A Coding Theoretic Approach for Evaluating Accumulate Distribution on Minimum Cut Capacity of Weighted Random Graphs

The multicast capacity of a directed network is closely related to the $s$-$t$ maximum flow, which is equal to the $s$-$t$ minimum cut capacity due to the max-flow min-cut theorem. If the topology of a network (or link capacities) is dynamically changing or have stochastic nature, it is not so trivial to predict statistical properties on the maximum flow. In this paper, we present a coding theoretic approach for evaluating the accumulate distribution of the minimum cut capacity of weighted random graphs. The main feature of our approach is to utilize the correspondence between the cut space of a graph and a binary LDGM (low-density generator-matrix) code with column weight 2. The graph ensemble treated in the paper is a weighted version of Erd\H{o}s-R\'{e}nyi random graph ensemble. The main contribution of our work is a combinatorial lower bound for the accumulate distribution of the minimum cut capacity. From some computer experiments, it is observed that the lower bound derived here reflects the actual statistical behavior of the minimum cut capacity.Comment: 5 pages, 2 figures, submitted to IEEE ISIT 201

The price of certainty: "waterslide curves" and the gap to capacity

The classical problem of reliable point-to-point digital communication is to achieve a low probability of error while keeping the rate high and the total power consumption small. Traditional information-theoretic analysis uses `waterfall' curves to convey the revolutionary idea that unboundedly low probabilities of bit-error are attainable using only finite transmit power. However, practitioners have long observed that the decoder complexity, and hence the total power consumption, goes up when attempting to use sophisticated codes that operate close to the waterfall curve. This paper gives an explicit model for power consumption at an idealized decoder that allows for extreme parallelism in implementation. The decoder architecture is in the spirit of message passing and iterative decoding for sparse-graph codes. Generalized sphere-packing arguments are used to derive lower bounds on the decoding power needed for any possible code given only the gap from the Shannon limit and the desired probability of error. As the gap goes to zero, the energy per bit spent in decoding is shown to go to infinity. This suggests that to optimize total power, the transmitter should operate at a power that is strictly above the minimum demanded by the Shannon capacity. The lower bound is plotted to show an unavoidable tradeoff between the average bit-error probability and the total power used in transmission and decoding. In the spirit of conventional waterfall curves, we call these `waterslide' curves.Comment: 37 pages, 13 figures. Submitted to IEEE Transactions on Information Theory. This version corrects a subtle bug in the proofs of the original submission and improves the bounds significantl

Visual encoding quality and scalability in information visualization

Information visualization seeks to amplify cognition through interactive visual representations of data. It comprises human processes, such as perception and cognition, and computer processes, such as visual encoding. Visual encoding consists in mapping data variables to visual variables, and its quality is critical to the effectiveness of information visualizations. The scalability of a visual encoding is the extent to which its quality is preserved as the parameters of the data grow. Scalable encodings offer good support for basic analytical tasks at scale by carrying design decisions that consider the limits of human perception and cognition. In this thesis, I present three case studies that explore different aspects of visual encoding quality and scalability: information loss, perceptual scalability, and discriminability. In the first study, I leverage information theory to model encoding quality in terms of information content and complexity. I examine how information loss and clutter affect the scalability of hierarchical visualizations and contribute an information-theoretic algorithm for adjusting these factors in visualizations of large datasets. The second study centers on the question of whether a data property (outlierness) can be lost in the visual encoding process due to saliency interference with other visual variables. I designed a controlled experiment to measure the effectiveness of motion outlier detection in complex multivariate scatterplots. The results suggest a saliency deficit effect whereby global saliency undermines support to tasks that rely on local saliency. Finally, I investigate how discriminability, a classic visualization criterion, can explain recent empirical results on encoding effectiveness and provide the foundation for automated evaluation of visual encodings. I propose an approach for discriminability evaluation based on a perceptually motivated image similarity measure

Systems biology approaches to the dynamics of gene expression and chemical reactions

Systems biology is an emergent interdisciplinary field of study whose main goal is to understand the global properties and functions of a biological system by investigating its structure and dynamics [74]. This high-level knowledge can be reached only with a coordinated approach involving researchers with different backgrounds in molecular biology, the various omics (like genomics, proteomics, metabolomics), computer science and dynamical systems theory. The history of systems biology as a distinct discipline began in the 1960s, and saw an impressive growth since year 2000, originated by the increased accumulation of biological information, the development of high-throughput experimental techniques, the use of powerful computer systems for calculations and database hosting, and the spread of Internet as the standard medium for information diffusion [77]. In the last few years, our research group tried to tackle a set of systems biology problems which look quite diverse, but share some topics like biological networks and system dynamics, which are of our interest and clearly fundamental for this field. In fact, the first issue we studied (covered in Part I) was the reverse engineering of large-scale gene regulatory networks. Inferring a gene network is the process of identifying interactions among genes from experimental data (tipically microarray expression profiles) using computational methods [6]. Our aim was to compare some of the most popular association network algorithms (the only ones applicable at a genome-wide level) in different conditions. In particular we verified the predictive power of similarity measures both of direct type (like correlations and mutual information) and of conditional type (partial correlations and conditional mutual information) applied on different kinds of experiments (like data taken at equilibrium or time courses) and on both synthetic and real microarray data (for E. coli and S. cerevisiae). In our simulations we saw that all network inference algorithms obtain better performances from data produced with \u201cstructural\u201d perturbations (like gene knockouts at steady state) than with just dynamical perturbations (like time course measurements or changes of the initial expression levels). Moreover, our analysis showed differences in the performances of the algorithms: direct methods are more robust in detecting stable relationships (like belonging to the same protein complex), while conditional methods are better at causal interactions (e.g. transcription factor\u2013binding site interactions), especially in presence of combinatorial transcriptional regulation. Even if time course microarray experiments are not particularly useful for inferring gene networks, they can instead give a great amount of information about the dynamical evolution of a biological process, provided that the measurements have a good time resolution. Recently, such a dataset has been published [119] for the yeast metabolic cycle, a well-known process where yeast cells synchronize with respect to oxidative and reductive functions. In that paper, the long-period respiratory oscillations were shown to be reflected in genome-wide periodic patterns in gene expression. As explained in Part II, we analyzed these time series in order to elucidate the dynamical role of post-transcriptional regulation (in particular mRNA stability) in the coordination of the cycle. We found that for periodic genes, arranged in classes according either to expression profile or to function, the pulses of mRNA abundance have phase and width which are directly proportional to the corresponding turnover rates. Moreover, the cascade of events which occurs during the yeast metabolic cycle (and their correlation with mRNA turnover) reflects to a large extent the gene expression program observable in other dynamical contexts such as the response to stresses or stimuli. The concepts of network and of systems dynamics return also as major arguments of Part III. In fact, there we present a study of some dynamical properties of the so-called chemical reaction networks, which are sets of chemical species among which a certain number of reactions can occur. These networks can be modeled as systems of ordinary differential equations for the species concentrations, and the dynamical evolution of these systems has been theoretically studied since the 1970s [47, 65]. Over time, several independent conditions have been proved concerning the capacity of a reaction network, regardless of the (often poorly known) reaction parameters, to exhibit multiple equilibria. This is a particularly interesting characteristic for biological systems, since it is required for the switch-like behavior observed during processes like intracellular signaling and cell differentiation. Inspired by those works, we developed a new open source software package for MATLAB, called ERNEST, which, by checking these various criteria on the structure of a chemical reaction network, can exclude the multistationarity of the corresponding reaction system. The results of this analysis can be used, for example, for model discrimination: if for a multistable biological process there are multiple candidate reaction models, it is possible to eliminate some of them by proving that they are always monostationary. Finally, we considered the related property of monotonicity for a reaction network. Monotone dynamical systems have the tendency to converge to an equilibrium and do not present chaotic behaviors. Most biological systems have the same features, and are therefore considered to be monotone or near-monotone [85, 116]. Using the notion of fundamental cycles from graph theory, we proved some theoretical results in order to determine how distant is a given biological network from being monotone. In particular, we showed that the distance to monotonicity of a network is equal to the minimal number of negative fundamental cycles of the corresponding J-graph, a signed multigraph which can be univocally associated to a dynamical system

Generalized asset integrity games

Generalized assets represent a class of multi-scale adaptive state-transition systems with domain-oblivious performance criteria. The governance of such assets must proceed without exact specifications, objectives, or constraints. Decision making must rapidly scale in the presence of uncertainty, complexity, and intelligent adversaries. This thesis formulates an architecture for generalized asset planning. Assets are modelled as dynamical graph structures which admit topological performance indicators, such as dependability, resilience, and efficiency. These metrics are used to construct robust model configurations. A normalized compression distance (NCD) is computed between a given active/live asset model and a reference configuration to produce an integrity score. The utility derived from the asset is monotonically proportional to this integrity score, which represents the proximity to ideal conditions. The present work considers the situation between an asset manager and an intelligent adversary, who act within a stochastic environment to control the integrity state of the asset. A generalized asset integrity game engine (GAIGE) is developed, which implements anytime algorithms to solve a stochastically perturbed two-player zero-sum game. The resulting planning strategies seek to stabilize deviations from minimax trajectories of the integrity score. Results demonstrate the performance and scalability of the GAIGE. This approach represents a first-step towards domain-oblivious architectures for complex asset governance and anytime planning

Geometric Inhomogeneous Random Graphs for Algorithm Engineering

The design and analysis of graph algorithms is heavily based on the worst case. In practice, however, many algorithms perform much better than the worst case would suggest. Furthermore, various problems can be tackled more efficiently if one assumes the input to be, in a sense, realistic. The field of network science, which studies the structure and emergence of real-world networks, identifies locality and heterogeneity as two frequently occurring properties. A popular model that captures these properties are geometric inhomogeneous random graphs (GIRGs), which is a generalization of hyperbolic random graphs (HRGs). Aside from their importance to network science, GIRGs can be an immensely valuable tool in algorithm engineering. Since they convincingly mimic real-world networks, guarantees about quality and performance of an algorithm on instances of the model can be transferred to real-world applications. They have model parameters to control the amount of heterogeneity and locality, which allows to evaluate those properties in isolation while keeping the rest fixed. Moreover, they can be efficiently generated which allows for experimental analysis. While realistic instances are often rare, generated instances are readily available. Furthermore, the underlying geometry of GIRGs helps to visualize the network, e.g.,~for debugging or to improve understanding of its structure. The aim of this work is to demonstrate the capabilities of geometric inhomogeneous random graphs in algorithm engineering and establish them as routine tools to replace previous models like the Erd\H{o}s-R{\\u27e}nyi model, where each edge exists with equal probability. We utilize geometric inhomogeneous random graphs to design, evaluate, and optimize efficient algorithms for realistic inputs. In detail, we provide the currently fastest sequential generator for GIRGs and HRGs and describe algorithms for maximum flow, directed spanning arborescence, cluster editing, and hitting set. For all four problems, our implementations beat the state-of-the-art on realistic inputs. On top of providing crucial benchmark instances, GIRGs allow us to obtain valuable insights. Most notably, our efficient generator allows us to experimentally show sublinear running time of our flow algorithm, investigate the solution structure of cluster editing, complement our benchmark set of arborescence instances with a density for which there are no real-world networks available, and generate networks with adjustable locality and heterogeneity to reveal the effects of these properties on our algorithms