9254987
Methodological frameworks for large-scale network analysis and design
This paper emphasizes the need for methodological frameworks for analysis and design of large scale networks which are independent of specific design innovations and their advocacy, with the aim of making networking a more systematic engineering discipline. Networking problems have largely confounded existing theory, and innovation based on intuition has dominated design. This paper will illustrate potential pitfalls of this practice. The general aim is to illustrate universal aspects of theoretical and methodological research that can be applied to network design and verification. The issues focused on will include the choice of models, including the relationship between flow and packet level descriptions, the need to account for uncertainty generated by modelling abstractions, and the challenges of dealing with network scale. The rigorous comparison of proposed schemes will be illustrated using various abstractions. While standard tools from robust control theory have been applied in this area, we will also illustrate how network-specific challenges can drive the development of new mathematics that expand their range of applicability, and how many enormous challenges remain.
6185794
Cross-layer optimization in TCP/IP networks
TCP-AQM can be interpreted as distributed primal-dual algorithms to maximize aggregate utility over source rates. We show that an equilibrium of TCP/IP, if exists, maximizes aggregate utility over both source rates and routes, provided congestion prices are used as link costs. An equilibrium exists if and only if this utility maximization problem and its Lagrangian dual have no duality gap. In this case, TCP/IP incurs no penalty in not splitting traffic across multiple paths. Such an equilibrium, however, can be unstable. It can be stabilized by adding a static component to link cost, but at the expense of a reduced utility in equilibrium. If link capacities are optimally provisioned, however, pure static routing, which is necessarily stable, is sufficient to maximize utility. Moreover single-path routing again achieves the same utility as multipath routing at optimality.
6775847
A first-principles approach to understanding the internet's router-level topology
A detailed understanding of the many facets of the Internet's topological structure is critical for evaluating the performance of networking protocols, for assessing the effectiveness of proposed techniques to protect the network from nefarious intrusions and attacks, or for developing improved designs for resource provisioning. Previous studies of topology have focused on interpreting measurements or on phenomenological descriptions and evaluation of graph-theoretic properties of topology generators. We propose a complementary approach of combining a more subtle use of statistics and graph theory with a first-principles theory of router-level topology that reflects practical constraints and tradeoffs. While there is an inevitable tradeoff between model complexity and fidelity, a challenge is to distill from the seemingly endless list of potentially relevant technological and economic issues the features that are most essential to a solid understanding of the intrinsic fundamentals of network topology. We claim that very simple models that incorporate hard technological constraints on router and link bandwidth and connectivity, together with abstract models of user demand and network performance, can successfully address this challenge and further resolve much of the confusion and controversy that has surrounded topology generation and evaluation.
5737470
A pragmatic approach to dealing with high-variability in network measurements
The Internet is teeming with high variability phenomena, from measured IP flow sizes to aspects of inferred router-level connectivity, but there still exists considerable debate about how best to deal with this encountered high variability and model it. While one popular approach favors modeling highly variable event sizes with conventional, finite variance distributions such as lognormal or Weibull distributions, Mandelbrot has argued for the last 40 years that there are compelling mathematical, statistical, and practical reasons for why infinite variance distributions are natural candidates for capturing the essence behind high variability phenomena. In this paper, we elaborate on Mandelbrot's arguments and present a methodology that often allows for a clear distinction between the two approaches. In particular, by requiring the resulting models to be resilient to ambiguities (i.e., robust to real-world deficiencies in the underlying network measurements) and internally self-consistent (i.e., insensitive with respect the duration, location, or time of the data collection), we provide a rigorous framework for a qualitative assessment of the observed high variability. We apply the proposed framework to assess previously reported findings about measured Internet traffic and inferred router- and AS-level connectivity. In the process, we also discuss what our approach has to say about recent discussions concerning network traffic being Poisson or self-similar and router-level or AS-level connectivity graphs of the Internet being scale-free or not.
21164331
Optimization model of internet protocols
Layered architecture is one of the most fundamental and influential structures of network design. Can we integrate the various protocol layers into a single coherent theory by regarding them as carrying out an asynchronous distributed primal-dual computation over the network to implicitly solve a global optimization problem? Different layers iterate on different subsets of the decision variables using local information to achieve individual optimalities, but taken together, these local algorithms attempt to achieve a global objective. Such a theory will expose the interconnection between protocol layers and can be used to study rigorously the performance tradeoff in protocol layering as different ways to distribute a centralized computation. In this talk, we describe some preliminary work towards this goal and discuss some of the difficulties of this approach.
32109138
Rewriting Queries for XML Integration Systems
A data integration system typically creates a target XML schema to represent an application domain and source schemas are mapped to the target schema. A user poses a query over the target schema, and the system rewrites the query into a set of queries over the data sources. Existing algorithms generate a set of static rules based on the target schema and mappings, and rewrite the target query using these rules. We design a flexible and dynamic approach that rewrites XML queries directly based on the mappings between the target and source schemas. Theoretical analysis and experiments on both synthetic and real-world datasets indicate that the proposed approach is efficient and scalable.
11083681
MARD: a new method to detect differential gene expression in treatment-control time courses
MOTIVATION
Characterizing the dynamic regulation of gene expression by time course experiments is becoming more and more important. A common problem is to identify differentially expressed genes between the treatment and control time course. It is often difficult to compare expression patterns of a gene between two time courses for the following reasons: (1) the number of sampling time points may be different or hard to be aligned between the treatment and the control time courses; (2) estimation of the function that describes the expression of a gene in a time course is difficult and error-prone due to the limited number of time points. We propose a novel method to identify the differentially expressed genes between two time courses, which avoids direct comparison of gene expression patterns between the two time courses.


RESULTS
Instead of attempting to 'align' and compare the two time courses directly, we first convert the treatment and control time courses into neighborhood systems that reflect the underlying relationships between genes. We then identify the differentially expressed genes by comparing the two gene relationship networks. To verify our method, we apply it to two treatment-control time course datasets. The results are consistent with the previous results and also give some new biologically meaningful findings.


AVAILABILITY
The algorithm in this paper is coded in C++ and is available from http://leili-lab.cmb.usc.edu/yeastaging/projects/MARD/
5082292
Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
MOTIVATION
It is important to predict the outcome of patients with diffuse large-B-cell lymphoma after chemotherapy, since the survival rate after treatment of this common lymphoma disease is <50%. Both clinically based outcome predictors and the gene expression-based molecular factors have been proposed independently in disease prognosis. However combining the high-dimensional genomic data and the clinically relevant information to predict disease outcome is challenging.


RESULTS
We describe an integrated clinicogenomic modeling approach that combines gene expression profiles and the clinically based International Prognostic Index (IPI) for personalized prediction in disease outcome. Dimension reduction methods are proposed to produce linear combinations of gene expressions, while taking into account clinical IPI information. The extracted summary measures capture all the regression information of the censored survival phenotype given both genomic and clinical data, and are employed as covariates in the subsequent survival model formulation. A case study of diffuse large-B-cell lymphoma data, as well as Monte Carlo simulations, both demonstrate that the proposed integrative modeling improves the prediction accuracy, delivering predictions more accurate than those achieved by using either clinical data or molecular predictors alone.
13836655
Dimension reduction methods for microarrays with application to censored survival data
MOTIVATION
Recent research has shown that gene expression profiles can potentially be used for predicting various clinical phenotypes, such as tumor class, drug response and survival time. While there has been extensive studies on tumor classification, there has been less emphasis on other phenotypic features, in particular, patient survival time or time to cancer recurrence, which are subject to right censoring. We consider in this paper an analysis of censored survival time based on microarray gene expression profiles.


RESULTS
We propose a dimension reduction strategy, which combines principal components analysis and sliced inverse regression, to identify linear combinations of genes, that both account for the variability in the gene expression levels and preserve the phenotypic information. The extracted gene combinations are then employed as covariates in a predictive survival model formulation. We apply the proposed method to a large diffuse large-B-cell lymphoma dataset, which consists of 240 patients and 7399 genes, and build a Cox proportional hazards model based on the derived gene expression components. The proposed method is shown to provide a good predictive performance for patient survival, as demonstrated by both the significant survival difference between the predicted risk groups and the receiver operator characteristics analysis.


AVAILABILITY
R programs are available upon request from the authors.


SUPPLEMENTARY INFORMATION
http://dna.ucdavis.edu/~hli/bioinfo-surv-supp.pdf.
46798
Lookahead Pathologies for Single Agent Search
Admissible and consistent heuristic functions are usually preferred in single-agent heuristic search as they guarantee optimal solutions with complete search methods such as A* and IDA*. Larger problems, however, frequently make a complete search intractable due to space and/or time limitations. In particular, a path-planning agent in a real-time strategy game may need to take an action before its complete search has the time to finish. In such cases, incomplete search techniques (such as RTA*, SRTA*, RTDP, DTA*) can be used. Such algorithms conduct a limited ply lookahead and then evaluate the states envisioned using a heuristic function. The action selected on the basis of such evaluations can be suboptimal due to the incompleteness of search and inaccuracies in the heuristic. It is usually believed that deeper lookahead increases the chances of taking the optimal action. In this paper, we demonstrate that this is not necessarily the case, even when admissible and consistent heuristic functions are used.