We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a high extent of functional homogeneity.

/pdf/detecting-overlapping-protein-complexes-in-protein-protein-1lmip46gqk.pdf

Detecting overlapping protein complexes in protein-protein interaction networks

Frequently, economic theory places shape restrictions on functional relationships between economic variables This paper develops a method to constrain the values of the first and second derivatives of nonparametric locally polynomial estimators We apply this technique to estimate the state price density (SPD), or risk-neutral density, implicit in the market prices of options The option pricing function must be monotonic and convex Simulations demonstrate that nonparametric estimates can be quite feasible in the small samples relevant for day-to-day option pricing, once appropriate theory-motivated shape restrictions are imposed Using S&P500 option prices, we show that unconstrained nonparametric estimators violate the constraints during more than half the trading days in 1999, unlike the constrained estimator we propose

Nonparametric Option Pricing under Shape Restrictions

Statistical models defined by imposing restrictions on marginal distributions of contingency tables have received considerable attention recently. This paper introduces a general definition of marginal log-linear parameters and describes conditions for a marginal log-linear parameter to be a smooth parameterization of the distribution and to be variation independent. Statistical models defined by imposing affine restrictions on the marginal log-linear parameters are investigated. These models generalize ordinary log-linear and multivariate logistic models. Sufficient conditions for a log-affine marginal model to be nonempty and to be a curved exponential family are given. Standard large-sample theory is shown to apply to maximum likelihood estimation of log-affine marginal models for a variety of sampling procedures.

/pdf/marginal-models-for-categorical-data-3c7s1pciiv.pdf

Marginal Models for Categorical Data

Summary. Much of the statistical methodology underlying the experimental design of phase 1 trials in oncology is intended for studies involving a single cytotoxic agent. The goal of these studies is to estimate the maximally tolerated dose, the highest dose that can be administered with an acceptable level of toxicity. A fundamental assumption of these methods is monotonicity of the dose–toxicity curve. This is a reasonable assumption for single-agent trials in which the administration of greater doses of the agent can be expected to produce dose-limiting toxicities in increasing proportions of patients. When studying multiple agents, the assumption may not hold because the ordering of the toxicity probabilities could possibly be unknown for several of the available drug combinations. At the same time, some of the orderings are known and so we describe the whole situation as that of a partial ordering. In this article, we propose a new two-dimensional dose-finding method for multiple-agent trials that simplifies to the continual reassessment method (CRM), introduced by O’Quigley, Pepe, and Fisher (1990, Biometrics 46, 33–48), when the ordering is fully known. This design enables us to relax the assumption of a monotonic dose–toxicity curve. We compare our approach and some simulation results to a CRM design in which the ordering is known as well as to other suggestions for partial orders.

Continual reassessment method for partial ordering.

This research describes some of the similarities and differences between additive conjoint measurement (a type of fundamental measurement) and the Rasch model. It seems that there are many similarities between the two frameworks, however, their differences are nontrivial. For instance, while conjoint measurement specifies measurement scales using a data-free, non-numerical axiomatic frame of reference, the Rasch model specifies measurement scales using a numerical frame of reference that is, by definition, data dependent. In order to circumvent difficulties that can be realistically imposed by this data dependence, this research formalizes new non-parametric item response models. These models are probabilistic measurement theory models in the sense that they explicitly integrate the axiomatic ideas of measurement theory with the statistical ideas of order-restricted inference and Markov Chain Monte Carlo. The specifications of these models are rather flexible, as they can represent any one of several models used in psychometrics, such as Mokken's (1971) monotone homogeneity model, Scheiblechner's (1995) isotonic ordinal probabilistic model, or the Rasch (1960) model. The proposed non-parametric item response models are applied to analyze both real and simulated data sets.

/pdf/the-rasch-model-additive-conjoint-measurement-and-new-models-3yt2xqqyxe.pdf

F. T. Wright

Papers

Order Restricted Statistical Inference.