We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.

/pdf/the-metacyc-database-of-metabolic-pathways-and-enzymes-and-4y3a7lo51l.pdf

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

We explore the effect of dimensionality on the nearest neighbor problem. We show that under a broad set of conditions (much broader than independent and identically distributed dimensions), as dimensionality increases, the distance to the nearest data point approaches the distance to the farthest data point. To provide a practical perspective, we present empirical results on both real and synthetic data sets that demonstrate that this effect can occur for as few as 10-15 dimensions. These results should not be interpreted to mean that high-dimensional indexing is never meaningful; we illustrate this point by identifying some high-dimensional workloads for which this effect does not occur. However, our results do emphasize that the methodology used almost universally in the database literature to evaluate high-dimensional indexing techniques is flawed, and should be modified. In particular, most such techniques proposed in the literature are not evaluated versus simple linear scan, and are evaluated over workloads for which nearest neighbor is not meaningful. Often, even the reported experiments, when analyzed carefully, show that linear scan would outperform the techniques being proposed on the workloads studied in high (10-15) dimensionality!.

When is nearest neighbor meaningful

Constraint integer programming (CIP) is a novel paradigm which integrates constraint programming (CP), mixed integer programming (MIP), and satisfiability (SAT) modeling and solving techniques. In this paper we discuss the software framework and solver SCIP (Solving Constraint Integer Programs), which is free for academic and non-commercial use and can be downloaded in source code. This paper gives an overview of the main design concepts of SCIP and how it can be used to solve constraint integer programs. To illustrate the performance and flexibility of SCIP, we apply it to two different problem classes. First, we consider mixed integer programming and show by computational experiments that SCIP is almost competitive to specialized commercial MIP solvers, even though SCIP supports the more general constraint integer programming paradigm. We develop new ingredients that improve current MIP solving technology. As a second application, we employ SCIP to solve chip design verification problems as they arise in the logic design of integrated circuits. This application goes far beyond traditional MIP solving, as it includes several highly non-linear constraints, which can be handled nicely within the constraint integer programming framework. We show anecdotally how the different solving techniques from MIP, CP, and SAT work together inside SCIP to deal with such constraint classes. Finally, experimental results show that our approach outperforms current state-of-the-art techniques for proving the validity of properties on circuits containing arithmetic.

/pdf/scip-solving-constraint-integer-programs-21j9hcniww.pdf

SCIP: solving constraint integer programs

Integer optimization problems are concerned with the efficient allocation of limited resources to meet a desired objective when some of the resources in question can only be divided into discrete parts. In such cases, the divisibility constraints on these resources, which may be people, machines, or other discrete inputs, may restrict the possible alternatives to a finite set. Nevertheless, there are usually too many alternatives to make complete enumeration a viable option for instances of realistic size. For example, an airline may need to determine crew schedules that minimize the total operating cost; an automotive manufacturer may want to determine the optimal mix of models to produce in order to maximize profit; or a flexible manufacturing facility may want to schedule production for a plant without knowing precisely what parts will be needed in future periods. In today’s changing and competitive industrial environment, the difference between ad hoc planning methods and those that use sophisticated mathematical models to determine an optimal course of action can determine whether or not a company survives.

/pdf/integer-and-combinatorial-optimization-9snwja6bti.pdf

Integer and Combinatorial Optimization

This thesis introduces the novel paradigm of constraint integer programming (CIP), which integrates constraint programming (CP) and mixed integer programming (MIP) modeling and solving techniques. It is supplemented by the software SCIP, which is a solver and framework for constraint integer programming that also features SAT solving techniques. SCIP is freely available in source code for academic and non-commercial purposes. Our constraint integer programming approach is a generalization of MIP that allows for the inclusion of arbitrary constraints, as long as they turn into linear constraints on the continuous variables after all integer variables have been fixed. The constraints, may they be linear or more complex, are treated by any combination of CP and MIP techniques: the propagation of the domains by constraint specific algorithms, the generation of a linear relaxation and its solving by LP methods, and the strengthening of the LP by cutting plane separation. The current version of SCIP comes with all of the necessary components to solve mixed integer programs. In the thesis, we cover most of these ingredients and present extensive computational results to compare different variants for the individual building blocks of a MIP solver. We focus on the algorithms and their impact on the overall performance of the solver. In addition to mixed integer programming, the thesis deals with chip design verification, which is an important topic of electronic design automation. Chip manufacturers have to make sure that the logic design of a circuit conforms to the specification of the chip. Otherwise, the chip would show an erroneous behavior that may cause failures in the device where it is employed. An important subproblem of chip design verification is the property checking problem, which is to verify whether a circuit satisfies a specified property. We show how this problem can be modeled as constraint integer program and provide a number of problem-specific algorithms that exploit the structure of the individual constraints and the circuit as a whole. Another set of extensive computational benchmarks compares our CIP approach to the current state-of-the-art SAT methodology and documents the success of our method.

/pdf/constraint-integer-programming-3f94hvr4hv.pdf

Constraint Integer Programming

http://users.encs.concordia.ca/~chvatal/workshop06/akm.pdf

Branching rules revisited

This paper reports on the fifth version of theMixed Integer Programming Library. The miplib 2010 is the first miplib release that has been assembled by a large group from academia and from industry, all of whom work in integer programming. There was mutual consent that the concept of the library had to be expanded in order to fulfill the needs of the community. The new version comprises 361 instances sorted into several groups. This includes the main benchmark test set of 87 instances, which are all solvable by today’s codes, and also the challenge test set with 164 instances, many of which are currently unsolved. For the first time, we include scripts to run automated tests in a predefined way. Further, there is a solution checker to test the accuracy of provided solutions using exact arithmetic.

Tobias Achterberg

Papers

SCIP: solving constraint integer programs

Constraint Integer Programming

Branching rules revisited

MIPLIB 2010 - Mixed Integer Programming Library version 5

Miplib 2003