Validation of nonlinear PCA

Linear principal component analysis (PCA) can be extended to a nonlinear PCA by using artificial neural networks. But the benefit of curved components requires a careful control of the model complexity. Moreover, standard techniques for model selection, including cross-validation and more generally the use of an independent test set, fail when applied to nonlinear PCA because of its inherent unsupervised characteristics. This paper presents a new approach for validating the complexity of nonlinear PCA models by using the error in missing data estimation as a criterion for model selection. It is motivated by the idea that only the model of optimal complexity is able to predict missing values with the highest accuracy. While standard test set validation usually favours over-fitted nonlinear PCA models, the proposed model validation approach correctly selects the optimal model complexity.Comment: 12 pages, 5 figure

A new mixture copula model for spatially correlated multiple variables with an environmental application

In environmental monitoring, multiple spatial variables are often sampled at a geographical location that can depend on each other in complex ways, such as non-linear and non-Gaussian spatial dependence. We propose a new mixture copula model that can capture those complex relationships of spatially correlated multiple variables and predict univariate variables while considering the multivariate spatial relationship. The proposed method is demonstrated using an environmental application and compared with three existing methods. Firstly, improvement in the prediction of individual variables by utilising multivariate spatial copula compares to the existing univariate pair copula method. Secondly, performance in prediction by utilising mixture copula in the multivariate spatial copula framework compares with an existing multivariate spatial copula model that uses a non-linear principal component analysis. Lastly, improvement in the prediction of individual variables by utilising the non-linear non-Gaussian multivariate spatial copula model compares to the linear Gaussian multivariate cokriging model. The results show that the proposed spatial mixture copula model outperforms the existing methods in the cross-validation of actual and predicted values at the sampled locations

Microbial life cycles link global modularity in regulation to mosaic evolution

Microbes are exposed to changing environments, to which they can respond by adopting various lifestyles such as swimming, colony formation or dormancy. These lifestyles are often studied in isolation, thereby giving a fragmented view of the life cycle as a whole. Here, we study lifestyles in the context of this whole. We first use machine learning to reconstruct the expression changes underlying life cycle progression in the bacterium Bacillus subtilis, based on hundreds of previously acquired expression profiles. This yields a timeline that reveals the modular organization of the life cycle. By analysing over 380 Bacillales genomes, we then show that life cycle modularity gives rise to mosaic evolution in which life stages such as motility and sporulation are conserved and lost as discrete units. We postulate that this mosaic conservation pattern results from habitat changes that make these life stages obsolete or detrimental. Indeed, when evolving eight distinct Bacillales strains and species under laboratory conditions that favour colony growth, we observe rapid and parallel losses of the sporulation life stage across species, induced by mutations that affect the same global regulator. We conclude that a life cycle perspective is pivotal to understanding the causes and consequences of modularity in both regulation and evolution

Do Household Financial Behaviors affect Poverty in Indonesia?: Evidence from Indonesian Family Life Survey

Poverty is a multidimensional phenomenon that can be measured by variety of approaches. The measurements of poverty based on consumption levels are not sufficient to explain various shortcomings faced by the poor. Household financial behavior that tends to be dynamic will indirectly affect household income patterns. Using data from the Indonesian Family Life Survey (IFLS) wave 5, this study aimed to identify the impact of household financial behavior on poverty in Indonesia. The results of analysis using Tobit Regression showed that the levels of financial vulnerability, financial literacy, education level, arisan or the rotating economy of savings and credit associations (ROSCAs), and total credit have a negative, significant relationship in influencing poverty. This means that when this variable increases, it will reduce poverty in Indonesia. Meanwhile, the location of residence, either in village or city, has a positive, significant relationship which implies that the location of residence has an impact on the poverty level in Indonesia

Estimating a mean-path from a set of 2-d curves

To perform many common industrial robotic tasks, e.g. deburring a work-piece, in small and medium size companies where a model of the work-piece may not be available, building a geometrical model of how to perform the task from a data set of human demonstrations is highly demanded. In many cases, however, the human demonstrations may be sub-optimal and noisy solutions to the problem of performing a task. For example, an expert may not completely remove the burrs that result in deburring residuals on the work-piece. Hence, we present an iterative algorithm to estimate a noise-free geometrical model of a work-piece from a given dataset of profiles with deburring residuals. In a case study, we compare the profiles obtained with the proposed method, nonlinear principal component analysis and Gaussian mixture model/Gaussian mixture regression. The comparison illustrates the effectiveness of the proposed method, in terms of accuracy, to compute a noise-free profile model of a task

The MIDAS touch: accurate and scalable missing-data imputation with deep learning

Principled methods for analyzing missing values, based chiefly on multiple imputation, have become increasingly popular yet can struggle to handle the kinds of large and complex data that are also becoming common. We propose an accurate, fast, and scalable approach to multiple imputation, which we call MIDAS (Multiple Imputation with Denoising Autoencoders). MIDAS employs a class of unsupervised neural networks known as denoising autoencoders, which are designed to reduce dimensionality by corrupting and attempting to reconstruct a subset of data. We repurpose denoising autoencoders for multiple imputation by treating missing values as an additional portion of corrupted data and drawing imputations from a model trained to minimize the reconstruction error on the originally observed portion. Systematic tests on simulated as well as real social science data, together with an applied example involving a large-scale electoral survey, illustrate MIDAS’s accuracy and efficiency across a range of settings. We provide open-source software for implementing MIDAS

Tensegrity and Recurrent Neural Networks: Towards an Ecological Model of Postural Coordination

Tensegrity systems have been proposed as both the medium of haptic perception and the functional architecture of motor coordination in animals. However, a full working model integrating those two aspects with some form of neural implementation is still lacking. A basic two-dimensional cross-tensegrity plant is designed and its mechanics simulated. The plant is coupled to a Recurrent Neural Network (RNN). The model’s task is to maintain postural balance against gravity despite the intrinsically unstable configuration of the plant. The RNN takes only proprioceptive input about the springs’ lengths and rate of length change and outputs minimum lengths for each spring which modulates their interaction with the plant’s inertial kinetics. Four artificial agents are evolved to coordinate the patterns of spring contractions in order to maintain dynamic equilibrium. A first study assesses quiet standing performance and reveals coordinative patterns between the tensegrity rods akin to humans’ strategy of anti-phase hip-ankle relative phase. The agents show a mixture of periodic and aperiodic trajectories of their Center of Mass. Moreover, the agents seem to tune to the anticipatory “time-to-balance” quantity in order to maintain their movements within a region of reversibility. A second study perturbs the systems with mechanical platform shifts and sensorimotor degradation. The agents’ response to the mechanical perturbation is robust. Dimensionality analysis of the RNNs’ unit activations reveals a pattern of degree of freedom recruitment after perturbation. In the degradation sub-study, different levels of noise are added to the RNN inputs and different levels of weakening gain are applied to the forces generated by the springs to mimic haptic degradation and muscular weakening in elderly humans. As expected, the systems perform less well, falling earlier than without the insults. However, the same systems re-evolved again under the degraded conditions see significant functional recovery. Overall, the dissertation supports the plausibility of RNN cum tensegrity models of haptics-guided postural coordination in humans