5,710 research outputs found
Efficient Algorithms for Moral Lineage Tracing
Lineage tracing, the joint segmentation and tracking of living cells as they
move and divide in a sequence of light microscopy images, is a challenging
task. Jug et al. have proposed a mathematical abstraction of this task, the
moral lineage tracing problem (MLTP), whose feasible solutions define both a
segmentation of every image and a lineage forest of cells. Their branch-and-cut
algorithm, however, is prone to many cuts and slow convergence for large
instances. To address this problem, we make three contributions: (i) we devise
the first efficient primal feasible local search algorithms for the MLTP, (ii)
we improve the branch-and-cut algorithm by separating tighter cutting planes
and by incorporating our primal algorithms, (iii) we show in experiments that
our algorithms find accurate solutions on the problem instances of Jug et al.
and scale to larger instances, leveraging moral lineage tracing to practical
significance.Comment: Accepted at ICCV 201
Submodular relaxation for inference in Markov random fields
In this paper we address the problem of finding the most probable state of a
discrete Markov random field (MRF), also known as the MRF energy minimization
problem. The task is known to be NP-hard in general and its practical
importance motivates numerous approximate algorithms. We propose a submodular
relaxation approach (SMR) based on a Lagrangian relaxation of the initial
problem. Unlike the dual decomposition approach of Komodakis et al., 2011 SMR
does not decompose the graph structure of the initial problem but constructs a
submodular energy that is minimized within the Lagrangian relaxation. Our
approach is applicable to both pairwise and high-order MRFs and allows to take
into account global potentials of certain types. We study theoretical
properties of the proposed approach and evaluate it experimentally.Comment: This paper is accepted for publication in IEEE Transactions on
Pattern Analysis and Machine Intelligenc
A practical fpt algorithm for Flow Decomposition and transcript assembly
The Flow Decomposition problem, which asks for the smallest set of weighted
paths that "covers" a flow on a DAG, has recently been used as an important
computational step in transcript assembly. We prove the problem is in FPT when
parameterized by the number of paths by giving a practical linear fpt
algorithm. Further, we implement and engineer a Flow Decomposition solver based
on this algorithm, and evaluate its performance on RNA-sequence data.
Crucially, our solver finds exact solutions while achieving runtimes
competitive with a state-of-the-art heuristic. Finally, we contextualize our
design choices with two hardness results related to preprocessing and weight
recovery. Specifically, -Flow Decomposition does not admit polynomial
kernels under standard complexity assumptions, and the related problem of
assigning (known) weights to a given set of paths is NP-hard.Comment: Introduces software package Toboggan: Version 1.0.
http://dx.doi.org/10.5281/zenodo.82163
Learning Combinatorial Node Labeling Algorithms
We present a graph neural network to learn graph coloring heuristics using
reinforcement learning. Our learned deterministic heuristics give better
solutions than classical degree-based greedy heuristics and only take seconds
to evaluate on graphs with tens of thousands of vertices. As our approach is
based on policy-gradients, it also learns a probabilistic policy as well. These
probabilistic policies outperform all greedy coloring baselines and a machine
learning baseline. Our approach generalizes several previous machine-learning
frameworks, which applied to problems like minimum vertex cover. We also
demonstrate that our approach outperforms two greedy heuristics on minimum
vertex cover
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