Not All Relations Are Equal: Relation-Balanced and Calibrated Graph Learning for Provenance-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. In contrast, Theia provides the richest semantic signal and shows the clearest improvements in ranking and node-level recovery for our reference model. Overall, these findings reinforce the importance of interpreting architectural claims in PIDS together with the benchmark properties and evaluation protocol that produced them.

Advanced persistent threat (APT) attacks remain difficult to detect due to their stealth, adaptability, and use of legitimate system components. Provenance-based intrusion detection systems (PIDS) offer a promising defense by capturing detailed relationships between system components and actions. However, current PIDS rely on predefined or subset-determined thresholds, which limit detection stability and the ability to detect any anomalous behavior in general. Furthermore, related work often neglects the role of process executables, which describe system activity by interacting through a process with files, network components, and other processes. We introduce GRASP, a PIDS based on masked self-supervised classification. GRASP masks the executable information of processes and learns to infer it from their two-hop provenance graph neighborhood, marking misclassified processes as anomalies. It captures behavior patterns for the learned executables without thresholding, making it robust against interference and unknown activities. Evaluations on the DARPA TC and OpTC datasets demonstrate that GRASP consistently detects anomalous behavior, including known attack-related activities, outperforming existing systems. Our PIDS identifies all documented attacks on datasets where the behavior of executables is learnable. In addition, compared to existing systems, GRASP uncovers potentially malicious anomalous behavior not labeled as an attack in the documentation.

Anomaly-based Intrusion Detection Systems (IDSs) ensure protection against malicious attacks on networked systems. While deep learning-based IDSs achieve effective performance, their limited trustworthiness due to black-box architectures remains a critical constraint. Despite existing explainable techniques offering insight into the alarms raised by IDSs, they lack process-based explanations grounded in packet-level sequencing analysis. In this paper, we propose a method that employs process mining techniques to enhance anomaly-based IDSs by providing process-based alarm severity ratings and explanations for alerts. Our method prioritizes critical alerts and maintains visibility into network behavior, while minimizing disruption by allowing misclassified benign traffic to pass. We apply the method to the publicly available USB-IDS-TC dataset, which includes anomalous traffic affected by different variants of the Slowloris DoS attack. Results show that our method is able to discriminate between low- to very-high-severity alarms while preserving up to 99.94% recall and 99.99% precision, effectively discarding false positives while providing different degrees of severity for the true positives.