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Articles 1 - 5 of 5
Full-Text Articles in Entire DC Network
Dmctcp: Desynchronized Multi-Channel Tcp For High Speed Access Networks With Tiny Buffers, Cheng Cui, Lin Xue, Chui Hui Chiu, Praveenkumar Kondikoppa, Seung Jong Park
Dmctcp: Desynchronized Multi-Channel Tcp For High Speed Access Networks With Tiny Buffers, Cheng Cui, Lin Xue, Chui Hui Chiu, Praveenkumar Kondikoppa, Seung Jong Park
Computer Science Faculty Research & Creative Works
The past few years have witnessed debate on how to improve link utilization of high-speed tiny-size buffer routers. Widely argued proposals for TCP traffic to realize acceptable link capacities mandate: (i) over-provisioned core link bandwidth; and (ii) non-bursty flows; and (iii) tens of thousands of asynchronous flows. However, in high-speed access networks where flows are bursty, sparse and synchronous, TCP traffic suffer severely from routers with tiny buffers. We propose a new congestion control algorithm called Desyn-chronized Multi-Channel TCP (DMCTCP) that creates a flow with multiple channels. It avoids TCP loss synchronization by desynchronizing channels, and it avoids sending rate …
Graph-Regularized Dual Lasso For Robust Eqtl Mapping, Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang
Graph-Regularized Dual Lasso For Robust Eqtl Mapping, Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang
Computer Science Faculty Research & Creative Works
Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and …
Mapreduce-Based Restmd: Enabling Large-Scale Sampling Tasks With Distributed Hpc Systems, Praveenkumar Kondikoppa, Richard Platania, Seung Jong Park, Tom Keyes, Jaegil Kim, Nayong Kim, Joohyun Kim, Shuju Bai
Mapreduce-Based Restmd: Enabling Large-Scale Sampling Tasks With Distributed Hpc Systems, Praveenkumar Kondikoppa, Richard Platania, Seung Jong Park, Tom Keyes, Jaegil Kim, Nayong Kim, Joohyun Kim, Shuju Bai
Computer Science Faculty Research & Creative Works
A novel implementation of Replica Exchange Statistical Temperature Molecular Dynamics (RESTMD), belonging to a generalized ensemble method and also known as parallel tempering, is presented. Our implementation employs the MapReduce (MR)-based iterative framework for launching RESTMD over high performance computing (HPC) clusters including our test bed system, Cyber-infrastructure for Reconfigurable Optical Networks (CRON) simulating a network-connected distributed system. Our main contribution is a new implementation of STMD plugged into the well-known CHARMM molecular dynamics package as well as the RESTMD implementation powered by the Hadoop that scales out in a cluster and across distributed systems effectively. To address challenges for …
Mapreduce Based Parallel Suffix Tree Construction For Human Genome, Umesh Chandra Satish, Praveenkumar Kondikoppa, Seung Jong Park, Manish Patil, Rahul Shah
Mapreduce Based Parallel Suffix Tree Construction For Human Genome, Umesh Chandra Satish, Praveenkumar Kondikoppa, Seung Jong Park, Manish Patil, Rahul Shah
Computer Science Faculty Research & Creative Works
Genome indexing is the basis for many bioinformatics applications. Read mapping (sequence alignment) is one such application where the goal is to align millions of short reads against reference genome. Several tools are available for read mapping which rely on different indexing techniques to expedite the alignment process. However, many of these contemporary alignment programs are sequential, memory intensive and cannot be easily scaled for larger genomes. Suffix tree is one of the most widely used data structures for indexing strings (genomes). Building a scalable suffix-tree based tool is particularly challenging due to the difficulties involved in parallel construction of …
Impact Of Loss Synchronization On Reliable High Speed Networks: A Model Based Simulation, Suman Kumar, Lin Xue, Seung Jong Park
Impact Of Loss Synchronization On Reliable High Speed Networks: A Model Based Simulation, Suman Kumar, Lin Xue, Seung Jong Park
Computer Science Faculty Research & Creative Works
Contemporary nature of network evolution demands for simulation models which are flexible, scalable, and easily implementable. In this paper, we propose a fluid-based model for performance analysis of reliable high-speed networks. In particular, this paper aims to study the dynamic relationship between congestion control algorithms and queue management schemes, in order to develop a better understanding of the causal linkages between the two. We propose a loss synchronization module which is user configurable. We validate our model through simulations under controlled settings. Also, we present a performance analysis to provide insights into two important issues concerning 10 Gbps high speed …