Statistical analysis of network data and evolution on GPUs: High-performance statistical computing

Network analysis typically involves as set of repetitive tasks that are particularly amenable to poor-man's parallelization. This is therefore an ideal application are for GPU architectures, which help to alleviate the tedium inherent to statistically sound analysis of network data. Here we will illustrate the use of GPUs in a range of applications, which include percolation processes on networks, the evolution of protein-protein interaction networks, and the fusion of different types of biomedical and disease data in the context of molecular interaction networks. We will pay particular attention to the numerical performance of different routines that are frequently invoked in network analysis problems. We conclude with a review over recent developments in the generation of random numbers that address the specific requirements posed by GPUs and high-performance computing needs

Benchmarking in cluster analysis: A white paper

To achieve scientific progress in terms of building a cumulative body of knowledge, careful attention to benchmarking is of the utmost importance. This means that proposals of new methods of data pre-processing, new data-analytic techniques, and new methods of output post-processing, should be extensively and carefully compared with existing alternatives, and that existing methods should be subjected to neutral comparison studies. To date, benchmarking and recommendations for benchmarking have been frequently seen in the context of supervised learning. Unfortunately, there has been a dearth of guidelines for benchmarking in an unsupervised setting, with the area of clustering as an important subdomain. To address this problem, discussion is given to the theoretical conceptual underpinnings of benchmarking in the field of cluster analysis by means of simulated as well as empirical data. Subsequently, the practicalities of how to address benchmarking questions in clustering are dealt with, and foundational recommendations are made

Using decision problems in public key cryptography

There are several public key establishment protocols as well as complete public key cryptosystems based on allegedly hard problems from combinatorial (semi)group theory known by now. Most of these problems are search problems, i.e., they are of the following nature: given a property P and the information that there are objects with the property P, find at least one particular object with the property P. So far, no cryptographic protocol based on a search problem in a non-commutative (semi)group has been recognized as secure enough to be a viable alternative to established protocols (such as RSA) based on commutative (semi)groups, although most of these protocols are more efficient than RSA is. In this paper, we suggest to use decision problems from combinatorial group theory as the core of a public key establishment protocol or a public key cryptosystem. By using a popular decision problem, the word problem, we design a cryptosystem with the following features: (1) Bob transmits to Alice an encrypted binary sequence which Alice decrypts correctly with probability "very close" to 1; (2) the adversary, Eve, who is granted arbitrarily high (but fixed) computational speed, cannot positively identify (at least, in theory), by using a "brute force attack", the "1" or "0" bits in Bob's binary sequence. In other words: no matter what computational speed we grant Eve at the outset, there is no guarantee that her "brute force attack" program will give a conclusive answer (or an answer which is correct with overwhelming probability) about any bit in Bob's sequence.Comment: 12 page

Effective Theories for Circuits and Automata

Abstracting an effective theory from a complicated process is central to the study of complexity. Even when the underlying mechanisms are understood, or at least measurable, the presence of dissipation and irreversibility in biological, computational and social systems makes the problem harder. Here we demonstrate the construction of effective theories in the presence of both irreversibility and noise, in a dynamical model with underlying feedback. We use the Krohn-Rhodes theorem to show how the composition of underlying mechanisms can lead to innovations in the emergent effective theory. We show how dissipation and irreversibility fundamentally limit the lifetimes of these emergent structures, even though, on short timescales, the group properties may be enriched compared to their noiseless counterparts.Comment: 11 pages, 9 figure

Computation in Finitary Stochastic and Quantum Processes

We introduce stochastic and quantum finite-state transducers as computation-theoretic models of classical stochastic and quantum finitary processes. Formal process languages, representing the distribution over a process's behaviors, are recognized and generated by suitable specializations. We characterize and compare deterministic and nondeterministic versions, summarizing their relative computational power in a hierarchy of finitary process languages. Quantum finite-state transducers and generators are a first step toward a computation-theoretic analysis of individual, repeatedly measured quantum dynamical systems. They are explored via several physical systems, including an iterated beam splitter, an atom in a magnetic field, and atoms in an ion trap--a special case of which implements the Deutsch quantum algorithm. We show that these systems' behaviors, and so their information processing capacity, depends sensitively on the measurement protocol.Comment: 25 pages, 16 figures, 1 table; http://cse.ucdavis.edu/~cmg; numerous corrections and update

JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

Continuous quantum error correction

We describe new implementations of quantum error correction that are continuous in time, and thus described by continuous dynamical maps. We evaluate the performance of such schemes using numerical simulations, and comment on the effectiveness and applicability of continuous error correction for quantum computing.Comment: 6 pages, 3 figures. Presented at QCMC '04 (Univ. of Strathclyde, Glasgow, UK, July 25-29, 2004