Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources

Integrative machine learning approach for multi-class SCOP protein fold classification

Classification and prediction of protein structure has been a central research theme in structural bioinformatics. Due to the imbalanced distribution of proteins over multi SCOP classification, most discriminative machine learning suffers the well-known ‘False Positives ’ problem when learning over these types of problems. We have devised eKISS, an ensemble machine learning specifically designed to increase the coverage of positive examples when learning under multiclass imbalanced data sets. We have applied eKISS to classify 25 SCOP folds and show that our learning system improved over classical learning methods

Renormings of Lp(Lq)L^p(L^q)

We investigate the best order of smoothness of $L^p(L^q)$. We prove in particular that there exists a $C^\infty$-smooth bump function on $L^p(L^q)$ if and only if $p$ and $q$ are both even integers and $p$ is a multiple of $q$.Comment: 18 pages; AMS-Te

Interaction of multiple particles with a solidification front : from compacted particle layer to particle trapping

The interaction of solidification fronts with objects such as particles, droplets, cells, or bubbles is a phenomenon with many natural and technological occurrences. For an object facing the front, it may yield various fates, from trapping to rejection, with large implications regarding the solidification pattern. However, whereas most situations involve multiple particles interacting with each other and the front, attention has focused almost exclusively on the interaction of a single, isolated object with the front. Here we address experimentally the interaction of multiple particles with a solidification front by performing solidification experiments of a monodisperse particle suspension in a Hele-Shaw cell, with precise control of growth conditions and real-time visualization. We evidence the growth of a particle layer ahead of the front at a close-packing volume fraction and we document its steady state value at various solidification velocities. We then extend single particle models to the situation of multiple particles by taking into account the additional force induced on an entering particle by viscous friction in the compacted particle layer. By a force balance model, this provides an indirect measure of the repelling mean thermomolecular pressure over a particle entering the front. The presence of multiple particles is found to increase it following a reduction of the thickness of the thin liquid film that separates particles and front. We anticipate the findings reported here to provide a relevant basis to understand many complex solidification situations in geophysics, engineering, biology, or food engineering, where multiple objects interact with the front and control the resulting solidification patterns.Comment: 13 pages, 10 figures, submitted to Langmui

Non-meanfield deterministic limits in chemical reaction kinetics far from equilibrium

A general mechanism is proposed by which small intrinsic fluctuations in a system far from equilibrium can result in nearly deterministic dynamical behaviors which are markedly distinct from those realized in the meanfield limit. The mechanism is demonstrated for the kinetic Monte-Carlo version of the Schnakenberg reaction where we identified a scaling limit in which the global deterministic bifurcation picture is fundamentally altered by fluctuations. Numerical simulations of the model are found to be in quantitative agreement with theoretical predictions.Comment: 4 pages, 4 figures (submitted to Phys. Rev. Lett.

New Jersey Radium Dial Workers and the Dynamics of Occupational Disease Litigation in the Early Twentieth Century, The

Between 1917 and 1923 over 800 women worked for the United States Radium Corporation ( USRC ) in Orange, New Jersey handpainting wrist-watch faces with a substance made luminescent by radioactive materials. While these workers were exposed to injurious, even mortal, levels of radiation, less than a dozen received any compensation for their injuries. These features compounded the workers\u27 legal problems once they entered the formal legal system by dramatically complicating attempts to prove causation, by raising the specter of the statute of limitations defense, and by playing a major role in the settlement negotiation process. As a consequence, even when some women did resort to the formal legal system for relief, they faced hurdles endemic to the legal process and a dynamic of litigation that favored and rewarded repeat-player defendants. This article examines the radium dial-painter episode in four main sections. The first section presents a basic, historical narrative of the dial-painter litigation. The second section identifies and explores the medical, legal, and sociological reasons why so few cases entered the legal system. In the third section, we will examine the legal doctrines that governed the workers\u27 claims against USRC. In the final section, we will examine how the basic architecture of the legal system presented conditions that dramatically affected the chances of success and recovery of the few claimants who entered the legal system and allowed powerful defendants to fashion to their benefit the overall course and outcome of the litigation

Dynamics of the Freezing Front During the Solidification of a Colloidal Alumina Aqueous Suspension: In Situ X-Ray Radiography, Tomography, and Modeling

International audienceIce templating of colloidal suspension is gaining interest in material science because it offers the possibility to shape advanced materials, and in particular porous ceramics. Recent investigations on this peculiar process show that a correlation between the morphology of the frozen suspension and the velocity of the freezing front do exist. The dynamics of the freezing front of a colloidal suspension of alumina is investigated in the present study by experimental tests, finite element numerical analysis and theoretical analytical calculations. The experimental tests are carried out by in situ X-ray radiography (investigation of the dynamics of the freezing front) and tomography (investigation of the resulting morphology of the frozen suspension). The finite element model is a continuous properties model; it is used for investigating the dynamics and the shape of the freezing front. The analytical model is based on the two-phase Stefan problem. We propose a solution for the dynamics of the solidification front based on the calculation of the diffusivity as a function of the particle fraction and local temperature

Improving Prolog Programs: Refactoring for Prolog

Refactoring is an established technique from the OO-community to restructure code: it aims at improving software readability, maintainability and extensibility. Although refactoring is not tied to the OO-paradigm in particular, its ideas have not been applied to Logic Programming until now. This paper applies the ideas of refactoring to Prolog programs. A catalogue is presented listing refactorings classified according to scope. Some of the refactorings have been adapted from the OO-paradigm, while others have been specifically designed for Prolog. Also the discrepancy between intended and operational semantics in Prolog is addressed by some of the refactorings. In addition, ViPReSS, a semi-automatic refactoring browser, is discussed and the experience with applying \vipress to a large Prolog legacy system is reported. Our main conclusion is that refactoring is not only a viable technique in Prolog but also a rather desirable one.Comment: To appear in ICLP 200