The Smith-Waterman (SW) algorithm is the best choice for searching similar regions between two DNA or protein sequences. However, it may become impracticable in some contexts due to its high computational demands. Consequently, the computer science community has focused on the use of modern parallel architectures such as Graphics Processing Units (GPUs), Xeon Phi accelerators and Field Programmable Gate Arrays (FGPAs) to speed up large-scale workloads. This paper presents and evaluates SWIFOLD: a Smith-Waterman parallel Implementation on FPGA with OpenCL for Long DNA sequences. First, we evaluate its performance and resource usage for different kernel configurations. Next, we carry out a performance comparison between our tool and other state-of-the-art implementations considering three different datasets. SWIFOLD offers the best average performance for small and medium test sets, achieving a performance that is independent of input size and sequence similarity. In addition, SWIFOLD provides competitive performance rates in comparison with GPU-based implementations on the latest GPU generation for the large dataset. The results suggest that SWIFOLD can be a serious contender for accelerating the SW alignment of DNA sequences of unrestricted size in an affordable way reaching on average 125 GCUPS and almost a peak of 270 GCUPS.

Addressing the huge amount of data continuously generated is an important challenge in the Machine Learning field. The need to adapt the traditional techniques or create new ones is evident. To do so, distributed technologies have to be used to deal with the significant scalability constraints due to the Big Data context. In many Big Data applications for classification, there are some classes that are highly underrepresented, leading to what is known as the imbalanced classification problem. In this scenario, learning algorithms are often biased towards the majority classes, treating minority ones as outliers or noise. Consequently, preprocessing techniques to balance the class distribution were developed. This can be achieved by suppressing majority instances (undersampling) or by creating minority examples (oversampling). Regarding the oversampling methods, one of the most widespread is the SMOTE algorithm, which creates artificial examples according to the neighborhood of each minority class instance. In this work, our objective is to analyze the SMOTE behavior in Big Data as a function of some key aspects such as the oversampling degree, the neighborhood value and, specially, the type of distributed design (local vs. global).

In this paper, a methodological data condensation approach for reducing tabular big datasets in classification problems is presented, named FDR${}^2$-BD. The key of our proposal is to analyze data in a dual way (vertical and horizontal), so as to provide a smart combination between feature selection to generate dense clusters of data and uniform sampling reduction to keep only a few representative samples from each problem area. Its main advantage is allowing the model’s predictive quality to be kept in a range determined by a user’s threshold. Its robustness is built on a hyper-parametrization process, in which all data are taken into consideration by following a k-fold procedure. Another significant capability is being fast and scalable by using fully optimized parallel operations provided by Apache Spark. An extensive experimental study is performed over 25 big datasets with different characteristics. In most cases, the obtained reduction percentages are above 95%, thus outperforming state-of-the-art solutions such as FCNN_MR that barely reach 70%. The most promising outcome is maintaining the representativeness of the original data information, with quality prediction values around 1% of the baseline.

The heterogeneous computing paradigm has led to the need for portable and efficient programming solutions that can leverage the capabilities of various hardware devices, such as NVIDIA, Intel, and AMD GPUs. This study evaluates the portability and performance of the SYCL and CUDA languages for one fundamental bioinformatics application (Smith-Waterman protein database search) across different GPU architectures, considering single and multi-GPU configurations from different vendors. The experimental work showed that, while both CUDA and SYCL versions achieve similar performance on NVIDIA devices, the latter demonstrated remarkable code portability to other GPU architectures, such as AMD and Intel. Furthermore, the architectural efficiency rates achieved on these devices were superior in 3 of the 4 cases tested. This brief study highlights the potential of SYCL as a viable solution for achieving both performance and portability in the heterogeneous computing ecosystem.

Bioinformatics and computational biology are two fields that have been exploiting GPUs for more than two decades, with being CUDA the most used programming language for them. However, as CUDA is an NVIDIA proprietary language, it implies a strong portability restriction to a wide range of heterogeneous architectures, like AMD or Intel GPUs. To face this issue, the Khronos group has recently proposed the SYCL standard, which is an open, royalty-free, cross-platform abstraction layer that enables the programming of a heterogeneous system to be written using standard, single-source C++ code. Over the past few years, several implementations of this SYCL standard have emerged, being oneAPI the one from Intel. This paper presents the migration process of theSW# suite, a biological sequence alignment tool developed in CUDA, to SYCL using Intel’s oneAPI ecosystem. The experimental results show thatSW# was completely migrated with a small programmer intervention in terms of hand-coding. In addition, it was possible to port the migrated code between different architectures (considering multiple vendor GPUs and also CPUs), with no noticeable performance degradation on five different NVIDIA GPUs. Moreover, performance remained stable when switching to another SYCL implementation. As a consequence, SYCL and its implementations can offer attractive opportunities for the bioinformatics community, especially considering the vast existence of CUDA-based legacy codes.