Diagnostic processes for complex cyber-physical systems often require extensive prior knowledge in the form of detailed system models or comprehensive training data. However, obtaining such information poses a significant challenge. To address this issue, we present a new diagnostic approach that operates with minimal prior knowledge, requiring only a basic understanding of subsystem relationships and data from nominal operations. Our method combines a neural network-based symptom generator, which employs subsystem-level anomaly detection, with a new graph diagnosis algorithm that leverages minimal causal relationship information between subsystems-information that is typically available in practice. Our experiments with fully controllable simulated datasets show that our method includes the true causal component in its diagnosis set for 82 p.c. of all cases while effectively reducing the search space in 73 p.c. of the scenarios. Additional tests on the real-world Secure Water Treatment dataset showcase the approach's potential for practical scenarios. Our results thus highlight our approach's potential for practical applications with large and complex cyber-physical systems where limited prior knowledge is available.