62878
Single-hop probing asymptotics in available bandwidth estimation: sample-path analysis
In this paper, we take the sample-path approach in analyzing the asymptotic behavior of single-hop bandwidth estimation under bursty cross-traffic and show that these results are provably different from those observed under fluid models of prior work. This difference, which we call the probing bias, is one of the previously unknown factors that can cause measurement inaccuracies in available bandwidth estimation. We present an analytical formulation of "packet probing," based on which we derive several major properties of the probing bias. We then experimentally observe the <i>probing bias</i> and investigate its quantitative relationship to several deciding factors such as probing packet size, probing train length, and cross-traffic burstiness. Both our analytical and experimental results show that the probing bias vanishes as the packet-train length or packet size increases. The vanishing rate is decided by the burstiness of cross-traffic.
16904687
What signals do packet-pair dispersions carry?
Although packet-pair probing has been used as one of the primary mechanisms to measure bottleneck capacity, cross-traffic intensity, and available bandwidth of end-to-end Internet paths, there is still no conclusive answer as to what information about the path is contained in the output packet-pair dispersions and how it is encoded. In this paper, we address this issue by deriving closed-form expression of packet-pair dispersion in the context of a single-hop path and general bursty cross-traffic arrival. Under the assumptions of cross-traffic stationarity and ASTA sampling, we examine the statistical properties of the information encoded in inter-packet spacings and derive the asymptotic average of the output packet-pair dispersions as a closed-form function of the input dispersion. We show that this result is different from what was obtained in prior work using fluid cross-traffic models and that this discrepancy has a significant impact on the accuracy of packet-pair bandwidth estimation.
353647
On Estimating Tight-Link Bandwidth Characteristics over Multi-Hop Paths
In this paper, we explore multi-hop bandwidth estimation assuming arbitrary cross-traffic at each node and develop a new probing method called Envelope that can asymptotically estimate not only the available bandwidth but also the raw capacity of the tight link. Envelope is based on a multi-link recursive extension of unbiased single-hop estimators proposed in the past (e.g., [14]) and a variation of the packet-cartouche technique [6]. Through extensive simulations, we evaluate Envelope in various network settings and cross-traffic conditions and find that it can measure tight-link bandwidth characteristics with accuracy that significantly surpasses that of the existing methods. We also find that Envelope can measure non-tight links in certain path and cross-traffic configurations.
8305231
Packet-pair bandwidth estimation: stochastic analysis of a single congested node
We examine the problem of estimating the capacity of bottleneck links and available bandwidth of end-to-end paths under non-negligible cross-traffic conditions. We present a simple stochastic analysis of the problem in the context of a single congested node and derive several results that allow the construction of asymptotically-accurate bandwidth estimators. We first develop a generic queuing model of an Internet router and solve the estimation problem assuming renewal cross-traffic at the bottleneck link. Noticing that the renewal assumption on Internet flows is too strong, we investigate an alternative filtering solution that asymptotically converges to the desired values of the bottleneck capacity and available bandwidth under arbitrary (including non-stationary) cross-traffic. This is one of the first methods that simultaneously estimates both types of bandwidth and is provably accurate. We finish the paper by discussing the impossibility of a similar estimator for paths with two or more congested routers.
35018228
Service-Level Management of Adaptive Distributed Network Applications
The paper is on generic service-level management tools that enable the reconfiguration of a distributed network application whenever there are resource-level changes or failures in the underlying network sub-systems. A network service is provided to client applications through a protocol module, with the latter exercising network infrastructure resources in a manner to meet the client requirements. Client requests for a network service instantiate the underlying protocol module with parameters specified at the service interface level, along with a prescription of critical properties to be enforced therein. At run-time, a management module may automatically monitor the service compliance to client-prescribed requirements, and notify the client whenever a service quality degradation is detected. The paper proposes a ‘function’-based model of service provisioning to realize our management approach. In this model, a service prescription conforms to generic interface templates based on an enumeration of the service attributes visible to clients, and how these attributes logically relate to one another in composing a client-level quality expectation. Our management model is independent of the specifics of problem-domain, which simplifies the development of distributed adaptive applications through a ‘software reuse’ of the management module. The paper presents the case study of an application: CDN, to demonstrate the usefulness of our model.
1211146
Multi-hop probing asymptotics in available bandwidth estimation: stochastic analysis
This paper analyzes the asymptotic behavior of packet-train probing over a multi-hop network path P carrying arbitrarily routed bursty cross-traffic flows. We examine the statistical mean of the packet-train output dispersions and its relationship to the input dispersion. We call this relationship the response curve of path P. We show that the real response curve Z is tightly lower-bounded by its multi-hop fluid counterpart F, obtained when every cross-traffic flow on P is hypothetically replaced with a constant-rate fluid flow of the same average intensity and routing pattern. The real curve Z asymptotically approaches its fluid counterpart F as probing packet size or packet train length increases. Most existing measurement techniques are based upon the single-hop fluid curve S associated with the bottleneck link in P. We note that the curve S coincides with F in a certain large-dispersion input range, but falls below F in the remaining small-dispersion input ranges. As an implication of these findings, we show that bursty cross-traffic in multi-hop paths causes negative bias (asymptotic underestimation) to most existing techniques. This bias can be mitigated by reducing the deviation of Z from S using large packet size or long packet-trains. However, the bias is not completely removable for the techniques that use the portion of S that falls below F.
17203041
Tight upper bounds for cell loss probabilities in ATM multiplexers and required bandwidth estimation
Estimating the cell loss probability in an ATM multiplexer is a key issue in network management and traffic control such as call admission control and bandwidth allocation. In this paper, we derive a new approximation to estimate the total and individual cell loss probabilities in an ATM multiplexer fed by a superposition of heterogeneous on-off sources with exponentially distributed on and off periods. Based on this approximation, a simple and accurate method is proposed to estimate the aggregate required bandwidth by a given mix of traffic to guarantee a given cell loss probability.
2696332
A boosting approach for motif modeling using ChIP-chip data
MOTIVATION
Building an accurate binding model for a transcription factor (TF) is essential to differentiate its true binding targets from those spurious ones. This is an important step toward understanding gene regulation.


RESULTS
This paper describes a boosting approach to modeling TF-DNA binding. Different from the widely used weight matrix model, which predicts TF-DNA binding based on a linear combination of position-specific contributions, our approach builds a TF binding classifier by combining a set of weight matrix based classifiers, thus yielding a non-linear binding decision rule. The proposed approach was applied to the ChIP-chip data of Saccharomyces cerevisiae. When compared with the weight matrix method, our new approach showed significant improvements on the specificity in a majority of cases.
17555727
A sensitivity analysis of low-power repeater insertion
In this paper, we perform the first quantitative study on the sensitivities of repeater power to available repeater width and candidate location, two key parameters of the dynamic programming (DP) based repeater insertion algorithms. Based on our analysis, we propose a simple yet effective scheme to select repeater widths and locations for DP-based algorithms, achieving an excellent trade-off between the solution quality and runtime. Experimental results have shown that, when combined with our sensitivity-guided scheme, the DP algorithm can attain more than 6 times speedup with negligible power degradation.
5601540
A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences
MOTIVATION
Transcription factors (TFs) regulate gene expression by recognizing and binding to specific regulatory regions on the genome, which in higher eukaryotes can occur far away from the regulated genes. Recently, Affymetrix developed the high-density oligonucleotide arrays that tile all the non-repetitive sequences of the human genome at 35 bp resolution. This new array platform allows for the unbiased mapping of in vivo TF binding sequences (TFBSs) using Chromatin ImmunoPrecipitation followed by microarray experiments (ChIP-chip). The massive dataset generated from these experiments pose great challenges for data analysis.


RESULTS
We developed a fast, scalable and sensitive method to extract TFBSs from ChIP-chip experiments on genome tiling arrays. Our method takes advantage of tiling array data from many experiments to normalize and model the behavior of each individual probe, and identifies TFBSs using a hidden Markov model (HMM). When applied to the data of p53 ChIP-chip experiments from an earlier study, our method discovered many new high confidence p53 targets including all the regions verified by quantitative PCR. Using a de novo motif finding algorithm MDscan, we also recovered the p53 motif from our HMM identified p53 target regions. Furthermore, we found substantial p53 motif enrichment in these regions comparing with both genomic background and the TFBSs identified earlier. Several of the newly identified p53 TFBSs are in the promoter region of known genes or associated with previously characterized p53-responsive genes.


SUPPLEMENTARY INFORMATION
Available at the following URL http://genome.dfci.harvard.edu/~xsliu/HMMTiling/index.html.
30635259
On global exponential stability of generalized stochastic neural networks with mixed time-delays
Abstract This paper is concerned with the global exponential stability analysis problem for a general class of stochastic neural networks with mixed time-delays. The mixed time-delays under consideration comprise both the discrete time-varying delays and the distributed time-delays. The main purpose of this paper is to establish easily verifiable conditions under which the delayed stochastic neural network is exponentially stable in the mean square in the presence of both the discrete and distributed delays. By employing a new Lyapunov–Krasovskii functional and conducting stochastic analysis, a linear matrix inequality (LMI) approach is developed to derive the criteria of the exponential stability. Furthermore, the main results are specialized to deal with the analysis problem for the global asymptotic stability within the same LMI framework. The proposed criteria can be readily checked by using some standard numerical packages such as the Matlab LMI toolbox. A simple example is provided to demonstrate the effectiveness and applicability of the proposed testing criteria.