2,506 research outputs found
Online Steiner Tree with Deletions
In the online Steiner tree problem, the input is a set of vertices that
appear one-by-one, and we have to maintain a Steiner tree on the current set of
vertices. The cost of the tree is the total length of edges in the tree, and we
want this cost to be close to the cost of the optimal Steiner tree at all
points in time. If we are allowed to only add edges, a tight bound of
on the competitiveness is known. Recently it was shown that if
we can add one new edge and make one edge swap upon every vertex arrival, we
can maintain a constant-competitive tree online.
But what if the set of vertices sees both additions and deletions? Again, we
would like to obtain a low-cost Steiner tree with as few edge changes as
possible. The original paper of Imase and Waxman had also considered this
model, and it gave a greedy algorithm that maintained a constant-competitive
tree online, and made at most edge changes for the first
requests. In this paper give the following two results.
Our first result is an online algorithm that maintains a Steiner tree only
under deletions: we start off with a set of vertices, and at each time one of
the vertices is removed from this set: our Steiner tree no longer has to span
this vertex. We give an algorithm that changes only a constant number of edges
upon each request, and maintains a constant-competitive tree at all times. Our
algorithm uses the primal-dual framework and a global charging argument to
carefully make these constant number of changes.
We then study the natural greedy algorithm proposed by Imase and Waxman that
maintains a constant-competitive Steiner tree in the fully-dynamic model (where
each request either adds or deletes a vertex). Our second result shows that
this algorithm makes only a constant number of changes per request in an
amortized sense.Comment: An extended abstract appears in the SODA 2014 conferenc
The Power of Dynamic Distance Oracles: Efficient Dynamic Algorithms for the Steiner Tree
In this paper we study the Steiner tree problem over a dynamic set of
terminals. We consider the model where we are given an -vertex graph
with positive real edge weights, and our goal is to maintain a tree
which is a good approximation of the minimum Steiner tree spanning a terminal
set , which changes over time. The changes applied to the
terminal set are either terminal additions (incremental scenario), terminal
removals (decremental scenario), or both (fully dynamic scenario). Our task
here is twofold. We want to support updates in sublinear time, and keep
the approximation factor of the algorithm as small as possible. We show that we
can maintain a -approximate Steiner tree of a general graph in
time per terminal addition or removal. Here,
denotes the stretch of the metric induced by . For planar graphs we achieve
the same running time and the approximation ratio of .
Moreover, we show faster algorithms for incremental and decremental scenarios.
Finally, we show that if we allow higher approximation ratio, even more
efficient algorithms are possible. In particular we show a polylogarithmic time
-approximate algorithm for planar graphs.
One of the main building blocks of our algorithms are dynamic distance
oracles for vertex-labeled graphs, which are of independent interest. We also
improve and use the online algorithms for the Steiner tree problem.Comment: Full version of the paper accepted to STOC'1
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Fully dynamic maintenance of euclidean minimum spanning trees
We maintain the minimum spanning tree of a point set in the plane, subject to point insertions and deletions, in time O(n^5/6 log1^2/2 n) per update operation. No nontrivial dynamic geometric minimum spanning tree algorithm was previously known. We reduce the problem to maintaining bichromatic closest pairs, which we also solve in the same time bounds. Our algorithm uses a novel construction, the ordered nearest neighbors of a sequence of points. Any point set or bichromatic point set can be ordered so that this graph is a simple path
Compressing DNA sequence databases with coil
Background: Publicly available DNA sequence databases such as GenBank are large, and are
growing at an exponential rate. The sheer volume of data being dealt with presents serious storage
and data communications problems. Currently, sequence data is usually kept in large "flat files,"
which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which
rarely achieves good compression ratios. While much research has been done on compressing
individual DNA sequences, surprisingly little has focused on the compression of entire databases
of such sequences. In this study we introduce the sequence database compression software coil.
Results: We have designed and implemented a portable software package, coil, for compressing
and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared
towards achieving high compression ratios at the expense of execution time and memory usage
during compression – the compression time represents a "one-off investment" whose cost is
quickly amortised if the resulting compressed file is transmitted many times. Decompression
requires little memory and is extremely fast. We demonstrate a 5% improvement in compression
ratio over state-of-the-art general-purpose compression tools for a large GenBank database file
containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental
additions to a sequence database.
Conclusion: coil presents a compelling alternative to conventional compression of flat files for the
storage and distribution of DNA sequence databases having a narrow distribution of sequence
lengths, such as EST data. Increasing compression levels for databases having a wide distribution of
sequence lengths is a direction for future work
Connectivity Oracles for Graphs Subject to Vertex Failures
We introduce new data structures for answering connectivity queries in graphs
subject to batched vertex failures. A deterministic structure processes a batch
of failed vertices in time and thereafter
answers connectivity queries in time. It occupies space . We develop a randomized Monte Carlo version of our data structure
with update time , query time , and space
for any failure bound . This is the first connectivity oracle for
general graphs that can efficiently deal with an unbounded number of vertex
failures.
We also develop a more efficient Monte Carlo edge-failure connectivity
oracle. Using space , edge failures are processed in time and thereafter, connectivity queries are answered in
time, which are correct w.h.p.
Our data structures are based on a new decomposition theorem for an
undirected graph , which is of independent interest. It states that
for any terminal set we can remove a set of
vertices such that the remaining graph contains a Steiner forest for with
maximum degree
Approximate Closest Community Search in Networks
Recently, there has been significant interest in the study of the community
search problem in social and information networks: given one or more query
nodes, find densely connected communities containing the query nodes. However,
most existing studies do not address the "free rider" issue, that is, nodes far
away from query nodes and irrelevant to them are included in the detected
community. Some state-of-the-art models have attempted to address this issue,
but not only are their formulated problems NP-hard, they do not admit any
approximations without restrictive assumptions, which may not always hold in
practice.
In this paper, given an undirected graph G and a set of query nodes Q, we
study community search using the k-truss based community model. We formulate
our problem of finding a closest truss community (CTC), as finding a connected
k-truss subgraph with the largest k that contains Q, and has the minimum
diameter among such subgraphs. We prove this problem is NP-hard. Furthermore,
it is NP-hard to approximate the problem within a factor , for
any . However, we develop a greedy algorithmic framework,
which first finds a CTC containing Q, and then iteratively removes the furthest
nodes from Q, from the graph. The method achieves 2-approximation to the
optimal solution. To further improve the efficiency, we make use of a compact
truss index and develop efficient algorithms for k-truss identification and
maintenance as nodes get eliminated. In addition, using bulk deletion
optimization and local exploration strategies, we propose two more efficient
algorithms. One of them trades some approximation quality for efficiency while
the other is a very efficient heuristic. Extensive experiments on 6 real-world
networks show the effectiveness and efficiency of our community model and
search algorithms
Finding and counting vertex-colored subtrees
The problems studied in this article originate from the Graph Motif problem
introduced by Lacroix et al. in the context of biological networks. The problem
is to decide if a vertex-colored graph has a connected subgraph whose colors
equal a given multiset of colors . It is a graph pattern-matching problem
variant, where the structure of the occurrence of the pattern is not of
interest but the only requirement is the connectedness. Using an algebraic
framework recently introduced by Koutis et al., we obtain new FPT algorithms
for Graph Motif and variants, with improved running times. We also obtain
results on the counting versions of this problem, proving that the counting
problem is FPT if M is a set, but becomes W[1]-hard if M is a multiset with two
colors. Finally, we present an experimental evaluation of this approach on real
datasets, showing that its performance compares favorably with existing
software.Comment: Conference version in International Symposium on Mathematical
Foundations of Computer Science (MFCS), Brno : Czech Republic (2010) Journal
Version in Algorithmic
Relaxing the Irrevocability Requirement for Online Graph Algorithms
Online graph problems are considered in models where the irrevocability
requirement is relaxed. Motivated by practical examples where, for example,
there is a cost associated with building a facility and no extra cost
associated with doing it later, we consider the Late Accept model, where a
request can be accepted at a later point, but any acceptance is irrevocable.
Similarly, we also consider a Late Reject model, where an accepted request can
later be rejected, but any rejection is irrevocable (this is sometimes called
preemption). Finally, we consider the Late Accept/Reject model, where late
accepts and rejects are both allowed, but any late reject is irrevocable. For
Independent Set, the Late Accept/Reject model is necessary to obtain a constant
competitive ratio, but for Vertex Cover the Late Accept model is sufficient and
for Minimum Spanning Forest the Late Reject model is sufficient. The Matching
problem has a competitive ratio of 2, but in the Late Accept/Reject model, its
competitive ratio is 3/2
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