A MEMORY EFFICIENT HARDWARE BASED PATTERN MATCHING AND PROTEIN ALIGNMENT SCHEMES FOR HIGHLY COMPLEX DATABASES

Protein sequence alignment to find correlation between different species, or genetic mutations etc. is the most computational intensive task when performing protein comparison. To speed-up the alignment, Systolic Arrays (SAs) have been used. In order to avoid the internal-loop problem which reduces the performance, pipeline interleaving strategy has been presented. This strategy is applied to an SA for Smith Waterman (SW) algorithm which is an alignment algorithm to locally align two proteins. In the proposed system, the above methodology has been extended to implement a memory efficient FPGA-hardware based Network Intrusion Detection System (NIDS) to speed up network processing. The pattern matching in Intrusion Detection Systems (IDS) is done using SNORT to find the pattern of intrusions. A Finite State Machine (FSM) based Processing Elements (PE) unit to achieve minimum number of states for pattern matching and bit wise early intrusion detection to increase the throughput by pipelining is presented

Hardware Acceleration of Network Intrusion Detection System Using FPGA

This thesis presents new algorithms and hardware designs for Signature-based Network Intrusion Detection System (SB-NIDS) optimisation exploiting a hybrid hardwaresoftware co-designed embedded processing platform. The work describe concentrates on optimisation of a complete SB-NIDS Snort application software on a FPGA based hardware-software target rather than on the implementation of a single functional unit for hardware acceleration. Pattern Matching Hardware Accelerator (PMHA) based on Bloom filter was designed to optimise SB-NIDS performance for execution on a Xilinx MicroBlaze soft-core processor. The Bloom filter approach enables the potentially large number of network intrusion attack patterns to be efficiently represented and searched primarily using accesses to FPGA on-chip memory. The thesis demonstrates, the viability of hybrid hardware-software co-designed approach for SB-NIDS. Future work is required to investigate the effects of later generation FPGA technology and multi-core processors in order to clearly prove the benefits over conventional processor platforms for SB-NIDS. The strengths and weaknesses of the hardware accelerators and algorithms are analysed, and experimental results are examined to determine the effectiveness of the implementation. Experimental results confirm that the PMHA is capable of performing network packet analysis for gigabit rate network traffic. Experimental test results indicate that our SB-NIDS prototype implementation on relatively low clock rate embedded processing platform performance is approximately 1.7 times better than Snort executing on a general purpose processor on PC when comparing processor cycles rather than wall clock time

FPGA-based High Throughput Regular Expression Pattern Matching for Network Intrusion Detection Systems

Network speeds and bandwidths have improved over time. However, the frequency of network attacks and illegal accesses have also increased as the network speeds and bandwidths improved over time. Such attacks are capable of compromising the privacy and confidentiality of network resources belonging to even the most secure networks. Currently, general-purpose processor based software solutions used for detecting network attacks have become inadequate in coping with the current network speeds. Hardware-based platforms are designed to cope with the rising network speeds measured in several gigabits per seconds (Gbps). Such hardware-based platforms are capable of detecting several attacks at once, and a good candidate is the Field-programmable Gate Array (FPGA). The FPGA is a hardware platform that can be used to perform deep packet inspection of network packet contents at high speed. As such, this thesis focused on studying designs that were implemented with Field-programmable Gate Arrays (FPGAs). Furthermore, all the FPGA-based designs studied in this thesis have attempted to sustain a more steady growth in throughput and throughput efficiency. Throughput efficiency is defined as the concurrent throughput of a regular expression matching engine circuit divided by the average number of look up tables (LUTs) utilised by each state of the engine"s automata. The implemented FPGA-based design was built upon the concept of equivalence classification. The concept helped to reduce the overall table size of the inputs needed to drive the various Nondeterministic Finite Automata (NFA) matching engines. Compared with other approaches, the design sustained a throughput of up to 11.48 Gbps, and recorded an overall reduction in the number of pattern matching engines required by up to 75%. Also, the overall memory required by the design was reduced by about 90% when synthesised on the target FPGA platform

QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction

In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with simple proof-of-concept examples to target both the genomics research community and quantum application developers in a self-contained manner. The details of the implementation are discussed for the various layers of the quantum full-stack accelerator design. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/prince-ph0en1x/QuASeR.Comment: 24 page

Techniques for Processing TCP/IP Flow Content in Network Switches at Gigabit Line Rates

The growth of the Internet has enabled it to become a critical component used by businesses, governments and individuals. While most of the traffic on the Internet is legitimate, a proportion of the traffic includes worms, computer viruses, network intrusions, computer espionage, security breaches and illegal behavior. This rogue traffic causes computer and network outages, reduces network throughput, and costs governments and companies billions of dollars each year. This dissertation investigates the problems associated with TCP stream processing in high-speed networks. It describes an architecture that simplifies the processing of TCP data streams in these environments and presents a hardware circuit capable of TCP stream processing on multi-gigabit networks for millions of simultaneous network connections. Live Internet traffic is analyzed using this new TCP processing circuit

An Interactive Relaxation Approach for Anomaly Detection and Preventive Measures in Computer Networks

It is proposed to develop a framework of detecting and analyzing small and widespread changes in specific dynamic characteristics of several nodes. The characteristics are locally measured at each node in a large network of computers and analyzed using a computational paradigm known as the Relaxation technique. The goal is to be able to detect the onset of a worm or virus as it originates, spreads-out, attacks and disables the entire network. Currently, selective disabling of one or more features across an entire subnet, e.g. firewalls, provides limited security and keeps us from designing high performance net-centric systems. The most desirable response is to surgically disable one or more nodes, or to isolate one or more subnets.The proposed research seeks to model virus/worm propagation as a spatio-temporal process. Such models have been successfully applied in heat-flow and evidence or gestalt driven perception of images among others. In particular, we develop an iterative technique driven by the self-assessed dynamic status of each node in a network. The status of each node will be updated incrementally in concurrence with its connected neighbors to enable timely identification of compromised nodes and subnets. Several key insights used in image analysis of line-diagrams, through an iterative and relaxation-driven node labeling method, are explored to help develop this new framework

Hardware acceleration for power efficient deep packet inspection

The rapid growth of the Internet leads to a massive spread of malicious attacks like viruses and malwares, making the safety of online activity a major concern. The use of Network Intrusion Detection Systems (NIDS) is an effective method to safeguard the Internet. One key procedure in NIDS is Deep Packet Inspection (DPI). DPI can examine the contents of a packet and take actions on the packets based on predefined rules. In this thesis, DPI is mainly discussed in the context of security applications. However, DPI can also be used for bandwidth management and network surveillance. DPI inspects the whole packet payload, and due to this and the complexity of the inspection rules, DPI algorithms consume significant amounts of resources including time, memory and energy. The aim of this thesis is to design hardware accelerated methods for memory and energy efficient high-speed DPI. The patterns in packet payloads, especially complex patterns, can be efficiently represented by regular expressions, which can be translated by the use of Deterministic Finite Automata (DFA). DFA algorithms are fast but consume very large amounts of memory with certain kinds of regular expressions. In this thesis, memory efficient algorithms are proposed based on the transition compressions of the DFAs. In this work, Bloom filters are used to implement DPI on an FPGA for hardware acceleration with the design of a parallel architecture. Furthermore, devoted at a balance of power and performance, an energy efficient adaptive Bloom filter is designed with the capability of adjusting the number of active hash functions according to current workload. In addition, a method is given for implementation on both two-stage and multi-stage platforms. Nevertheless, false positive rates still prevents the Bloom filter from extensive utilization; a cache-based counting Bloom filter is presented in this work to get rid of the false positives for fast and precise matching. Finally, in future work, in order to estimate the effect of power savings, models will be built for routers and DPI, which will also analyze the latency impact of dynamic frequency adaption to current traffic. Besides, a low power DPI system will be designed with a single or multiple DPI engines. Results and evaluation of the low power DPI model and system will be produced in future