Comment on ``Solidification of a Supercooled Liquid in a Narrow Channel''

Comment on PRL v. 86, p. 5084 (2001) [cond-mat/0101016]. We point out that the authors' simulations are consistent with the known theory of steady-state solutions in this system

On the Propagation of Slip Fronts at Frictional Interfaces

The dynamic initiation of sliding at planar interfaces between deformable and rigid solids is studied with particular focus on the speed of the slip front. Recent experimental results showed a close relation between this speed and the local ratio of shear to normal stress measured before slip occurs (static stress ratio). Using a two-dimensional finite element model, we demonstrate, however, that fronts propagating in different directions do not have the same dynamics under similar stress conditions. A lack of correlation is also observed between accelerating and decelerating slip fronts. These effects cannot be entirely associated with static local stresses but call for a dynamic description. Considering a dynamic stress ratio (measured in front of the slip tip) instead of a static one reduces the above-mentioned inconsistencies. However, the effects of the direction and acceleration are still present. To overcome this we propose an energetic criterion that uniquely associates, independently on the direction of propagation and its acceleration, the slip front velocity with the relative rise of the energy density at the slip tip.Comment: 15 pages, 6 figure

Implicit Decomposition for Write-Efficient Connectivity Algorithms

The future of main memory appears to lie in the direction of new technologies that provide strong capacity-to-performance ratios, but have write operations that are much more expensive than reads in terms of latency, bandwidth, and energy. Motivated by this trend, we propose sequential and parallel algorithms to solve graph connectivity problems using significantly fewer writes than conventional algorithms. Our primary algorithmic tool is the construction of an $o(n)$-sized "implicit decomposition" of a bounded-degree graph $G$ on $n$ nodes, which combined with read-only access to $G$ enables fast answers to connectivity and biconnectivity queries on $G$. The construction breaks the linear-write "barrier", resulting in costs that are asymptotically lower than conventional algorithms while adding only a modest cost to querying time. For general non-sparse graphs on $m$ edges, we also provide the first $o(m)$ writes and $O(m)$ operations parallel algorithms for connectivity and biconnectivity. These algorithms provide insight into how applications can efficiently process computations on large graphs in systems with read-write asymmetry

A Cost-based Optimizer for Gradient Descent Optimization

As the use of machine learning (ML) permeates into diverse application domains, there is an urgent need to support a declarative framework for ML. Ideally, a user will specify an ML task in a high-level and easy-to-use language and the framework will invoke the appropriate algorithms and system configurations to execute it. An important observation towards designing such a framework is that many ML tasks can be expressed as mathematical optimization problems, which take a specific form. Furthermore, these optimization problems can be efficiently solved using variations of the gradient descent (GD) algorithm. Thus, to decouple a user specification of an ML task from its execution, a key component is a GD optimizer. We propose a cost-based GD optimizer that selects the best GD plan for a given ML task. To build our optimizer, we introduce a set of abstract operators for expressing GD algorithms and propose a novel approach to estimate the number of iterations a GD algorithm requires to converge. Extensive experiments on real and synthetic datasets show that our optimizer not only chooses the best GD plan but also allows for optimizations that achieve orders of magnitude performance speed-up.Comment: Accepted at SIGMOD 201

MODBASE, a database of annotated comparative protein structure models and associated resources.

MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)

Setting school-level outcome standards

To establish international standards for medical schools, an appropriate panel of experts must decide on performance standards. A pilot test of such standards was set in the context of a multidimensional (multiple-choice question examination, objective structured clinical examination, faculty observation) examination at 8 leading schools in China. Methods  A group of 16 medical education leaders from a broad array of countries met over a 3-day period. These individuals considered competency domains, examination items, and the percentage of students who could fall below a cut-off score if the school was still to be considered as meeting competencies. This 2-step process started with a discussion of the borderline school and the relative difficulty of a borderline school in achieving acceptable standards in a given competency domain. Committee members then estimated the percentage of students falling below the standard that is tolerable at a borderline school and were allowed to revise their ratings after viewing pilot data. Results  Tolerable failure rates ranged from 10% to 26% across competency domains and examination types. As with other standard-setting exercises, standard deviations from initial to final estimates of the tolerable failure rates fell, but the cut-off scores did not change significantly. Final, but not initial cut-off scores were correlated with student failure rates ( r =  0.59, P  = 0.03). Discussion  This paper describes a method to set school-level outcome standards at an international level based on prior established standard-setting methods. Further refinement of this process and validation using other examinations in other countries will be needed to achieve accurate international standards.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71572/1/j.1365-2929.2005.02374.x.pd