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AbstractRecent work has established that large informatics graphs such as social and information networks have non-trivial tree-like structure when viewed at moderate size scales. Here, we present results from the first detailed empirical evaluation of the use of tree decomposition (TD) heuristics for structure identification and extraction in social graphs. Although TDs have historically been used in structural graph theory and scientific computing, we show that—even with existing TD heuristics developed for those very different areas—TD methods can identify interesting structure in a wide range of realistic informatics graphs. Our main contributions are the following: we show that TD methods can identify structures that correlate strongly with the core-periphery structure of realistic networks, even when using simple greedy heuristics; we show that the peripheral bags of these TDs correlate well with low-conductance communities (when they exist) found using local spectral computations; and we show that several types of large-scale “ground-truth” communities, defined by demographic metadata on the nodes of the network, are well-localized in the large-scale and/or peripheral structures of the TDs. Our other main contributions are the following: we provide detailed empirical results for TD heuristics on toy and synthetic networks to establish a baseline to understand better the behavior of the heuristics on more complex real-world networks; and we prove a theorem providing formal justification for the intuition that the only two impediments to low-distortion hyperbolic embedding are high tree-width and long geodesic cycles. Our results suggest future directions for improved TD heuristics that are more appropriate for realistic social graphs.

Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome. Our software implementation is available at https://github.com/spacegraphcats/spacegraphcatsunder the 3-Clause BSD License.