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As a traditional algorithm, the string match meets a challenge with the development of the massive volume of data be-cause of gene sequencing. Surveys show that there will be a huge amount of short read segments during the process of gene sequencing and the need for a highly efficient is urgent. The BWA is an effective algorithm to deal with the short read mapping. Compared with other short read mapping...
Modern reconfigurable computing chips, such as FPGAs, offer an unprecedented opportunity to achieving both multifunctionality and real-time responsiveness for memoryintensive embedded applications. However, how to cost-effectively synthesize application-specific hardware constructs that fully exploit memory-level parallelism remains to be a key challenge. To address this problem, we propose a new...
Sparse matrix-vector multiplication (SMVM) is a fundamental operation in many scientific and engineering applications. In many cases sparse matrices have thousands of rows and columns where most of the entries are zero, while non-zero data is spread over the matrix. This sparsity of data locality reduces the effectiveness of data cache in general-purpose processors quite reducing their performance...
In order to process real-time phased array ultrasound imaging, to improve imaging resolution, and achieve on-line defect detection, total focusing method (TFM) imaging algorithm is used for the complete data, thrust reversers the focus and algorithm in different positions, the computational problems of large data can be solved by the FPGA parallel algorithms. After that, the total focusing method...
This paper presents a compact and low-power digital implementation of the Roughness Index, which provides an estimate of the fixed-pattern noise present in an infrared video stream. This noise is caused by imperfections in the fabrication of the focal plane array and its readout circuitry, in addition to other time-variant processes. The index is continuously used during normal operation of the imager...
Partial evaluation is a common optimization technique in compiler design. It is also used in hardware synthesis for simplifying modules with constant signals. In this paper we introduce a new evaluation method for imperative programs in high-level synthesis, which benefits from control data, whose values do not vary in different program executions and are thus determinable in advance. The key aspect...
String matching is a ubiquitous problem that arises in a wide range of applications in computing, e.g., packet routing, intrusion detection, web querying, and genome analysis. Due to its importance, dozens of algorithms and several data structures have been developed over the years. A recent breakthrough in this field is the FM-index, a data structure that synergistically combines the Burrows-Wheeler...
The security of digital images attracts much attention recently. For images the transformation can be implemented at two levels, the first one consists of the pixel value permutation and the second one consists of position permutation. In this paper, we propose an encryption scheme for digital images with new pixel position permutation method based on Evolvable Hardware (EHW). In this work, we use...
This paper introduces an implementation of a general purpose fuzzy logic controller for use with general purpose embedded processors. This controller is used in the applications of maximum power point tracker of photovoltaic energy system as an application. However, the proposed model is very flexible to be applied in various and different applications. The design is made to be scalable in terms of...
The matrix LU decomposition is the key kernel of the Linpack benchmark. Based on the analysis of the theory Gaussian elimination, this paper proposes a parallel model of implementing the LU decomposition on FPGAs. The model has the pivoting operation and different architecture with former designs. Experimental results show the floating-point performance of our designs achieves 3371.40 MFLOPS at 110...
Efficient utilization of massive data, such as full-text search has become important in view of the growing needs for Web search and genome analysis. High-speed search and small storage space are required to handle massive amounts of data. For high-speed search, generally, a data structure such as index which needs additional storage space is required. Recently, compressed suffix array, which is a...
Satellites gather information from different sensors and send it using a temporal connection with very limited bandwidth. The bandwidth demand can be highly reduced if the satellite preprocesses the data and only sends relevant information. FPGAs offer the necessary flexibility and performance to carry out this preprocessing step. We have designed and implemented the well-known PPI algorithm for hyper...
In the field of RNA secondary structure prediction, the Zuker algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50% on Zuker. FPGA chips provide a new approach to accelerate the Zuker algorithm by exploiting fine-grained custom design. Zuker...
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