A Modern Look at Freedman's Box Model

This paper revisits the box model, a metaphor developed by David Freedman to explain sampling distributions and  statistical inference to introductory statistics students. The basic idea is to represent all random phenomena in terms of drawing tickets at random from a box. In this way, random sampling from a population can be described in the same way as everyday phenomena, like coin tossing and card dealing. For Freedman, box models were merely a thought experiment; calculations were still done using normal approximations. In this paper, we propose a more modern view that treats the box model as a practical simulation framework for conducting inference. We show how concepts in introductory statistics and probability classes can be motivated by simulating from a box model. To facilitate this simulation-based approach to teaching box models, we developed an online, open-source "box model simulator"

Fair Evaluation of Global Network Aligners

Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different networks, and alignment strategy (AS), which uses these similarities to rapidly identify high-scoring alignments. Different methods use both different NCFs and different ASs. Thus, it is unclear whether the superiority of a method comes from its NCF, its AS, or both. We already showed on MI-GRAAL and IsoRankN that combining NCF of one method and AS of another method can lead to a new superior method. Here, we evaluate MI-GRAAL against newer GHOST to potentially further improve alignment quality. Also, we approach several important questions that have not been asked systematically thus far. First, we ask how much of the node similarity information in NCF should come from sequence data compared to topology data. Existing methods determine this more-less arbitrarily, which could affect the resulting alignment(s). Second, when topology is used in NCF, we ask how large the size of the neighborhoods of the compared nodes should be. Existing methods assume that larger neighborhood sizes are better. We find that MI-GRAAL's NCF is superior to GHOST's NCF, while the performance of the methods' ASs is data-dependent. Thus, the combination of MI-GRAAL's NCF and GHOST's AS could be a new superior method for certain data. Also, which amount of sequence information is used within NCF does not affect alignment quality, while the inclusion of topological information is crucial. Finally, larger neighborhood sizes are preferred, but often, it is the second largest size that is superior, and using this size would decrease computational complexity. Together, our results give several general recommendations for a fair evaluation of network alignment methods.Comment: 19 pages. 10 figures. Presented at the 2014 ISMB Conference, July 13-15, Boston, M

Parametric Analysis of the Selective Laser Sintering Process

Qualitative and quantitative analyses are required to develop Selective Laser Sintering into a viable Manufacturing process. A simplified mathematical model for sintering incorporating the heat tJ;ansfer equation. and the sintering rate equation, but using temperature independent thermal properties, is presented in this paper. A practical result is the calculation of sintering depthdeftned as the depth of powder where the void fraction is less than 0.1 as a function of control parameters, such as the laser power intensity, the laser scanning velocity, and the initial bedtemperature. We derive the general behavior of laser sintering. A comparison of model predictions with laser sinterlng tests is provided.Mechanical Engineerin

A Model for Partial Viscous Sintering

A mathematical model describing the sintering rate of a viscous material powder bed is presented. This model assumes that the powder bed is composed of cubic packed, equal-size spherical particles. The sintering rate equation is derived in terms of a unit cell dimension or the relative density of a powder bed. A mathematical factor, fraction of sintering, is introduced to explain the phenomena of partial sintering. Key words: model, viscous sintering.Mechanical Engineerin

On Coordinating Collaborative Objects

A collaborative object represents a data type (such as a text document) designed to be shared by a group of dispersed users. The Operational Transformation (OT) is a coordination approach used for supporting optimistic replication for these objects. It allows the users to concurrently update the shared data and exchange their updates in any order since the convergence of all replicas, i.e. the fact that all users view the same data, is ensured in all cases. However, designing algorithms for achieving convergence with the OT approach is a critical and challenging issue. In this paper, we propose a formal compositional method for specifying complex collaborative objects. The most important feature of our method is that designing an OT algorithm for the composed collaborative object can be done by reusing the OT algorithms of component collaborative objects. By using our method, we can start from correct small collaborative objects which are relatively easy to handle and incrementally combine them to build more complex collaborative objects.Comment: In Proceedings FOCLASA 2010, arXiv:1007.499