We show that several problems of compacting orthogonal graph drawings to use
the minimum number of rows or the minimum possible area cannot be approximated
to within better than a polynomial factor in polynomial time unless P = NP.
However, there is a fixed-parameter-tractable algorithm for testing whether a
drawing can be compacted to a given number of rows.
In this paper, we study methods for improving the efficiency and privacy of
compressed DNA sequence comparison computations, under various querying
scenarios. For instance, one scenario involves a querier, Bob, who wants to
test if his DNA string, $Q$, is close to a DNA string, $Y$, owned by a data
owner, Alice, but Bob does not want to reveal $Q$ to Alice and Alice is willing
to reveal $Y$ to Bob \emph{only if} it is close to $Q$. We describe a
privacy-enhanced method for comparing two compressed DNA sequences, which can
be used to achieve the goals of such a scenario.
We implement a new algorithm for listing all maximal cliques in sparse graphs
due to Eppstein, L\"offler, and Strash (ISAAC 2010) and analyze its performance
on a large corpus of real-world graphs. Our analysis shows that this algorithm
is the first to offer a practical solution to listing all maximal cliques in
large sparse graphs. All other theoretically-fast algorithms for sparse graphs
have been shown to be significantly slower than the algorithm of Tomita et al.
(Theoretical Computer Science, 2006) in practice. However, the algorithm of
Tomita et al.
We give efficient data-oblivious algorithms for several fundamental geometric
problems that are relevant to geographic information systems, including planar
convex hulls and all-nearest neighbors. Our methods are "data-oblivious" in
that they don't perform any data-dependent operations, with the exception of
operations performed inside low-level blackbox circuits having a constant
number of inputs and outputs.
We present techniques for maintaining subgraph frequencies in a dynamic
graph, using data structures that are parameterized in terms of h, the h-index
of the graph. Our methods extend previous results of Eppstein and Spiro for
maintaining statistics for undirected subgraphs of size three to directed
subgraphs and to subgraphs of size four. For the directed case, we provide a
data structure to maintain counts for all 3-vertex induced subgraphs in O(h)
amortized time per update. For the undirected case, we maintain the counts of
size-four subgraphs in O(h^2) amortized time per update.
We study the classic graph drawing problem of drawing a planar graph using
straight-line edges with a prescribed convex polygon as the outer face. Unlike
previous algorithms for this problem, which may produce drawings with
exponential area, our method produces drawings with polynomial area. In
addition, we allow for collinear points on the boundary, provided such vertices
do not create overlapping edges.
We show that every graph of maximum degree three can be drawn in three
dimensions with at most two bends per edge, and with 120-degree angles between
any two edge segments meeting at a vertex or a bend. We show that every graph
of maximum degree four can be drawn in three dimensions with at most three
bends per edge, and with 109.5-degree angles, i.e., the angular resolution of
the diamond lattice, between any two edge segments meeting at a vertex or bend.
We study the maximum flow problem in directed H-minor-free graphs where H can
be drawn in the plane with one crossing. If a structural decomposition of the
graph as a clique-sum of planar graphs and graphs of constant complexity is
given, we show that a maximum flow can be computed in O(n log n) time. In
particular, maximum flows in directed K_{3,3}-minor-free graphs and directed
K_5-minor-free graphs can be computed in O(n log n) time without additional
assumptions.
Simple rectilinear polygons (i.e. rectilinear polygons without holes or
cutpoints) can be regarded as finite rectangular cell complexes coordinatized
by two finite dendrons. The intrinsic $l_1$-metric is thus inherited from the
product of the two finite dendrons via an isometric embedding. The rectangular
cell complexes that share this same embedding property are called ramified
rectilinear polygons.
We introduce the straggler identification problem, in which an algorithm must
determine the identities of the remaining members of a set after it has had a
large number of insertion and deletion operations performed on it, and now has
relatively few remaining members. The goal is to do this in o(n) space, where n
is the total number of identities. The straggler identification problem has
applications, for example, in determining the set of unacknowledged packets in
a high-bandwidth multicast data stream.
This paper considers pairs of optimization problems that are defined from a
single input and for which it is desired to find a good approximation to either
one of the problems. In many instances, it is possible to efficiently find an
approximation of this type that is better than known inapproximability lower
bounds for either of the two individual optimization problems forming the pair.
In particular, we find either a $(1+\epsilon)$-approximation to $(1,2)$-TSP or
a $1/\epsilon$-approximation to maximum independent set, from a given graph, in
linear time.
We describe an algorithm for finding the tight span of a finite metric space;
the tight span is a construction for embedding arbitrary metrics into
$L_\infty$ spaces analogous to the Euclidean convex hull. Our algorithm is
incremental, and applies to any space for which the tight span is homeomorphic
to a subset of the Euclidean plane. After a new point is added to the metric
space our algorithm can update the tight span in time linear in the number of
points already added; this is optimal with respect to the size of the input, an
$n\times n$ distance matrix.