Weighted Additive Spanners

A emph{spanner} of a graph $G$ is a subgraph $H$ that approximately preserves shortest path distances in $G$. Spanners are commonly applied to compress computation on metric spaces corresponding to weighted input graphs. Classic spanner constructions can seamlessly handle edge weights, so long as error is measured emph{multiplicatively}. In this work, we investigate whether one can similarly extend constructions of spanners with purely emph{additive} error to weighted graphs. These extensions are not immediate, due to a key lemma about the size of shortest path neighborhoods that fails for weighted graphs. Despite this, we recover a suitable amortized version, which lets us prove direct extensions of classic $+2$ and $+4$ unweighted spanners (both all-pairs and pairwise) to $+2W$ and $+4W$ weighted spanners, where $W$ is the maximum edge weight. Specifically, we show that a weighted graph $G$ contains all-pairs (pairwise) $+2W$ and $+4W$ weighted spanners of size $O(n^{3/2})$ and $widetilde{O}(n^{7/5})$ ($O(np^{1/3})$ and $O(np^{2/7})$) respectively. For a technical reason, the $+6$ unweighted spanner becomes a $+8W$ weighted spanner; closing this error gap is an interesting remaining open problem. That is, we show that $G$ contains all-pairs (pairwise) $+8W$ weighted spanners of size $O(n^{4/3})$ ($O(np^{1/4})$).

Distributed Weighted Matching via Randomized Composable Coresets

Maximum weight matching is one of the most fundamental combinatorial optimization problems with a wide range of applications in data mining and bioinformatics. Developing distributed weighted matching algorithms is challenging due to the sequential nature of efficient algorithms for this problem. In this paper, we develop a simple distributed algorithm for the problem on general graphs with approximation guarantee of $2+varepsilon$ that (nearly) matches that of the sequential greedy algorithm. A key advantage of this algorithm is that it can be easily implemented in only two rounds of computation in modern parallel computation frameworks such as MapReduce. We also demonstrate the efficiency of our algorithm in practice on various graphs (some with half a trillion edges) by achieving objective values always close to what is achievable in the centralized setting.

Reconciling Multiple Genes Trees via Segmental Duplications and Losses

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost $delta$ and $lambda$, respectively. We show that the problem is polynomial-time solvable when $delta leq lambda$ (via LCA-mapping), while if $delta > lambda$ the problem is NP-hard, even when $lambda = 0$ and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are $delta/lambda$ and the number $d$ of segmental duplications, of time complexity $O(lceil frac{delta}{lambda} rceil^{d} cdot n cdot frac{delta}{lambda})$. Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.

Compact Routing Messages in Self-Healing Trees

Existing compact routing schemes, e.g., Thorup and Zwick [SPAA 2001] and Chechik [PODC 2013], often have no means to tolerate failures, once the system has been setup and started. This paper presents, to our knowledge, the first self-healing compact routing scheme. Besides, our schemes are developed for low memory nodes, i.e., nodes need only $O(log^2 n)$ memory, and are thus, compact schemes. We introduce two algorithms of independent interest: The first is CompactFT, a novel compact version (using only $O(log n)$ local memory) of the self-healing algorithm Forgiving Tree of Hayes et al. [PODC 2008]. The second algorithm (CompactFTZ) combines CompactFT with Thorup-Zwicks tree-based compact routing scheme [SPAA 2001] to produce a fully compact self-healing routing scheme. In the self-healing model, the adversary deletes nodes one at a time with the affected nodes self-healing locally by adding few edges. CompactFT recovers from each attack in only $O(1)$ time and $Delta$ messages, with only +3 degree increase and $O(log Delta)$ graph diameter increase, over any sequence of deletions ($Delta$ is the initial maximum degree). Additionally, CompactFTZ guarantees delivery of a packet sent from sender s as long as the receiver t has not been deleted, with only an additional $O(y log Delta)$ latency, where $y$ is the number of nodes that have been deleted on the path between $s$ and $t$. If $t$ has been deleted, $s$ gets informed and the packet removed from the network.

Computing the Greedy Spanner in Linear Space

The greedy spanner is a high-quality spanner: its total weight, edge count and maximal degree are asymptotically optimal and in practice significantly better than for any other spanner with reasonable construction time. Unfortunately, all known algorithms that compute the greedy spanner of n points use Omega(n^2) space, which is impractical on large instances. To the best of our knowledge, the largest instance for which the greedy spanner was computed so far has about 13,000 vertices. We present a O(n)-space algorithm that computes the same spanner for points in R^d running in O(n^2 log^2 n) time for any fixed stretch factor and dimension. We discuss and evaluate a number of optimizations to its running time, which allowed us to compute the greedy spanner on a graph with a million vertices. To our knowledge, this is also the first algorithm for the greedy spanner with a near-quadratic running time guarantee that has actually been implemented.