6 citations · 10 across the 13 of their papers we have counts for
16 papers
Reconciling Inconsistent Molecular Structures from Biochemical Databases
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg +1
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discove…
Representing catalytic mechanisms with rule composition
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph tra…
Efficient Modular Graph Transformation Rule Application
Jakob L. Andersen, Rolf Fagerberg, Juri Kolčák +3
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in…
Graph Transformation for Enzymatic Mechanisms
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and e…
Fragile Complexity of Adaptive Algorithms
Prosenjit Bose, Pilar Cano, Rolf Fagerberg +3
The fragile complexity of a comparison-based algorithm is if each input element participates in comparisons. In this paper, we explore the fragile complexity of al…
Fragile Complexity of Comparison-Based Algorithms
Peyman Afshani, Rolf Fagerberg, David Hammer +5
We initiate a study of algorithms with a focus on the computational complexity of individual elements, and introduce the fragile complexity of comparison-based algorithms as the ma…
Biased Predecessor Search
Prosenjit Bose, Rolf Fagerberg, John Howat +1
We consider the problem of performing predecessor searches in a bounded universe while achieving query times that depend on the distribution of queries. We obtain several data stru…
On Plane Constrained Bounded-Degree Spanners
Prosenjit Bose, Rolf Fagerberg, André van Renssen +1
Let be a finite set of points in the plane and a set of non-crossing line segments with endpoints in . The visibility graph of with respect to , denoted $Vis(P,S)…
Competitive Local Routing with Constraints
Prosenjit Bose, Rolf Fagerberg, André van Renssen +1
Let be a set of vertices in the plane and a set of non-crossing line segments between vertices in , called constraints. Two vertices are visible if the straight line…
Optimal local routing on Delaunay triangulations defined by empty equilateral triangles
Prosenjit Bose, Rolf Fagerberg, André van Renssen +1
We present a deterministic local routing algorithm that is guaranteed to find a path between any pair of vertices in a half--graph (the half--graph is equivalent to the D…
Continuous Yao Graphs
Luis Barba, Prosenjit Bose, Jean-Lou De Carufel +5
In this paper, we introduce a variation of the well-studied Yao graphs. Given a set of points and an angle , we define the continuous Yao grap…
On the Complexity of Reconstructing Chemical Reaction Networks
Rolf Fagerberg, Christoph Flamm, Daniel Merkle +2
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, d…
New and Improved Spanning Ratios for Yao Graphs
Luis Barba, Prosenjit Bose, Mirela Damian +7
For a set of points in the plane and a fixed integer , the Yao graph partitions the space around each point into equiangular cones of angle , and connects…
De-amortizing Binary Search Trees
Prosenjit Bose, Sébastien Collette, Rolf Fagerberg +1
We present a general method for de-amortizing essentially any Binary Search Tree (BST) algorithm. In particular, by transforming Splay Trees, our method produces a BST that has the…
An O(loglog n)-Competitive Binary Search Tree with Optimal Worst-Case Access Times
Prosenjit Bose, Karim Douïeb, Vida Dujmovic +1
We present the zipper tree, an -competitive online binary search tree that performs each access in worst-case time. This shows that for binary search tr…
Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts
Philip Bille, Rolf Fagerberg, Inge Li Goertz
We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary com…