Algorithms to Explore the Structure and Evolution of Biological Networks

High-throughput experimental protocols have revealed thousands of relationships amongst genes and proteins under various conditions. These putative associations are being aggressively mined to decipher the structural and functional architecture of the cell. One useful tool for exploring this data has been computational network analysis. In this thesis, we propose a collection of novel algorithms to explore the structure and evolution of large, noisy, and sparsely annotated biological networks. We first introduce two information-theoretic algorithms to extract interesting patterns and modules embedded in large graphs. The first, graph summarization, uses the minimum description length principle to find compressible parts of the graph. The second, VI-Cut, uses the variation of information to non-parametrically find groups of topologically cohesive and similarly annotated nodes in the network. We show that both algorithms find structure in biological data that is consistent with known biological processes, protein complexes, genetic diseases, and operational taxonomic units. We also propose several algorithms to systematically generate an ensemble of near-optimal network clusterings and show how these multiple views can be used together to identify clustering dynamics that any single solution approach would miss. To facilitate the study of ancient networks, we introduce a framework called ``network archaeology'') for reconstructing the node-by-node and edge-by-edge arrival history of a network. Starting with a present-day network, we apply a probabilistic growth model backwards in time to find high-likelihood previous states of the graph. This allows us to explore how interactions and modules may have evolved over time. In experiments with real-world social and biological networks, we find that our algorithms can recover significant features of ancestral networks that have long since disappeared. Our work is motivated by the need to understand large and complex biological systems that are being revealed to us by imperfect data. As data continues to pour in, we believe that computational network analysis will continue to be an essential tool towards this end

Exploiting cloud utility models for profit and ruin

A key characteristic that has led to the early adoption of public cloud computing is the utility pricing model that governs the cost of compute resources consumed. Similar to public utilities like gas and electricity, cloud consumers only pay for the resources they consume and only for the time they are utilized. As a result and pursuant to a Cloud Service Provider\u27s (CSP) Terms of Agreement, cloud consumers are responsible for all computational costs incurred within and in support of their rented computing environments whether these resources were consumed in good faith or not. While initial threat modeling and security research on the public cloud model has primarily focused on the confidentiality and integrity of data transferred, processed, and stored in the cloud, little attention has been paid to the external threat sources that have the capability to affect the financial viability of cloud-hosted services. Bounded by a utility pricing model, Internet-facing web resources hosted in the cloud are vulnerable to Fraudulent Resource Consumption (FRC) attacks. Unlike an application-layer DDoS attack that consumes resources with the goal of disrupting short-term availability, a FRC attack is a considerably more subtle attack that instead targets the utility model over an extended time period. By fraudulently consuming web resources in sufficient volume (i.e. data transferred out of the cloud), an attacker is able to inflict significant fraudulent charges to the victim. This work introduces and thoroughly describes the FRC attack and discusses why current application-layer DDoS mitigation schemes are not applicable to a more subtle attack. The work goes on to propose three detection metrics that together form the criteria for detecting a FRC attack from that of normal web activity and an attribution methodology capable of accurately identifying FRC attack clients. Experimental results based on plausible and challenging attack scenarios show that an attacker, without knowledge of the training web log, has a difficult time mimicking the self-similar and consistent request semantics of normal web activity necessary to carryout a successful FRC attack

Approximate Inference for Determinantal Point Processes

In this thesis we explore a probabilistic model that is well-suited to a variety of subset selection tasks: the determinantal point process (DPP). DPPs were originally developed in the physics community to describe the repulsive interactions of fermions. More recently, they have been applied to machine learning problems such as search diversification and document summarization, which can be cast as subset selection tasks. A challenge, however, is scaling such DPP-based methods to the size of the datasets of interest to this community, and developing approximations for DPP inference tasks whose exact computation is prohibitively expensive. A DPP defines a probability distribution over all subsets of a ground set of items. Consider the inference tasks common to probabilistic models, which include normalizing, marginalizing, conditioning, sampling, estimating the mode, and maximizing likelihood. For DPPs, exactly computing the quantities necessary for the first four of these tasks requires time cubic in the number of items or features of the items. In this thesis, we propose a means of making these four tasks tractable even in the realm where the number of items and the number of features is large. Specifically, we analyze the impact of randomly projecting the features down to a lower-dimensional space and show that the variational distance between the resulting DPP and the original is bounded. In addition to expanding the circumstances in which these first four tasks are tractable, we also tackle the other two tasks, the first of which is known to be NP-hard (with no PTAS) and the second of which is conjectured to be NP-hard. For mode estimation, we build on submodular maximization techniques to develop an algorithm with a multiplicative approximation guarantee. For likelihood maximization, we exploit the generative process associated with DPP sampling to derive an expectation-maximization (EM) algorithm. We experimentally verify the practicality of all the techniques that we develop, testing them on applications such as news and research summarization, political candidate comparison, and product recommendation

Learning Scheduling Algorithms for Data Processing Clusters

Efficiently scheduling data processing jobs on distributed compute clusters requires complex algorithms. Current systems, however, use simple generalized heuristics and ignore workload characteristics, since developing and tuning a scheduling policy for each workload is infeasible. In this paper, we show that modern machine learning techniques can generate highly-efficient policies automatically. Decima uses reinforcement learning (RL) and neural networks to learn workload-specific scheduling algorithms without any human instruction beyond a high-level objective such as minimizing average job completion time. Off-the-shelf RL techniques, however, cannot handle the complexity and scale of the scheduling problem. To build Decima, we had to develop new representations for jobs' dependency graphs, design scalable RL models, and invent RL training methods for dealing with continuous stochastic job arrivals. Our prototype integration with Spark on a 25-node cluster shows that Decima improves the average job completion time over hand-tuned scheduling heuristics by at least 21%, achieving up to 2x improvement during periods of high cluster load