On the Complexity of Reconstructing Chemical Reaction Networks

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, due to the available methods, analyses regarding network properties are typically made on standard graphs derived from the full hypergraph description, e.g.\ on the so-called species and reaction graphs. However, a reconstruction of the underlying hypergraph from these graphs is not necessarily unique. In this paper, we address the problem of reconstructing a hypergraph from its species and reaction graph and show NP-completeness of the problem in its Boolean formulation. Furthermore we study the problem empirically on random and real world instances in order to investigate its computational limits in practice

On Optimal Balance in B-Trees: What Does It Cost to Stay in Perfect Shape?

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

Cache-Oblivious Data Structures and Algorithms for Undirected Breadth-First Search and Shortest Paths

We present improved cache-oblivious data structures and algorithms for breadth-first search (BFS) on undirected graphs and the single-source shortest path (SSSP) problem on undirected graphs with non-negative edge weights. For the SSSP problem, our result closes the performance gap between the currently best cache-aware algorithm and the cache-oblivious counterpart. Our cache-oblivious SSSP-algorithm takes nearly full advantage of block transfers for dense graphs. The algorithm relies on a new data structure, called bucket heap, which is the first cache-oblivious priority queue to efficiently support a weak DECREASEKEY operation. For the BFS problem, we reduce the number of I/Os for sparse graphs by a factor of nearly sqrt{B}, where B is the cache-block size, nearly closing the performance gap between the currently best cache-aware and cache-oblivious algorithms

An Experimental Study of External Memory Algorithms for Connected Components

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

Reconciling Inconsistent Molecular Structures from Biochemical Databases

Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the chemical structure for a given compound is not necessarily consistent between databases. This paper presents StructRecon, a novel tool for resolving unique and correct molecular structures from database identifiers. StructRecon traverses the cross-links between database entries in different databases to construct what we call an identifier graph, which offers a more complete view of the total information available on a particular compound across all the databases. In order to reconcile discrepancies between databases, we first present an extensible model for chemical structure which supports multiple independent levels of detail, allowing standardisation of the structure to be applied iteratively. In some cases, our standardisation approach results in multiple structures for a given compound, in which case a random walk-based algorithm is used to select the most likely structure among incompatible alternates. We applied StructRecon to the EColiCore2 model, resolving a unique chemical structure for 85.11 % of identifiers. StructRecon is open-source and modular, which enables the potential support for more databases in the future.Comment: 14 pages, 4 figures, accepted at ISBRA 202

Continuous Yao Graphs

In this paper, we introduce a variation of the well-studied Yao graphs. Given a set of points $S\subset \mathbb{R}^2$ and an angle $0 < \theta \leq 2\pi$, we define the continuous Yao graph $cY(\theta)$ with vertex set $S$ and angle $\theta$ as follows. For each $p,q\in S$, we add an edge from $p$ to $q$ in $cY(\theta)$ if there exists a cone with apex $p$ and aperture $\theta$ such that $q$ is the closest point to $p$ inside this cone. We study the spanning ratio of $cY(\theta)$ for different values of $\theta$. Using a new algebraic technique, we show that $cY(\theta)$ is a spanner when $\theta \leq 2\pi /3$. We believe that this technique may be of independent interest. We also show that $cY(\pi)$ is not a spanner, and that $cY(\theta)$ may be disconnected for $\theta > \pi$.Comment: 7 pages, 7 figures. Presented at CCCG 201

Fragile Complexity of Adaptive Algorithms

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 Θ(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 kth smallest element has expected fragile complexity O(log log k) for the element selected. Deterministically finding the minimum element has fragile complexity Θ(log (Inv ) ) and Θ(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 Θ(log (Inv ) ). Deterministic sorting has fragile complexity Θ(log (Inv ) ) but it has fragile complexity Θ(log n) regardless of the number of runs.SCOPUS: cp.kinfo:eu-repo/semantics/publishe