AD in Fortran, Part 1: Design

We propose extensions to Fortran which integrate forward and reverse Automatic Differentiation (AD) directly into the programming model. Irrespective of implementation technology, embedding AD constructs directly into the language extends the reach and convenience of AD while allowing abstraction of concepts of interest to scientific-computing practice, such as root finding, optimization, and finding equilibria of continuous games. Multiple different subprograms for these tasks can share common interfaces, regardless of whether and how they use AD internally. A programmer can maximize a function F by calling a library maximizer, XSTAR=ARGMAX(F,X0), which internally constructs derivatives of F by AD, without having to learn how to use any particular AD tool. We illustrate the utility of these extensions by example: programs become much more concise and closer to traditional mathematical notation. A companion paper describes how these extensions can be implemented by a program that generates input to existing Fortran-based AD tools

Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DECOMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 512^3. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike other high performance computing benchmarks, for this problem size, the time to solution will not be improved by simply building a bigger supercomputer.Comment: 10 page

Comprehensive Review of Opinion Summarization

The abundance of opinions on the web has kindled the study of opinion summarization over the last few years. People have introduced various techniques and paradigms to solving this special task. This survey attempts to systematically investigate the different techniques and approaches used in opinion summarization. We provide a multi-perspective classification of the approaches used and highlight some of the key weaknesses of these approaches. This survey also covers evaluation techniques and data sets used in studying the opinion summarization problem. Finally, we provide insights into some of the challenges that are left to be addressed as this will help set the trend for future research in this area.unpublishednot peer reviewe

Novel Techniques and Their Applications to Health Foods, Agricultural and Medical Biotechnology: Functional Genomics and Basic Epigenetic Controls in Plant and Animal Cells

Selected applications of novel techniques for analyzing Health Food formulations, as well as for advanced investigations in Agricultural and Medical Biotechnology aimed at defining the multiple connections between functional genomics and epigenomic, fundamental control mechanisms in both animal and plant cells are being reviewed with the aim of unraveling future developments and policy changes that are likely to open new niches for Biotechnology and prevent the shrinking or closing of existing markets. Amongst the selected novel techniques with applications in both Agricultural and Medical Biotechnology are: immobilized bacterial cells and enzymes, microencapsulation and liposome production, genetic manipulation of microorganisms, development of novel vaccines from plants, epigenomics of mammalian cells and organisms, and biocomputational tools for molecular modeling related to disease and Bioinformatics. Both fundamental and applied aspects of the emerging new techniques are being discussed in relation to their anticipated, marked impact on future markets and present policy changes that are needed for success in either Agricultural or Medical Biotechnology. The novel techniques are illustrated with figures presenting the most important features of representative and powerful tools which are currently being developed for both immediate and long term applications in Agriculture, Health Food formulation and production, pharmaceuticals and Medicine. The research aspects are naturally emphasized in our review as they are key to further developments in Biotechnology; however, the course adopted for the implementation of biotechnological applications, and the policies associated with biotechnological applications are clearly the determining factors for future Biotechnology successes, be they pharmaceutical, medical or agricultural

Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators.

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych.uic.edu in their daily work and guided the development, refinement and expansion of the system into a suite of tools intended for use by the wider scientific community