text: We consider the problem of inferring the topology of a network with M sources and N receivers (an M-by- N network), by sending probes between the sources and receivers. Prior work has shown that this problem can be decomposed into two parts: first, infer smaller subnetwork components (1-by- N's or 2-by-2's) and then merge them to identify the M-by- N topology. We focus on the second part, which had previously received less attention in the literature. We assume that a 1-by- N topology is given and that all 2-by-2 components can be queried and learned using end-to-end probes. The problem is which 2-by-2's to query and how to merge them with the given 1-by- N, so as to exactly identify the 2-by- N topology, and optimize a number of performance metrics, including the number of queries (which directly translates into measurement bandwidth), time complexity, and memory usage. We provide a lower bound, [N 2], on the number of 2-by-2's required by any active learning algorithm and propose two greedy algorithms. The first algorithm follows the framework of multiple hypothesis testing, in particular Generalized Binary Search (GBS). The second algorithm is called the Receiver Elimination Algorithm (REA) and follows a bottom-up approach. It requires exactly N-1 steps, which is much less than all (2N) possible 2-by-2's. Simulation results demonstrate that both algorithms correctly identify the 2-by- N topology and are near-optimal, but REA is more efficient in practice.
  @cite_4: 
  @cite_28: We consider the task of topology discovery of sparse random graphs using end-to-end random measurements (e.g., delay) between a subset of nodes, referred to as the participants. The rest of the nodes are hidden, and do not provide any information for topology discovery. We consider topology discovery under two routing models: (a) the participants exchange messages along the shortest paths and obtain end-to-end measurements, and (b) additionally, the participants exchange messages along the second shortest path. For scenario (a), our proposed algorithm results in a sub-linear edit-distance guarantee using a sub-linear number of uniformly selected participants. For scenario (b), we obtain a much stronger result, and show that we can achieve consistent reconstruction when a sub-linear number of uniformly selected nodes participate. This implies that accurate discovery of sparse random graphs is tractable using an extremely small number of participants. We finally obtain a lower bound on the number of participants required by any algorithm to reconstruct the original random graph up to a given edit distance. We also demonstrate that while consistent discovery is tractable for sparse random graphs using a small number of participants, in general, there are graphs which cannot be discovered by any algorithm even with a significant number of participants, and with the availability of end-to-end information along all the paths between the participants. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2013
  @cite_1: Knowledge of a network's topology and internal characteristics such as delay times or losses is crucial to maintain seamless operation of network services. Network tomography is a useful approach to infer such knowledge from end-to-end measurements between nodes at the periphery of the network, as it does not require cooperation of routers and other internal nodes. Most current tomography algorithms are single-source methods, which use multicast probes or synchronized unicast packet trains to measure covariances between destinations from a single vantage point and recover a tree topology from these measurements. Multi-source tomography, on the other hand, uses pairwise hop counts or latencies and consequently overcomes the difficulties associated with obtaining measurements for single-source methods. However, topology recovery is complicated by the fact that the paths along which measurements are taken do not form a tree in the network. Motivated by recent work suggesting that these measurements can be well-approximated by tree metrics, we present two algorithms that use selective pairwise distance measurements between peripheral nodes to construct a tree whose end-to-end distances approximate those in the network. Our first algorithm accommodates measurements perturbed by additive noise, while our second considers a novel noise model that captures missing measurements and the network's deviations from a tree topology. Both algorithms provably use O (p polylog p) pairwise measurements to construct a tree approximation on p end hosts. We present extensive simulated and real-world experiments to evaluate both of our algorithms.
  @cite_40: Abstract Models of complex phenomena often consist of hypothetical entities called “hidden causes,” which cannot be observed directly and yet play a major role in understanding those phenomena. This paper examines the computational roles of these constructs, and addresses the question of whether they can be discovered from empirical observations. Causal models are treated as trees of binary random variables where the leaves are accessible to direct observation, and the internal nodes—representing hidden causes—account for interleaf dependencies. In probabilistic terms, every two leaves are conditionally independent given the value of some internal node between them. We show that if the mechanism which drives the visible variables is indeed tree structured, then it is possible to uncover the topology of the tree uniquely by observing pairwise dependencies among the leaves. The entire tree structure, including the strengths of all internal relationships, can be reconstructed in time proportional to n log n , where n is the number of leaves.
  @cite_45: Probablistic models are becoming increasingly important in analyzing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analyzing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it is accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time presents the state of the art in this new and important field.
summary: Topology inference problems have also been studied in the context of phylogenetic trees @cite_45 @cite_4 . The work in @cite_1 built on @cite_40 and proposed robust algorithms for multiple source tree topology inference. The work in @cite_28 inferred the topology of sparse random graphs using end-to-end measurements between a small subset of nodes. However, the quartet structures and the way we measure them are different in our case due to the nature of active probing in network tomography (see problem formulation in ).