Shibdas Bandyopadhyay

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We propose a new algorithm, PMS6, for the (l,d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. The run time ratio PMS5/PMS6, where PMS5 is the fastest previously known algorithm for motif discovery in large instances, ranges from a high of 2.20 for the(More)
Organizations in both public and private sectors have become increasingly dependent on electronic data processing. Protecting these important data is of utmost concern to the organizations and cryptography is one of the primary ways to do the job. Public Key Cryptography is used to protect digital data going through an insecure channel from one place to(More)
An agent is a computer software that is capable of taking independent action on behalf of its user or owner. It is an entity with goals, actions and domain knowledge, situated in an environment. Multiagent systems comprises of multiple autonomous, interacting computer software, or agents. These systems can successfully emulate the entities active in a(More)
We develop a radix sort algorithm, GRS, suitable to sort multifield records on a graphics processing unit (GPU). We assume the By Field layout for records to be sorted. GRS is benchmarked against the radix sort algorithm, SDK, in NVIDIA's CUDA SDK 3.0 [14] as well as the radix sort algorithm, SRTS, of Merrill and Grimshaw [11]. Although SRTS is faster than(More)
We adapt merge sort for a single SPU of the Cell Broadband Engine. This adaptation takes advantage of the vector instructions supported by the SPU. Experimental results indicate that our merge sort adaptation is faster than other sort algorithms (e.g., AA sort, Cell sort, quick sort) proposed for the SPU as well as faster than our SPU adaptations of shaker(More)
We extend the fastest comparison based (sample sort) and non-comparison based (radix sort) number sorting algorithms on a GPU to sort large multifield records. Two extensions - direct (the entire record is moved whenever its key is to be moved) and indirect ((key, index) pairs are sorted using the direct extension and then records are ordered according to(More)
2.1 Graphics Processing Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 2.2 Sorting Numbers on GPUs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 2.2.1 SDK Radix Sort Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .(More)
We develop an efficient multicore algorithm, PMS6MC, for the (l, d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. PMS6MC is based on PMS6, which is currently the fastest single-core algorithm for motif discovery in large instances. The speedup,(More)