Papers.

High-Fidelity RF Gun Simulations with the Parallel 3D Finite Element Particle-In-Cell Code Pic3P

SLAC’s Advanced Computations Department (ACD) has developed the first parallel Finite Element 3D Particle‐In‐Cell (PIC) code, Pic3P, for simulations of RF guns and other spacecharge dominated beam‐cavity interactions. Pic3P solves the complete set of Maxwell‐Lorentz equations and thus includes space charge, retardation and wakefield effects from first principles. Pic3P uses higher‐order Finite Element methods on unstructured conformal meshes. A novel scheme for causal adaptive refinement and dynamic load balancing enable unprecedented simulation accuracy, aiding the design and operation of the next generation of accelerator facilities. Application to the Linac Coherent Light Source (LCLS) RF gun is presented.

Sensory transformations and the use of multiple reference frames for reach planning

Shows that the brain plans reaches using multiple reference frames simultaneously rather than a single optimal one, because each sensory transformation adds noise; a multiple-reference-frame model explains observed reach-error patterns.

Not all quiet on the noise front.

Diurnal dependence of ELF/VLF hiss and its relation to chorus at L = 2.4

Physical Binding Pocket Induction for Affinity Prediction

Computational methods for predicting ligand affinity where no protein structure is known generally take the form of regression analysis based on molecular features that have only a tangential relationship to a protein/ligand binding event. Such methods have limited utility when structural variation moves beyond congeneric series. We present a novel approach, based on the multiple-instance learning method of Compass, where a physical model of a binding site is induced from ligands and their corresponding activity data. The model consists of molecular fragments that can account for multiple positions of literal protein residues. We demonstrate the method on 5HT1a ligands by training on a series with limited scaffold variation and testing on numerous ligands with variant scaffolds. Predictive error was between 0.5 and 1.0 log units (0.7–1.4 kcal/mol), with statistically significant rank correlations. Accurate activity predictions of novel ligands were demonstrated using a validation approach where a small number of ligands of limited structural variation known at a fixed time point were used to make predictions on a blind test set of widely varying molecules, some discovered at a much later time-point.

On the size of Boyer–Moore automata

Composite Inelastic Dark Matter

Using Atom Interferometry to Search for New Forces

Endogenous growth and adverse selection in entrepreneurship

Information systems special issue on ACM CIKM 2007

Using intrinsic data skew to improve hash join performance.

An integrated approach to high-level information fusion

Entry and exit by new versus existing firms

Mining meaning from Wikipedia

On the parametric variation of case and agreement

Taxonomy-Driven Lumping for Sequence Mining

Improving peer connectivity in wide-area overlays of virtual workstations

Representing uncertain data: models, properties, and algorithms

Collective Quartics from Simple Groups

Keynote Talk: Mining the Web 2.0 for Improved Image Search

Towards a Pan-European Learning Resource Exchange Infrastructure

Two-Dimensional Distributed Inverted Files

Universal XForms for Dynamic XQuery Generation

A Federated Authorization Service for Bridging Learning Object Distribution Models

Packaging Mathematical Structures

Java on 1000 Cores: Tales of Hardware/Software Co-design

Improved Team Performance Using EEG- and Context-Based Cognitive-State Classifications for a Vehicle Crew

Using Context to Identify Difficult Driving Situations in Unstructured Environments

Validating Safety and Security Requirements for Partitioned Architectures

A Study of the Impact of Index Updates on Distributed Query Processing for Web Search

Path Planning among Movable Obstacles: A Probabilistically Complete Approach

Beginning Scala

Ssort: Peak Analysis for Efficient String Sorting

Structured Text Retrieval Models

Structured Document Retrieval

Prenatal diagnosis of primary pulmonary hypoplasia in fraternal twins

Markovian Network Interdiction and the Four Color Theorem

Building on Quicksand

Reviews how fault tolerance and replication schemes have evolved as systems scaled out, and argues for designing around eventual consistency, idempotence and commutative operations rather than classic ACID recovery.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

Wakefield Computations for the CLIC PETS using the Parallel Finite Element Time-Domain Code T3P

In recent years, SLAC's Advanced Computations Department (ACD) has developed the high-performance parallel 3D electromagnetic time-domain code, T3P, for simulations of wakefields and transients in complex accelerator structures. T3P is based on advanced higher-order Finite Element methods on unstructured grids with quadratic surface approximation. Optimized for large-scale parallel processing on leadership supercomputing facilities, T3P allows simulations of realistic 3D structures with unprecedented accuracy, aiding the design of the next generation of accelerator facilities. Applications to the Compact Linear Collider (CLIC) Power Extraction and Transfer Structure (PETS) are presented.

User Modeling of Parallel Workloads

The goal of workload modeling is to predict a computer’s workload well enough to design it correctly. A poor model will lead to degraded performance and user satisfaction. Analyzing logs from multiple real parallel computers uncovers several statistical features – locality of sampling, daily cycles, weekly cycles, self similarity and flurries – that are missing from current workload models. Their practical importance is demonstrated by two new kinds of scheduling algorithms – adaptive scheduling and shortest job backfill first scheduling – which achieve an average 10% bottom- line performance gain and 35% stability gain on the production workloads. The second part of this book presents a user based workload model. It identifies four stable user types and five stable session types. It then deduces model parameters, the distributions of the arrival and activity patterns for both users and sessions, their dependencies and temporal structure. The methodology and statistical toolset is explained to make it easier to reuse in other domains. The insights and practical advice provided will be of use to anyone building or operating a large-scale parallel computer.

Type Constructor Polymorphism for Scala: Theory and Practice (Type constructor polymorfisme voor Scala: theorie en praktijk)

Towards the understanding of information dynamics in large scale networked systems

Towards a Scalable Enterprise Content Analytics Platform

Timed Annotations - Enhancing MUC7 Metadata by the Time It Takes to Annotate Named Entities.

THE DYNAMIC RELATIONSHIP BETWEEN ENTREPRENEURSHIP AND ECONOMIC GROWTH: EVIDENCE FROM U.S. MANUFACTURING INDUSTRIES (INTERACTIVE PAPER)

Suggesting Email View Filters for Triage and Search

Growing email volumes cause flooded inboxes and swelled email archives, making search and new email processing difficult. While emails have rich metadata, such as recipients and folders, suitable for creating filtered views, it is often difficult to choose appropriate filters for new inbox messages without first examining messages. In this work, we consider a system that automatically suggests relevant view filters to the user for the currently viewed messages. We propose several ranking algorithms for suggesting useful filters. Our work suggests that such systems quickly filter groups of inbox messages and find messages more easily during search. 1

STANLEY (Sandia Text ANaLysis Extensible librarY) Ver. 1.1

Some Linguistic Considerations of Entity Resolution and Retrieval

Semi-Supervised Active Learning for Sequence Labeling.