Theory-driven learning : using intra-example relationships to constrain learning

We describe an incremental learning algorithm, called theory-driven learning, that creates rules to predict the effect of actions. Theory-driven learning exploits knowledge of regularities among rules to constrain the learning problem. We demonstrate that this knowledge enables the learning system to rapidly converge on accurate predictive rules and to tolerate more complex training data. An algorithm for incrementally learning these regularities is described and we provide evidence that the resulting regularities are sufficiently general to facilitate learning in new domains

Model selection in cosmology

Model selection aims to determine which theoretical models are most plausible given some data, without necessarily considering preferred values of model parameters. A common model selection question is to ask when new data require introduction of an additional parameter, describing a newly discovered physical effect. We review model selection statistics, then focus on the Bayesian evidence, which implements Bayesian analysis at the level of models rather than parameters. We describe our CosmoNest code, the first computationally efficient implementation of Bayesian model selection in a cosmological context. We apply it to recent WMAP satellite data, examining the need for a perturbation spectral index differing from the scaleinvariant (Harrison–Zel'dovich) case

Diffusion and permeation in binary solutions: Application to\ud protein ultrafiltration

During the ultrafiltration of colloidal solutions the particles can form a porous medium (filter cake) or a diffuse boundary layer (concentration polarization) above the semipermeable membrane depending on the magnitude of the filtration pressure. In order to provide a unified description of these phenomena the present work develops some connections between irreversible thermodynamics and poroelasticity. In particular, Fick’s and Darcy’s laws are shown to provide an equivalent description except in two limiting cases – infinite dilution and infinite rigidity of the solute. A new expression for the generalized Stokes-Einstein equation is also obtained, which incorporates the poroelastic Biot-Willis coefficient accounting for the compressibility of the solvent. The theory is utilized to predict the pressure and concentration profiles during the ultrafiltration of a protein solution. The model captures the formation of a diffuse polarization layer at low pressures and a nearly rigid filter cake at higher pressures, as well as intermediate stages. The predicted Darcy pressure profile across the polarization layer is in good quantitative agreement with experimental measurements

A practical Bayesian framework for backpropagation networks

A quantitative and practical Bayesian framework is described for learning of mappings in feedforward networks. The framework makes possible (1) objective comparisons between solutions using alternative network architectures, (2) objective stopping rules for network pruning or growing procedures, (3) objective choice of magnitude and type of weight decay terms or additive regularizers (for penalizing large weights, etc.), (4) a measure of the effective number of well-determined parameters in a model, (5) quantified estimates of the error bars on network parameters and on network output, and (6) objective comparisons with alternative learning and interpolation models such as splines and radial basis functions. The Bayesian "evidence" automatically embodies "Occam's razor," penalizing overflexible and overcomplex models. The Bayesian approach helps detect poor underlying assumptions in learning models. For learning models well matched to a problem, a good correlation between generalization ability and the Bayesian evidence is obtained

Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

A Stochastic Complexity Perspective of Induction in Economics and Inference in Dynamics

Rissanen's fertile and pioneering minimum description length principle (MDL) has been viewed from the point of view of statistical estimation theory, information theory, as stochastic complexity theory -.i.e., a computable approximation to Kolomogorov Complexity - or Solomonoff's recursion theoretic induction principle or as analogous to Kolmogorov's sufficient statistics. All these - and many more - interpretations are valid, interesting and fertile. In this paper I view it from two points of view: those of an algorithmic economist and a dynamical system theorist. >From these points of view I suggest, first, a recasting of Jevons's sceptical vision of induction in the light of MDL; and a complexity interpretation of an undecidable question in dynamics.

Strain controlled biaxial stretch: An experimental characterization of natural rubber

In this paper we provide new experimental data showing the response of 40A natural rubber in uniaxial, pure shear and biaxial tension. Real-time biaxial strain control allows for independent and automatic variation of the velocity of extension and retraction of each actuator to maintain the pre-selected deformation rate within the gage area of the specimen. The remaining part of the paper focuses on the Valanis-Landel hypothesis that is used to verify and validate the consistency of the data. We use a three term Ogden model to derive stress-stretch relations to validate the experimental data. The material model parameters are determined using the primary loading path in uniaxial and equibiaxial tension. Excellent agreement is found when the model is used to predict the response in biaxial tension for different maximum in-plane stretches. The application of the Valanis-Landel hypothesis also results in excellent agreement with the theoretical prediction

Mathematical modelling plant signalling networks

During the last two decades, molecular genetic studies and the completion of the sequencing of the Arabidopsis thaliana genome have increased knowledge of hormonal regulation in plants. These signal transduction pathways act in concert through gene regulatory and signalling networks whose main components have begun to be elucidated. Our understanding of the resulting cellular processes is hindered by the complex, and sometimes counter-intuitive, dynamics of the networks, which may be interconnected through feedback controls and cross-regulation. Mathematical modelling provides a valuable tool to investigate such dynamics and to perform in silico experiments that may not be easily carried out in a laboratory. In this article, we firstly review general methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This sub-cellular analysis paves the way for more comprehensive mathematical studies of hormonal transport and signalling in a multi-scale setting