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Application-Level Optimization of Big Data Transfers Through Pipelining, Parallelism and Concurrency In end-to-end data transfers, there are several factors affecting the data transfer throughput, such as the network characteristics (e.g. network bandwidth, round-trip-time, background traffic); end-system characteristics (e.g. NIC capacity, number of CPU cores and their clock rate, number of disk drives and their I/O rate); and the dataset characteristics (e.g. average file size, dataset size, file size distribution). Optimization of big data transfers over inter-cloud and intra-cloud networks is a challenging task that requires joint-consideration of all of these parameters. This optimization task becomes even more challenging when transferring datasets comprised of heterogeneous file sizes (i.e. large files and small files mixed). Previous work in this area only focuses on the end-system and network characteristics however does not provide models regarding the dataset characteristics. In this study, we analyze the effects of the three most important transfer parameters that are used to enhance data transfer throughput: pipelining, parallelism and concurrency. We provide models and guidelines to set the best values for these parameters and present two different transfer optimization algorithms that use the models developed.The tests conducted over high-speed networking and cloud testbeds show that our algorithms outperform the most popular data transfer tools like Globus Online and UDT in majority of the cases.