Skynet: Workflow-Level Anomaly Detection for Agentic AI via Semantic and Structural Modeling
Organizations: Virginia Tech Arlington, VA, USA · WashU St. Louis, MO, USA · Virginia Tech Blacksburg, VA, USA
Abstract
Agentic AI systems execute complex tasks through long-horizon workflows of planning, tool use, and multi-agent coordination. Task failures in these systems often originate from a single step, such as an injected prompt or a flawed plan, and are then amplified through downstream dependencies as the corrupted step propagates across many subsequent agents and tool calls. Existing defenses either target a specific class of attacks or failures, or inspect individual prompts and steps in isolation. Both leave the global dependency structure of a workflow unexamined, and miss the inconsistencies that only emerge when the execution is viewed as a whole. We argue that anomaly detection for agentic AI must reason at the workflow level, where global execution structure exposes signals that local checks cannot see. We present Skynet, a principled workflow-level anomaly detection framework that turns observed multi-agent execution into directed workflow graphs and scores them against learned benign behavior. Skynet jointly models the semantic execution context and the structural organization of inter-agent delegation, tool invocation, and data-flow dependencies, and trains only on benign workflows. Because training never sees attacks or failures, this design naturally extends to zero-day detection: any execution that violates benign workflow regularities surfaces as off-manifold geometry under a single decision rule. We evaluate Skynet on three public agentic safety and failure benchmarks. It sustains high recall together with a sub-1% false positive rate, with per-workflow and per-step latencies low enough for online monitoring of agentic AI runtimes.
Figures & tables
| Agent-SafetyBench | AgentErrorBench | ATBench | Combined | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Method | Acc | Prec | Rec | F1 | FPR | Acc | Prec | Rec | F1 | FPR | Acc | Prec | Rec | F1 | FPR | Acc | Prec | Rec | F1 | FPR |
| Skynet | 99.26 | 95.69 | 100.00 | 97.80 | 0.89 | 99.34 | 97.56 | 100.00 | 98.77 | 0.89 | 91.41 | 98.80 | 82.70 | 90.03 | 0.89 | 93.36 | 99.31 | 89.36 | 94.07 | 0.89 |
| F-GAE | 97.86 | 90.91 | 99.10 | 94.83 | 2.14 | 98.05 | 93.02 | 98.50 | 95.68 | 2.14 | 88.94 | 90.12 | 84.31 | 87.12 | 2.14 | 90.87 | 93.44 | 86.92 | 90.06 | 2.14 |
| TraceAegis | 96.62 | 86.89 | 96.40 | 91.40 | 3.38 | 96.83 | 89.19 | 94.50 | 91.77 | 3.38 | 67.43 | 61.54 | 34.61 | 44.27 | 3.38 | 75.92 | 78.48 | 58.42 | 66.98 | 3.38 |
| Guardian | 99.85 | 99.11 | 100.00 | 99.55 | 0.18 | 99.87 | 99.50 | 100.00 | 99.75 | 0.18 | 61.57 | 98.91 | 18.31 | 30.90 | 0.18 | 70.29 | 99.75 | 49.75 | 66.39 | 0.18 |
| TopoGCL | 95.69 | 80.15 | 98.20 | 88.26 | 4.80 | 92.78 | 86.43 | 86.00 | 86.22 | 4.80 | 56.56 | 70.33 | 12.88 | 21.77 | 4.80 | 64.23 | 92.74 | 42.70 | 58.47 | 4.80 |
| Subclass | Acc | Prec | Rec | F1 | FPR | |
|---|---|---|---|---|---|---|
| AgentErrorBench (failure type) | ||||||
| inefficient_plan | 46 | 99.18 | 90.20 | 100.00 | 94.85 | 0.89 |
| over_simplification | 20 | 99.14 | 80.00 | 100.00 | 88.89 | 0.89 |
| progress_misjudge | 20 | 99.14 | 80.00 | 100.00 | 88.89 | 0.89 |
| constraint_ignorance | 13 | 99.13 | 72.22 | 100.00 | 83.87 | 0.89 |
| hallucination | 13 | 99.13 | 72.22 | 100.00 | 83.87 | 0.89 |
| Variant | Acc | Prec | Rec | F1 | FPR |
|---|---|---|---|---|---|
| Full Skynet | 96.64 | 99.48 | 94.80 | 97.08 | 0.71 |
| w/o structural branch | 94.09 | 99.32 | 90.59 | 94.76 | 0.89 |
| w/o counterfactual views | 94.09 | 99.19 | 90.72 | 94.76 | 1.07 |
| w/o workflow-aware aug. | 95.84 | 99.30 | 93.54 | 96.33 | 0.98 |
| single-mode inference | 79.42 | 99.25 | 65.59 | 78.99 | 0.71 |
| Component | Total (s) | Mean (s) | P95 (s) |
|---|---|---|---|
| Per-workflow component cost (offline) | |||
| Graph construction | 0.2249 | 0.0225 | 0.0882 |
| Encoder forward (sem. struct.) | 0.5816 | 0.0582 | 0.1437 |
| Mode scoring (batched) | 0.0013 | 0.0001 | — |
| End-to-end per workflow | — | 0.0808 | 0.2282 |
| End-to-end scalability by workflow size | |||
Anomaly Detection
Anomaly detection finds rare or unexpected patterns in data, from defective products and system faults to fraud and security threats.
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