Predictive gene lists for breast cancer prognosis: a topographic visualisation study

Background: The controversy surrounding the non-uniqueness of predictive gene lists (PGL) of small selected subsets of genes from very large potential candidates as available in DNA microarray experiments is now widely acknowledged 1. Many of these studies have focused on constructing discriminative semi-parametric models and as such are also subject to the issue of random correlations of sparse model selection in high dimensional spaces. In this work we outline a different approach based around an unsupervised patient-specific nonlinear topographic projection in predictive gene lists. Methods: We construct nonlinear topographic projection maps based on inter-patient gene-list relative dissimilarities. The Neuroscale, the Stochastic Neighbor Embedding(SNE) and the Locally Linear Embedding(LLE) techniques have been used to construct two-dimensional projective visualisation plots of 70 dimensional PGLs per patient, classifiers are also constructed to identify the prognosis indicator of each patient using the resulting projections from those visualisation techniques and investigate whether a-posteriori two prognosis groups are separable on the evidence of the gene lists. A literature-proposed predictive gene list for breast cancer is benchmarked against a separate gene list using the above methods. Generalisation ability is investigated by using the mapping capability of Neuroscale to visualise the follow-up study, but based on the projections derived from the original dataset. Results: The results indicate that small subsets of patient-specific PGLs have insufficient prognostic dissimilarity to permit a distinction between two prognosis patients. Uncertainty and diversity across multiple gene expressions prevents unambiguous or even confident patient grouping. Comparative projections across different PGLs provide similar results. Conclusion: The random correlation effect to an arbitrary outcome induced by small subset selection from very high dimensional interrelated gene expression profiles leads to an outcome with associated uncertainty. This continuum and uncertainty precludes any attempts at constructing discriminative classifiers. However a patient's gene expression profile could possibly be used in treatment planning, based on knowledge of other patients' responses. We conclude that many of the patients involved in such medical studies are intrinsically unclassifiable on the basis of provided PGL evidence. This additional category of 'unclassifiable' should be accommodated within medical decision support systems if serious errors and unnecessary adjuvant therapy are to be avoided.

On the Uniform Decay of the Local Energy

It is proved in [1],[2] that in odd dimensional spaces any uniform decay of the local energy implies that it must decay exponentially. We extend this to even dimensional spaces and to more general perturbations (including the transmission problem) showing that any uniform decay of the local energy implies that it must decay like O(t^(−2n) ), t ≫ 1 being the time and n being the space dimension.

On Parabolic Subgroups and Hecke Algebras of some Fractal Groups

* The authors thank the “Swiss National Science Foundation” for its support.

The Point of Continuity Property: Descriptive Complexity and Ordinal Index

∗ Supported by D.G.I.C.Y.T. Project No. PB93-1142

Hilbert-Smith Conjecture for K - Quasiconformal Groups

MSC 2010: 30C60

Triangular Models and Asymptotics of Continuous Curves with Bounded and Unbounded Semigroup Generators

2000 Mathematics Subject Classification: Primary 47A48, Secondary 60G12.

Criterion of Normality of the Completely Regular Topology of Separate Continuity

2000 Mathematics Subject Classification: 54C10, 54D15, 54G12.

Algebraic duality theorems for infinite LP problems

In this paper we consider a primal-dual infinite linear programming problem-pair, i.e. LPs on infinite dimensional spaces with infinitely many constraints. We present two duality theorems for the problem-pair: a weak and a strong duality theorem. We do not assume any topology on the vector spaces, therefore our results are algebraic duality theorems. As an application, we consider transferable utility cooperative games with arbitrarily many players.

Universal Non-Debye Scaling in the Density of States of Amorphous Solids.

At the jamming transition, amorphous packings are known to display anomalous vibrational modes with a density of states (DOS) that remains constant at low frequency. The scaling of the DOS at higher packing fractions remains, however, unclear. One might expect to find a simple Debye scaling, but recent results from effective medium theory and the exact solution of mean-field models both predict an anomalous, non-Debye scaling. Being mean-field in nature, however, these solutions are only strictly valid in the limit of infinite spatial dimension, and it is unclear what value they have for finite-dimensional systems. Here, we study packings of soft spheres in dimensions 3 through 7 and find, away from jamming, a universal non-Debye scaling of the DOS that is consistent with the mean-field predictions. We also consider how the soft mode participation ratio evolves as dimension increases.

Some results on orbifold quotients and related objects

The quotient of a finite-dimensional Euclidean space by a finite linear group inherits different structures from the initial space, e.g. a topology, a metric and a piecewise linear structure. The question when such a quotient is a manifold leads to the study of finite groups generated by reflections and rotations, i.e. by orthogonal transformations whose fixed point subspace has codimension one or two. We classify such groups and thereby complete earlier results by M. A. Mikhaîlova from the 70s and 80s. Moreover, we show that a finite group is generated by reflections and) rotations if and only if the corresponding quotient is a Lipschitz-, or equivalently, a piecewise linear manifold (with boundary). For the proof of this statement we show in addition that each piecewise linear manifold of dimension up to four on which a finite group acts by piecewise linear homeomorphisms admits a compatible smooth structure with respect to which the group acts smoothly. This solves a challenge by Thurston and confirms a conjecture by Kwasik and Lee. In the topological category a counterexample to the above mentioned characterization is given by the binary icosahedral group. We show that this is the only counterexample up to products. In particular, we answer the question by Davis of when the underlying space of an orbifold is a topological manifold. As a corollary of our results we generalize a fixed point theorem by Steinberg on unitary reflection groups to finite groups generated by reflections and rotations. As an application thereof we answer a question by Petrunin on quotients of spheres.

Discontinuous Galerkin Methods on hp-Anisotropic Meshes I: A Priori Error Analysis

We consider the a priori error analysis of hp-version interior penalty discontinuous Galerkin methods for second-order partial differential equations with nonnegative characteristic form under weak assumptions on the mesh design and the local finite element spaces employed. In particular, we prove a priori hp-error bounds for linear target functionals of the solution, on (possibly) anisotropic computational meshes with anisotropic tensor-product polynomial basis functions. The theoretical results are illustrated by a numerical experiment.

Complex functions with Geogebra

Complex functions, generally feature some interesting peculiarities, seen as extensions real functions, complementing the study of real analysis. However, the visualization of some complex functions properties requires the simultaneous visualization of two-dimensional spaces. The multiple Windows of GeoGebra, combined with its ability of algebraic computation with complex numbers, allow the study of the functions defined from ℂ to ℂ through traditional techniques and by the use of Domain Colouring. Here, we will show how we can use GeoGebra for the study of complex functions, using several representations and creating tools which complement the tools already provided by the software. Our proposals designed for students of the first year of engineering and science courses can and should be used as an educational tool in collaborative learning environments. The main advantage in its use in individual terms is the promotion of the deductive reasoning (conjecture / proof). In performed the literature review few references were found involving this educational topic and by the use of a single software.

Numerical enclosures of the optimal cost of the Kantorovitch’s mass transportation problem

International audience

Credit risk & forward price models

Doutoramento em Gestão

An extended Weyl-Wigner transformation for special finite spaces

We extend the Weyl-Wigner transformation to those particular degrees of freedom described by a finite number of states using a technique of constructing operator bases developed by Schwinger. Discrete transformation kernels are presented instead of continuous coordinate-momentum pair system and systems such as the one-dimensional canonical continuous coordinate-momentum pair system and the two-dimensional rotation system are described by special limits. Expressions are explicitly given for the spin one-half case. © 1988.