarks, outperforms fixed-invariance baselines on Colored MNIST, achieves state-of-the-art accuracy on three DomainBed benchmarks (PACS, VLCS, OfficeHome), and degrades gracefully under structural misspecification and limited environment diversity. Code is available at: https://github.com/ArmanBehnam/sacrl.

Causal action verifiers gate an agent's state-changing tool calls by checking whether each proposed intervention is identifiable against a committed action-state graph, and they issue a certificate that carries the identification argument and a one-sided lower confidence bound. One such verifier, CIVeX, reports zero false executions on a confounded tool-use benchmark. We red-team it by corrupting only the committed graph. Omitting a single bidirected edge takes it from zero false executions to 15.3% at the benchmark's published confounding strength, with 91% of its executions harmful and utility falling from +2.27 to +0.35. Reversing one arrowhead, so that a mediator is committed as a confounder, gives 48.9% false executions and no correct ones. Every one of these actions carries an internally valid certificate. An attestation step that tests each observationally certified execution against a bounded randomised sample detected both attacks, with 2 false alarms in 555 executions on a truthful graph; refusing what fails the test, or cannot be tested, gave zero false executions in every setting we measured. It does not restore beneficial execution: at the published strength 97.1% of beneficial actions are still never executed, because the same misspecification rejects them before attestation runs. Those rejections carry certificates too, and auditing them works, but its cost scales with the number of rejections rather than the number of executions. Recovering safety costs 127 experiments per 1,050 actions; recovering the lost value costs 614 more, at which point the audited verifier makes the honest graph's decisions on every instance and spends exactly its experiment budget. An audit that inspects only executions protects against wrongful action. Wrongful inaction has to be paid for separately.

Count data pose a challenge for score-matching-based causal discovery: derivatives are unavailable, and simply replacing them with finite differences does not generally suffice for causal discovery. We generalize SCORE's constant-curvature criterion (Rolland et al., 2022) by conditioning on the node's value, yielding the conditional curvature score (CCS) for ordering. We also extend curvature-based parent recovery through the off-diagonal curvature score (OCS), enabling directed acyclic graph (DAG) recovery with both scores constructed from score functions for continuous data and concrete scores for counts. In the bivariate setting, zero CCS exactly characterizes a semiparametric generalized linear model (GLM) conditional form in which the conditional family need not be specified in advance, unlike in classical GLMs. For bivariate semiparametric GLM DAGs under our regularity condition, canonical-parameter nonlinearity is necessary and sufficient for identifiability. In multivariate DAGs, this nonlinearity enables DAG recovery through CCS and OCS. Our framework identifies a new class of semiparametric GLM DAGs that strictly contains the nonlinear Gaussian ANM class identified by SCORE. We introduce DISCO (DIscrete SCOre), a count-DAG recovery algorithm that estimates CCS and OCS using discrete diffusion. Experiments demonstrate accurate DAG recovery across Poisson, negative binomial, binomial, and mixed-family settings, as well as scalability to 1,000-node DAGs on a single GPU.

We study causal structure learning from observational data in linear Gaussian structural causal models in the presence of directed cycles and an unknown number of exogenous latent confounders, bounded by a given maximum. We derive the covariance of the observed variables and introduce marginal quasi-equivalence, which characterizes when different causal models share a full-dimensional subset of the observational distributions they can generate. We formulate structure learning as minimization of the Gaussian negative log-likelihood with a logarithmically scaled complexity penalty that counts directed edges and latent variables. For a fixed number of observed variables and a fixed upper bound on latent variables, we establish consistency of global score minimizers up to marginal quasi-equivalence under algebraic faithfulness, structural minimality, and model-overlap assumptions. We parameterize the inclusion of directed edges and candidate latent variables using Bernoulli gates, whose continuous probabilities are optimized jointly with the structural coefficients. Averaging the penalized negative log-likelihood over these gates yields an objective with a closed-form differentiable complexity penalty. We prove that this expected objective has the same global infimum as the corresponding discrete structure-learning objective. Experimental results show that our approach achieves lower recovery error than previous methods in several experimental settings.

A wide range of methods have been proposed, including physics-informed neural networks, which are powerful but do not guarantee identifiability of the dynamics, symbolic regression, which requires a set of precomputed operations, and causal discovery, which is more principled but usually relies on strong assumptions that physical systems may violate. In this work, we develop a theory-grounded method and prove that under a set of permissive assumptions, the structural drivers and drift of stochastic delayed differential equations are identifiable. Our method outperforms others on a benchmark for driver identifiability, and on a second benchmark to evaluate physical consistency of the learned dynamics.

Supervised causal discovery learns to infer causal structure for a new dataset from training datasets paired with structural labels. These training pairs are typically simulated, making the simulator both a source of supervision and a carrier of assumptions about causal graphs, mechanisms, and noise. Understanding the resulting predictions therefore requires examining how these assumptions supplement the information available in observational data, which may be compatible with multiple causal graphs. This paper examines that relationship across representative methods available through June 2026. We organize these methods by prediction target, prediction granularity, encoder, structural decoder, and training regime to relate what each method predicts to how it uses data and simulator-based supervision. Using this framework, we distinguish two questions: whether the target is identifiable under the assumed model class, and whether a trained predictor generalizes beyond its training distribution. Restrictions on mechanisms and noise can make otherwise ambiguous causal directions identifiable, but predictive accuracy under those restrictions does not establish transfer when they change. This distinction motivates evaluation that matches metrics to the identifiable graph target and tests changes in graphs, mechanisms, and noise between training and deployment. Extending such evaluation to real data also requires documenting the external causal evidence and uncertainty behind benchmark reference graphs. Together, these analyses guide method comparison and identify open questions in transfer, test-time adaptation, and uncertainty assessment.

Causal discovery from observational data is a fundamental yet challenging task in scientific research. While existing approaches are primarily based on conditional independence tests, structure scores, or restrictive functional assumptions, we propose Decoupled Causal Discovery (DCD), a novel decoupling-based perspective that does not rely on these methodologies. DCD directly identifies the Markov boundary (MB) by decoupling non-target variables via weighting functions, such that only variables within the MB preserve dependence with the target under the decoupled distribution. Building on this, DCD iteratively constructs the Completed Partially Directed Acyclic Graph (CPDAG) by exploiting structural asymmetries within the MBs. We establish the theoretical identifiability, soundness, and completeness of DCD. Empirical evaluations demonstrate that DCD achieves strong performance, particularly excelling in challenging noise regimes.

Causal discovery from observational data is fundamental to statistics and machine learning, yet determining causal direction without interventions necessitates structural assumptions. Existing identifiability research primarily focuses on continuous variables under additive noise models, often neglecting mixed datasets containing ordinal scales, counts, and continuous measurements. This paper investigates causal discovery in Directed Acyclic Graphs (DAGs) where nodes follow either an ordinal distribution (via an ordered logit model) or a regular one-parameter exponential family distribution. We prove that the edge direction between an ordinal and an exponential family node is distributionally identifiable for generic parameter values. Our findings generalize previous Ordinal-Poisson results to the broader exponential family. Computationally, we introduce a score-based exhaustive search and a masked continuous optimization framework using DAGMA for larger graphs. Numerical results validate the theory, recovering edge orientations within a Markov equivalence class that are unidentifiable under classical structural equation models.

We study the problem of recovering the parameters of a multivariate Ornstein-Uhlenbeck (OU) process from steady-state observational and interventional data. In many applications, such as large-scale gene perturbation experiments, only stationary "snapshot" measurements are available, making standard stochastic differential equation estimation methods that rely on time-series trajectories inapplicable. We first establish an identifiability result: one intervention per strongly connected component (SCC) of the drift graph suffices to recover all OU process parameters generically up to a global scaling factor. This holds provided that the SCC condensation graph is connected with a single root and certain spectral nondegeneracy assumptions hold. We propose a recursive learning algorithm that orders SCCs topologically and, for each component, isolates its marginal dynamics and solves a linear system derived from the steady-state moment equations, leveraging parameters recovered for upstream components. Building on this theoretical foundation, we propose a regularized least-squares estimator that jointly minimizes residuals of the steady-state mean and covariance equations across observational and interventional data. Experimental results validate our theoretical findings in recovering parameters of the underlying OU process.

The problem of identifiability in linear parametric models (LPMs) whose nodes follow either an ordered logit model or a regular one-parameter exponential family is evaluated. The results go beyond classical structural equation models as well as results for nodes with observations from a homogeneous family of distributions. The main result establishes that the orientation of every edge joining an ordinal node to an exponential-family node is identifiable from the joint distribution alone at every parameter value, provided the ordinal node has at least three categories and the exponential-family node at least three points of support, with no restriction on the sufficient statistic. Converses show that both requirements are necessary: the three-category requirement is binding only for affine sufficient statistics, and the three-point requirement is binding under the canonical link. The guarantee extends to orienting every such mixed ordinal-exponential family edge of a given $d$-node undirected skeleton. Numerical experiments illustrate the theoretical results by successfully separating orientations within a Markov equivalence class, which are indistinguishable by conditional independence alone.

We propose Low-Rank Quantile Surfaces (LRQS), a bivariate causal model in which, in the causal direction, an unknown monotone transformation of the conditional quantile surface admits a low-rank functional decomposition. LRQS subsumes location-scale noise models and post-nonlinear heteroscedastic noise models, while allowing multiple quantile bases to represent changes beyond location-scale effects. We prove generic identifiability of LRQS: the transformed quantile surface is low rank in the causal direction, whereas reverse representability under the corresponding constraints occurs only for exceptional, fine-tuned cause marginals. We provide a simple-yet-powerful causal score using a nonparametric fitting procedure that alternates between rank-constrained approximation of discretized quantile surfaces and isotonic estimation of the unknown monotone transformation. Experiments on synthetic mechanisms with higher-rank distributional shape variation and strong nonlinear distortions, together with standard bivariate benchmarks, show that LRQS is especially effective when conditional distributional shape or observation distortion goes beyond existing location-scale assumptions.

In the natural sciences, symmetries and cause-effect relationships are ubiquitous. Yet for complex machine-learning tasks, like world-modeling in reinforcement learning, they appear difficult to harness. We propose a formal description of statistical systems based on symmetries in data leaving causal mechanisms invariant. The result is an abstract, simple and general mathematical language for causal reasoning. This paper provides formal descriptions of models and queries, setting up this language, and the formal infrastructure and strategies for their mathematically rigorous identification from data within this formalism. This approach reproduces and matches standard theoretical results on IID data and transport of experimental and non-experimental data. But its main purpose is to unify and substantially extend the scope of causal reasoning, in going beyond IID data and in approaching complex causal queries not captured by do- or soft-interventions. This new perspective on causally relevant aspects of data-modeling additionally sheds new light on well-known structures like c-components or hedges but also includes aspects of missing data and is inherently well-suited for the description of transfer and robustness properties.

Differentiable causal discovery methods increasingly encode expert priors as forbidden-edge constraints enforced by an Augmented Lagrangian (ALM) penalty, on the assumption that a data-adaptive relaxation mechanism will discount and eventually override a rule the data consistently contradicts. We show this design, which we call \emph{guide, not bind}, fails for two independent, precisely characterized reasons, and that directly repairing both restores it only partially. First, sequential penalty-ramping ALM suppresses a wrongly-forbidden true edge before any counterfactual check can detect it: we give three necessary conditions any adaptive relaxation must satisfy to avoid this (Proposition~\ref{prop:conditions}), prove that DADU---the natural relaxation rule this paper introduces as the object of study---violates all three (Corollary~\ref{cor:dadu_failure}), and confirm the failure across 3{,}072 training runs spanning graphs from 4 to 32 nodes, where a single wrong prior suppresses a true edge in 87--97% of trials under DADU. Second, and independent of any fix to the mechanism, we prove in closed form that the standard correlation-matching objective ties a true edge and its reverse to an identical cost of exactly $2r^2$ (Lemma~\ref{lem:tie}), not because the underlying equal-variance model is unidentifiable, but because normalizing to correlation discards exactly the variance information that would make it identifiable; covariance matching instead separates the two directions by a provable margin of at least $w_0^4$ (Lemma~\ref{lem:separation}).

Short observational pricing panels often contain many data points but very few actual price changes. This paper shows that this sparsity creates a hidden source of error that standard statistical methods miss. When estimating price effects, most of the uncertainty does not come from sample size within a panel, but from the specific history of price movements observed. Standard confidence intervals fail because they only measure variation within the panel, ignoring this broader design-level error. Using simulations, we find that this cross-design variation accounts for most of the estimation error, causing standard methods to significantly understate uncertainty. First, we show that cross-design error decreases predictably as the total volume of price variation increases. Second, adding more data from regions that share the same price trends does not fix the issue; true precision improves only when combining data across units with independent price trajectories. Third, applying a simple variance-component adjustment across independently priced units restores accurate statistical coverage. We confirm these findings in real-world store scanner data, showing that products and pricing zones behave as if they have far fewer independent price movements than their raw counts suggest. Ultimately, reliable inference in passive pricing data requires genuine, independent variation, which can be achieved through controlled regional price testing.

LLM benchmark scores can be precise even when the observation protocol does not identify the behavioral property they are intended to measure. In a controlled, solver-grounded setting, we formalize a protocol-level identifiability audit over a finite behavioral policy class: given policies H, observation support O, and estimand $τ$, we test whether O separates every pair with different $τ$. The audit requires zero model calls and resolves our diagnostic case: base-only observation collapses seven frozen deterministic policies into one equivalence class; full support yields seven classes and no cross-estimand collisions; every leave-one-out support retains a constructive collision witness. Empirically, both constrained-generation variants have pair-validity 1.0, yet base accuracy and selective-response fidelity diverge - 0.620 versus 0.324 across six balanced oracle-transition directions (cluster-bootstrap 95% CI [0.600, 0.642] vs. [0.304, 0.345]) - and the gap recurs on a second deterministic source (0.646 vs. 0.331). The audit also synthesizes a minimum identifying support $O^*$ for the frozen policy class: two cells instead of the full 36-cell tensor. This case shows how evaluation-design validity can be checked structurally before model inference and why base correctness does not determine intervention-response fidelity.

Probabilities of causation (PoCs) characterize individual causal responses that cannot be directly observed and therefore generally require partial identification. Tian and Pearl first derived theoretically sharp bounds for binary PoCs, including the probability of necessity (PN), the probability of sufficiency (PS), and the probability of necessity and sufficiency (PNS). Mueller et al. subsequently tightened the bounds for binary PNS by incorporating causal information encoded in covariates and mediators. More recently, Li and Pearl, as well as Shu et al., extended PoCs to multivalued settings and derived corresponding theoretical bounds. These developments naturally raise the question of whether additional causal knowledge can further tighten the bounds in multivalued settings. This paper addresses this question by deriving tighter bounds for multivalued PoCs through the incorporation of causal information encoded in covariates and mediators. We illustrate the theoretical results with toy examples, while simulation studies further demonstrate that the proposed bounds are tighter than existing nonbinary bounds.

The Relativity of Causal Knowledge (RCK) explains how a network of agents with different structural causal models can exchange causal knowledge through a shared interventionally consistent abstraction, or backbone. We ask the prior identification question that this transport mechanism presupposes: when is that backbone determined by the agents' private causal knowledge? In the basic two-agent common-effect case, two private causes influence one shared outcome and each agent identifies only the single-cause causal marginal relevant to its own perspective. We show that, under standard compatibility, non-degeneracy, and local overlap assumptions, those local causal marginals do not identify a unique backbone. Infinitely many joint intervention kernels can induce exactly the same private reports while disagreeing on joint interventions. We then give a conditional recovery result. Additive separability removes the hidden interaction degree of freedom, but observational residual summaries remain insufficient. Identification becomes possible when agents communicate causally identified response functions. An education value-added example illustrates why this is first a communication problem, and only then a policy-composition problem.

Probabilistic logic programming is a formalism of statistical relational artificial intelligence that supports causal queries, including interventions from outside the system. When the structure of a probabilistic logic program is learned from data, however, only probabilistic information is used, and a single probability distribution may be compatible with several causal orders. This leads to ambiguity in interventional reasoning, raising the question of when the causal order is uniquely determined by the distribution. Exploiting the relationship between acyclic probabilistic logic programs and Bayesian networks, we derive conditions under which the probabilistic information encoded in a program determines a unique causal order. We also incorporate constraints arising from relational structure by taking into account prescribed sets of causal symmetries induced by the underlying relational vocabulary. The result is a method for verifying when a learned probabilistic logic program supports well-defined intervention semantics.

Generative models can reproduce an observational distribution while encoding an incorrect causal structure. We study a sequential game in which a structural causal generator proposes observational and interventional distributions, while an adversarial experimentalist selects interventions intended to maximally falsify the generator. The discriminator is therefore not merely a real-versus-synthetic classifier: it is indexed by an intervention and tests whether the generator reproduces the corresponding post-intervention law. We introduce Adversarial Causal Intervention Falsification (ACIF), formulate oracle and implementable versions of the game, and distinguish three objects that are often conflated: observational fit, interventional equivalence over an admissible query class, and point identification of a structural causal model. For finite model and intervention classes, we prove: (i) an exact reduction of the adversarial objective to a worst-intervention integral probability metric; (ii) identification up to interventional equivalence, with point identification under a separating intervention family; (iii) existence of mixed-strategy equilibria; (iv) finite-sample uniform convergence and margin-based model-selection guarantees; and (v) a logarithmic elimination guarantee for a disagreement-driven sequential design under a balanced-separation condition. We also give a complete linear-Gaussian example in which two observationally indistinguishable causal directions are separated by a single well-chosen intervention. The framework clarifies what an adversarial causal discriminator can and cannot certify, and provides a principled bridge between causal generative modeling, active causal discovery, and experimental design.

Causal inference has traditionally centered on scalar outcomes: whether a patient recovers, how much a worker earns, or how many visits a website receives. Modern studies increasingly ask causal questions about outcomes with richer form, such as clinical notes, open-ended survey responses, and images. A hospital may want to know how an AI documentation tool changes the notes physicians write, or how a nurse training program alters what patients say in survey responses. For such outcomes, the usual average treatment effect is ill-defined: one cannot meaningfully subtract one text or image from another. To this end, we propose a causal query for unstructured outcomes. The key idea is to learn what features of the outcome are most causally affected by the treatment, which we call the maximally contrasting feature (MCF). To estimate the MCF, we learn a feature-scoring function that maps each outcome to a scalar and exposes the sharpest contrast between treated and control potential outcomes. We develop identification conditions and estimation algorithms for this query, and extend it to heterogeneous effects by allowing the feature-scoring function to depend on observed covariates. We also handle settings where both the treatment and the outcome are unstructured. Empirical studies on text and images show that the algorithm recovers salient aspects of an outcome changed by a treatment.

Estimating causal effects from real-world spatiotemporal data is challenging due to hidden confounders and interference. Standard causal identification methods assume conditional exchangeability given observed covariates, which fails whenever hidden confounders affect both treatment and outcomes - a common setting in domains such as climate, environmental policy, epidemiology, and regional economics. In this paper, we propose a novel spatiotemporal proximal causal inference framework that extends proximal identification theory to spatiotemporal settings. The proposed method jointly captures local and neighborhood-level confounding information by introducing treatment- and outcome-inducing proxies, and we derive a spatiotemporal outcome confounding bridge function that identifies the potential outcome without requiring direct recovery of the hidden confounder. We establish the identifiability of this bridge function under proxy exclusion restrictions and a spatiotemporal completeness condition, and show that the resulting estimator recovers the outcome through a proximal generalization of the g-computation formula. To operationalize this identification result, we propose a neural architecture that learns proxies via transformer-based spatiotemporal encoders - coupled with a conditional mutual information critic to enforce exclusion restrictions and a moment-matching network to guarantee that the learned bridge function satisfies the underlying identifying equation. We further introduce a stabilized weighting scheme to address treatment support imbalance. Experiments on synthetic datasets demonstrate that our approach achieves comparable performance to baseline causal inference methods, while providing, to our knowledge, the first theoretically grounded outcomes for the hidden confounding in the presence of spatiotemporal interference through a proximal causal inference framework.

A calibrated stochastic world model can reveal how uncertain a future is without revealing why it branches. The same conditional future law can arise because an observation aliases physical states or because dynamics remain random after the declared full state is fixed. We prove that ordinary transitions cannot identify these two sources, even for a perfect probabilistic predictor. ClosurePairs makes them identifiable by crossing compatible microstates with repeated exogenous disturbances and estimating state, noise, and state-noise interaction variance. The central consequence is operational: under finite hierarchical sampling, forecast difficulty governs the useful compute scale, while the alias/process composition provides complementary information about its direction-resolving the current state or sampling future randomness. ClosurePairs recovers source attribution at unchanged likelihood, reduces equal-budget decomposition error in a nonlinear interaction benchmark, and supports observation-only routing. On exact-marginal MetaWorld twins, an output-only allocator is at chance while a Closure-supervised probe on frozen JEPA-WM features routes 89.8-100%. In an independent ManiSkill PushCube confirmation, a stochastic RSSM's outputs and latents remain at chance, whereas an RGB-only Closure probe routes 100% under both ID and geometry/camera OOD over five seeds, matching direct allocation rather than exceeding it. Across five unseen allocation menus, the same Closure probe routes 92.5%/90.4% ID/OOD with no new oracle labels, versus 37.9%/32.9% for a frozen direct allocator. ClosurePairs is therefore an identifiable, reusable mechanism target that cannot be recovered from forecast quality alone.

Learning causal graphs from interventional data is a challenging problem with broad applications. In molecular biology, for example, a central goal is to uncover gene regulatory networks from large-scale perturbation data. An ideal algorithm for this task should scale to thousands of nodes, incorporate interventions even when their targets are unknown, quantify uncertainty, and provide identifiability guarantees. However, existing approaches---e.g. approaches using score-based optimization or approximate Bayesian inference---often fail to meet all of these criteria. To address these limitations, we develop Amortized Bayesian Causal Discovery of Extended Factor Graphs (ABCDEFG). Our method guarantees exact acyclicity, scales to graphs with thousands of nodes, and naturally handles interventions even when their targets are unknown. Additionally, ABCDEFG estimates a posterior distribution whose maximum a posteriori estimate provably identifies the true causal graph up to an equivalence class. On simulated datasets, ABCDEFG achieves state-of-the-art accuracy, producing a well-calibrated posterior distribution while outperforming previous score-based and approximate Bayesian methods. Applied to large-scale single-cell perturbation data, ABCDEFG identifies both established and novel gene targets of growth factors.

Pearl's structural causal model (SCM) framework, built on directed acyclic graphs (DAGs) and the do-calculus, is the dominant formal language for causal reasoning. Yet it carries two structural restrictions: every relationship must be pre-specified as a directed causal edge, and feedback cycles are forbidden. This paper examines two classes of phenomena that strain these restrictions. First, symmetric physical and economic constraints, the ideal gas law being the canonical case, carry no intrinsic causal direction. Direction emerges only under intervention, and which variable is solved for must be specified as part of the intervention. We formalize such constraints as causal zeros within an Extended Causal Model by adding an activation operator, subject to local solvability and graph-admissibility conditions. Second, for the class of finite-propagation state-space systems considered here, we treat apparent instantaneous cycles as artifacts of suppressed time and ground both causal zeros and feedback in Causal Differential Equations (CDEs). In these, the transient regime is a time-unrolled acyclic causal process, and causal zeros arise as the defining functions of attracting equilibrium manifolds; periodic and chaotic attractors define further regimes of the same dynamics, treated through attractor-relative intervention. We give the extended do-calculus, identifiability conditions, counterfactual semantics, and open problems.

Estimating contemporaneous bidirectional interactions from observational data is difficult because each outcome is endogenous to the other, while flexible regressions may capture only reduced-form dependence. This paper proposes SEM-DNN, a heteroscedastic neural simultaneous-equation estimator that learns reciprocal structural interactions without external instruments. Identification exploits conditional covariance diagonalization: when structural shocks have zero conditional means, are conditionally uncorrelated given predetermined covariates, and exhibit nonproportional conditional variances, only the true interaction coefficients diagonalize the conditional residual covariance across the feature space. The method jointly approximates nonlinear structural mean functions and feature-dependent variances using a diagonal Gaussian quasi-likelihood that incorporates the simultaneous-system Jacobian. We establish unique identification and positive-definite local curvature of the profiled population criterion and show that, under neural-profile compatibility conditions, the implemented neural criterion inherits this curvature despite nonunique network parameterizations. The coefficients admit a causal interpretation when the structural equations represent autonomous mechanisms that remain invariant under the relevant interventions. Monte Carlo experiments with nonlinear, high-dimensional nuisance functions and non-Gaussian shocks show that SEM-DNN recovers structural effects more reliably than parametric, kernel-based, and separate-equation neural alternatives as information increases, although at greater computational cost. An application to ready-to-eat cereal scanner data illustrates how the method can study contemporaneous price-sales feedback and assess identification strength, residual diagonalization, variance calibration, and optimization sensitivity.

Digital twins are often used to predict how a system would respond to an intervention. In systems with feedback, a twin must reproduce an equilibrium counterfactual, and a twin developed in one domain may fail after mechanisms change. We study when these predictions can be validated and transported. For equilibrium causal games, we give conditions on the mechanisms, equilibrium selection, and intervention design under which agreement with experimental distributions identifies the counterfactual of interest. We show why agreement of means and covariances is insufficient for distributional queries. We then introduce cyclic selection diagrams and derive criteria for direct reuse and for hybrid models that combine invariant source mechanisms with target information. An impossibility result constructs systems that agree under every experiment in a finite design but disagree on the target counterfactual, showing that validation requires structural assumptions. For linear models, we derive intervention requirements that depend on the mechanisms that changed, the observation model, and graph support. When point identification fails, we characterize the remaining range of query values. We also provide statistical tests for reconstructed means and covariances and illustrate the theory in synthetic feedback systems.

Power grids, markets, and interacting populations, settle into feedback driven equilibria observed through unknown sensors. Our Equilibrium Causal Game (ECG) joins a game to its cyclic causal model, hidden inputs, sensor map, and rules for interventions and equilibrium selection; interventions edit declared objects and recompute equilibrium. Under stated conditions, ECG-separation is sound but incomplete in our examples. Back-door/half-trek routes identify observed queries. Yet for an untouched rotationally symmetric Gaussian block, second moments determine only a source-frame rotation, across which distinct-variable effects generically change. Unknown sensing creates a separate ambiguity. In passive stable linear models without self-effects, unknown wiring and full-rank unknown sensing leave $B$ completely unidentified for $d\ge2$. Under LiNG, non-Gaussianity removes the source rotation; mechanism interventions separate sensing from interactions. With unknown support, invariant sensing, aligned responses, and well-posed single-target interventions identify $(H,B)$ up to declared equivalence. Of $d$ targets, $d-1$ suffice exactly when the sole untargeted node directly parents all others; otherwise $d$ are needed. Acquisition probes are excluded; known wiring gives no universal count. With nonlinear sensing, isotropic Gaussian source blocks admit hidden twists within and across blocks in labelled environments preserving required radial laws. Conversely, under stated positivity, informative one-block changes, rank, and irreducibility conditions, the finest independent source-block representation is identified within the stated alternative class up to block permutation and blockwise coordinate changes, but not downstream mechanisms or the sensor/interaction split. Together, these results show which causal conclusions equilibrium data support and which require targeted experiments.

We formalize verification in causal graphical models: deciding whether a given observational formula identifies a target interventional distribution. This opens a problem complementary to identification, asking not whether any identifying formula exists, but whether the given formula is identifying. We show that even sound and complete solutions to identification do not solve verification. We propose a falsifier as a first practical route forward, prove that it induces an almost-surely correct verifier for regular exponential-family models, and use the resulting verifier to develop the gateway test, which finds all sets admissible for use in a front-door formula.