Topological Additive Numbering of Directed Acyclic Graphs

We propose to study a problem that arises naturally from both Topological Numbering of Directed Acyclic Graphs, and Additive Coloring (also known as Lucky Labeling). Let $D$ be a digraph and $f$ a labeling of its vertices with positive integers; denote by $S(v)$ the sum of labels over all neighbors of each vertex $v$. The labeling $f$ is called \emph{topological additive numbering} if $S(u) < S(v)$ for each arc $(u,v)$ of the digraph. The problem asks to find the minimum number $k$ for which $D$ has a topological additive numbering with labels belonging to $\{ 1, \ldots, k \}$, denoted by $\eta_t(D)$. We characterize when a digraph has topological additive numberings, give a lower bound for $\eta_t(D)$, and provide an integer programming formulation for our problem, characterizing when its coefficient matrix is totally unimodular. We also present some families for which $\eta_t(D)$ can be computed in polynomial time. Finally, we prove that this problem is \np-Hard even when its input is restricted to planar bipartite digraphs

The Multiobjective Average Network Flow Problem: Formulations, Algorithms, Heuristics, and Complexity

Integrating value focused thinking with the shortest path problem results in a unique formulation called the multiobjective average shortest path problem. We prove this is NP-complete for general graphs. For directed acyclic graphs, an efficient algorithm and even faster heuristic are proposed. While the worst case error of the heuristic is proven unbounded, its average performance on random graphs is within 3% of the optimal solution. Additionally, a special case of the more general biobjective average shortest path problem is given, allowing tradeoffs between decreases in arc set cardinality and increases in multiobjective value; the algorithm to solve the average shortest path problem provides all the information needed to solve this more difficult biobjective problem. These concepts are then extended to the minimum cost flow problem creating a new formulation we name the multiobjective average minimum cost flow. This problem is proven NP-complete as well. For directed acyclic graphs, two efficient heuristics are developed, and although we prove the error of any successive average shortest path heuristic is in theory unbounded, they both perform very well on random graphs. Furthermore, we define a general biobjective average minimum cost flow problem. The information from the heuristics can be used to estimate the efficient frontier in a special case of this problem trading off total flow and multiobjective value. Finally, several variants of these two problems are discussed. Proofs are conjectured showing the conditions under which the problems are solvable in polynomial time and when they remain NP-complete

Pattern Mining and Events Discovery in Molecular Dynamics Simulations Data

Molecular dynamics simulation method is widely used to calculate and understand a wide range of properties of materials. A lot of research efforts have been focused on simulation techniques but relatively fewer works are done on methods for analyzing the simulation results. Large-scale simulations usually generate massive amounts of data, which make manual analysis infeasible, particularly when it is necessary to look into the details of the simulation results. In this dissertation, we propose a system that uses computational method to automatically perform analysis of simulation data, which represent atomic position-time series. The system identifies, in an automated fashion, the micro-level events (such as the bond formation/breaking) that are connected to large movements of the atoms, which is considered to be relevant to the diffusion property of the material. The challenge is how to discover such interesting atomic activities which are the key to understanding macro-level (bulk) properties of material. Furthermore, simply mining the structure graph of a material (the graph where the constituent atoms form nodes and the bonds between the atoms form edges) offers little help in this scenario. It is the patterns among the atomic dynamics that may be good candidate for underlying mechanisms. We propose an event-graph model to model the atomic dynamics and propose a graph mining algorithm to discover popular subgraphs in the event graph. We also analyze such patterns in primitive ring mining process and calculate the distributions of primitive rings during large and normal movement of atoms. Because the event graph is a directed acyclic graph, our mining algorithm uses a new graph encoding scheme that is based on topological- sorting. This encoding scheme also ensures that our algorithm enumerates candidate subgraphs without any duplication. Our experiments using simulation data of silica liquid show the effectiveness of the proposed mining system

Optimality of Orthogonal Access for One-dimensional Convex Cellular Networks

It is shown that a greedy orthogonal access scheme achieves the sum degrees of freedom of all one-dimensional (all nodes placed along a straight line) convex cellular networks (where cells are convex regions) when no channel knowledge is available at the transmitters except the knowledge of the network topology. In general, optimality of orthogonal access holds neither for two-dimensional convex cellular networks nor for one-dimensional non-convex cellular networks, thus revealing a fundamental limitation that exists only when both one-dimensional and convex properties are simultaneously enforced, as is common in canonical information theoretic models for studying cellular networks. The result also establishes the capacity of the corresponding class of index coding problems