17355175
Packing Steiner Trees: Separation Algorithms
In this paper, we investigate separation problems for classes of inequalities valid for the polytope associated with the Steiner tree packing problem, a problem that arises, e.g., in very large-scale integration (VLSI) routing. The separation problem for Steiner partition inequalities is \NP-hard in general. We show that it can be solved in polynomial time for those instances that come up in switchbox routing. Our algorithm uses dynamic programming techniques. These techniques are also applied to the much more complicated separation problem for alternating cycle inequalities. In this case, we can compute in polynomial time, given some point $y$, a lower bound for the gap $\alpha-a^Ty$ over all alternating cycle inequalities $a^Tx\ge\alpha$. This gives rise to a very effective separation heuristic. A by-product of our algorithm is the solution of a combinatorial optimization problem that is interesting in its own right: find a shortest path in a graph where the "length" of a path is its usual length minus the length of its longest edge.
145836
Packing Steiner trees: polyhedral investigations
LetG=(V, E) be a graph andT⊆V be a node set. We call an edge setS a Steiner tree forT ifS connects all pairs of nodes inT. In this paper we address the following problem, which we call the weighted Steiner tree packing problem. Given a graphG=(V, E) with edge weightswe, edge capacitiesce,e∈E, and node setT1,…,TN, find edge setsS1,…,SN such that eachSk is a Steiner tree forTk, at mostce of these edge sets use edgee for eache∈E, and the sum of the weights of the edge sets is minimal. Our motivation for studying this problem arises from a routing problem in VLSI-design, where given sets of points have to be connected by wires. We consider the Steiner tree packing problem from a polyhedral point of view and define an associated polyhedron, called the Steiner tree packing polyhedron. The goal of this paper is to (partially) describe this polyhedron by means of inequalities. It turns out that, under mild assumptions, each inequality that defines a facet for the (single) Steiner tree polyhedron can be lifted to a facet-defining inequality for the Steiner tree packing polyhedron. The main emphasis of this paper lies on the presentation of so-called joint inequalities that are valid and facet-defining for this polyhedron. Inequalities of this kind involve at least two Steiner trees. The classes of inequalities we have found form the basis of a branch & cut algorithm. This algorithm is described in our companion paper (in this issue).
5379517
Packing Steiner Trees: Further Facets
Abstract In this paper we continue the investigations in [3] for the Steiner tree packing polyhedron. We present several new classes of valid inequalities and give sufficient (and necessary) conditions for these inequalities to be facet-definining. It is intended to incorporate these inequalities into an existing cutting plane algorithm that is applicable to practical problems arising in the design of electronic curcuits.
18494896
The steiner tree packing problem in VLSI design
In this paper we describe several versions of the routing problem arising in VLSI design and indicate how the Steiner tree packing problem can be used to model these problems mathematically. We focus on switchbox routing problems and provide integer programming formulations for routing in the knock-knee and in the Manhattan model. We give a brief sketch of cutting plane algorithms that we developed and implemented for these two models. We report on computational experiments using standard test instances. Our codes are able to determine optimum solutions in most cases, and in particular, we can show that some of the instances have no feasible solution if Manhattan routing is used instead of knock-knee routing.
5189033
Routing in grid graphs by cutting planes
In this paper we study the following problem, which we call the weighted routing problem. Let be given a graphG = (V, E) with non-negative edge weightswe ∈ ℝ+ and letN,N ≥ 1, be a list of node sets. The weighted routing problem consists in finding mutually disjoint edge setsS1,...,SN such that, for eachk ∈ {1, ...,N}, the subgraph (V(Sk),Sk) contains an [s, t]-path for alls, t ∈ Tk and the sum of the weights of the edge sets is minimal. Our motivation for studying this problem arises from the routing problem in VLSI-design, where given sets of points have to be connected by wires. We consider the weighted routing problem from a polyhedral point of view. We define an appropriate polyhedron and try to (partially) describe this polyhedron by means of inequalities. We describe our separation algorithms for some of the presented classes of inequalities. Based on these separation routines we have implemented a branch and cut algorithm. Our algorithm is applicable to an important subclass of routing problems arising in VLSI-design, namely to switchbox routing problems where the underlying graph is a grid graph and the list of node sets is located on the outer face of the grid. We report on our computational experience with this class of problem instances.
10352274
The AMPERE Algorithm - Area-Based Masking with the Performance Equation
The18th International Florida Artificial Intelligence Research Symposium (FLAIRS-2005), May 16th-18th, Clearwater Beach, Florida
14479325
Bus catcher: a context sensitive prototype system for public transportation users
In this paper we describe the architectural andfunctional characteristics of Bus Catcher, a contextsensitive prototype system for public transportation users.Bus Catcher assists mobile users in planning their busrides by providing timely and accurate information aboutcurrent bus locations and estimated arrival times. Acomplete report on the implementation together with apreliminary evaluation of the system is provided in thispaper.
23372292
A Calculus for Schemas in Z
The popularity and flexibility of the Z notation can largely be attributed to its notion of schemas. We describe these schemas and illustrate their various common uses in Z. We also present a collection of logical laws for manipulating these schemas. These laws are capable of supporting reasoning about the Z schema calculus in its full generality. This is demonstrated by presenting some theorems about the removability of schemas from Z specifications, together with outline proofs. We survey briefly models against which this logical system may be proven sound, and other related logics for Z.
33375279
Mapping PDB chains to UniProtKB entries
MOTIVATION
UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file.


RESULTS
We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.


AVAILABILITY
The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.
14876854
Security principles for public-resource modeling research
Large-scale distributed computing projects have many security concerns due to their public and often "open" nature. Climateprediction.net (CPDN) is taking the concept of public-resource, high-throughput grid computing a stage further, by using it for a major piece of modeling research. The aim is to harness the spare CPU cycles of potentially millions of individual users' PCs to run a massive ensemble of climate simulations. In doing so it has been faced with a range of security and integrity issues beyond those encountered by previous projects but likely also to confront similar initiatives in the future. This paper introduces the project and its software architecture, and outlines a threat model for such situations, including threats to participants, threats to the experiment and threats to other stakeholders. It goes on to discuss how these threats have been addressed, with the procedures presented expected to form a valuable foundation for an increasing number of similar projects.