The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic systems with a large variety of applications. We introduce a novel method of the graph transformation model construction, combining generative and dynamical viewpoints to give a fully automated data-driven model inference method. The method takes the input dynamical properties, given as a "snapshot" of the dynamics encoded by explicit transitions, and constructs a compatible model. The obtained model is guaranteed to be minimal, thus framing the approach as model compression (from a set of transitions into a set of rules). The compression is permissive to a lossy case, where the constructed model is allowed to exhibit behavior outside of the input transitions, thus suggesting a completion of the input dynamics. The task of graph transformation model inference is naturally highly challenging due to the combinatorics involved. We tackle the exponential explosion by proposing a heuristically minimal translation of the task into a well-established problem, set cover, for which highly optimized solutions exist. We further showcase how our results relate to Kolmogorov complexity expressed in terms of graph transformation.

Two standard textbook problems illustrating dynamic programming are to find the longest common subsequence (LCS) between two strings and to find the longest palindromic subsequence (LPS) of a single string. A popular claim is that the longest palindromic subsequence in a string can be computed as the longest common subsequence between the string and the reversed string. We prove that the correctness of this claim depends on how the longest common subsequence is computed. In particular, we prove that the classical dynamic programming solution by Wagner and Fischer [JACM 1974] for finding an LCS in fact does find an LPS, while a slightly different LCS backtracking strategy makes the algorithm fail to always report a palindrome.

The fragile complexity of a comparison-based algorithm is $f(n)$ if each input element participates in $O(f(n))$ comparisons. In this paper, we explore the fragile complexity of algorithms adaptive to various restrictions on the input, i.e., algorithms with a fragile complexity parameterized by a quantity other than the input size~$n$. We show that searching for the predecessor in a sorted array has fragile complexity $\Theta(\log k)$, where $k$ is the rank of the query element, both in a randomized and a deterministic setting. For predecessor searches, we also show how to optimally reduce the amortized fragile complexity of the elements in the array. We also prove the following results: Selecting the $k$th smallest element has expected fragile complexity $O(\log\log k)$ for the element selected. Deterministically finding the minimum element has fragile complexity $\Theta(\log(\INV))$ and $\Theta(\log(\RUNS))$, where $\INV$ is the number of inversions in a sequence and $\RUNS$ is the number of increasing runs in a sequence. Deterministically finding the median has fragile complexity $O(\log(\RUNS) + \log\log n)$ and $\Theta(\log (\INV))$. Deterministic sorting has fragile complexity $\Theta(\log (\INV))$ but it has fragile complexity $\Theta(\log n)$ regardless of the number of runs.

We empirically investigate algorithms for solving Connected Components in the external memory model. In particular, we study whether the randomized O(Sort(E)) algorithm by Karger, Klein, and Tarjan can be implemented to compete with practically promising and simpler algorithms having only slightly worse theoretical cost, namely Borůvka’s algorithm and the algorithm by Sibeyn and collaborators. For all algorithms, we develop and test a number of tuning options. Our experiments are executed on a large set of different graph classes including random graphs, grids, geometric graphs, and hyperbolic graphs. Among our findings are: The Sibeyn algorithm is a very strong contender due to its simplicity and due to an added degree of freedom in its internal workings when used in the Connected Components setting. With the right tunings, the Karger-Klein-Tarjan algorithm can be implemented to be competitive in many cases. Higher graph density seems to benefit Karger-Klein-Tarjan relative to Sibeyn. Borůvka’s algorithm is not competitive with the two others.

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 environmentally friendly. While several aspects of this complex problem are computationally assisted, the drafting of catalytic mechanisms, i.e. the specification of the chemical steps-and hence intermediate states-that the enzyme is meant to implement, is largely left to human expertise. The ability to capture specific chemistries of multistep catalysis in a fashion that enables its computational construction and design is therefore highly desirable and would equally impact the elucidation of existing enzymatic reactions whose mechanisms are unknown. RESULTS: We use the mathematical framework of graph transformation to express the distinction between rules and reactions in chemistry. We derive about 1000 rules for amino acid side chain chemistry from the M-CSA database, a curated repository of enzymatic mechanisms. Using graph transformation, we are able to propose hundreds of hypothetical catalytic mechanisms for a large number of unrelated reactions in the Rhea database. We analyze these mechanisms to find that they combine in chemically sound fashion individual steps from a variety of known multistep mechanisms, showing that plausible novel mechanisms for catalysis can be constructed computationally. AVAILABILITY AND IMPLEMENTATION: The source code of the initial prototype of our approach is available at https://github.com/Nojgaard/mechsearch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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 maximal number of comparisons any individual element takes part in. We give a number of upper and lower bounds on the fragile complexity for fundamental problems, including Minimum, Selection, Sorting and Heap Construction. The results include both deterministic and randomized upper and lower bounds, and demonstrate a separation between the two settings for a number of problems. The depth of a comparator network is a straight-forward upper bound on the worst case fragile complexity of the corresponding fragile algorithm. We prove that fragile complexity is a different and strictly easier property than the depth of comparator networks, in the sense that for some problems a fragile complexity equal to the best network depth can be achieved with less total work and that with randomization, even a lower fragile complexity is possible.

Any B-tree has height at least ceil[log_B(n)]. Static B-trees achieving this height are easy to build. In the dynamic case, however, standard B-tree rebalancing algorithms only maintain a height within a constant factor of this optimum. We investigate exactly how close to ceil[log_B(n)] the height of dynamic B-trees can be maintained as a function of the rebalancing cost. In this paper, we prove a lower bound on the cost of maintaining optimal height ceil[log_B(n)], which shows that this cost must increase from Omega(1/B) to Omega(n/B) rebalancing per update as n grows from one power of B to the next. We also provide an almost matching upper bound, demonstrating this lower bound to be essentially tight. We then give a variant upper bound which can maintain near-optimal height at low cost. As two special cases, we can maintain optimal height for all but a vanishing fraction of values of n using Theta(log_B(n)) amortized rebalancing cost per update and we can maintain a height of optimal plus one using O(1/B) amortized rebalancing cost per update. More generally, for any rebalancing budget, we can maintain (as n grows from one power of B to the next) optimal height essentially up to the point where the lower bound requires the budget to be exceeded, after which optimal height plus one is maintained. Finally, we prove that this balancing scheme gives B-trees with very good storage utilization.

We present a deterministic local routing algorithm that is guaranteed to find a path between any pair of vertices in a half-$\theta_6$-graph (the half-$\theta_6$-graph is equivalent to the Delaunay triangulation where the empty region is an equilateral triangle). The length of the path is at most $5/\sqrt{3} \approx 2.887$ times the Euclidean distance between the pair of vertices. Moreover, we show that no local routing algorithm can achieve a better routing ratio, thereby proving that our routing algorithm is optimal. This is somewhat surprising because the spanning ratio of the half-$\theta_6$-graph is 2, meaning that even though there always exists a path whose length is at most twice the Euclidean distance, we cannot always find such a path when routing locally. Since every triangulation can be embedded in the plane as a half-$\theta_6$-graph using $O(\log n)$ bits per vertex coordinate via Schnyder's embedding scheme [W. Schnyder, Embedding planar graphs on the grid, in Proceedings of the 1st Annual ACM--SIAM Symposium on Discrete Algorithms (SODA 1990), ACM, New York, SIAM, Philadelphia, 1990, pp. 138--148], our result provides a competitive local routing algorithm for every such embedded triangulation. Finally, we show how our routing algorithm can be adapted to provide a routing ratio of $15/\sqrt{3} \approx 8.660$ on two bounded degree subgraphs of the half-$\theta_6$-graph.

For a set of points in the plane and a fixed integer k > 0, the Yao graph Yk partitions the space around each point into k equiangular cones of angle θ = 2π/k, and connects each point to a nearest neighbor in each cone. It is known for all Yao graphs, with the sole exception of Y5, whether or not they are geometric spanners. In this paper we close this gap by showing that for odd k ≥ 5, the spanning ratio of Yk is at most 1/(1−2sin(3θ/8)), which gives the first constant upper bound for Y5, and is an improvement over the previous bound of 1/(1−2sin(θ/2)) for odd k ≥ 7. We further reduce the upper bound on the spanning ratio for Y5 from 10.9 to 2 + √3 ≈ 3.74, which falls slightly below the lower bound of 3.79 established for the spanning ratio of ⊝5 (⊝-graphs differ from Yao graphs only in the way they select the closest neighbor in each cone). This is the first such separation between a Yao and ⊝-graph with the same number of cones. We also give a lower bound of 2.87 on the spanning ratio of Y5. Finally, we revisit the Y6 graph, which plays a particularly important role as the transition between the graphs (k > 6) for which simple inductive proofs are known, and the graphs (k ≤ 6) whose best spanning ratios have been established by complex arguments. Here we reduce the known spanning ratio of Y6 from 17.6 to 5.8, getting closer to the spanning ratio of 2 established for ⊝6.

The triplet and quartet distances are distance measures to compare two rooted and two unrooted trees, respectively. The leaves of the two trees should have the same set of n labels. The distances are defined by enumerating all subsets of three labels (triplets) and four labels (quartets), respectively, and counting how often the induced topologies in the two input trees are different. In this paper we present efficient algorithms for computing these distances. We show how to compute the triplet distance in time O(n log n) and the quartet distance in time O(dn log n), where d is the maximal degree of any node in the two trees. Within the same time bounds, our framework also allows us to compute the parameterized triplet and quartet distances, where a parameter is introduced to weight resolved (binary) topologies against unresolved (non-binary) topologies. The previous best algorithm for computing the triplet and parameterized triplet distances have O(n2) running time, while the previous best algorithms for computing the quartet distance include an O(d9n log n) time algorithm and an O(n2.688) time algorithm, where the latter can also compute the parameterized quartet distance. Since d ≤ n, our algorithms improve on all these algorithms.

The triplet distance is a distance measure that compares two rooted trees on the same set of leaves by enumerating all sub-sets of three leaves and counting how often the induced topologies of the tree are equal or different. We present an algorithm that computes the triplet distance between two rooted binary trees in time O (n log2 n). The algorithm is related to an algorithm for computing the quartet distance between two unrooted binary trees in time O (n log n). While the quartet distance algorithm has a very severe overhead in the asymptotic time complexity that makes it impractical compared to O (n2) time algorithms, we show through experiments that the triplet distance algorithm can be implemented to give a competitive wall-time running time.

We present a deterministic local routing scheme that is guaranteed to find a path between any pair of vertices in a half-θ6-graph whose length is at most 5/ √ 3 = 2.886... times the Euclidean distance between the pair of vertices.The half-θ6graph is identical to the Delaunay triangulation where the empty region is an equilateral triangle.Moreover, we show that no local routing scheme can achieve a better competitive spanning ratio thereby implying that our routing scheme is optimal.This is somewhat surprising because the spanning ratio of the half-θ6-graph is 2. Since every triangulation can be embedded in the plane as a half-θ6-graph using O(log n) bits per vertex coordinate via Schnyder's embedding scheme (SODA 1990), our result provides a competitive local routing scheme for every such embedded triangulation.

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 compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck.

We analyze the problem of sparse-matrix dense-vector multiplication (SpMV) in the I/O-model. The task of SpMV is to compute y := Ax, where A is a sparse N x N matrix and x and y are vectors. Here, sparsity is expressed by the parameter k that states that A has a total of at most kN nonzeros, i.e., an average number of k nonzeros per column. The extreme choices for parameter k are well studied special cases, namely for k=1 permuting and for k=N dense matrix-vector multiplication.

BACKGROUND: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Theta(n3) algorithm upon which all existing implementations are based. RESULTS: In this paper we present techniques for speeding up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2) but the worst-case remains O(n3). We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Theta(n2) on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical neighbor-joining method. CONCLUSION: The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances.

We present the first cache-oblivious data structure for planar orthogonal range counting, and improve on previous results for cache-oblivious planar orthogonal range searching.Our range counting structure uses O(N log2 N) space and answers queries using O(logB N) memory transfers, where B is the block size of any memory level in a multilevel memory hierarchy. Using bit manipulation techniques, the space can be further reduced to O(N). The structure can also be modified to support more general semigroup range sum queries in O(logB N) memory transfers, using O(N log2 N) space for three-sided queries and O(N log22 N/log2 log2 N) space for four-sided queries.Based on the O(N log N) space range counting structure, we develop a data structure that uses O(N log2 N) space and answers three-sided range queries in O(logB N+T/B) memory transfers, where T is the number of reported points. Based on this structure, we present a general four-sided range searching structure that uses O(N log22 N/log2 log2 N) space and answers queries in O(logB N + T/B) memory transfers.

Tight bounds on the cost of cache-oblivious searching are proved. It is shown that no cache-oblivious search structure can guarantee that a search performs fewer than lg e log/sub B/N block transfers between any two levels of the memory hierarchy. This lower bound holds even if all of the block sizes are limited to be powers of 2. A modified version of the van Emde Boas layout is proposed, whose expected block transfers between any two levels of the memory hierarchy arbitrarily close to [lg e + O(lg lg B/ lgB)] logB N + O(1). This factor approaches lg e /spl ap/ 1.443 as B increases. The expectation is taken over the random placement of the first element of the structure in memory. As searching in the disk access model (DAM) can be performed in log/sub B/N + 1 block transfers, this result shows a separation between the 2-level DAM and cache-oblivious memory-hierarchy models. By extending the DAM model to k levels, multilevel memory hierarchies can be modeled. It is shown that as k grows, the search costs of the optimal k-level DAM search structure and of the optimal cache-oblivious search structure rapidly converge. This demonstrates that for a multilevel memory hierarchy, a simple cache-oblivious structure almost replicates the performance of an optimal parameterized k-level DAM structure.

In this paper, we present lower bounds for permuting and sorting in the cache-oblivious model. We prove that (1) I/O optimal cache-oblivious comparison based sorting is not possible without a tall cache assumption, and (2) there does not exist an I/O optimal cache-oblivious algorithm for permuting, not even in the presence of a tall cache assumption.Our results for sorting show the existence of an inherent trade-off in the cache-oblivious model between the strength of the tall cache assumption and the overhead for the case M » B, and show that Funnelsort and recursive binary mergesort are optimal algorithms in the sense that they attain this trade-off.