Parameter-efficient fine-tuning (PEFT) methods, such as LoRA, offer compact and effective alternatives to full model fine-tuning by introducing low-rank updates to pretrained weights. However, most existing approaches rely on global low-rank structures, which can overlook spatial patterns spread across the parameter space. In this work, we propose Localized LoRA, a generalized framework that models weight updates as a composition of low-rank matrices applied to structured blocks of the weight matrix. This formulation enables dense, localized updates throughout the parameter space—without increasing the total number of trainable parameters. We provide a formal comparison between global, diagonal-local, and fully localized low-rank approximations, and show that our method consistently achieves lower approximation error under matched parameter budgets. Experiments on both synthetic and practical settings demonstrate that Localized LoRA offers a more expressive and adaptable alternative to existing methods, enabling efficient fine-tuning with improved performance.

Online bilevel optimization (OBO) is a powerful framework for machine learning problems where both outer and inner objectives evolve over time, requiring dynamic updates. Current OBO approaches rely on deterministic \textit{window-smoothed} regret minimization, which may not accurately reflect system performance when functions change rapidly. In this work, we introduce a novel search direction and show that both first- and zeroth-order (ZO) stochastic OBO algorithms leveraging this direction achieve sublinear {stochastic bilevel regret without window smoothing}. Beyond these guarantees, our framework enhances efficiency by: (i) reducing oracle dependence in hypergradient estimation, (ii) updating inner and outer variables alongside the linear system solution, and (iii) employing ZO-based estimation of Hessians, Jacobians, and gradients. Experiments on online parametric loss tuning and black-box adversarial attacks validate our approach.

BACKGROUND: Metabolomics is a high-throughput technology that measures small molecule metabolites in cells, tissues or biofluids. Analysis of metabolomics data is a multi-step process that involves data processing, quality control and normalization, followed by statistical and bioinformatics analysis. The latter step often involves pathway analysis to aid biological interpretation of the data. This approach is limited to endogenous metabolites that can be readily mapped to metabolic pathways. An alternative to pathway analysis that can be used for any classes of metabolites, including unknown compounds that are ubiquitous in untargeted metabolomics data, involves defining metabolite-metabolite interactions using experimental data. Our group has developed several network-based methods that use partial correlations of experimentally determined metabolite measurements. These were implemented in CorrelationCalculator and Filigree, two software tools for the analysis of metabolomics data we developed previously. The latter tool implements the Differential Network Enrichment Analysis (DNEA) algorithm. This analysis is useful for building differential networks from metabolomics data containing two experimental groups and identifying differentially enriched metabolic modules. While Filigree is a user-friendly tool, it has certain limitations when used for the analysis of large-scale metabolomics datasets. RESULTS: We developed the DNEA R package for the data-driven network analysis of metabolomics data. We present the DNEA workflow and functionality, algorithm enhancements implemented with respect to the package's predecessor, Filigree, and discuss best practices for analyses. We tested the performance of the DNEA R package and illustrated its features using publicly available metabolomics data from the environmental determinants of diabetes in the young. To our knowledge, this package is the only publicly available tool designed for the construction of biological networks and subsequent enrichment testing for datasets containing exogenous, secondary, and unknown compounds. This greatly expands the scope of traditional enrichment analysis tools that can be used to analyze a relatively small set of well-annotated metabolites. CONCLUSIONS: The DNEA R package is a more flexible and powerful implementation of our previously published software tool, Filigree. The modular structure of the package, along with the parallel processing framework built into the most computationally extensive steps of the algorithm, make it a powerful tool for the analysis of large and complex metabolomics datasets.

Logistic regression is a key method for modeling the probability of a binary outcome based on a collection of covariates. However, the classical formulation of logistic regression relies on the independent sampling assumption, which is often violated when the outcomes interact through an underlying network structure, such as over a temporal/spatial domain or on a social network. This necessitates the development of models that can simultaneously handle both the network 'peer-effect' (arising from neighborhood interactions) and the effect of (possibly) high-dimensional covariates. In this paper, we develop a framework for incorporating such dependencies in a high-dimensional logistic regression model by introducing a quadratic interaction term, as in the Ising model, designed to capture the pairwise interactions from the underlying network. The resulting model can also be viewed as an Ising model, where the node-dependent external fields linearly encode the high-dimensional covariates. We propose a penalized maximum pseudo-likelihood method for estimating the network peer-effect and the effect of the covariates (the regression coefficients), which, in addition to handling the high-dimensionality of the parameters, conveniently avoids the computational intractability of the maximum likelihood approach. Under various standard regularity conditions, we show that the corresponding estimate attains the classical high-dimensional rate of consistency. In particular, our results imply that even under network dependence it is possible to consistently estimate the model parameters at the same rate as in classical (independent) logistic regression, when the true parameter is sparse and the underlying network is not too dense. Consequently, we derive the rates of consistency of our proposed estimator for various natural graph ensembles, such as bounded degree graphs, sparse Erd\H{o}s-Rényi random graphs, and stochastic block models. We also develop an efficient algorithm for computing the estimates and validate our theoretical results in numerical experiments. An application to selecting genes in clustering spatial transcriptomics data is also discussed.

We study effect propagation in a causal directed acyclic graph (DAG), with the goal of providing a flow-based decomposition of the effect (i.e., change in the outcome variable) as a result of changes in the source variables. We first compare various ideas on causality to quantify effect propagation, such as direct and indirect effects, path-specific effects, and degree of responsibility. We discuss the shortcomings of such approaches and propose a flow-based methodology, which we call recursive Shapley value (RSV). By considering a broader set of counterfactuals than existing methods, RSV obeys a unique adherence to four desirable flow-based axioms. Further, we provide a general path-based characterization of RSV for an arbitrary non-parametric structural equations model (SEM) defined on the underlying DAG. Interestingly, for the special class of linear SEMs, RSV exhibits a simple and tractable characterization (and hence, computation), which recovers the classical method of path coefficients and is equivalent to path-specific effects. For non-parametric SEMs, we use our general characterization to develop an unbiased Monte-Carlo estimation procedure with an exponentially decaying sample complexity. We showcase the application of RSV on two challenging problems on causality (causal overdetermination and causal unfairness).

In network analysis, it is common to work with a collection of graphs that exhibit heterogeneity. For example, neuroimaging data from patient cohorts are increasingly available. A critical analytical task is to identify communities, and graph Laplacian-based methods are routinely used. However, these methods are currently limited to a single network and also do not provide measures of uncertainty on the community assignment. In this work, we first propose a probabilistic network model called the ”Spiked Laplacian Graph” that considers an observed network as a transform of the Laplacian and degree matrices of the network generating process, with the Laplacian eigenvalues modeled by a modified spiked structure. This effectively reduces the number of parameters in the eigenvectors, and their sign patterns allow efficient estimation of the underlying community structure. Further, the posterior distribution of the eigenvectors provides uncertainty quantification for the community estimates. Second, we introduce a Bayesian non-parametric approach to address the issue of heterogeneity in a collection of graphs. Theoretical results are established on the posterior consistency of the procedure and provide insights on the trade-off between model resolution and accuracy. We illustrate the performance of the methodology on synthetic data sets, as well as a neuroscience study related to brain activity in working memory.

Vector autoregression has been widely used for modeling and analysis of multivariate time series data. In high-dimensional settings, model parameter regularization schemes inducing sparsity yield interpretable models and achieved good forecasting performance. However, in many data applications, such as those in neuroscience, the Granger causality graph estimates from existing vector autoregression methods tend to be quite dense and difficult to interpret, unless one compromises on the goodness-of-fit. To address this issue, this paper proposes to incorporate a commonly used structural assumption --- that the ground-truth graph should be largely connected, in the sense that it should only contain at most a few components. We take a Bayesian approach and develop a novel tree-rank prior distribution for the regression coefficients. Specifically, this prior distribution forces the non-zero coefficients to appear only on the union of a few spanning trees. Since each spanning tree connects $p$ nodes with only $(p-1)$ edges, it effectively achieves both high connectivity and high sparsity. We develop a computationally efficient Gibbs sampler that is scalable to large sample size and high dimension. In analyzing test-retest functional magnetic resonance imaging data, our model produces a much more interpretable graph estimate, compared to popular existing approaches. In addition, we show appealing properties of this new method, such as efficient computation, mild stability conditions and posterior consistency.

We consider the problem of constructing asymptotically valid confidence intervals for the change point in a high-dimensional covariance shift setting. A novel estimator for the change point parameter is developed, and its asymptotic distribution under high dimensional scaling obtained. We establish that the proposed estimator exhibits a sharp $O_p(\psi^{-2})$ rate of convergence, wherein $\psi$ represents the jump size between model parameters before and after the change point. Further, the form of the asymptotic distributions under both a vanishing and a non-vanishing regime of the jump size are characterized. In the former case, it corresponds to the argmax of an asymmetric Brownian motion, while in the latter case to the argmax of an asymmetric random walk. We then obtain the relationship between these distributions, which allows construction of regime (vanishing vs non-vanishing) adaptive confidence intervals. Easy to implement algorithms for the proposed methodology are developed and their performance illustrated on synthetic and real data sets.

Many modern machine learning problems require solving min-max saddle point games, whose computational complexity is NP-hard in general. To overcome this issue, most available algorithms aim for finding a first-order Nash equilibrium solution that always exists under mild assumptions. However, the proposed algorithms for obtaining such solutions are non-adaptive and also exhibit slow convergence rates in real settings. Further, most algorithms are centralized in nature and cannot be adapted to a decentralized architecture in a straightforward manner. This study aims to address these issues by introducing general two-step adaptive algorithms for obtaining first-order Nash equilibrium solutions of min-max games in both single-node and decentralized architectures. We also obtain the non-asymptotic convergence rates of the algorithms assuming the objective functions satisfy the weak Minty variational inequality condition which is standard in recent literature. Finally, we illustrate the performance of the proposed algorithms by using them to train neural networks which are more robust against adversarial attacks compared to neural networks trained using existing algorithms.

This study presents a novel video recommendation system for an algebra virtual learning environment (VLE) that leverages ideas and methods from engagement measurement, item response theory, and reinforcement learning. Following Vygotsky's Zone of Proximal Development (ZPD) theory, but considering low affect and high affect students separately, we developed a system of five categories of video recommendations: 1) Watch new video; 2) Review current topic video with a new tutor; 3) Review segment of current video with current tutor; 4) Review segment of current video with a new tutor; 5) Watch next video in curriculum sequence. The category of recommendation was determined by student scores on a quiz and a sensor-free engagement detection model. New video recommendations (i.e., category 1) were selected based on a novel reinforcement learning algorithm that takes input from an item response theory model. The recommendation system was evaluated in a large field experiment, both before and after school closures due to the COVID-19 pandemic. The results show evidence of effectiveness of the video recommendation algorithm during the period of normal school operations, but the effect disappears after school closures. Implications for teacher orchestration of technology for normal classroom use and periods of school closure are discussed.

Previous research has shown that providing video recommendations to students in virtual learning environments implemented at scale positively affects student achievement. However, it is also critical to evaluate whether the treatment effects are heterogeneous, and whether they depend on contextual variables such as disadvantaged student status and characteristics of the school settings. The current study extends the evaluation of a novel video recommendation system by performing an exploratory search for sources of heterogeneity of treatment effects. This study's design is a multi-site randomized controlled trial with an assignment at the student level across three large and diverse school districts in the southeast United States. The study occurred in Spring 2021, when some students were in regular classrooms and others in online classrooms. The results of the current study replicate positive effects found in a previous field experiment that occurred in Spring 2020, at the onset of the COVID-19 pandemic. Then, causal forests were used to investigate the heterogeneity of treatment effects. This study contributes to the literature on content sequencing systems and recommendation systems by showing how these systems can disproportionally benefit the groups of students who had higher levels of previous algebra ability, followed more recommendations, learned remotely, were Hispanic, and received free or reduced-price lunch, which has implications for the fairness of implementation of educational technology solutions.

The rapid development of high-throughput technologies has enabled the generation of data from biological or disease processes that span multiple layers, like genomic, proteomic or metabolomic data, and further pertain to multiple sources, like disease subtypes or experimental conditions. In this work, we propose a general statistical framework based on Gaussian graphical models for horizontal (i.e. across conditions or subtypes) and vertical (i.e. across different layers containing data on molecular compartments) integration of information in such datasets. We start with decomposing the multi-layer problem into a series of two-layer problems. For each two-layer problem, we model the outcomes at a node in the lower layer as dependent on those of other nodes in that layer, as well as all nodes in the upper layer. We use a combination of neighborhood selection and group-penalized regression to obtain sparse estimates of all model parameters. Following this, we develop a debiasing technique and asymptotic distributions of inter-layer directed edge weights that utilize already computed neighborhood selection coefficients for nodes in the upper layer. Subsequently, we establish global and simultaneous testing procedures for these edge weights. Performance of the proposed methodology is evaluated on synthetic and real data.

We introduce a general tensor model suitable for data analytic tasks for heterogeneous datasets, wherein there are joint low-rank structures within groups of observations, but also discriminative structures across different groups. To capture such complex structures, a double core tensor (DCOT) factorization model is introduced together with a family of smoothing loss functions. By leveraging the proposed smoothing function, the model accurately estimates the model factors, even in the presence of missing entries. A linearized ADMM method is employed to solve regularized versions of DCOT factorizations, that avoid large tensor operations and large memory storage requirements. Further, we establish theoretically its global convergence, together with consistency of the estimates of the model parameters. The effectiveness of the DCOT model is illustrated on several real-world examples including image completion, recommender systems, subspace clustering, and detecting modules in heterogeneous Omics multi-modal data, since it provides more insightful decompositions than conventional tensor methods.

Due to increasing rates of adoption of electric vehicles (EVs), there is a strong need to deploy the necessary charging station infrastructure, together with routing strategies to manage traffic flow and congestion. This study addresses the location-routing problem (LRP) for a general EV charging system with stochastic charging requests regarding their locations, arrival times and charging times. The objective is to develop an efficient routing strategy of EVs to charging stations, as well as to determine the optimal charging station locations so as to minimize the demand’s mean response time. Under some regularity assumptions on the mean waiting time at each charging station (e.g. system operates in a light or heavy traffic regime), we show that the optimization problem can be formulated as a partition-based clustering problem with size constraints. This relaxation of the problem formulation enables us to develop a novel data-driven approach for solving the charging station LRP, without requiring detailed stochastic models for the EV’s charging requests, as well as the queueing behavior of the charging stations. An algorithm along with two size adjustment strategies are developed to solve the obtained clustering problem and illustrated on urban areas of Seattle with various types of distance, vehicle speeds, distributions for charging request locations, and inter-arrival time densities.

There is increasing interest in identifying changes in the underlying states of brain networks. The availability of large scale neuroimaging data creates a strong need to develop fast, scalable methods for detecting and localizing in time such changes and also identify their drivers, thus enabling neuroscientists to hypothesize about potential mechanisms. This paper presents a fast method for detecting break points in exceedingly long time series neurogimaging data, based on vector autoregressive (Granger causal) models. It uses a multi-step strategy based on a regularized objective function that leads to fast identification of candidate break points, followed by clustering steps to select the final set of break points and subsequent estimation with false positives control of the underlying Granger causal networks. The latter provide insights into key changes in network connectivity that led to the presence of break points. The proposed methodology is illustrated on synthetic data varying in their length, dimensionality, number of break points, strength of signal and also applied to EEG data related to visual tasks.

Adaptive momentum methods have recently attracted a lot of attention for training of deep neural networks. They use an exponential moving average of past gradients of the objective function to update both search directions and learning rates. However, these methods are not suited for solving min-max optimization problems that arise in training generative adversarial networks. In this paper, we propose an adaptive momentum min-max algorithm that generalizes adaptive momentum methods to the non-convex min-max regime. Further, we establish non-asymptotic rates of convergence for it when used in a reasonably broad class of non-convex min-max optimization problems. Experimental results illustrate its superior performance vis-a-vis benchmark methods for solving such problems.

Clustering of time series data exhibits a number of challenges not present in other settings, notably the problem of registration (alignment) of observed signals. Typical approaches include pre-registration to a user-specified template or time warping approaches which attempt to optimally align series with a minimum of distortion. For many signals obtained from recording or sensing devices, these methods may be unsuitable as a template signal is not available for pre-registration, while the distortion of warping approaches may obscure meaningful temporal information. We propose a new method for automatic time series alignment within a clustering problem. Our approach, Temporal Registration using Optimal Unitary Transformations (TROUT), is based on a novel dissimilarity measure between time series that is easy to compute and automatically identifies optimal alignment between pairs of time series. By embedding our new measure in a optimization formulation, we retain well-known advantages of computational and statistical performance. We provide an efficient algorithm for TROUT-based clustering and demonstrate its superior performance over a range of competitors.

We study the attribution problem in a graphical model, wherein the objective is to quantify how the effect of changes at the source nodes propagates through the graph. We develop a model-agnostic flow-based attribution method, called recursive Shapley value (RSV). RSV generalizes a number of existing node-based methods and uniquely satisfies a set of flow-based axioms. In addition to admitting a natural characterization for linear models and facilitating mediation analysis for non-linear models, RSV satisfies a mix of desirable properties discussed in the recent literature, including implementation invariance, sensitivity, monotonicity, and affine scale invariance.

MOTIVATION: When metabolites are analyzed by electrospray ionization (ESI)-mass spectrometry, they are usually detected as multiple ion species due to the presence of isotopes, adducts and in-source fragments. The signals generated by these degenerate features (along with contaminants and other chemical noise) obscure meaningful patterns in MS data, complicating both compound identification and downstream statistical analysis. To address this problem, we developed Binner, a new tool for the discovery and elimination of many degenerate feature signals typically present in untargeted ESI-LC-MS metabolomics data. RESULTS: Binner generates feature annotations and provides tools to help users visualize informative feature relationships that can further elucidate the underlying structure of the data. To demonstrate the utility of Binner and to evaluate its performance, we analyzed data from reversed phase LC-MS and hydrophilic interaction chromatography (HILIC) platforms and demonstrated the accuracy of selected annotations using MS/MS. When we compared Binner annotations of 75 compounds previously identified in human plasma samples with annotations generated by three similar tools, we found that Binner achieves superior performance in the number and accuracy of annotations while simultaneously minimizing the number of incorrectly annotated principal ions. Data reduction and pattern exploration with Binner have allowed us to catalog a number of previously unrecognized complex adducts and neutral losses generated during the ionization of molecules in LC-MS. In summary, Binner allows users to explore patterns in their data and to efficiently and accurately eliminate a significant number of the degenerate features typically found in various LC-MS modalities. AVAILABILITY AND IMPLEMENTATION: Binner is written in Java and is freely available from http://binner.med.umich.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We consider the problem of estimating the location of a single change point in a network generated by a dynamic stochastic block model mechanism. This model produces community structure in the network that exhibits change at a single time epoch. We propose two methods of estimating the change point, together with the model parameters, before and after its occurrence. The first employs a least-squares criterion function and takes into consideration the full structure of the stochastic block model and is evaluated at each point in time. Hence, as an intermediate step, it requires estimating the community structure based on a clustering algorithm at every time point. The second method comprises the following two steps: in the first one, a least-squares function is used and evaluated at each time point, but ignoring the community structure and only considering a random graph generating mechanism exhibiting a change point. Once the change point is identified, in the second step, all network data before and after it are used together with a clustering algorithm to obtain the corresponding community structures and subsequently estimate the generating stochastic block model parameters. The first method, since it requires knowledge of the community structure and hence clustering at every point in time, is significantly more computationally expensive than the second one. On the other hand, it requires a significantly less stringent identifiability condition for consistent estimation of the change point and the model parameters than the second method; however, it also requires a condition on the misclassification rate of misallocating network nodes to their respective communities that may fail to hold in many realistic settings. Despite the apparent stringency of the identifiability condition for the second method, we show that networks generated by a stochastic block mechanism exhibiting a change in their structure can easily satisfy this condition under a multitude of scenarios, including merging/splitting communities, nodes joining another community, etc. Further, for both methods under their respective identifiability and certain additional regularity conditions, we establish rates of convergence and derive the asymptotic distributions of the change point estimators. The results are illustrated on synthetic data. In summary, this work provides an in-depth investigation of the novel problem of change point analysis for networks generated by stochastic block models, identifies key conditions for the consistent estimation of the change point, and proposes a computationally fast algorithm that solves the problem in many settings that occur in applications. Finally, it discusses challenges posed by employing clustering algorithms in this problem, that require additional investigation for their full resolution.

High dimensional piecewise stationary graphical models represent a versatile class for modelling time varying networks arising in diverse application areas, including biology, economics, and social sciences. There has been recent work in offline detection and estimation of regime changes in the topology of sparse graphical models. However, the online setting remains largely unexplored, despite its high relevance to applications in sensor networks and other engineering monitoring systems, as well as financial markets. To that end, this work introduces a novel scalable online algorithm for detecting an unknown number of abrupt changes in the inverse covariance matrix of sparse Gaussian graphical models with small delay. The proposed algorithm is based upon monitoring the conditional log-likelihood of all nodes in the network and can be extended to a large class of continuous and discrete graphical models. We also investigate asymptotic properties of our procedure under certain mild regularity conditions on the graph size, sparsity level, number of samples, and pre- and post-changes in the topology of the network. Numerical works on both synthetic and real data illustrate the good performance of the proposed methodology both in terms of computational and statistical efficiency across numerous experimental settings.

A factor-augmented vector autoregressive (FAVAR) model is defined by a VAR equation that captures lead-lag correlations amongst a set of observed variables $X$ and latent factors $F$, and a calibration equation that relates another set of observed variables $Y$ with $F$ and $X$. The latter equation is used to estimate the factors that are subsequently used in estimating the parameters of the VAR system. The FAVAR model has become popular in applied economic research, since it can summarize a large number of variables of interest as a few factors through the calibration equation and subsequently examine their influence on core variables of primary interest through the VAR equation. However, there is increasing need for examining lead-lag relationships between a large number of time series, while incorporating information from another high-dimensional set of variables. Hence, in this paper we investigate the FAVAR model under high-dimensional scaling. We introduce an appropriate identification constraint for the model parameters, which when incorporated into the formulated optimization problem yields estimates with good statistical properties. Further, we address a number of technical challenges introduced by the fact that estimates of the VAR system model parameters are based on estimated rather than directly observed quantities. The performance of the proposed estimators is evaluated on synthetic data. Further, the model is applied to commodity prices and reveals interesting and interpretable relationships between the prices and the factors extracted from a set of global macroeconomic indicators.

Electricity distribution networks have undergone rapid change with the introduction of smart meter technology, that have advanced sensing and communications capabilities, resulting in improved measurement and control functions. However, the same capabilities have enabled various cyber-attacks. A particular attack focuses on electricity theft, where the attacker alters (increases) the electricity consumption measurements recorded by the smart meter of other users, while reducing her own measurement. Thus, such attacks, since they maintain the total amount of power consumed at the distribution transformer are hard to detect by techniques that monitor mean levels of consumption patterns. To address this data integrity problem, we develop statistical techniques that utilize information on higher order statistics of electricity consumption and thus are capable of detecting such attacks and also identify the users (attacker and victims) involved. The models work both for independent and correlated electricity consumption streams. The results are illustrated on synthetic data, as well as emulated attacks leveraging real consumption data.

We study the impact of an online tutoring program, AnimalWatch, for algebra readiness on mathematics achievements of grade 6 students. We use the data from a randomized experimental design conducted on 69 teachers and 2025 students in California in the academic years 2011-2012. After a brief description of the experimental design and the system implementation, we analyze the treatment effect of employing AnimalWatch using the popular hierarchical linear models and find a small positive effect. We further use the logged system usage data such as time spent in the system, modules completed, correct/incorrect/no-answers records of students in each login to analyze how system implementation and usage helped different students. Our results provide insights into the limitations in implementing such a study in a real world setting and suggests recommendations for future research.

We study the usage of a self-guided online tutoring platform called Algebra Nation, which is widely by middle school and high school students who take the End-of-Course Algebra I exam at the end of the school year. This article aims to study how the platform contributes to increasing students' exam scores by examining users' logs over a three year period. The platform under consideration was used by more than 36,000 students in the first year, to nearly 67,000 by the third year, thus enabling us to examine how usage patterns evolved and influenced students' performance at scale. We first identify which Algebra Nation usage factors in conjunction with math overall preparation and socioeconomic factors contribute to the students' exam performance. Subsequently, we investigate the effect of increased teacher familiarity level with the Algebra Nation on students' scores across different grades through mediation analysis. The results show that the indirect effect of teacher's familiarity with the platform through increasing student's usage dosage is more significant in higher grades.

MOTIVATION: Functional enrichment testing methods can reduce data comprising hundreds of altered biomolecules to smaller sets of altered biological 'concepts' that help generate testable hypotheses. This study leveraged differential network enrichment analysis methodology to identify and validate lipid subnetworks that potentially differentiate chronic kidney disease (CKD) by severity or progression. RESULTS: We built a partial correlation interaction network, identified highly connected network components, applied network-based gene-set analysis to identify differentially enriched subnetworks, and compared the subnetworks in patients with early-stage versus late-stage CKD. We identified two subnetworks 'triacylglycerols' and 'cardiolipins-phosphatidylethanolamines (CL-PE)' characterized by lower connectivity, and a higher abundance of longer polyunsaturated triacylglycerols in patients with severe CKD (stage ≥4) from the Clinical Phenotyping Resource and Biobank Core. These finding were replicated in an independent cohort, the Chronic Renal Insufficiency Cohort. Using an innovative method for elucidating biological alterations in lipid networks, we demonstrated alterations in triacylglycerols and cardiolipins-phosphatidylethanolamines that precede the clinical outcome of end-stage kidney disease by several years. AVAILABILITY AND IMPLEMENTATION: A complete list of NetGSA results in HTML format can be found at http://metscape.ncibi.org/netgsa/12345-022118/cric_cprobe/022118/results_cric_cprobe/main.html. The DNEA is freely available at https://github.com/wiggie/DNEA. Java wrapper leveraging the cytoscape.js framework is available at http://js.cytoscape.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: The diversity of biological omics data provides richness of information, but also presents an analytic challenge. While there has been much methodological and theoretical development on the statistical handling of large volumes of biological data, far less attention has been devoted to characterizing their veracity and variability. RESULTS: We propose a method of statistically quantifying heterogeneity among multiple groups of datasets, derived from different omics modalities over various experimental and/or disease conditions. It draws upon strategies from analysis of variance and principal component analysis in order to reduce dimensionality of the variability across multiple data groups. The resulting hypothesis-based inference procedure is demonstrated with synthetic and real data from a cell line study of growth factor responsiveness based on a factorial experimental design. AVAILABILITY AND IMPLEMENTATION: Source code and datasets are freely available at https://github.com/yangzi4/gPCA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: Pathway enrichment extensively used in the analysis of Omics data for gaining biological insights into the functional roles of pre-defined subsets of genes, proteins and metabolites. A large number of methods have been proposed in the literature for this task. The vast majority of these methods use as input expression levels of the biomolecules under study together with their membership in pathways of interest. The latest generation of pathway enrichment methods also leverages information on the topology of the underlying pathways, which as evidence from their evaluation reveals, lead to improved sensitivity and specificity. Nevertheless, a systematic empirical comparison of such methods is still lacking, making selection of the most suitable method for a specific experimental setting challenging. This comparative study of nine network-based methods for pathway enrichment analysis aims to provide a systematic evaluation of their performance based on three real data sets with different number of features (genes/metabolites) and number of samples. RESULTS: The findings highlight both methodological and empirical differences across the nine methods. In particular, certain methods assess pathway enrichment due to differences both across expression levels and in the strength of the interconnectedness of the members of the pathway, while others only leverage differential expression levels. In the more challenging setting involving a metabolomics data set, the results show that methods that utilize both pieces of information (with NetGSA being a prototypical one) exhibit superior statistical power in detecting pathway enrichment. CONCLUSION: The analysis reveals that a number of methods perform equally well when testing large size pathways, which is the case with genomic data. On the other hand, NetGSA that takes into consideration both differential expression of the biomolecules in the pathway, as well as changes in the topology exhibits a superior performance when testing small size pathways, which is usually the case for metabolomics data.

Tensors of order three or higher have found applications in diverse fields, including image and signal processing, data mining, biomedical engineering, and link analysis, to name a few. In many applications that involve, for example, time series or other ordered data, the corresponding tensor has a distinguishing orientation that exhibits a low tubal structure. This has motivated the introduction of the tubal rank and the corresponding tubal singular value decomposition in the literature. In this work, we develop randomized algorithms for many common tensor operations, including tensor low-rank approximation and decomposition, together with tensor multiplication. The proposed tubal focused algorithms employ a small number of lateral and/or horizontal slices of the underlying third order tensor that come with relative error guarantees for the quality of the obtained solutions. The performance of the proposed algorithms is illustrated on diverse imaging applications, including mass spectrometry data and image and video recovery from incomplete and noisy data. The results show both good computational speed-up vis-a-vis conventional completion algorithms and good accuracy.

MOTIVATION: Recent technological advances in mass spectrometry, development of richer mass spectral libraries and data processing tools have enabled large scale metabolic profiling. Biological interpretation of metabolomics studies heavily relies on knowledge-based tools that contain information about metabolic pathways. Incomplete coverage of different areas of metabolism and lack of information about non-canonical connections between metabolites limits the scope of applications of such tools. Furthermore, the presence of a large number of unknown features, which cannot be readily identified, but nonetheless can represent bona fide compounds, also considerably complicates biological interpretation of the data. RESULTS: Leveraging recent developments in the statistical analysis of high-dimensional data, we developed a new Debiased Sparse Partial Correlation algorithm (DSPC) for estimating partial correlation networks and implemented it as a Java-based CorrelationCalculator program. We also introduce a new version of our previously developed tool Metscape that enables building and visualization of correlation networks. We demonstrate the utility of these tools by constructing biologically relevant networks and in aiding identification of unknown compounds. AVAILABILITY AND IMPLEMENTATION: http://metscape.med.umich.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dynamical systems comprising of multiple components that can be partitioned into distinct blocks originate in many scientific areas. A pertinent example is the interactions between financial assets and selected macroeconomic indicators, which has been studied at aggregate level---e.g. a stock index and an employment index---extensively in the macroeconomics literature. A key shortcoming of this approach is that it ignores potential influences from other related components (e.g. Gross Domestic Product) that may impact the system's dynamics and structure and thus produces incorrect results. To mitigate this issue, we consider a multi-block linear dynamical system with Granger-causal ordering between blocks, wherein the blocks' temporal dynamics are described by vector autoregressive processes and are influenced by blocks higher in the system hierarchy. We derive the maximum likelihood estimator for the posited model for Gaussian data in the high- dimensional setting based on appropriate regularization schemes for the parameters of the block components. To optimize the underlying non-convex likelihood function, we develop an iterative algorithm with convergence guarantees. We establish theoretical properties of the maximum likelihood estimates, leveraging the decomposability of the regularizers and a careful analysis of the iterates. Finally, we develop testing procedures for the null hypothesis of whether a block Granger-causes another block of variables. The performance of the model and the testing procedures are evaluated on synthetic data, and illustrated on a data set involving log-returns of the US S&P100 component stocks and key macroeconomic variables for the 2001--16 period.

MOTIVATION: Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of changes in cellular activity in response to treatments and/or in disease states. Methods that use existing pathway network information have been shown to outperform simpler methods that only take into account pathway membership. However, despite significant progress in understanding the association amongst members of biological pathways, and expansion of data bases containing information about interactions of biomolecules, the existing network information may be incomplete or inaccurate and is not cell-type or disease condition-specific. RESULTS: We propose a constrained network estimation framework that combines network estimation based on cell- and condition-specific high-dimensional Omics data with interaction information from existing data bases. The resulting pathway topology information is subsequently used to provide a framework for simultaneous testing of differences in expression levels of pathway members, as well as their interactions. We study the asymptotic properties of the proposed network estimator and the test for pathway enrichment, and investigate its small sample performance in simulated and real data settings. AVAILABILITY AND IMPLEMENTATION: The proposed method has been implemented in the R-package netgsa available on CRAN. CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online.

MOTIVATION: Recent advances in high-throughput omics technologies have enabled biomedical researchers to collect large-scale genomic data. As a consequence, there has been growing interest in developing methods to integrate such data to obtain deeper insights regarding the underlying biological system. A key challenge for integrative studies is the heterogeneity present in the different omics data sources, which makes it difficult to discern the coordinated signal of interest from source-specific noise or extraneous effects. RESULTS: We introduce a novel method of multi-modal data analysis that is designed for heterogeneous data based on non-negative matrix factorization. We provide an algorithm for jointly decomposing the data matrices involved that also includes a sparsity option for high-dimensional settings. The performance of the proposed method is evaluated on synthetic data and on real DNA methylation, gene expression and miRNA expression data from ovarian cancer samples obtained from The Cancer Genome Atlas. The results show the presence of common modules across patient samples linked to cancer-related pathways, as well as previously established ovarian cancer subtypes. AVAILABILITY AND IMPLEMENTATION: The source code repository is publicly available at https://github.com/yangzi4/iNMF. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Analyzing multi-layered graphical models provides insight into understanding the conditional relationships among nodes within layers after adjusting for and quantifying the effects of nodes from other layers. We obtain the penalized maximum likelihood estimator for Gaussian multi-layered graphical models, based on a computational approach involving screening of variables, iterative estimation of the directed edges between layers and undirected edges within layers and a final refitting and stability selection step that provides improved performance in finite sample settings. We establish the consistency of the estimator in a high-dimensional setting. To obtain this result, we develop a strategy that leverages the biconvexity of the likelihood function to ensure convergence of the developed iterative algorithm to a stationary point, as well as careful uniform error control of the estimates over iterations. The performance of the maximum likelihood estimator is illustrated on synthetic data.

Gaussian graphical models capture dependence relationships between random variables through the pattern of nonzero elements in the corresponding inverse covariance matrices. To date, there has been a large body of literature on both computational methods and analytical results on the estimation of a single graphical model. However, in many application domains, one has to estimate several related graphical models, a problem that has also received attention in the literature. The available approaches usually assume that all graphical models are globally related. On the other hand, in many settings different relationships between subsets of the node sets exist between different graphical models. We develop methodology that jointly estimates multiple Gaussian graphical models, assuming that there exists prior information on how they are structurally related. For many applications, such information is available from external data sources. The proposed method consists of first applying neighborhood selection with a group lasso penalty to obtain edge sets of the graphs, and a maximum likelihood refit for estimating the nonzero entries in the inverse covariance matrices. We establish consistency of the proposed method for sparse high-dimensional Gaussian graphical models and examine its performance using simulation experiments. Applications to a climate data set and a breast cancer data set are also discussed.

The Internet, as a global system of interconnected networks, carries an extensive array of information resources and services. Key requirements include good quality-of-service and protection of the infrastructure from nefarious activity [e.g., distributed denial of service (DDoS) attacks]. Network monitoring is essential to network engineering, capacity planning, and prevention/mitigation of threats. We develop an open-source architecture, All-packet MONitor (AMON), for online monitoring and analysis of multi-gigabit network streams. It leverages the high-performance packet monitor PF_RING and is readily deployable on commodity hardware. AMON examines all packets, partitions traffic into sub-streams by using rapid hashing and computes certain real-time data products. The resulting data structures provide views of the intensity and connectivity structure of network traffic at the time-scale of routing. The proposed integrated framework includes modules for the identification of heavy-hitters as well as for visualization and statistical detection at the time-of-onset of high-impact events such as DDoS. This allows operators to quickly visualize and diagnose attacks, and limit offline and time-consuming post-mortem analysis. We demonstrate our system in the context of real-world attack incidents, and validate it against state-of-the-art alternatives. AMON has been deployed and is currently processing multi-gigabit live Internet traffic at Merit Network. It is extensible and allows the addition of further statistical and filtering modules for real-time forensics.

To facilitate the adoption of electric vehicles (EVs) and their plug-in hybrid (PHEVs) counterparts and to avoid straining the capacity of the power grid there is a strong need for developing a network of fast charging facilities and coordinate their service. Incorporation of EVs in the vehicle fleet would decrease green house gas emissions and overall dependency on fossil fuels. A key issue in charging EVs is that the corresponding time is fairly large, which can lead to very long delays. Hence, for the network of charging stations to provide good quality of service to customers, we first propose an admission control mechanism based on pricing for a single charging station. Subsequently, we develop a decentralized routing scheme of EV drivers, employing a game theoretic model. The latter entices drivers through price incentives to require charging from less busy stations, thus leading to a more efficient utilization of power across the network, while it enhances profit for the charging facilities operator. Of note, the proposed scheme does not require advanced monitoring tools for power usage and pricing calculations. The drivers receive and send back the necessary information through the a communications infrastructure and the routing is initiated only when the network has exceeded a critical threshold. The numerical results illustrate the discussed benefits of the proposed scheme.

MOTIVATION: Reverse engineering of gene regulatory networks remains a central challenge in computational systems biology, despite recent advances facilitated by benchmark in silico challenges that have aided in calibrating their performance. A number of approaches using either perturbation (knock-out) or wild-type time-series data have appeared in the literature addressing this problem, with the latter using linear temporal models. Nonlinear dynamical models are particularly appropriate for this inference task, given the generation mechanism of the time-series data. In this study, we introduce a novel nonlinear autoregressive model based on operator-valued kernels that simultaneously learns the model parameters, as well as the network structure. RESULTS: A flexible boosting algorithm (OKVAR-Boost) that shares features from L2-boosting and randomization-based algorithms is developed to perform the tasks of parameter learning and network inference for the proposed model. Specifically, at each boosting iteration, a regularized Operator-valued Kernel-based Vector AutoRegressive model (OKVAR) is trained on a random subnetwork. The final model consists of an ensemble of such models. The empirical estimation of the ensemble model's Jacobian matrix provides an estimation of the network structure. The performance of the proposed algorithm is first evaluated on a number of benchmark datasets from the DREAM3 challenge and then on real datasets related to the In vivo Reverse-Engineering and Modeling Assessment (IRMA) and T-cell networks. The high-quality results obtained strongly indicate that it outperforms existing approaches. AVAILABILITY: The OKVAR-Boost Matlab code is available as the archive: http://amis-group.fr/sourcecode-okvar-boost/OKVARBoost-v1.0.zip. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

In order to increase the penetration of electric vehicles, a network of fast charging stations that can provide drivers with a certain level of quality of service (QoS) is needed. However, given the strain that such a network can exert on the power grid, and the mobility of loads represented by electric vehicles, operating it efficiently is a challenging and complex problem. In this paper, we examine a network of charging stations equipped with an energy storage device and propose a scheme that allocates power to them from the grid, as well as routes customers. We examine three scenarios, gradually increasing their complexity. In the first one, all stations have identical charging capabilities and energy storage devices, draw constant power from the grid and no routing decisions of customers are considered. It represents the current state of affairs and serves as a baseline for evaluating the performance of the proposed scheme. In the second scenario, power to the stations is allocated in an optimal manner from the grid and in addition a certain percentage of customers can be routed to nearby stations. In the final scenario, optimal allocation of both power from the grid and customers to stations is considered. The three scenarios are evaluated using real traffic traces corresponding to weekday rush hour from a large metropolitan area in the US. The results indicate that the proposed scheme offers substantial improvements of performance compared to the current mode of operation; namely, more customers can be served with the same amount of power, thus enabling the station operators to increase their profitability. Further, the scheme provides guarantees to customers in terms of the probability of being blocked (and hence not served) by the closest charging station to their location. Overall, the paper addresses key issues related to the efficient operation, both from the perspective of the power grid and the drivers satisfaction, of a network of charging stations.

In this paper, we conduct feasibility studies on the average delay space for Cloud computing, and we propose a heuristic method to control the vector of average delays, subject to predefined delay constraints. Our work is strongly motivated by the fact that delay control plays a critical role to improve Service Level Agreements (SLA) between users and Cloud service providers, which is necessary for empowering online business. Specifically, our main contributions are two-fold: First, the feasible regions of various routing algorithms for the system's dispatcher are investigated in depth. Second, a simple heuristic algorithm is designed, to move the average delay point along the feasible direction until achieving the delay constraints. Average delay is dependent on multiple factors such as job size, inter-arrival time, flow rate, and the dispatching rules of the system. Therefore, we vary their distribution, parameters and routing rules to examine how the feasible regions move or change. After establishing the feasible delay space, then by moving along the feasible directions, we show that a simple heuristic algorithm can achieve the delay constraints for a two queue system.

A massive amount of energy consumption currently stems from the transportation sector. Therefore, improvements in power usage by commuting vehicles are being studied and becoming an increasingly popular research topic. In particular, there is a growing need to model the envisioned smart infrastructure, including charging stations, some of which might include energy storage devices and swappable, pre-charged batteries. For such new stations, power management is indeed crucial for operation costs, driver convenience, and overall smart grid efficiency. Information technology, communications and vehicle intelligence need to play a crucial role in this process. In this paper, we describe a quantitative model and propose a guiding and control system for the charging of PHEVs in a future smart infrastructure. Specifically, we describe an algorithm that can be used for the joint guidance and power control of smarter electric vehicles in the smart grid. We envision it as part of a larger Smart Guide for the Smart Grid (SGSG) system. Its function is to guide PHEV drivers, directing them to the appropriate charging station, while attempting to achieve an optimization goal at the same time. Our algorithm aims at a joint guiding and power control, in order to heuristically maximize the weighted sum of the average of throughput and energy cost consumption from multiple vehicle charging stations, while satisfying a cost constraint at each station, as well as system stability.

BACKGROUND: Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. RESULTS: This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. CONCLUSIONS: The ontology based information retrieval system described in this paper (OBIRS) is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help.

In this paper, we propose the use of network decomposition under an optimal resource allocation framework. We develop a methodology where recursive formulas can be utilized for calculating the desired end-to-end performance bounds (i.e., backlog bound violation probability) of flows traversing tandem, acyclic queueing networks. We use those performance metrics in an optimization framework that allocates resources to network services with specific quality-of-service requirements. Finally, we evaluate our framework and compare its performance against a system utilizing deterministic bounds obtained from network calculus.

Heterogeneous computing platforms such as Grid and Cloud computing are becoming prevalent and available online. As a result, resource management in these platforms is fundamentally critical to their global performance. Under the assumption of jobs comprised of subtasks forming DAG jobs, we focus on how to increase utilization and achieve near-optimal throughput performance on heterogeneous platforms. Our analysis and proposed algorithm are analytically derived and establish that, by aggregating multiple jobs using good scheduling, a near-optimal throughput can be achieved. Consequently, its limit is asymptotically converging to a certain value and can be written in the form of the service time of subtasks. Furthermore, our analysis shows how to explicitly compute the optimal throughput of computing systems, an important task for such a complex scheduling problem. In addition, we derive a simple super-job scheduling and show that its performance in term of throughput is better than the well-known Heterogeneous Earliest-Finish-Time (HEFT) algorithm.

We propose models for the joint distribution of two modalities for network flow volumes. While these models are motivated by computer network applications, the underlying structural assumptions are more generally applicable. In the case of computer network flow volumes, this corresponds to joint modeling for packet and byte volumes and enables computer network tomography, whose goal is to estimate characteristics of source-destination flows based on aggregate link measurements. Network tomography is a prototypical example of a linear inverse problem on graphs. We introduce two generative models for the relation between packet and byte volumes, establish identifiability of their parameters, and discuss different estimating procedures. The proposed estimators of the flow characteristics are evaluated using both simulated and emulated data. Finally, the proposed models allow us to estimate parameters of the packet size distribution, thus providing additional insights into the composition of network traffic.

In this paper, a novel approach to the problem of estimating the heavy-tail exponent α >; 0 of a distribution is proposed. It is based on the fact that block-maxima of size m scale at a rate m1/αfor independent, as well as for a number of dependent data. This scaling rate can be captured well by the max-spectrum plot of the data that leads to regression based estimators for α. Consistency and asymptotic normality of these estimators is established for independent data under mild conditions on the behavior of the tail of the distribution. The proposed estimators have an important computational advantage over existing methods; namely, they can be calculated and updated sequentially in an on-line fashion without having to store the entire data set. Practical issues on the automatic selection of tuning parameters for the estimators and corresponding confidence intervals are also addressed. Extensive numerical simulations show that the proposed method is competitive for both small and large sample sizes, robust to contaminants and continues to work under the presence of substantial amount of dependence. The proposed estimators are used to illustrate the close connection between long-range dependence and heavy tails over an Internet traffic trace.

We develop a probabilistic framework for global modeling of the traffic over a computer network. The model integrates existing single-link (-flow) traffic models with the routing over the network to capture the global traffic behavior. It arises from a limit approximation of the traffic fluctuations as the time-scale and the number of users sharing the network grow. The resulting probability model is comprised of a Gaussian and/or a stable, infinite variance components. They can be succinctly described and handled by certain 'space-time' random fields. The model is validated against real data and applied to predict traffic fluctuations over unobserved links from a limited set of observed links.

Network models are widely used to capture interactions among component of complex systems, such as social and biological. To understand their behavior, it is often necessary to analyze functionally related components of the system, corresponding to subsystems. Therefore, the analysis of subnetworks may provide additional insight into the behavior of the system, not evident from individual components. We propose a novel approach for incorporating available network information into the analysis of arbitrary subnetworks. The proposed method offers an efficient dimension reduction strategy using Laplacian eigenmaps with Neumann boundary conditions, and provides a flexible inference framework for analysis of subnetworks, based on a group-penalized principal component regression model on graphs. Asymptotic properties of the proposed inference method, as well as the choice of the tuning parameter for control of the false positive rate are discussed in high dimensional settings. The performance of the proposed methodology is illustrated using simulated and real data examples from biology.

MOTIVATION: Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms. Discovering regulatory interactions among genes is therefore an important problem in systems biology. Whole-genome expression data over time provides an opportunity to determine how the expression levels of genes are affected by changes in transcription levels of other genes, and can therefore be used to discover regulatory interactions among genes. RESULTS: In this article, we propose a novel penalization method, called truncating lasso, for estimation of causal relationships from time-course gene expression data. The proposed penalty can correctly determine the order of the underlying time series, and improves the performance of the lasso-type estimators. Moreover, the resulting estimate provides information on the time lag between activation of transcription factors and their effects on regulated genes. We provide an efficient algorithm for estimation of model parameters, and show that the proposed method can consistently discover causal relationships in the large p, small n setting. The performance of the proposed model is evaluated favorably in simulated, as well as real, data examples. AVAILABILITY: The proposed truncating lasso method is implemented in the R-package 'grangerTlasso' and is freely available at http://www.stat.lsa.umich.edu/~shojaie/.

In this paper, we present a distributed algorithm to dynamically allocate the available resources of a service-oriented network to delay sensitive network services. We use a utility-based framework to differentiate services based on both their relative profitability and quality-of-service requirements. Our performance metric is the end-to-end delay that a service class experiences in the network. We use network calculus to obtain a deterministic upper bound of this delay and we incorporate this information into our optimization problem formulation. We leverage a moving average control scheme to capture traffic shifts in real time, which makes our solution to react adaptively to traffic dynamics. Finally, we evaluate our system using real traces of instant messaging service traffic.

Advances in networking technology have enabled network engineers to use sampled data from routers to estimate network flow volumes and track them over time. However, low sampling rates result in large noise in traffic volume estimates. We propose to combine data on individual flows obtained from sampling with highly aggregate data obtained from SNMP measurements (similar to those used in network tomography) for the tracking problem at hand. Specifically, we introduce a linearized state space model for the estimation of network traffic flow volumes from combined SNMP and sampled data. Further, we formulate the problem of obtaining optimal sampling rates under router resource constraints as an experiment design problem. Theoretically it corresponds to the problem of optimal design for estimation of conditional means for state space models and we present the associated convex programs for a simple approach to it. The usefulness of the approach in the context of network monitoring is illustrated through an extensive numerical study.

Graph-based learning provides a useful approach for modeling data in classification problems. In this modeling scenario, the relationship between labeled and unlabeled data impacts the construction and performance of classifiers, and therefore a semi-supervised learning framework is adopted. We propose a graph classifier based on kernel smoothing. A regularization framework is also introduced, and it is shown that the proposed classifier optimizes certain loss functions. Its performance is assessed on several synthetic and real benchmark data sets with good results, especially in settings where only a small fraction of the data are labeled.

Switched processing systems (SPS) represent a canonical model for many areas of applications of communication, computer and manufacturing systems. They are characterized by flexible, interdependent service capabilities and multiple classes of job traffic flows. Recently, increased attention has been paid to the issue of improving quality of service (QoS) performance in terms of delays and backlogs of the associated scheduling policies, rather than simply maximizing the system's throughput. In this study, we investigate a measurement based dynamic service allocation policy that significantly improves performance with respect to delay metrics. The proposed policy solves a linear program at selected points in time that are in turn determined by a monitoring strategy that detects 'significant' changes in the intensities of the input processes. The proposed strategy is illustrated on a small SPS subject to different types of input traffic.

In this paper, we consider the problem of non-parametric estimation of network flow characteristics, namely packet lengths and byte sizes, based on sampled flow data. We propose two different approaches to deal with the problem at hand. The first one is based on single stage Bernoulli sampling of packets and their corresponding byte sizes. Subsequently, the flow length distribution is estimated by an adaptive expectation- maximization (EM) algorithm that in addition provides an estimate for the number of active flows. The estimation of the flow sizes (in bytes) is accomplished through a random effects regression model that utilizes the flow length information previously obtained. A variation of this approach, particularly suited for mixture distributions that appear in real network traces, is also considered. The second approach relies on a two-stage sampling procedure, which in the first stage samples flows amongst the active ones, while in the second stage samples packets from the sampled flows. Subsequently, the flow length distribution is estimated using another EM algorithm and the flow byte sizes based on a regression model. The proposed approaches are illustrated and compared on a number of synthetic and real data sets.

In this paper, we consider the problem of nonparametric estimation of the original length of traffic flows, based on sampled flow data. The proposed approach is a two-step one. In the first stage, the flow length distribution is estimated by an expectation-maximization (EM) algorithm that in addition provides an estimate for the number of active flows in the link. In the second stage, two estimators are derived for the original flow length, using information from the posterior distribution previously obtained. The proposed approach is illustrated on a number of synthetic and real data sets.

An algorithm for generating sample paths of linear fractional stable motion (LFSM) is introduced. It is based on the approximation of LFSM by a linear process and exhibits low computational complexity. A detailed analysis of the error term involved in the approximation is provided, which in turn guides the user on selecting the size of the generated sequence.