VCDF: A Validated Consensus-Driven Framework for Time Series Causal Discovery

Causal discovery with instantaneous effects in multivariate time series is challenging, as the instantaneous structure must be acyclic. Prior methods enforce this by either separating instantaneous and lagged estimation into multi-stage pipelines or imposing algebraic acyclicity constraints via complex augmented Lagrangian optimization, both of which incur high computational cost. In this work, we propose a different approach: we learn a differentiable permutation of variables using the Gumbel--Sinkhorn operator and triangularize the instantaneous coefficient matrix of a Structural Vector Autoregressive (SVAR) model in the learned order. This converts acyclicity from a hard constraint into a parameterization and keeps it valid throughout optimization. In doing so, our method enables unified, continuous optimization with gradient-based learning, leading to improved efficiency in time--series causal discovery. Across three real-world benchmarks, our method achieves the best overall performance compared with 12 baselines in both discovery accuracy and efficiency. On the large-scale benchmark, it further demonstrates strong scalability, achieving more than a 6x speedup over competing methods.

Time-series causal discovery methods rely on assumptions such as stationarity, regular sampling, and bounded temporal dependence. When these assumptions are violated, structure learning can produce confident but misleading causal graphs without warning. We introduce Causal-Audit, a framework that formalizes assumption validation as calibrated risk assessment. The framework computes effect-size diagnostics across five assumption families (stationarity, irregularity, persistence, nonlinearity, and confounding proxies), aggregates them into four calibrated risk scores with uncertainty intervals, and applies an abstention-aware decision policy that recommends methods (e.g., PCMCI+, VAR-based Granger causality) only when evidence supports reliable inference. The semi-automatic diagnostic stage can also be used independently for structured assumption auditing in individual studies. Evaluation on a synthetic atlas of 500 data-generating processes (DGPs) spanning 10 violation families demonstrates well-calibrated risk scores (AUROC > 0.95), a 62% false positive reduction among recommended datasets, and 78% abstention on severe-violation cases. On 21 external evaluations from TimeGraph (18 categories) and CausalTime (3 domains), recommend-or-abstain decisions are consistent with benchmark specifications in all cases. An open-source implementation of our framework is available.

The widespread availability of complex time series data in various domains such as environmental science, epidemiology, and economics demands robust causal discovery methods that can identify intricate contemporaneous and lagged relationships in non-stationary, nonlinear, and noisy settings. Existing constraint-based methods often rely heavily on conditional independence tests that degrade for limited data samples and complex distributions, while score-based methods impose strong statistical assumptions. Recent methods address special cases such as change point detection or distribution shifts, but struggle to provide a unified solution. We propose the Transformer Integrated Temporal Causal Discovery (TTCD) Framework, a novel end-to-end approach that learns contemporaneous and lagged causal relations from non-stationary time series. TTCD introduces a Non-Stationary Feature Learner integrating temporal and frequency-domain attention with dynamic non-stationarity profiling, and a custom Causal Structure Learner. A key innovation is reconstruction-guided causal signal distillation, to distill essential causal signals through the reconstruction process of the transformer decoder, which mitigates noise and spurious correlations while preserving meaningful dependencies. The Causal Structure Learner operates on distilled reconstructed signals to infer the underlying causal graph without restrictive assumptions on noise distributions or data generation processes. Experiments on synthetic, benchmark, and real world datasets show that TTCD consistently outperforms state-of-the-art baselines in both accuracy and consistency with domain knowledge, demonstrating the approach's effectiveness for causal discovery in challenging real world contexts.