SoK: Timestamps Are Not a Time Model: Rethinking Temporal Reasoning in Host-Based Intrusion Detection

Provenance-based intrusion detection systems (PIDS) frequently report strong performance, but the conclusions drawn from these results can be highly sensitive to benchmarking choices and evaluation protocols. We investigate this dependency by re-evaluating representative PIDS on public datasets that meet our audit, labeling, and calibration requirements. Focusing primarily on the audited DARPA TC E3 datasets, we apply a unified protocol with temporally separated test periods and validation-only checkpoint selection and threshold calibration, and ask which architectural claims are empirically supported. We find that alerting success and investigation utility can diverge sharply, as several systems surface attacks without providing enough process-level context to support forensic investigation. Across the four primary datasets, a simple allowlist built from executable names and paths observed during training matches or exceeds the selected learned baselines on key operating-point metrics, showing that comparable performance on these metrics is achievable using lexical novelty alone. Quantifying semantic signal quality through feature completeness and field entropy helps explain why several audited E3 datasets support alerting performance without reliably separating model architectures. Theia, however, provides the richest semantic signal and is the only primary dataset on which our reference model, Theseus, clearly improves both ranking and node-level recovery over the other learned systems. Overall, these findings reinforce the importance of interpreting architectural claims in PIDS together with the benchmark properties and evaluation protocol that produced them.

This paper addresses the problem of attack detection in cyber-physical systems without any knowledge of the plant model or its structure. A remotely located plant transmits sensor measurements to an operator over a network that is assumed to be under attack. We consider two classes of attacks: model-free replay attacks and model-based stealthy attacks. For the latter, we derive closed-form expressions for the optimal stealthy attack policy against a $χ^2$ detector, for both linear and nonlinear systems. We then propose a model-structure-free detector based on TimesFM, a time-series foundation model developed by Google Research, which serves as a surrogate residual generator operating in a zero-shot fashion. We show empirically that the TimesFM-based detector achieves a comparable or superior attack detection performance. The efficacy of the proposed approach is demonstrated numerically on the IEEE 14-bus power system. We also demonstrate that TimesFM predictions can serve as a substitute for corrupted measurements, a practical mitigation technique when classical redundancy assumptions fail.

Recent deep learning approaches for network intrusion detection increasingly incorporate temporal architectures such as recurrent networks and Transformers, often reporting near-perfect performance on CIC-IDS2017. However, many existing studies neither supply their temporal modules with genuine sequence inputs nor evaluate under realistic, leakage-free conditions, making it unclear whether reported gains arise from true sequence-modeling capability. In this work, we reformulate CIC-IDS2017 as a temporal intrusion-detection task by constructing ordered flow sequences from network conversations and benchmarking nine classical and deep learning architectures under a random split, two leakage-free splits, and a padding-scheme ablation. The central finding is that padding convention, not architecture, determines the Transformer's performance: on genuinely sequential (non-padded) windows the Transformer achieves the highest macro-F1 of any model in the experiment (0.89); under zero-pad+mask evaluation it drops markedly (-0.24 macro-F1), while LSTM, GRU, and 1D-CNN remain stable. Under leakage-free group evaluation the Random Forest is the most robust model (+0.009), while the Transformer's false-alarm rate grows from 0.04% to 2.7%, a 67-fold increase invisible under conventional protocols. These findings demonstrate that evaluation methodology -- specifically padding convention and split protocol -- has a larger effect on reported performance than architectural choice, and that widely used random splits with repeat-last padding can overestimate model robustness by up to 0.24 macro-F1. We advocate leakage-free splits, explicit padding disclosure, and sequence-aware benchmarking as standard practice in future IDS research. Code and implementation details are available at https://github.com/zachmocz/temporal-ids-bench.