An optimal algorithm for global termination detection in shared-memory asynchronous multiprocessor systems

In the literature, the problem of global termination detection in parallel systems is usually solved by message passing. In shared-memory systems, this problem can also be solved by using exclusively accessible variables with locking mechanisms. In this paper, we present an algorithm that solves the problem of global termination detection in shared-memory asynchronous multiprocessor systems without using locking. We assume a reasonable computation model in which concurrent reading does not require locking and concurrent writing different values without locking results in an arbitrary one of the values being actually written. For a system of n processors, the algorithm allocates a working space of 2n + 1 bits. The worst case time complexity of the algorithm is n + 2√n + 1, which we prove is the lower bound under a reasonable model of computation. © 1997 IEEE.published_or_final_versio

Improving the time complexity of message-optimal distributed algorithms for minimum-weight spanning trees

A distributed algorithm is presented that constructs the minimum-weight spanning tree of an undirected connected graph with distinct node identities. Initially, each node knows only the weight of each of its adjacent edges. When the algorithm terminates, each node knows which of its adjacent edges are edges of the tree. For a graph with n nodes and e edges, the total number of messages required by this algorithm is at most 5n log n + 2e, where each message contains at most one edge weight plus 3 + log n bits. Although the algorithm presented here has the same message complexity as the previously known algorithm due to R.G. Gallager, P.A. Humblet, and P.M. Spira, the time complexity of the algorithm presented improves from Gallager's O(n log n) to O(n log n) time units, where log k is the number of times the log function must be applied to k to obtain a result less than or equal to one. A worst case of Ω(n log n) is also possible. In addition, when the network is synchronous, the algorithm presented is modified further to solve the same problem with the same message complexity but in O(n) time.published_or_final_versio

A simple and economical method for improving whole genome alignment

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PnpProbs: A better multiple sequence alignment tool by better handling of guide trees

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Online pricing for multi-type of Items

LNCS v. 7285 entitled: Frontiers in algorithmics and algorithmic aspects in information and management: joint international conference, FAW-AAIM 2012 ... proceedingsIn this paper, we study the problem of online pricing for bundles of items. Given a seller with k types of items, m of each, a sequence of users {u 1, u 2, ...} arrives one by one. Each user is single-minded, i.e., each user is interested only in a particular bundle of items. The seller must set the price and assign some amount of bundles to each user upon his/her arrival. Bundles can be sold fractionally. Each u i has his/her value function v i (·) such that v i (x) is the highest unit price u i is willing to pay for x bundles. The objective is to maximize the revenue of the seller by setting the price and amount of bundles for each user. In this paper, we first show that the lower bound of the competitive ratio for this problem is Ω(logh + logk), where h is the highest unit price to be paid among all users. We then give a deterministic online algorithm, Pricing, whose competitive ratio is O (√k·log h log k). When k = 1 the lower and upper bounds asymptotically match the optimal result O(logh). © 2012 Springer-Verlag.postprin

Online algorithms for 1-space bounded multi dimensional bin packing and hypercube packing

In this paper, we study 1-space bounded multi-dimensional bin packing and hypercube packing. A sequence of items arrive over time, each item is a d-dimensional hyperbox (in bin packing) or hypercube (in hypercube packing), and the length of each side is no more than 1. These items must be packed without overlapping into d-dimensional hypercubes with unit length on each side. In d-dimensional space, any two dimensions i and j define a space P ij. When an item arrives, we must pack it into an active bin immediately without any knowledge of the future items, and 90 {ring operator}-rotation on any plane P ij is allowed. The objective is to minimize the total number of bins used for packing all these items in the sequence. In the 1-space bounded variant, there is only one active bin for packing the current item. If the active bin does not have enough space to pack the item, it must be closed and a new active bin is opened. For d-dimensional bin packing, an online algorithm with competitive ratio 4 d is given. Moreover, we consider d-dimensional hypercube packing, and give a 2 d+1-competitive algorithm. These two results are the first study on 1-space bounded multi dimensional bin packing and hypercube packing. © 2012 The Author(s).published_or_final_versionSpringer Open Choice, 28 May 201

An efficient algorithm for optimizing whole genome alignment with noise

Motivation: This paper is concerned with algorithms for aligning two whole genomes so as to identify regions that possibly contain conserved genes. Motivated by existing heuristic-based software tools, we initiate the study of an optimization problem that attempts to uncover conserved genes with a global concern. Another interesting feature in our formulation is the tolerance of noise, which also complicates the optimization problem. A brute-force approach takes time exponential in the noise level. Results: We show how an insight into the optimization structure can lead to a drastic improvement in the time and space requirement [precisely, to O(k2n2) and O(k2n), respectively, where n is the size of the input and k is the noise level]. The reduced space requirement allows us to implement the new algorithm, called MaxMinCluster, on a PC. It is exciting to see that when tested with different real data sets, MaxMinCluster consistently uncovers a high percentage of conserved genes that have been published by GenBank. Its performance is indeed favorably compared to MUMmer (perhaps the most popular software tool for uncovering conserved genes in a whole-genome scale). © Oxford University Press 2004; all rights reserved.published_or_final_versio

A simple algorithm for finding all k-edge-connected components

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Nutrient supplemented serum-free medium increases cardiomyogenesis efficiency of human pluripotent stem cells.

AIM: To development of an improved p38 MAPK inhibitor-based serum-free medium for embryoid body cardiomyocyte differentiation of human pluripotent stem cells. METHODS: Human embryonic stem cells (hESC) differentiated to cardiomyocytes (CM) using a p38 MAPK inhibitor (SB203580) based serum-free medium (SB media). Nutrient supplements known to increase cell viability were added to SB medium. The ability of these supplements to improve cardiomyogenesis was evaluated by measurements of cell viability, total cell count, and the expression of cardiac markers via flow cytometry. An improved medium containing Soy hydrolysate (HySoy) and bovine serum albumin (BSA) (SupSB media) was developed and tested on 2 additional cell lines (H1 and Siu-hiPSC). Characterization of the cardiomyocytes was done by immunohistochemistry, electrophysiology and quantitative real-time reverse transcription-polymerase chain reaction. RESULTS: hESC cell line, HES-3, differentiating in SB medium for 16 d resulted in a cardiomyocyte yield of 0.07 +/- 0.03 CM/hESC. A new medium (SupSB media) was developed with the addition of HySoy and BSA to SB medium. This medium resulted in 2.6 fold increase in cardiomyocyte yield (0.21 +/- 0.08 CM/hESC). The robustness of SupSB medium was further demonstrated using two additional pluripotent cell lines (H1, hESC and Siu1, hiPSC), showing a 15 and 9 fold increase in cardiomyocyte yield respectively. The age (passage number) of the pluripotent cells did not affect the cardiomyocyte yields. Embryoid body (EB) cardiomyocytes formed in SupSB medium expressed canonical cardiac markers (sarcomeric alpha-actinin, myosin heavy chain and troponin-T) and demonstrated all three major phenotypes: nodal-, atrial- and ventricular-like. Electrophysiological characteristics (maximum diastolic potentials and action potential durations) of cardiomyocytes derived from SB and SupSB media were similar. CONCLUSION: The nutrient supplementation (HySoy and BSA) leads to increase in cell viability, cell yield and cardiac marker expression during cardiomyocyte differentiation, translating to an overall increase in cardiomyocyte yield.published_or_final_versio

GLProbs: Aligning multiple sequences adaptively

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