Nonparametric Bayesian sparse factor models with application to gene expression modeling

A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data $\mathbf{Y}$ is modeled as a linear superposition, $\mathbf{G}$, of a potentially infinite number of hidden factors, $\mathbf{X}$. The Indian Buffet Process (IBP) is used as a prior on $\mathbf{G}$ to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated data sets based on a known sparse connectivity matrix for E. Coli, and on three biological data sets of increasing complexity.

Bayesian and L1 Approaches to Sparse Unsupervised Learning

The use of L1 regularisation for sparse learning has generated immense research interest, with successful application in such diverse areas as signal acquisition, image coding, genomics and collaborative filtering. While existing work highlights the many advantages of L1 methods, in this paper we find that L1 regularisation often dramatically underperforms in terms of predictive performance when compared with other methods for inferring sparsity. We focus on unsupervised latent variable models, and develop L1 minimising factor models, Bayesian variants of "L1", and Bayesian models with a stronger L0-like sparsity induced through spike-and-slab distributions. These spike-and-slab Bayesian factor models encourage sparsity while accounting for uncertainty in a principled manner and avoiding unnecessary shrinkage of non-zero values. We demonstrate on a number of data sets that in practice spike-and-slab Bayesian methods outperform L1 minimisation, even on a computational budget. We thus highlight the need to re-assess the wide use of L1 methods in sparsity-reliant applications, particularly when we care about generalising to previously unseen data, and provide an alternative that, over many varying conditions, provides improved generalisation performance.

Assessment of CFD models for shock boundary-layer interaction

A workshop on the computational fluid dynamics (CFD) prediction of shock boundary-layer interactions (SBLIs) was held at the 48th AIAA Aerospace Sciences Meeting. As part of the workshop numerous CFD analysts submitted solutions to four experimentally measured SBLIs. This paper describes the assessment of the CFD predictions. The assessment includes an uncertainty analysis of the experimental data, the definition of an error metric and the application of that metric to the CFD solutions. The CFD solutions provided very similar levels of error and in general it was difficult to discern clear trends in the data. For the Reynolds Averaged Navier-Stokes methods the choice of turbulence model appeared to be the largest factor in solution accuracy. Large-eddy simulation methods produced error levels similar to RANS methods but provided superior predictions of normal stresses.

Factor analysis based VTS and JUD noise estimation and compensation

Model based compensation schemes are a powerful approach for noise robust speech recognition. Recently there have been a number of investigations into adaptive training, and estimating the noise models used for model adaptation. This paper examines the use of EM-based schemes for both canonical models and noise estimation, including discriminative adaptive training. One issue that arises when estimating the noise model is a mismatch between the noise estimation approximation and final model compensation scheme. This paper proposes FA-style compensation where this mismatch is eliminated, though at the expense of a sensitivity to the initial noise estimates. EM-based discriminative adaptive training is evaluated on in-car and Aurora4 tasks. FA-style compensation is then evaluated in an incremental mode on the in-car task. © 2011 IEEE.

Factor analysis based VTS discriminative adaptive training

Vector Taylor Series (VTS) model based compensation is a powerful approach for noise robust speech recognition. An important extension to this approach is VTS adaptive training (VAT), which allows canonical models to be estimated on diverse noise-degraded training data. These canonical model can be estimated using EM-based approaches, allowing simple extensions to discriminative VAT (DVAT). However to ensure a diagonal corrupted speech covariance matrix the Jacobian (loading matrix) relating the noise and clean speech is diagonalised. In this work an approach for yielding optimal diagonal loading matrices based on minimising the expected KL-divergence between the diagonal loading matrix and "correct" distributions is proposed. The performance of DVAT using the standard and optimal diagonalisation was evaluated on both in-car collected data and the Aurora4 task. © 2012 IEEE.

Effects of turbulent reynolds number on the performance of algebraic flame surface density models for large eddy simulation in the thin reaction zones regime: A direct numerical simulation analysis

A direct numerical simulation (DNS) database of freely propagating statistically planar turbulent premixed flames with a range of different turbulent Reynolds numbers has been used to assess the performance of algebraic flame surface density (FSD) models based on a fractal representation of the flame wrinkling factor. The turbulent Reynolds number Ret has been varied by modifying the Karlovitz number Ka and the Damköhler number Da independently of each other in such a way that the flames remain within the thin reaction zones regime. It has been found that the turbulent Reynolds number and the Karlovitz number both have a significant influence on the fractal dimension, which is found to increase with increasing Ret and Ka before reaching an asymptotic value for large values of Ret and Ka. A parameterisation of the fractal dimension is presented in which the effects of the Reynolds and the Karlovitz numbers are explicitly taken into account. By contrast, the inner cut-off scale normalised by the Zel'dovich flame thickness ηi/δz does not exhibit any significant dependence on Ret for the cases considered here. The performance of several algebraic FSD models has been assessed based on various criteria. Most of the algebraic models show a deterioration in performance with increasing the LES filter width. © 2012 Mohit Katragadda et al.

Model reductions for inference: generality of pairwise, binary, and planar factor graphs.

We offer a solution to the problem of efficiently translating algorithms between different types of discrete statistical model. We investigate the expressive power of three classes of model-those with binary variables, with pairwise factors, and with planar topology-as well as their four intersections. We formalize a notion of "simple reduction" for the problem of inferring marginal probabilities and consider whether it is possible to "simply reduce" marginal inference from general discrete factor graphs to factor graphs in each of these seven subclasses. We characterize the reducibility of each class, showing in particular that the class of binary pairwise factor graphs is able to simply reduce only positive models. We also exhibit a continuous "spectral reduction" based on polynomial interpolation, which overcomes this limitation. Experiments assess the performance of standard approximate inference algorithms on the outputs of our reductions.

Factorial comparison of working memory models.

Three questions have been prominent in the study of visual working memory limitations: (a) What is the nature of mnemonic precision (e.g., quantized or continuous)? (b) How many items are remembered? (c) To what extent do spatial binding errors account for working memory failures? Modeling studies have typically focused on comparing possible answers to a single one of these questions, even though the result of such a comparison might depend on the assumed answers to both others. Here, we consider every possible combination of previously proposed answers to the individual questions. Each model is then a point in a 3-factor model space containing a total of 32 models, of which only 6 have been tested previously. We compare all models on data from 10 delayed-estimation experiments from 6 laboratories (for a total of 164 subjects and 131,452 trials). Consistently across experiments, we find that (a) mnemonic precision is not quantized but continuous and not equal but variable across items and trials; (b) the number of remembered items is likely to be variable across trials, with a mean of 6.4 in the best model (median across subjects); (c) spatial binding errors occur but explain only a small fraction of responses (16.5% at set size 8 in the best model). We find strong evidence against all 6 documented models. Our results demonstrate the value of factorial model comparison in working memory.

The user-value of rural electrification: An analysis and adoption of existing models and theories

User-value is a determining factor for product acceptance in product design. Research on rural electrification to date, however, does not draw sufficient attention to the importance of user-value with regard to the overall success of a project. This is evident from the analysis of project reports and applicable indicators from agencies active in the sector. Learning from the design, psychology and sociology literatures, it is important that rural electrification projects incorporate the value perception of the end-user and extend their success beyond the commonly used criteria of financial value, the appropriateness of the technology, capacity building and technology uptake. Creating value for the end-user is particularly important for project acceptance and the sustainability of a scheme once it has been handed over to the local community. In this research paper, existing theories and models of value-theory are transposed and applied to community operated rural electrification schemes and a user-value framework is developed. Furthermore, the importance of value to the end-user is clarified. Current literature on product design reveals that user-value has different properties, many of which are applicable to rural electrification. Five value pillars and their sub-categories important for the users of rural electrification projects are identified, namely: functional; social significance; epistemic; emotional; and cultural values. These pillars provide the main structure for the conceptual framework developed in this research paper. It is proposed that by targeting the values of the end-user, the key factors of user-value applicable to rural electrification projects will be identified and the sustainability of the project will be better ensured. © 2014 The Authors.