Hardness of Exact Distance Queries in Sparse Graphs Through Hub Labeling

A distance labeling scheme is an assignment of bit-labels to the vertices of an undirected, unweighted graph such that the distance between any pair of vertices can be decoded solely from their labels. An important class of distance labeling schemes is that of hub labelings, where a node $v \in G$ stores its distance to the so-called hubs $S_v \subseteq V$, chosen so that for any $u,v \in V$ there is $w \in S_u \cap S_v$ belonging to some shortest $uv$ path. Notice that for most existing graph classes, the best distance labelling constructions existing use at some point a hub labeling scheme at least as a key building block. Our interest lies in hub labelings of sparse graphs, i.e., those with $|E(G)| = O(n)$, for which we show a lowerbound of $\frac{n}{2^{O(\sqrt{\log n})}}$ for the average size of the hubsets. Additionally, we show a hub-labeling construction for sparse graphs of average size $O(\frac{n}{RS(n)^{c}})$ for some $0 < c < 1$, where $RS(n)$ is the so-called Ruzsa-Szemer{\'e}di function, linked to structure of induced matchings in dense graphs. This implies that further improving the lower bound on hub labeling size to $\frac{n}{2^{(\log n)^{o(1)}}}$ would require a breakthrough in the study of lower bounds on $RS(n)$, which have resisted substantial improvement in the last 70 years. For general distance labeling of sparse graphs, we show a lowerbound of $\frac{1}{2^{O(\sqrt{\log n})}} SumIndex(n)$, where $SumIndex(n)$ is the communication complexity of the Sum-Index problem over $Z_n$. Our results suggest that the best achievable hub-label size and distance-label size in sparse graphs may be $\Theta(\frac{n}{2^{(\log n)^c}})$ for some $0<c < 1$

Going the distance for protein function prediction: a new distance metric for protein interaction networks

Due to an error introduced in the production process, the x-axes in the first panels of Figure 1 and Figure 7 are not formatted correctly. The correct Figure 1 can be viewed here: http://dx.doi.org/10.1371/annotation/343bf260-f6ff-48a2-93b2-3cc79af518a9In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.MC, HZ, NMD and LJC were supported in part by National Institutes of Health (NIH) R01 grant GM080330. JP was supported in part by NIH grant R01 HD058880. This material is based upon work supported by the National Science Foundation under grant numbers CNS-0905565, CNS-1018266, CNS-1012910, and CNS-1117039, and supported by the Army Research Office under grant W911NF-11-1-0227 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Algorithms for Landmark Hub Labeling

Landmark-based routing and Hub Labeling (HL) are shortest path planning techniques, both of which rely on storing shortest path distances between selected pairs of nodes in a preprocessing phase to accelerate query answering. In Landmark-based routing, stored distances to landmark nodes are used to obtain distance lower bounds that guide A* search from node s to node t. With HL, tight upper bounds for shortest path distances between any s-t-pair can be interfered from their stored node labels, making HL an efficient distance oracle. However, for shortest path retrieval, the oracle has to be called once per edge in said path. Furthermore, HL often suffers from a large space consumption as many node pair distances have to be stored in the labels to allow for correct query answering. In this paper, we propose a novel technique, called Landmark Hub Labeling (LHL), which integrates the landmark concept into HL. We prove better worst-case path retrieval times for LHL in case it is path-consistent (a new labeling property we introduce). Moreover, we design efficient (approximation) algorithms that produce path-consistent LHL with small label size and provide parametrized upper bounds, depending on the highway dimension h or the geodesic transversal number gt of the graph. Finally, we show that the space consumption of LHL is smaller than that of (hierarchical) HL, both in theory and in experiments on real-world road networks

Simpler, faster and shorter labels for distances in graphs

We consider how to assign labels to any undirected graph with n nodes such that, given the labels of two nodes and no other information regarding the graph, it is possible to determine the distance between the two nodes. The challenge in such a distance labeling scheme is primarily to minimize the maximum label lenght and secondarily to minimize the time needed to answer distance queries (decoding). Previous schemes have offered different trade-offs between label lengths and query time. This paper presents a simple algorithm with shorter labels and shorter query time than any previous solution, thereby improving the state-of-the-art with respect to both label length and query time in one single algorithm. Our solution addresses several open problems concerning label length and decoding time and is the first improvement of label length for more than three decades. More specifically, we present a distance labeling scheme with label size (log 3)/2 + o(n) (logarithms are in base 2) and O(1) decoding time. This outperforms all existing results with respect to both size and decoding time, including Winkler's (Combinatorica 1983) decade-old result, which uses labels of size (log 3)n and O(n/log n) decoding time, and Gavoille et al. (SODA'01), which uses labels of size 11n + o(n) and O(loglog n) decoding time. In addition, our algorithm is simpler than the previous ones. In the case of integral edge weights of size at most W, we present almost matching upper and lower bounds for label sizes. For r-additive approximation schemes, where distances can be off by an additive constant r, we give both upper and lower bounds. In particular, we present an upper bound for 1-additive approximation schemes which, in the unweighted case, has the same size (ignoring second order terms) as an adjacency scheme: n/2. We also give results for bipartite graphs and for exact and 1-additive distance oracles