8 research outputs found
A greedy algorithm for multicut and integral multiflow in rooted trees
We present an O(min(Kn,n2)) algorithm to solve the maximum integral multiflow and minimum multicut problems in rooted trees, where K is the number of commodities and n is the number of vertices. These problems are NP-hard in undirected trees but polynomial in directed trees. In the algorithm we propose, we first use a greedy procedure to build the multiflow then we use duality properties to obtain the multicut and prove the optimality
Partitioning Graph Drawings and Triangulated Simple Polygons into Greedily Routable Regions
A greedily routable region (GRR) is a closed subset of , in
which each destination point can be reached from each starting point by
choosing the direction with maximum reduction of the distance to the
destination in each point of the path.
Recently, Tan and Kermarrec proposed a geographic routing protocol for dense
wireless sensor networks based on decomposing the network area into a small
number of interior-disjoint GRRs. They showed that minimum decomposition is
NP-hard for polygons with holes.
We consider minimum GRR decomposition for plane straight-line drawings of
graphs. Here, GRRs coincide with self-approaching drawings of trees, a drawing
style which has become a popular research topic in graph drawing. We show that
minimum decomposition is still NP-hard for graphs with cycles, but can be
solved optimally for trees in polynomial time. Additionally, we give a
2-approximation for simple polygons, if a given triangulation has to be
respected.Comment: full version of a paper appearing in ISAAC 201
Maximum Weight Disjoint Paths in Outerplanar Graphs via Single-Tree Cut Approximators
Since 1997 there has been a steady stream of advances for the maximum
disjoint paths problem. Achieving tractable results has usually required
focusing on relaxations such as: (i) to allow some bounded edge congestion in
solutions, (ii) to only consider the unit weight (cardinality) setting, (iii)
to only require fractional routability of the selected demands (the
all-or-nothing flow setting). For the general form (no congestion, general
weights, integral routing) of edge-disjoint paths ({\sc edp}) even the case of
unit capacity trees which are stars generalizes the maximum matching problem
for which Edmonds provided an exact algorithm. For general capacitated trees,
Garg, Vazirani, Yannakakis showed the problem is APX-Hard and Chekuri, Mydlarz,
Shepherd provided a -approximation. This is essentially the only setting
where a constant approximation is known for the general form of \textsc{edp}.
We extend their result by giving a constant-factor approximation algorithm for
general-form \textsc{edp} in outerplanar graphs. A key component for the
algorithm is to find a {\em single-tree} cut approximator for
outerplanar graphs. Previously cut approximators were only known via
distributions on trees and these were based implicitly on the results of Gupta,
Newman, Rabinovich and Sinclair for distance tree embeddings combined with
results of Anderson and Feige.Comment: 19 pages, 6 figure
Parameterized Algorithms for Zero Extension and Metric Labelling Problems
We consider the problems Zero Extension and Metric Labelling under the paradigm of parameterized complexity. These are natural, well-studied problems with important applications, but have previously not received much attention from this area.
Depending on the chosen cost function mu, we find that different algorithmic approaches can be applied to design FPT-algorithms: for arbitrary mu we parameterize by the number of edges that cross the cut (not the cost) and show how to solve Zero Extension in time O(|D|^{O(k^2)} n^4 log n) using randomized contractions. We improve this running time with respect to both parameter and input size to O(|D|^{O(k)} m) in the case where mu is a metric. We further show that the problem admits a polynomial sparsifier, that is, a kernel of size O(k^{|D|+1}) that is independent of the metric mu.
With the stronger condition that mu is described by the distances of leaves in a tree, we parameterize by a gap parameter (q - p) between the cost of a true solution q and a `discrete relaxation\u27 p and achieve a running time of O(|D|^{q-p} |T|m + |T|phi(n,m)) where T is the size of the tree over which mu is defined and phi(n,m) is the running time of a max-flow computation. We achieve a similar result for the more general Metric Labelling, while also allowing mu to be the distance metric between an arbitrary subset of nodes in a tree using tools from the theory of VCSPs. We expect the methods used in the latter result to have further applications
Cuts and Partitions in Graphs/Trees with Applications
Both the maximum agreement forest problem and the multicut on trees problem are NP-hard, thus cannot be solved efficiently if P /=NP. The maximum agreement forest problem was motivated in the study of evolution trees in bioinformatics, in which we are given two leaf-labeled trees and are asked to find a maximum forest that is a subgraph of both trees. The multicuton trees problem has applications in networks, in which we are given a forest and a set of pairs of termianls and are asked to find a cut that separates all pairs of terminals.
We develop combinatorial and algorithmic techniques that lead to improved parameterized algorithms, approximation algorithms, and kernelization algorithms for these problems. For the maximum agreement forest problem, we proceed from the bottommost level of trees and extend solutions to whole trees. With this technique, we show that the maxi- mum agreement forest problem is fixed-parameterized tractable in general trees, resolving an open problem in this area. We also provide the first constant ratio approximation algorithm for the problem in general trees. For the multicut on trees problem, we take a new look at the problem through the eyes of vertex cover problem. This connection allows us to develop an kernelization algorithm for the problem, which gives an upper bound of O(k3) on the kernel size, significantly improving the previous best upper bound O(k6). We further exploit this connection to give a parameterized algorithm for the problem that runs in time Oâ (1.62k), thus improving the previous best algorithm of running time Oâ (2k). In the protein complex prediction problem, which comes directly from the study of bioinformatics, we are given a protein-protein interaction network, and are asked to find dense regions in this graph. We formulate this problem as a graph clustering problem and develop an algorithm to refine the results for identifying protein complexes. We test our algorithm on yeast protein- protein interaction networks, and we show that our algorithm is able to identify complexes more accurately than other existing algorithms
Learning-based Segmentation for Connectomics
Recent advances in electron microscopy techniques make it possible to acquire highresolution, isotropic volume images of neural circuitry. In connectomics, neuroscientists seek to obtain the circuit diagram involving all neurons and synapses in such a volume image. Mapping neuron connectivity requires tracing each and every neural process through terabytes of image data. Due to the size and complexity of these volume images, fully automated analysis methods are desperately needed. In this thesis, I consider automated, machine learning-based neurite segmentation approaches based on a simultaneous merge decision of adjacent supervoxels.
- Given a learned likelihood of merging adjacent supervoxels, Chapter 4 adapts a probabilistic graphical model which ensures that merge decisions are consistent
and the surfaces of final segments are closed. This model can be posed as a multicut optimization problem and is solved with the cutting-plane method. In order to scale to large datasets, a fast search for (and good choice of) violated cycle constraints is crucial. Quantitative experiments show that the proposed closed-surface regularization significantly improves segmentation performance.
- In Chapter 5, I investigate whether the edge weights of the previous model can be chosen to minimize the loss with respect to non-local segmentation quality measures (e.g. Rand Index). Suitable w are obtained from a structured learning approach. In the Structured Support Vector Machine formulation, a novel fast enumeration scheme is used to find the most violated constraint. Quantitative experiments show that structured learning can improve upon unstructured methods. Furthermore, I introduce a new approximate, hierarchical and blockwise optimization approach for large-scale multicut segmentation. Using this method, high-quality approximate solutions for large problem instances are found quickly.
- Chapter 6 introduces another novel approximate scheme for multicut segmentation -- Cut, Glue&Cut -- which is based on the move-making paradigm. First, the graph is recursively partitioned into small regions (cut phase). Then, for any two adjacent regions, alternative cuts of these two regions define possible moves (glue&cut phase). The proposed algorithm finds segmentations that are { as measured by a loss function { as close to the ground-truth as the global optimum found by exact solvers, while being significantly faster than existing methods.
- In order to jointly label resulting segments as well as to label the boundaries between segments, Chapter 7 proposes the Asymmetric Multi-way Cut model, a variant of Multi-way Cut. In this new model, within-class cuts are allowed for some labels, while being forbidden for other labels. Qualitative experiments show when such a formulation can be beneficial. In particular, an application to joint neurite and cell organelle labeling in EM volume images is discussed.
- Custom software tools that can cope with the large data volumes common in the field of connectomics are a prerequisite for the implementation and evaluation of novel segmentation techniques. Chapter 3 presents version 1.0 of ilastik, a joint effort of multiple researchers. I have co-written its volume viewing component, volumina. ilastik provides an interactive pixel classification work
ow on largerthan-RAM datasets as well as a semi-automated segmentation module useful for acquiring gold standard segmentations. Furthermore, I describe new software for
dealing with hierarchies of cell complexes as well as for blockwise image processing operations on large datasets.
The different segmentation methods presented in this thesis provide a promising direction towards reaching the required reliability as well as the required data throughput
necessary for connectomics applications