Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Graphics Processing Unit Computing

Markov clustering is becoming a key algorithm with in bioinformatics for determining clusters in networks. For instance, clustering protein interaction networks is helping find genes implicated in diseases such as cancer. However, with fast sequencing and other technologies generating vast amounts of data on biological networks, performance and scalability issues are becoming a critical limiting factorin applications. Meanwhile, Graphics Processing (GPU)computing, which uses a massively parallel computing environment in the GPU card, is becoming a very powerful, efficient and low cost option to achieve substantial performance gains over CPU approaches. This paper introduces a very fast Markov clustering algorithm (MCL) based on massive parallel computing in GPU. We use the Compute Unified Device Architecture (CUDA) to allow the GPU to perform parallel sparse matrix-matrix computations and parallel sparse Markov matrix normalizations, which are at the heart of the clustering algorithm. The key to optimizing our CUDA Markov Clustering (CUDAMCL) was utilizing ELLACK-R sparse data format to allow the effective and fine-grain massively parallel processing to cope with the sparse nature of interaction networks datasets in bioinformatics applications. CUDA also allows us to use on-chip memory on the GPU efficiently, to lower the latency time thus circumventing a major issue in other parallel computing environments, such as Message Passing Interface (MPI). Here we describe the GPU algorithm and its application to several real world problems as well as to artificial datasets. We find that the principle factor causing variation in performance of the GPU approach is the relative sparseness of networks. Comparing GPU computation times against a modern quad-core CPU on the published(relatively sparse) standard BIOGRID protein interaction networks with 5156 and 23175 nodes, speed factors of 4 times and 9 were obtained, respectively. On the Human Protein Reference Database, the speed of clustering of 19599 proteins was improved by a factor of 7 by the GPU algorithm. However, on artificially generated densely connected networks with 1600 to 4800 nodes, speedups by a factor in the range 40 to 120 times were readily obtained. As the results show, in all cases the GPU implementation is significantly faster than the original MCL running on CPU. Such approaches are allowing large-scale parallel computation on off-the-shelf desktop machines that were previously only possible on super-computing architectures, and have the potential to significantly change the way bioinformaticians and biologists compute and interact with their data.