As the primary vehicle for most organized cybercrimes, malicious software (or malware) has become one of the most serious threats to computer systems and the Internet. With the recent advent of automated malware development toolkits, it has become relatively easy, even for marginally skilled adversaries, to create and mutate malware, bypassing Anti-Virus (AV) detection. This has led to a surge in the number of new malware threats and has created several major challenges for the AV industry. AV companies typically receive tens of thousands of suspicious samples daily. However, the overwhelming number of new malware easily overtax the available human resources at AV companies, making them less responsive to emerging threats and leading to poor detection rates. To address these issues, this dissertation proposes several new and scalable systems to facilitate malware analysis and detection, with the focus on a central theme: ``automation and scalability". This dissertation makes four primary contributions. First, it builds a large-scale malware database management system called SMIT that addresses the challenges of determining whether a suspicious sample is indeed malicious. SMIT exploits the insight that most new malicious samples are simple syntactic variations of existing malware. Thus, one way to ascertain the maliciousness of an unknown sample is to check if it is sufficiently similar to any existing malware. SMIT is designed to make such decisions efficiently using malware's function call graph---a high-level structural representation that is less susceptible to the low-level obfuscation employed by malware writers to evade detection. Second, the dissertation develops an automatic malware clustering system called MutantX. By quickly grouping similar samples into clusters, MutantX allows malware analysts to focus on representative samples and automatically generate labels based on samples’ association with existing groups. Third, this dissertation introduces a signature-generation system, called Hancock, that automatically creates high-quality string signatures with extremely low false-positive rates. Finally, observing that two widely used malware analysis approaches---i.e., static and dynamic analyses---have their respective pros and cons, this dissertation proposes a novel system that optimally integrates static-feature and dynamic-behavior based malware clusterings, mitigating their respective shortcomings without losing their merits
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