Prediction of secondary structures for large RNA molecules

The prediction of correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. Among the major obstacles is the fact that accurate calculations scale as O(n⁴), so the computational requirements become prohibitive as the length increases. We present a new parallel multicore and scalable program called GTfold, which is one to two orders of magnitude faster than the de facto standard programs mfold and RNAfold for folding large RNA viral sequences and achieves comparable accuracy of prediction. We analyze the algorithm's concurrency and describe the parallelism for a shared memory environment such as a symmetric multiprocessor or multicore chip. We are seeing a paradigm shift to multicore chips and parallelism must be explicitly addressed to continue gaining performance with each new generation of systems. We provide a rigorous proof of correctness of an optimized algorithm for internal loop calculations called internal loop speedup algorithm (ILSA), which reduces the time complexity of internal loop computations from O(n⁴) to O(n³) and show that the exact algorithms such as ILSA are executed with our method in affordable amount of time. The proof gives insight into solving these kinds of combinatorial problems. We have documented detailed pseudocode of the algorithm for predicting minimum free energy secondary structures which provides a base to implement future algorithmic improvements and improved thermodynamic model in GTfold. GTfold is written in C/C++ and freely available as open source from our website.M.S.Committee Chair: Bader, David; Committee Co-Chair: Heitsch, Christine; Committee Member: Harvey, Stephen; Committee Member: Vuduc, Richar

Topology dependence of PPM-based Internet Protocol traceback schemes

Multiple schemes that utilize probabilistic packet marking (PPM) have been proposed to deal with Distributed Denial of Service (DDoS) attacks by reconstructing their attack graphs and identifying the attack sources. In the first part of this dissertation, we present our contribution to the family of PPM-based schemes for Internet Protocol (IP) traceback. Our proposed approach, Prediction-Based Scheme (PBS), consists of marking and traceback algorithms that reduce scheme convergence times by dealing with the problems of data loss and incomplete attack graphs exhibited by previous PPM-based schemes. Compared to previous PPM-based schemes, the PBS marking algorithm ensures that traceback is possible with about 54% as many total network packets, while the traceback algorithm takes about 33% as many marked packets for complete attack path construction. In the second part of this dissertation, we tackle the problem of scheme evaluation and comparison across discrepant network topologies. Previous research in this area has overlooked the influence of network topology on scheme performance and often utilized disparate and simplistic network abstractions to evaluate and compare these schemes. Our approach to this problem involves the evaluation of selected PPM-based schemes across a set of 60 Internet-like topologies and the adaptation of the network motif approach to provide a common ground for comparing the schemes\u27 performances in different network topologies. This approach allows us to determine the level of structural similarity between network topologies and consequently enables the comparison of scheme performance even when the schemes are implemented on different topologies. Furthermore, we identify three network-dependent factors that affect different PPM-based schemes uniquely causing a variation in, and discrepancy between, scheme performance from one network to another. Results indicate that scheme performance is dependent on the network upon which it is implemented, i.e. the value of the PPM-based schemes\u27 convergence times and their rankings vary depending on the underlying network topology. We show how the identified network factors contribute, individually and collectively, to the scheme performance in large-scale networks. Additionally, we identify five superfamilies from the 60 considered networks and find that networks within a superfamily also exhibit similar PPM-based scheme performance. To complement our results, we present an analytical model showing a link between scheme performance in any superfamily, and the motifs exhibited by the networks in that superfamily. Our work highlights a need for multiple network evaluation of network protocols. To this end, we demonstrate a method of identifying structurally similar network topologies among which protocol performance is potentially comparable. Our work also presents an effective way of comparing general network protocol performance in which the protocol is evaluated on specific representative networks instead of an entire set of networks

DoS and DDoS Attacks: Defense, Detection and Traceback Mechanisms - A Survey

Denial of Service (DoS) or Distributed Denial of Service (DDoS) attacks are typically explicit attempts to exhaust victim2019;s bandwidth or disrupt legitimate users2019; access to services. Traditional architecture of internet is vulnerable to DDoS attacks and it provides an opportunity to an attacker to gain access to a large number of compromised computers by exploiting their vulnerabilities to set up attack networks or Botnets. Once attack network or Botnet has been set up, an attacker invokes a large-scale, coordinated attack against one or more targets. Asa result of the continuous evolution of new attacks and ever-increasing range of vulnerable hosts on the internet, many DDoS attack Detection, Prevention and Traceback mechanisms have been proposed, In this paper, we tend to surveyed different types of attacks and techniques of DDoS attacks and their countermeasures. The significance of this paper is that the coverage of many aspects of countering DDoS attacks including detection, defence and mitigation, traceback approaches, open issues and research challenges

On packet marking and Markov modeling for IP Traceback: A deep probabilistic and stochastic analysis

From many years, the methods to defend against Denial of Service attacks have been very attractive from different point of views, although network security is a large and very complex topic. Different techniques have been proposed and so-called packet marking and IP tracing procedures have especially demonstrated a good capacity to face different malicious attacks. While host-based DoS attacks are more easily traced and managed, network-based DoS attacks are a more challenging threat. In this paper, we discuss a powerful aspect of the IP traceback method, which allows a router to mark and add information to attack packets on the basis of a fixed probability value. We propose a potential method for modeling the classic probabilistic packet marking algorithm as Markov chains, allowing a closed form to be obtained for evaluating the correct number of received marked packets in order to build a meaningful attack graph and analyze how marking routers must behave to minimize the overall overhead

Fundamental Design Issues in Anonymous Peer-to-peer Distributed Hash Table Protocols

Ph.D

Impact of denial of service solutions on network quality of service

The Internet has become a universal communication network tool. It has evolved from a platform that supports best-effort traffic to one that now carries different traffic types including those involving continuous media with quality of service (QoS) requirements. As more services are delivered over the Internet, we face increasing risk to their availability given that malicious attacks on those Internet services continue to increase. Several networks have witnessed denial of service (DoS) and distributed denial of service (DDoS) attacks over the past few years which have disrupted QoS of network services, thereby violating the Service Level Agreement (SLA) between the client and the Internet Service Provider (ISP). Hence DoS or DDoS attacks are major threats to network QoS. In this paper we survey techniques and solutions that have been deployed to thwart DoS and DDoS attacks and we evaluate them in terms of their impact on network QoS for Internet services. We also present vulnerabilities that can be exploited for QoS protocols and also affect QoS if exploited. In addition, we also highlight challenges that still need to be addressed to achieve end-to-end QoS with recently proposed DoS/DDoS solutions

Algorithms for Reconstructing DDoS Attack Graphs using Probabilistic Packet Marking

DoS and DDoS attacks are widely used and pose a constant threat. Here we explore Probability Packet Marking (PPM), one of the important methods for reconstructing the attack-graph and detect the attackers. We present two algorithms. Differently from others, their stopping time is not fixed a priori. It rather depends on the actual distance of the attacker from the victim. Our first algorithm returns the graph at the earliest feasible time, and turns out to guarantee high success probability. The second algorithm enables attaining any predetermined success probability at the expense of a longer runtime. We study the performance of the two algorithms theoretically, and compare them to other algorithms by simulation. Finally, we consider the order in which the marks corresponding to the various edges of the attack graph are obtained by the victim. We show that, although edges closer to the victim tend to be discovered earlier in the process than farther edges, the differences are much smaller than previously thought.Comment: 30 pages, 4 figures, 4 table

Adaptive Response System for Distributed Denial-of-Service Attacks

The continued prevalence and severe damaging effects of the Distributed Denial of Service (DDoS) attacks in today’s Internet raise growing security concerns and call for an immediate response to come up with better solutions to tackle DDoS attacks. The current DDoS prevention mechanisms are usually inflexible and determined attackers with knowledge of these mechanisms, could work around them. Most existing detection and response mechanisms are standalone systems which do not rely on adaptive updates to mitigate attacks. As different responses vary in their “leniency” in treating detected attack traffic, there is a need for an Adaptive Response System. We designed and implemented our DDoS Adaptive ResponsE (DARE) System, which is a distributed DDoS mitigation system capable of executing appropriate detection and mitigation responses automatically and adaptively according to the attacks. It supports easy integrations for both signature-based and anomaly-based detection modules. Additionally, the design of DARE’s individual components takes into consideration the strengths and weaknesses of existing defence mechanisms, and the characteristics and possible future mutations of DDoS attacks. These components consist of an Enhanced TCP SYN Attack Detector and Bloom-based Filter, a DDoS Flooding Attack Detector and Flow Identifier, and a Non Intrusive IP Traceback mechanism. The components work together interactively to adapt the detections and responses in accordance to the attack types. Experiments conducted on DARE show that the attack detection and mitigation are successfully completed within seconds, with about 60% to 86% of the attack traffic being dropped, while availability for legitimate and new legitimate requests is maintained. DARE is able to detect and trigger appropriate responses in accordance to the attacks being launched with high accuracy, effectiveness and efficiency. We also designed and implemented a Traffic Redirection Attack Protection System (TRAPS), a stand-alone DDoS attack detection and mitigation system for IPv6 networks. In TRAPS, the victim under attack verifies the authenticity of the source by performing virtual relocations to differentiate the legitimate traffic from the attack traffic. TRAPS requires minimal deployment effort and does not require modifications to the Internet infrastructure due to its incorporation of the Mobile IPv6 protocol. Experiments to test the feasibility of TRAPS were carried out in a testbed environment to verify that it would work with the existing Mobile IPv6 implementation. It was observed that the operations of each module were functioning correctly and TRAPS was able to successfully mitigate an attack launched with spoofed source IP addresses