Government-Industry Cooperative Fisheries Research in the North Pacific under the MSFCMA

The National Marine Fisheries Service’s Alaska Fisheries Science Center (AFSC) has a long and successful history of conducting research in cooperation with the fishing industry. Many of the AFSC’s annual resource assessment surveys are carried out aboard chartered commercial vessels and the skill and experience of captains and crew are integral to the success of this work. Fishing companies have been contracted to provide vessels and expertise for many different types of research, including testing and evaluation of survey and commercial fishing gear and development of improved methods for estimating commercial catch quantity and composition. AFSC scientists have also participated in a number of industry-initiated research projects including development of selective fishing gears for bycatch reduction and evaluating and improving observer catch composition sampling. In this paper, we describe the legal and regulatory provisions for these types of cooperative work and present examples to illustrate the process and identify the requirements for successful cooperative research

Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project)

More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information. We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platformsComment: Presented at DEIT, Data Engineering and Internet Technology, 2011 IEEE: CFP1113L-CD

Optimal Vertex Cover for the Small-World Hanoi Networks

The vertex-cover problem on the Hanoi networks HN3 and HN5 is analyzed with an exact renormalization group and parallel-tempering Monte Carlo simulations. The grand canonical partition function of the equivalent hard-core repulsive lattice-gas problem is recast first as an Ising-like canonical partition function, which allows for a closed set of renormalization group equations. The flow of these equations is analyzed for the limit of infinite chemical potential, at which the vertex-cover problem is attained. The relevant fixed point and its neighborhood are analyzed, and non-trivial results are obtained both, for the coverage as well as for the ground state entropy density, which indicates the complex structure of the solution space. Using special hierarchy-dependent operators in the renormalization group and Monte-Carlo simulations, structural details of optimal configurations are revealed. These studies indicate that the optimal coverages (or packings) are not related by a simple symmetry. Using a clustering analysis of the solutions obtained in the Monte Carlo simulations, a complex solution space structure is revealed for each system size. Nevertheless, in the thermodynamic limit, the solution landscape is dominated by one huge set of very similar solutions.Comment: RevTex, 24 pages; many corrections in text and figures; final version; for related information, see http://www.physics.emory.edu/faculty/boettcher

On implicational bases of closure systems with unique critical sets

We show that every optimum basis of a finite closure system, in D.Maier's sense, is also right-side optimum, which is a parameter of a minimum CNF representation of a Horn Boolean function. New parameters for the size of the binary part are also established. We introduce a K-basis of a general closure system, which is a refinement of the canonical basis of Duquenne and Guigues, and discuss a polynomial algorithm to obtain it. We study closure systems with the unique criticals and some of its subclasses, where the K-basis is unique. A further refinement in the form of the E-basis is possible for closure systems without D-cycles. There is a polynomial algorithm to recognize the D-relation from a K-basis. Thus, closure systems without D-cycles can be effectively recognized. While E-basis achieves an optimum in one of its parts, the optimization of the others is an NP-complete problem.Comment: Presented on International Symposium of Artificial Intelligence and Mathematics (ISAIM-2012), Ft. Lauderdale, FL, USA Results are included into plenary talk on conference Universal Algebra and Lattice Theory, June 2012, Szeged, Hungary 29 pages and 2 figure

Convex Independence in Permutation Graphs

A set C of vertices of a graph is P_3-convex if every vertex outside C has at most one neighbor in C. The convex hull \sigma(A) of a set A is the smallest P_3-convex set that contains A. A set M is convexly independent if for every vertex x \in M, x \notin \sigma(M-x). We show that the maximal number of vertices that a convexly independent set in a permutation graph can have, can be computed in polynomial time

Approximately coloring graphs without long induced paths

It is an open problem whether the 3-coloring problem can be solved in polynomial time in the class of graphs that do not contain an induced path on $t$ vertices, for fixed $t$. We propose an algorithm that, given a 3-colorable graph without an induced path on $t$ vertices, computes a coloring with $\max\{5,2\lceil{\frac{t-1}{2}}\rceil-2\}$ many colors. If the input graph is triangle-free, we only need $\max\{4,\lceil{\frac{t-1}{2}}\rceil+1\}$ many colors. The running time of our algorithm is $O((3^{t-2}+t^2)m+n)$ if the input graph has $n$ vertices and $m$ edges

Percolation of satisfiability in finite dimensions

The satisfiability and optimization of finite-dimensional Boolean formulas are studied using percolation theory, rare region arguments, and boundary effects. In contrast with mean-field results, there is no satisfiability transition, though there is a logical connectivity transition. In part of the disconnected phase, rare regions lead to a divergent running time for optimization algorithms. The thermodynamic ground state for the NP-hard two-dimensional maximum-satisfiability problem is typically unique. These results have implications for the computational study of disordered materials.Comment: 4 pages, 4 fig