Hans L. Bodlaender

Bio: Hans L. Bodlaender is an academic researcher from Utrecht University. The author has contributed to research in topics: Treewidth & Pathwidth. The author has an hindex of 68, co-authored 427 publications receiving 19826 citations. Previous affiliations of Hans L. Bodlaender include Eindhoven University of Technology.

A Linear-Time Algorithm for Finding Tree-Decompositions of Small Treewidth

Abstract: In this paper, we give for constant $k$ a linear-time algorithm that, given a graph $G=(V,E)$, determines whether the treewidth of $G$ is at most $k$ and, if so, finds a tree-decomposition of $G$ with treewidth at most $k$. A consequence is that every minor-closed class of graphs that does not contain all planar graphs has a linear-time recognition algorithm. Another consequence is that a similar result holds when we look instead for path-decompositions with pathwidth at most some constant $k$.

A tourist guide through treewidth

Abstract: A short overview is given of many recent results in algorithmic graph theory that deal with the notions treewidth, and pathwidth. We discuss algorithms that find tree-decompositions, algorithms that use tree-decompositions to solve hard problems efficiently, graph minor theory, and some applications. The paper contains an extensive bibliography.

A linear time algorithm for finding tree-decompositions of small treewidth

Abstract: In this paper, we give for constant $k$ a linear-time algorithm that, given a graph $G=(V,E)$, determines whether the treewidth of $G$ is at most $k$ and, if so, finds a tree-decomposition of $G$ with treewidth at most $k$. A consequence is that every minor-closed class of graphs that does not contain all planar graphs has a linear-time recognition algorithm. Another consequence is that a similar result holds when we look instead for path-decompositions with pathwidth at most some constant $k$.

Pattern Recognition and Machine Learning

Abstract: Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Random graphs

Abstract: We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Graphical Models, Exponential Families, and Variational Inference

Abstract: The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building large-scale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fields, including bioinformatics, communication theory, statistical physics, combinatorial optimization, signal and image processing, information retrieval and statistical machine learning. Many problems that arise in specific instances — including the key problems of computing marginals and modes of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing likelihoods, marginal probabilities and most probable configurations. We describe how a wide variety of algorithms — among them sum-product, cluster variational methods, expectation-propagation, mean field methods, max-product and linear programming relaxation, as well as conic programming relaxations — can all be understood in terms of exact or approximate forms of these variational representations. The variational approach provides a complementary alternative to Markov chain Monte Carlo as a general source of approximation methods for inference in large-scale statistical models.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Abstract: MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

A Dynamic Survey of Graph Labeling

Abstract: A graph labeling is an assignment of integers to the vertices or edges, or both, subject to certain conditions. Graph labelings were first introduced in the late 1960s. In the intervening years dozens of graph labelings techniques have been studied in over 1000 papers. Finding out what has been done for any particular kind of labeling and keeping up with new discoveries is difficult because of the sheer number of papers and because many of the papers have appeared in journals that are not widely available. In this survey I have collected everything I could find on graph labeling. For the convenience of the reader the survey includes a detailed table of contents and index.