A method of generating graphical models for providing security analysis in computer networks that in one embodiment includes the steps of generating a type abstract graph independent of particular networks that models abstract dependency relationships among attributes and exploits; generating network-specific attack graphs by combining the type abstract graph with specific network information; monitoring an intruder alert; and generating a real-time attack graph by correlating the intruder alert with the network-specific attack graph. The real-time attack graph can be generated using reachability checking, bridging, and exploit prediction based on consequence alerts and may further include the step of calculating the likelihood of queries using a Bayesian network model. The method may also include the steps of inferring unobserved attacks that may have been missed by intrusion detection sensors, and projecting on which hosts and using what exploits additional intruder attacks may occur. The method may further include the step of comparing alternate actions by computation, wherein the alternate actions include the step of patching some vulnerabilities, and wherein the specific network information includes network topology. The specific network information may also include firewall rules.