Search results for "clusterin"

Restricted Neighborhood Search Clustering Revisited: An Evolutionary Computation Perspective

2013

Protein-protein interaction networks have been broadly studied in the last few years, in order to understand the behavior of proteins inside the cell. Proteins interacting with each other often share common biological functions or they participate in the same biological process. Thus, discovering protein complexes made of groups of proteins strictly related, can be useful to predict protein functions. Clustering techniques have been widely employed to detect significative biological complexes. In this paper, we integrate one of the most popular network clustering techniques, namely the Restricted Neighborhood Search Clustering (RNSC), with evolutionary computation. The two cost functions in…

Automatic detection of cervical cells in Pap-smear images using polar transform and k-means segmentation

2016

We introduce a novel method of cell detection and segmentation based on a polar transformation. The method assumes that the seed point of each candidate is placed inside the nucleus. The polar representation, built around the seed, is segmented using k-means clustering into one candidate-nucleus cluster, one candidate-cytoplasm cluster and up to three miscellaneous clusters, representing background or surrounding objects that are not part of the candidate cell. For assessing the natural number of clusters, the silhouette method is used. In the segmented polar representation, a number of parameters can be conveniently observed and evaluated as fuzzy memberships to the non-cell class, out of …

The Three Steps of Clustering in the Post-Genomic Era: A Synopsis

2011

Clustering is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from Statistics to Computer Science. Following Handl et al., it can be summarized as a three step process: (a) choice of a distance function; (b) choice of a clustering algorithm; (c) choice of a validation method. Although such a purist approach to clustering is hardly seen in many areas of science, genomic data require that level of attention, if inferences made from cluster analysis have to be of some relevance to biomedical research. Unfortunately, the high dimensionality of the data and their noisy nature makes cluster analysis of genomic data particul…

Prevention of Dominant IgG Adsorption on Nanocarriers in IgG‐Enriched Blood Plasma by Clusterin Precoating

2019

Abstract Nanocarriers for medical applications must work reliably within organisms, independent of the individual differences in the blood proteome. Variation in the blood proteome, such as immunoglobulin levels, is a result of environmental, nutrition, and constitution conditions. This variation, however, should not influence the behavior of nanocarriers in biological media. The composition of the protein corona is investigated to understand the influence varying immunoglobulin levels in the blood plasma have on the interactions with nanocarriers. Specifically, the composition of the nanocarriers' coronas is analyzed after incubation in plasma with normal or elevated immunoglobulin G (IgG)…

Statistical Indexes for Computational and Data Driven Class Discovery in Microarray Data

2009

Restricted Neighborhood search clustering revisited: an evolutionary computation perspective

2013

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistic…

2008

Abstract Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster…

A PARTITION TYPE METHOD FOR CLUSTERING MIXED DATA

1990

In this paper, we propose a method for clustering mixed data. The method is a nonhierarchical one, and deals simultaneously with variables of three main kinds: numerical, ordinal, and nominal. It is based on the minimization of a particular criterion f(G。) over all the partitions G。of n entities in m distinct clusters. The criterion is founded on a peculiar kind of internal standardized mean diversity of the entities, according to the three types of variables. The algorithm to get the best partition is also presented: it starts from a non-random choice of the first partition; the results are compared with those obtained by a random assignment to a first partition. In order to show the usefu…

A new approach for clustering of effects in quantile regression

2017

In this paper we aim at nding similarities among the coefficients from a multivariate regression. Using a quantile regression coefficients modeling, the effect of each covariate, given a response (also multivariate) is a curve in the multidimensional space of the percentiles. Collecting all the curves, describing the effects of each covariate on each response variable, we could be able to assess if only one or more covariates have same effects on different responses.

Scalable robust clustering method for large and sparse data

2018

Datasets for unsupervised clustering can be large and sparse, with significant portion of missing values. We present here a scalable version of a robust clustering method with the available data strategy. Moreprecisely, a general algorithm is described and the accuracy and scalability of a distributed implementation of the algorithm is tested. The obtained results allow us to conclude the viability of the proposed approach. peerReviewed