Parallel and private generalized suffix tree construction and query on genomic data.

BACKGROUND: Several technological advancements and digitization of healthcare data have provided the scientific community with a large quantity of genomic data. Such datasets facilitated a deeper understanding of several diseases and our health in general. Strikingly, these genome datasets require a large storage volume and present technical challenges in retrieving meaningful information. Furthermore, the privacy aspects of genomic data limit access and often hinder timely scientific discovery. METHODS: In this paper, we utilize the Generalized Suffix Tree (GST); their construction and applications have been fairly studied in related areas. The main contribution of this article is the proposal of a privacy-preserving string query execution framework using GSTs and an additional tree-based hashing mechanism. Initially, we start by introducing an efficient GST construction in parallel that is scalable for a large genomic dataset. The secure indexing scheme allows the genomic data in a GST to be outsourced to an untrusted cloud server under encryption. Additionally, the proposed methods can perform several string search operations (i.e., exact, set-maximal matches) securely and efficiently using the outlined framework. RESULTS: The experimental results on different datasets and parameters in a real cloud environment exhibit the scalability of these methods as they also outperform the state-of-the-art method based on Burrows-Wheeler Transformation (BWT). The proposed method only takes around 36.7s to execute a set-maximal match whereas the BWT-based method takes around 160.85s, providing a 4× speedup.

Evolving convolutional neural network parameters through the genetic algorithm for the breast cancer classification problem.

Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer mortality in women around the world. However, it can be controlled effectively by early diagnosis, followed by effective treatment. Clinical specialists take the advantages of computer-aided diagnosis (CAD) systems to make their diagnosis as accurate as possible. Deep learning techniques, such as the convolutional neural network (CNN), due to their classification capabilities on learned feature methods and ability of working with complex images, have been widely adopted in CAD systems. The parameters of the network, including the weights of the convolution filters and the weights of the fully connected layers, play a crucial role in the classification accuracy of any CNN model. The back-propagation technique is the most frequently used approach for training the CNN. However, this technique has some disadvantages, such as getting stuck in local minima. In this study, we propose to optimize the weights of the CNN using the genetic algorithm (GA). The work consists of designing a CNN model to facilitate the classification process, training the model using three different optimizers (mini-batch gradient descent, Adam, and GA), and evaluating the model through various experiments on the BreakHis dataset. We show that the CNN model trained through the GA performs as well as the Adam optimizer with a classification accuracy of 85%.

A Micro-Level Compensation-Based Cost Model for Resource Allocation in a Fog Environment.

Fog computing aims to support applications requiring low latency and high scalability by using resources at the edge level. In general, fog computing comprises several autonomous mobile or static devices that share their idle resources to run different services. The providers of these devices also need to be compensated based on their device usage. In any fog-based resource-allocation problem, both cost and performance need to be considered for generating an efficient resource-allocation plan. Estimating the cost of using fog devices prior to the resource allocation helps to minimize the cost and maximize the performance of the system. In the fog computing domain, recent research works have proposed various resource-allocation algorithms without considering the compensation to resource providers and the cost estimation of the fog resources. Moreover, the existing cost models in similar paradigms such as in the cloud are not suitable for fog environments as the scaling of different autonomous resources with heterogeneity and variety of offerings is much more complicated. To fill this gap, this study first proposes a micro-level compensation cost model and then proposes a new resource-allocation method based on the cost model, which benefits both providers and users. Experimental results show that the proposed algorithm ensures better resource-allocation performance and lowers application processing costs when compared to the existing best-fit algorithm.

An OpenMP-based tool for finding longest common subsequence in bioinformatics.

OBJECTIVE: Finding the longest common subsequence (LCS) among sequences is NP-hard. This is an important problem in bioinformatics for DNA sequence alignment and pattern discovery. In this research, we propose new CPU-based parallel implementations that can provide significant advantages in terms of execution times, monetary cost, and pervasiveness in finding LCS of DNA sequences in an environment where Graphics Processing Units are not available. For general purpose use, we also make the OpenMP-based tool publicly available to end users. RESULT: In this study, we develop three novel parallel versions of the LCS algorithm on: (i) distributed memory machine using message passing interface (MPI); (ii) shared memory machine using OpenMP, and (iii) hybrid platform that utilizes both distributed and shared memory using MPI-OpenMP. The experimental results with both simulated and real DNA sequence data show that the shared memory OpenMP implementation provides at least two-times absolute speedup than the best sequential version of the algorithm and a relative speedup of almost 7. We provide a detailed comparison of the execution times among the implementations on different platforms with different versions of the algorithm. We also show that removing branch conditions negatively affects the performance of the CPU-based parallel algorithm on OpenMP platform.

Mapping iterative medical imaging algorithm on cell accelerator.

Algebraic reconstruction techniques require about half the number of projections as that of Fourier backprojection methods, which makes these methods safer in terms of required radiation dose. Algebraic reconstruction technique (ART) and its variant OS-SART (ordered subset simultaneous ART) are techniques that provide faster convergence with comparatively good image quality. However, the prohibitively long processing time of these techniques prevents their adoption in commercial CT machines. Parallel computing is one solution to this problem. With the advent of heterogeneous multicore architectures that exploit data parallel applications, medical imaging algorithms such as OS-SART can be studied to produce increased performance. In this paper, we map OS-SART on cell broadband engine (Cell BE). We effectively use the architectural features of Cell BE to provide an efficient mapping. The Cell BE consists of one powerPC processor element (PPE) and eight SIMD coprocessors known as synergetic processor elements (SPEs). The limited memory storage on each of the SPEs makes the mapping challenging. Therefore, we present optimization techniques to efficiently map the algorithm on the Cell BE for improved performance over CPU version. We compare the performance of our proposed algorithm on Cell BE to that of Sun Fire ×4600, a shared memory machine. The Cell BE is five times faster than AMD Opteron dual-core processor. The speedup of the algorithm on Cell BE increases with the increase in the number of SPEs. We also experiment with various parameters, such as number of subsets, number of processing elements, and number of DMA transfers between main memory and local memory, that impact the performance of the algorithm.