MDL Convergence Speed for Bernoulli Sequences

The Minimum Description Length principle for online sequence estimation/prediction in a proper learning setup is studied. If the underlying model class is discrete, then the total expected square loss is a particularly interesting performance measure: (a) this quantity is finitely bounded, implying convergence with probability one, and (b) it additionally specifies the convergence speed. For MDL, in general one can only have loss bounds which are finite but exponentially larger than those for Bayes mixtures. We show that this is even the case if the model class contains only Bernoulli distributions. We derive a new upper bound on the prediction error for countable Bernoulli classes. This implies a small bound (comparable to the one for Bayes mixtures) for certain important model classes. We discuss the application to Machine Learning tasks such as classification and hypothesis testing, and generalization to countable classes of i.i.d. models.Comment: 28 page

Solomonoff Induction Violates Nicod's Criterion

Nicod's criterion states that observing a black raven is evidence for the hypothesis H that all ravens are black. We show that Solomonoff induction does not satisfy Nicod's criterion: there are time steps in which observing black ravens decreases the belief in H. Moreover, while observing any computable infinite string compatible with H, the belief in H decreases infinitely often when using the unnormalized Solomonoff prior, but only finitely often when using the normalized Solomonoff prior. We argue that the fault is not with Solomonoff induction; instead we should reject Nicod's criterion.Comment: ALT 201

Bayesian DNA copy number analysis

BACKGROUND: Some diseases, like tumors, can be related to chromosomal aberrations, leading to changes of DNA copy number. The copy number of an aberrant genome can be represented as a piecewise constant function, since it can exhibit regions of deletions or gains. Instead, in a healthy cell the copy number is two because we inherit one copy of each chromosome from each our parents. Bayesian Piecewise Constant Regression (BPCR) is a Bayesian regression method for data that are noisy observations of a piecewise constant function. The method estimates the unknown segment number, the endpoints of the segments and the value of the segment levels of the underlying piecewise constant function. The Bayesian Regression Curve (BRC) estimates the same data with a smoothing curve. However, in the original formulation, some estimators failed to properly determine the corresponding parameters. For example, the boundary estimator did not take into account the dependency among the boundaries and succeeded in estimating more than one breakpoint at the same position, losing segments. RESULTS: We derived an improved version of the BPCR (called mBPCR) and BRC, changing the segment number estimator and the boundary estimator to enhance the fitting procedure. We also proposed an alternative estimator of the variance of the segment levels, which is useful in case of data with high noise. Using artificial data, we compared the original and the modified version of BPCR and BRC with other regression methods, showing that our improved version of BPCR generally outperformed all the others. Similar results were also observed on real data. CONCLUSION: We propose an improved method for DNA copy number estimation, mBPCR, which performed very well compared to previously published algorithms. In particular, mBPCR was more powerful in the detection of the true position of the breakpoints and of small aberrations in very noisy data. Hence, from a biological point of view, our method can be very useful, for example, to find targets of genomic aberrations in clinical cancer samples

Revisiting the Core Ontology and Problem in Requirements Engineering

In their seminal paper in the ACM Transactions on Software Engineering and Methodology, Zave and Jackson established a core ontology for Requirements Engineering (RE) and used it to formulate the "requirements problem", thereby defining what it means to successfully complete RE. Given that stakeholders of the system-to-be communicate the information needed to perform RE, we show that Zave and Jackson's ontology is incomplete. It does not cover all types of basic concerns that the stakeholders communicate. These include beliefs, desires, intentions, and attitudes. In response, we propose a core ontology that covers these concerns and is grounded in sound conceptual foundations resting on a foundational ontology. The new core ontology for RE leads to a new formulation of the requirements problem that extends Zave and Jackson's formulation. We thereby establish new standards for what minimum information should be represented in RE languages and new criteria for determining whether RE has been successfully completed.Comment: Appears in the proceedings of the 16th IEEE International Requirements Engineering Conference, 2008 (RE'08). Best paper awar

Fermionic Molecular Dynamics for nuclear dynamics and thermodynamics

A new Fermionic Molecular Dynamics (FMD) model based on a Skyrme functional is proposed in this paper. After introducing the basic formalism, some first applications to nuclear structure and nuclear thermodynamics are presentedComment: 5 pages, Proceedings of the French-Japanese Symposium, September 2008. To be published in Int. J. of Mod. Phys.

A viscoelastic Rivlin-Ericksen material model applicable to glacier ice

We present a viscoelastic constitutive relation which describes transient creep of a modified second grade fluid enhanced with elastic properties of a solid. The material law describes a Rivlin-Ericksen material and is a generalization of existing material laws applied to study the viscoelastic properties of ice. The intention is to provide a formulation tailored to reproduce the viscoelastic behaviour of ice ranging from the instantaneous elastic response, to recoverable deformation, to viscous, stationary flow at the characteristic minimum creep rate associated with the deformation of polycrystalline ice. We numerically solve the problem of a slab of material shearing down a uniformly inclined plate. The equations are made dimensionless in a form in which elastic effects and/or the influence of higher order terms (i.e., strain accelerations) can be compared with viscous creep at the minimum creep rate by means of two dimensionless parameters. We discuss the resulting material behaviour and the features exhibited at different parameter combinations. Also, a viable range of the non-dimensional parameters is estimated in the scale analysis

Modelling debris flows down general channels

This paper is an extension of the single-phase cohesionless dry granular avalanche model over curved and twisted channels proposed by Pudasaini and Hutter (2003). It is a generalisation of the Savage and Hutter (1989, 1991) equations based on simple channel topography to a two-phase fluid-solid mixture of debris material. Important terms emerging from the correct treatment of the kinematic and dynamic boundary condition, and the variable basal topography are systematically taken into account. For vanishing fluid contribution and torsion-free channel topography our new model equations exactly degenerate to the previous Savage-Hutter model equations while such a degeneration was not possible by the Iverson and Denlinger (2001) model, which, in fact, also aimed to extend the Savage and Hutter model. The model equations of this paper have been rigorously derived; they include the effects of the curvature and torsion of the topography, generally for arbitrarily curved and twisted channels of variable channel width. The equations are put into a standard conservative form of partial differential equations. From these one can easily infer the importance and influence of the pore-fluid-pressure distribution in debris flow dynamics. The solid-phase is modelled by applying a Coulomb dry friction law whereas the fluid phase is assumed to be an incompressible Newtonian fluid. Input parameters of the equations are the internal and bed friction angles of the solid particles, the viscosity and volume fraction of the fluid, the total mixture density and the pore pressure distribution of the fluid at the bed. Given the bed topography and initial geometry and the initial velocity profile of the debris mixture, the model equations are able to describe the dynamics of the depth profile and bed parallel depth-averaged velocity distribution from the initial position to the final deposit. A shock capturing, total variation diminishing numerical scheme is implemented to solve the highly non-linear equations. Simulation results present the combined effects of curvature, torsion and pore pressure on the dynamics of the flow over a general basal topography. These simulation results reveal new physical insight of debris flows over such non-trivial topography. Model equations are applied to laboratory avalanche and debris-flow-flume tests. Very good agreement between the theory and experiments is established

The Trouble with Trebles: What Violates G.S. 75-1.1?

At first glance the North Carolina Unfair and Deceptive Trade Practices Act appears to be a broad, almost unconstitutionally vague statute. Its federal counterpart, the Federal Trade Commission Act, evoked similar responses when it was first enforced. Like the FTC Act, North Carolina General Statute § 75-1.1 has taken shape through judicial interpretation and legislative modification. (North Carolina General Statutes hereinafter referred to as G.S.). As this process has proceeded over the last decade or so, many aspects of the scope and application of the statute have been determined. No general answer, however, has been given to the question of just what does violate the statute. The boundary between a simple breach of contract, rendering one liable for at most simple damages, and an unfair trade practice, rendering one liable for treble damages and attorney\u27s fees, remains ill-defined. The significance of the question is clear, both to the used car dealer and his customer arguing over an $800 automobile, and to the businessman whose$8,000,000 deal falls through. This problem is highlighted, but not illuminated, by the conflict of analytical processes between the Supreme Court of North Carolina and the U.S. Court of Appeals for the Fourth Circuit. This conflict is evidence of uncertainty in the objectives of the statute and uncertainty among the judiciary as to the basic desirability of the statutory remedy