With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden on aligning them. For example, aligning sequences to a human reference genome can take tens or even hundreds of hours. The current de facto standard approach for alignment is based on the guided dynamic programming method. Although this takes a long time and could potentially benefit from high-throughput graphic processing units (GPUs), the existing GPU-accelerated approaches often compromise the algorithm's structure, due to the GPU-unfriendly nature of the computational pattern. Unfortunately, such compromise in the algorithm is not tolerable in the field, because sequence alignment is a part of complicated bioinformatics analysis pipelines. In such circumstances, we propose AGAThA, an exact and efficient GPU-based acceleration of guided sequence alignment. We diagnose and address the problems of the algorithm being unfriendly to GPUs, which comprises strided/redundant memory accesses and workload imbalances that are difficult to predict. According to the experiments on modern GPUs, AGAThA achieves 18.8× speedup against the CPU-based baseline, 9.6× against the best GPU-based baseline, and 3.6× against GPU-based algorithms with different heuristics.

Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit exploiting the full computational capability of modern GPUs. This paper presents SALoBa, a GPU-accelerated sequence alignment library focused on seed extension. Based on the analysis of previous work with real-world sequencing data, we propose techniques to exploit the data locality and improve work-load balancing. The experimental results reveal that SALoBa significantly improves the seed extension kernel compared to state-of-the-art GPU-based methods.

Packing is the most common analysis avoidance technique for hiding malware. Also, packing can make it harder for the security researcher to identify the behaviour of malware and increase the analysis time. In order to analyze the packed malware, we need to perform unpacking first to release the packing. In this paper, we focus on unpacking and its related technologies to analyze the packed malware. Through extensive analysis on previous unpacking studies, we pay attention to four important drawbacks: no phase integration, no detection combination, no real-restoration, and no unpacking verification. To resolve these four drawbacks, in this paper, we present an all-in-one structure of the unpacking system that performs packing detection, unpacking (i.e., restoration), and verification phases in an integrated framework. For this, we first greatly increase the packing detection accuracy in the detection phase by combining four existing and new packing detection techniques. We then improve the unpacking phase by using the state-of-the-art static and dynamic unpacking techniques. We also present a verification algorithm evaluating the accuracy of unpacking results. Experimental results show that the proposed all-in-one unpacking system performs all of the three phases well in an integrated framework. In particular, the proposed hybrid detection method is superior to the existing methods, and the system performs unpacking very well up to 100% of restoration accuracy for most of the files except for a few packers.

Real-time data stream processing technologies such as Apache Storm and Apache Spark are being actively studied to deal with large-capacity data streams that generated rapidly in real time. Because it is difficult to use most real-time processing techniques alone, it is common to use it with a messaging system that supports input and output of data streams. Apache Kafka is a representative distributed messaging system, specialized in delivering large amounts of real-time log data. However, if the production rate of data in Kafka is faster than the consumption rate, data starvation problem may arise. In order to solve the starvation problem, a load shedding technique is needed to limit the incoming data and maintain system performance when the system is under load. Thus, in this paper confirmed the starvation problem that can occur in Kafka, and we designed and implemented a load shedding engine to solve this problem and proposed a solution to the starvation problem in Kafka based on the performance experiment.

Recently, the risk of information disclosure is increasing significantly. Accordingly, privacy-preserving data mining (PPDM) is being actively studied to obtain accurate mining results while preserving the data privacy. We here focus on secure similar document detection (SSDD), which identifies similar documents of two parties when each party does not disclose its own sensitive documents to the another party. In this paper, we propose an efficient two-step protocol that exploits a feature selection as a lower-dimensional transformation, and we present discriminative feature selections to maximize the performance of the protocol. The proposed protocol consists of two steps: thefilteringstep and thepostprocessingstep. For the feature selection, we first consider the simplest one, random projection (RP), and propose its two-step solution,SSDD-RP. We then present two discriminative feature selections and their solutions:SSDD-LFwhich selects a few dimensions locally frequent in the current querying vector andSSDD-GFwhich selects ones globally frequent in the set of all document vectors. We finally propose a hybrid one,SSDD-HF, which takes advantage of bothSSDD-LFandSSDD-GF. We empirically show that the proposed two-step protocol significantly outperforms the previous one-step protocol by three or four orders of magnitude.