How well do we understand the clusters found in microarray data?

Clare, A. and King R.D. (2002) How well do we understand the clusters found in microarray data? In In Silico Biol. 2, 0046

Topological changes in a two-dimensional foam cluster

Cox, S.J., Vaz, M.F. and Weaire, D. (2003) Topological changes in a two-dimensional foam cluster. The European Physical Journal E - Soft Matter . 11:29-35.

Simultaneous ant colony optimisation algorithms for learning linguistic fuzzy rules

M. Galea and Q. Shen. Simultaneous ant colony optimisation algorithms for learning linguistic fuzzy rules. A. Abraham, C. Grosan and V. Ramos (Eds.), Swarm Intelligence in Data Mining, pages 75-99.

Ocena wiarygodności metod identyfikacji strumieni meteoroidowych

Wydział Fizyki:Instytut Obserwatorium Astronomiczne

Pricing Algorithms For a Two-sided Internet Advertisement Market

The Google AdSense Program is a successful internet advertisement program where Google places contextual adverts on third-party websites and shares the resulting revenue with each publisher. Advertisers have budgets and bid on ad slots while publishers set reserve prices for the ad slots on their websites. Following previous modelling efforts, we model the program as a two-sided market with advertisers on one side and publishers on the other. We show a reduction from the Generalised Assignment Problem (GAP) to the problem of computing the revenue maximising allocation and pricing of publisher slots under a first-price auction. GAP is APX-hard but a (1-1/e) approximation is known. We compute truthful and revenue-maximizing prices and allocation of ad slots to advertisers under a second-price auction. The auctioneer's revenue is within (1-1/e) second-price optimal.

Mapping Parallel Iterative Algorithms onto Workstation Networks

For communication-intensive parallel applications, the maximum degree of concurrency achievable is limited by the communication throughput made available by the network. In previous work [HPS94], we showed experimentally that the performance of certain parallel applications running on a workstation network can be improved significantly if a congestion control protocol is used to enhance network performance. In this paper, we characterize and analyze the communication requirements of a large class of supercomputing applications that fall under the category of fixed-point problems, amenable to solution by parallel iterative methods. This results in a set of interface and architectural features sufficient for the efficient implementation of the applications over a large-scale distributed system. In particular, we propose a direct link between the application and network layer, supporting congestion control actions at both ends. This in turn enhances the system's responsiveness to network congestion, improving performance. Measurements are given showing the efficacy of our scheme to support large-scale parallel computations.

How Good are Genetic Algorithms at Finding Large Cliques: An Experimental Study

This paper investigates the power of genetic algorithms at solving the MAX-CLIQUE problem. We measure the performance of a standard genetic algorithm on an elementary set of problem instances consisting of embedded cliques in random graphs. We indicate the need for improvement, and introduce a new genetic algorithm, the multi-phase annealed GA, which exhibits superior performance on the same problem set. As we scale up the problem size and test on \hard" benchmark instances, we notice a degraded performance in the algorithm caused by premature convergence to local minima. To alleviate this problem, a sequence of modi cations are implemented ranging from changes in input representation to systematic local search. The most recent version, called union GA, incorporates the features of union cross-over, greedy replacement, and diversity enhancement. It shows a marked speed-up in the number of iterations required to find a given solution, as well as some improvement in the clique size found. We discuss issues related to the SIMD implementation of the genetic algorithms on a Thinking Machines CM-5, which was necessitated by the intrinsically high time complexity (O(n3)) of the serial algorithm for computing one iteration. Our preliminary conclusions are: (1) a genetic algorithm needs to be heavily customized to work "well" for the clique problem; (2) a GA is computationally very expensive, and its use is only recommended if it is known to find larger cliques than other algorithms; (3) although our customization e ort is bringing forth continued improvements, there is no clear evidence, at this time, that a GA will have better success in circumventing local minima.

On the Performance of Polynomial-time CLIQUE Approximation Algorithms on Very Large Graphs

The performance of a randomized version of the subgraph-exclusion algorithm (called Ramsey) for CLIQUE by Boppana and Halldorsson is studied on very large graphs. We compare the performance of this algorithm with the performance of two common heuristic algorithms, the greedy heuristic and a version of simulated annealing. These algorithms are tested on graphs with up to 10,000 vertices on a workstation and graphs as large as 70,000 vertices on a Connection Machine. Our implementations establish the ability to run clique approximation algorithms on very large graphs. We test our implementations on a variety of different graphs. Our conclusions indicate that on randomly generated graphs minor changes to the distribution can cause dramatic changes in the performance of the heuristic algorithms. The Ramsey algorithm, while not as good as the others for the most common distributions, seems more robust and provides a more even overall performance. In general, and especially on deterministically generated graphs, a combination of simulated annealing with either the Ramsey algorithm or the greedy heuristic seems to perform best. This combined algorithm works particularly well on large Keller and Hamming graphs and has a competitive overall performance on the DIMACS benchmark graphs.

A Spectrum of TCP-Friendly Window-Based Congestion Control Algorithms

The increased diversity of Internet application requirements has spurred recent interests in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The parameterization of these control rules is done so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. In this paper, we define a new spectrum of window-based congestion control algorithms that are TCP-friendly as well as TCP-compatible under RED. Contrary to previous memory-less controls, our algorithms utilize history information in their control rules. Our proposed algorithms have two salient features: (1) They enable a wider region of TCP-friendliness, and thus more flexibility in trading off among smoothness, aggressiveness, and responsiveness; and (2) they ensure a faster convergence to fairness under a wide range of system conditions. We demonstrate analytically and through extensive ns simulations the steady-state and transient behaviors of several instances of this new spectrum of algorithms. In particular, SIMD is one instance in which the congestion window is increased super-linearly with time since the detection of the last loss. Compared to recently proposed TCP-friendly AIMD and binomial algorithms, we demonstrate the superiority of SIMD in: (1) adapting to sudden increases in available bandwidth, while maintaining competitive smoothness and responsiveness; and (2) rapidly converging to fairness and efficiency.

A Spectrum of TCP-friendly Window-Based Congestion Control Algorithms

The increasing diversity of Internet application requirements has spurred recent interest in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The control rules are parameterized so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. This paper presents a comprehensive study of a new spectrum of window-based congestion controls, which are TCP-friendly as well as TCP-compatible under RED. Our controls utilize history information in their control rules. By doing so, they improve the transient behavior, compared to recently proposed slowly-responsive congestion controls such as general AIMD and binomial controls. Our controls can achieve better tradeoffs among smoothness, aggressiveness, and responsiveness, and they can achieve faster convergence. We demonstrate analytically and through extensive ns simulations the steady-state and transient behavior of several instances of this new spectrum.

Cluster-Based Optimizations for Distributed Hash Tables

We consider the problem of performing topological optimizations of distributed hash tables. Such hash tables include Chord and Tapestry and are a popular building block for distributed applications. Optimizing topologies over one dimensional hash spaces is particularly difficult as the higher dimensionality of the underlying network makes close fits unlikely. Instead, current schemes are limited to heuristically performing local optimizations finding the best of small random set of peers. We propose a new class of topology optimizations based on the existence of clusters of close overlay members within the underlying network. By constructing additional overlays for each cluster, a significant portion of the search procedure can be performed within the local cluster with a corresponding reduction in the search time. Finally, we discuss the effects of these additional overlays on spatial locality and other load balancing scheme.

On Clustering Images Using Compression

The need for the ability to cluster unknown data to better understand its relationship to know data is prevalent throughout science. Besides a better understanding of the data itself or learning about a new unknown object, cluster analysis can help with processing data, data standardization, and outlier detection. Most clustering algorithms are based on known features or expectations, such as the popular partition based, hierarchical, density-based, grid based, and model based algorithms. The choice of algorithm depends on many factors, including the type of data and the reason for clustering, nearly all rely on some known properties of the data being analyzed. Recently, Li et al. proposed a new universal similarity metric, this metric needs no prior knowledge about the object. Their similarity metric is based on the Kolmogorov Complexity of objects, the objects minimal description. While the Kolmogorov Complexity of an object is not computable, in "Clustering by Compression," Cilibrasi and Vitanyi use common compression algorithms to approximate the universal similarity metric and cluster objects with high success. Unfortunately, clustering using compression does not trivially extend to higher dimensions. Here we outline a method to adapt their procedure to images. We test these techniques on images of letters of the alphabet.

Load Balancing a Cluster of Web Servers using Distributed Packet Rewriting

In this paper, we propose and evaluate an implementation of a prototype scalable web server. The prototype consists of a load-balanced cluster of hosts that collectively accept and service TCP connections. The host IP addresses are advertised using the Round Robin DNS technique, allowing any host to receive requests from any client. Once a client attempts to establish a TCP connection with one of the hosts, a decision is made as to whether or not the connection should be redirected to a different host---namely, the host with the lowest number of established connections. We use the low-overhead Distributed Packet Rewriting (DPR) technique to redirect TCP connections. In our prototype, each host keeps information about connections in hash tables and linked lists. Every time a packet arrives, it is examined to see if it has to be redirected or not. Load information is maintained using periodic broadcasts amongst the cluster hosts.

Popularity-Aware GreedyDual-Size Web Proxy Caching Algorithms

Web caching aims to reduce network traffic, server load, and user-perceived retrieval delays by replicating "popular" content on proxy caches that are strategically placed within the network. While key to effective cache utilization, popularity information (e.g. relative access frequencies of objects requested through a proxy) is seldom incorporated directly in cache replacement algorithms. Rather, other properties of the request stream (e.g. temporal locality and content size), which are easier to capture in an on-line fashion, are used to indirectly infer popularity information, and hence drive cache replacement policies. Recent studies suggest that the correlation between these secondary properties and popularity is weakening due in part to the prevalence of efficient client and proxy caches (which tend to mask these correlations). This trend points to the need for proxy cache replacement algorithms that directly capture and use popularity information. In this paper, we (1) present an on-line algorithm that effectively captures and maintains an accurate popularity profile of Web objects requested through a caching proxy, (2) propose a novel cache replacement policy that uses such information to generalize the well-known GreedyDual-Size algorithm, and (3) show the superiority of our proposed algorithm by comparing it to a host of recently-proposed and widely-used algorithms using extensive trace-driven simulations and a variety of performance metrics.

Eliminating Redundant Training Data Using Unsupervised Clustering Techniques

Training data for supervised learning neural networks can be clustered such that the input/output pairs in each cluster are redundant. Redundant training data can adversely affect training time. In this paper we apply two clustering algorithms, ART2 -A and the Generalized Equality Classifier, to identify training data clusters and thus reduce the training data and training time. The approach is demonstrated for a high dimensional nonlinear continuous time mapping. The demonstration shows six-fold decrease in training time at little or no loss of accuracy in the handling of evaluation data.