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Maximal Interaction Two-Mode Clustering

Most classical approaches for two-mode clustering of a data matrix are designed to attain homogeneous row by column clusters (blocks, biclusters), that is, biclusters with a small variation of data values within the blocks. In contrast, this article deals with methods that look for a biclustering with a large interaction between row and column clusters. Thereby an aggregated, ...

Erratum to: KSC-N: Clustering of Hierarchical Time Profile Data

Erratum to: Psychometrika Joke Heylen, Iven Van Mechelen, Philippe Verduyn, And Eva Ceulemans The order of the authors in the original online version of the above article was incorrect. The

Physical activity and relaxation in the work setting to reduce the need for recovery: what works for whom?

participated in the “Be Active & Relax study. Funding This project was funded by Fonds Nuts Ohra. The contribution of Iven van Mechelen was funded by the Research Fund KU Leuven (Award Number: GOA/15/003) and

Quint: An R package for the identification of subgroups of clients who differ in which treatment alternative is best for them

In the analysis of randomized controlled trials (RCTs), treatment effect heterogeneity often occurs, implying differences across (subgroups of) clients in treatment efficacy. This phenomenon is typically referred to as treatment-subgroup interactions. The identification of subgroups of clients, defined in terms of pretreatment characteristics that are involved in a ...

Not Just a Sum? Identifying Different Types of Interplay between Constituents in Combined Interventions

Motivation Experiments in which the effect of combined manipulations is compared with the effects of their pure constituents have received a great deal of attention. Examples include the study of combination therapies and the comparison of double and single knockout model organisms. Often the effect of the combined manipulation is not a mere addition of the effects of its ...

SCA with rotation to distinguish common and distinctive information in linked data

Often data are collected that consist of different blocks that all contain information about the same entities (e.g., items, persons, or situations). In order to unveil both information that is common to all data blocks and information that is distinctive for one or a few of them, an integrated analysis of the whole of all data blocks may be most useful. Interesting classes of ...

Inferring protein–protein interaction complexes from immunoprecipitation data

Background Protein–protein interactions in cells are widely explored using small–scale experiments. However, the search for protein complexes and their interactions in data from high throughput experiments such as immunoprecipitation is still a challenge. We present "4N", a novel method for detecting protein complexes in such data. Our method is a heuristic algorithm based on Near ...

ADPROCLUS: a graphical user interface for fitting additive profile clustering models to object by variable data matrices

In many areas of psychology, one is interested in disclosing the underlying structural mechanisms that generated an object by variable data set. Often, based on theoretical or empirical arguments, it may be expected that these underlying mechanisms imply that the objects are grouped into clusters that are allowed to overlap (i.e., an object may belong to more than one cluster). In ...

A flexible framework for sparse simultaneous component based data integration

1 Background High throughput data are complex and methods that reveal structure underlying the data are most useful. Principal component analysis, frequently implemented as a singular value decomposition, is a popular technique in this respect. Nowadays often the challenge is to reveal structure in several sources of information (e.g., transcriptomics, proteomics) that are ...

Desequens: An R package for the variance decomposition of sequential processes

SOFIE FREDERICKX PETER KUPPENS FRANCIS TUERLINCKX IVEN VAN MECHELEN Katholieke Universiteit Leuven Leuven Belgium Recently, Kuppens, Van Mechelen, and Rijmen (2008) developed a method that allows

DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes

Background In systems biology it is common to obtain for the same set of biological entities information from multiple sources. Examples include expression data for the same set of orthologous genes screened in different organisms and data on the same set of culture samples obtained with different high-throughput techniques. A major challenge is to find the important biological ...

Integrating functional genomics data using maximum likelihood based simultaneous component analysis

Background In contemporary biology, complex biological processes are increasingly studied by collecting and analyzing measurements of the same entities that are collected with different analytical platforms. Such data comprise a number of data blocks that are coupled via a common mode. The goal of collecting this type of data is to discover biological mechanisms that underlie the ...

A structured overview of simultaneous component based data integration

Background Data integration is currently one of the main challenges in the biomedical sciences. Often different pieces of information are gathered on the same set of entities (e.g., tissues, culture samples, biomolecules) with the different pieces stemming, for example, from different measurement techniques. This implies that more and more data appear that consist of two or more ...

Joint mapping of genes and conditions via multidimensional unfolding analysis

Van Mechelen 2 0 Department of Psychology, Leiden University , 2300 RB Leiden , The Netherlands 1 Department of Microbial and Molecular Systems, Catholic University of Leuven , 3000 Leuven , Belgium 2

Using Ribosomal Protein Genes as Reference: A Tale of Caution

BackgroundHousekeeping genes are needed in every tissue as their expression is required for survival, integrity or duplication of every cell. Housekeeping genes commonly have been used as reference genes to normalize gene expression data, the underlying assumption being that they are expressed in every cell type at approximately the same level. Often, the terms “reference genes” ...

Not guppies, nor goldfish, but tumble dryers, Noriega, Jesse Jackson, panties, car crashes, bird books, and Stevie Wonder

This paper focuses on theguppy effect (Osherson & Smith, 1981), that is, on the existence of examples of conjunctive concepts that are more typical of the conjunction than of both constituents. The most frequently given examples of this effect,guppy andgoldfish, are shown not to be more typical of the conjunctionpet fish than offish in two between-subjects and one within-subjects ...

Part-instance association in the categorization of acts

Rips and Conrad (1989) found a kind-part reciprocal effect in models of the mind, in that one mental activity is part of another if the second is a kind of the first, and vice versa. In the present paper, we hypothesize that a formally analogous effect occurs at the level of activity instances. In particular, we hypothesize that an act is judged to be an instance of an act category ...

Predicting conjunction typicalities by component typicalities

In two studies, we investigated to what extent typicalities in conjunctive concepts phrased as relative clauses—such aspets that are also birds—can be predicted from simple functions of constituent typicalities and from extensions of such functions. In a first study, analyses of a large aggregated data set, based on seven different experiments, showed that a calibrated minimum rule ...

Dominance and noncommutativity effects in concept conjunctions: Extensional or intensional basis?

Dominance and noncommutativity effects are investigated in relative clause descriptions of five conjunctive concepts (birds andpets, sports andgames, vehicles andmachines, office equipment andwriting implements, andshoes andsports equipment). Both asymmetry phenomena are studied at the extensional level (using membership ratings) and at the intensional level (using ...