Distributed Connectivity Decomposition

We present time-efficient distributed algorithms for decomposing graphs with large edge or vertex connectivity into multiple spanning or dominating trees, respectively. As their primary applications, these decompositions allow us to achieve information flow with size close to the connectivity by parallelizing it along the trees. More specifically, our distributed decomposition algorithms are as follows: (I) A decomposition of each undirected graph with vertex-connectivity $k$ into (fractionally) vertex-disjoint weighted dominating trees with total weight $\Omega(\frac{k}{\log n})$, in $\widetilde{O}(D+\sqrt{n})$ rounds. (II) A decomposition of each undirected graph with edge-connectivity $\lambda$ into (fractionally) edge-disjoint weighted spanning trees with total weight $\lceil\frac{\lambda-1}{2}\rceil(1-\varepsilon)$, in $\widetilde{O}(D+\sqrt{n\lambda})$ rounds. We also show round complexity lower bounds of $\tilde{\Omega}(D+\sqrt{\frac{n}{k}})$ and $\tilde{\Omega}(D+\sqrt{\frac{n}{\lambda}})$ for the above two decompositions, using techniques of [Das Sarma et al., STOC'11]. Moreover, our vertex-connectivity decomposition extends to centralized algorithms and improves the time complexity of [Censor-Hillel et al., SODA'14] from $O(n^3)$ to near-optimal $\tilde{O}(m)$. As corollaries, we also get distributed oblivious routing broadcast with $O(1)$-competitive edge-congestion and $O(\log n)$-competitive vertex-congestion. Furthermore, the vertex connectivity decomposition leads to near-time-optimal $O(\log n)$-approximation of vertex connectivity: centralized $\widetilde{O}(m)$ and distributed $\tilde{O}(D+\sqrt{n})$. The former moves toward the 1974 conjecture of Aho, Hopcroft, and Ullman postulating an $O(m)$ centralized exact algorithm while the latter is the first distributed vertex connectivity approximation

Content Distribution by Multiple Multicast Trees and Intersession Cooperation: Optimal Algorithms and Approximations

In traditional massive content distribution with multiple sessions, the sessions form separate overlay networks and operate independently, where some sessions may suffer from insufficient resources even though other sessions have excessive resources. To cope with this problem, we consider the universal swarming approach, which allows multiple sessions to cooperate with each other. We formulate the problem of finding the optimal resource allocation to maximize the sum of the session utilities and present a subgradient algorithm which converges to the optimal solution in the time-average sense. The solution involves an NP-hard subproblem of finding a minimum-cost Steiner tree. We cope with this difficulty by using a column generation method, which reduces the number of Steiner-tree computations. Furthermore, we allow the use of approximate solutions to the Steiner-tree subproblem. We show that the approximation ratio to the overall problem turns out to be no less than the reciprocal of the approximation ratio to the Steiner-tree subproblem. Simulation results demonstrate that universal swarming improves the performance of resource-poor sessions with negligible impact to resource-rich sessions. The proposed approach and algorithm are expected to be useful for infrastructure-based content distribution networks with long-lasting sessions and relatively stable network environment

Coding limits on the number of transcription factors

Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms. We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction. The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/BMCGenomics2006.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590034/ http://www.biomedcentral.com/1471-2164/7/23

Convolutional Neural Networks over Tree Structures for Programming Language Processing

Programming language processing (similar to natural language processing) is a hot research topic in the field of software engineering; it has also aroused growing interest in the artificial intelligence community. However, different from a natural language sentence, a program contains rich, explicit, and complicated structural information. Hence, traditional NLP models may be inappropriate for programs. In this paper, we propose a novel tree-based convolutional neural network (TBCNN) for programming language processing, in which a convolution kernel is designed over programs' abstract syntax trees to capture structural information. TBCNN is a generic architecture for programming language processing; our experiments show its effectiveness in two different program analysis tasks: classifying programs according to functionality, and detecting code snippets of certain patterns. TBCNN outperforms baseline methods, including several neural models for NLP.Comment: Accepted at AAAI-1