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PubMed2004

A knowledge-based clustering algorithm driven by Gene Ontology.

We have developed an algorithm for inferring the degree of similarity between genes by using the graph-based structure of Gene Ontology (GO). We applied this knowledge-based similarity metric to a clique-finding algorithm for detecting sets of related genes with biological classifications. We also combined it with an expression-based distance metric to produce a co-cluster analysis, which accentuates genes with both similar expression profiles and similar biological characteristics and identifies gene clusters that are more stable and biologically meaningful. These algorithms are demonstrated in the analysis of MPRO cell differentiation time series experiments.

Algorithms↗
PubMed2004

Rejection-free geometric cluster algorithm for complex fluids.

We present a novel, generally applicable Monte Carlo algorithm for the simulation of fluid systems. Geometric transformations are used to identify clusters of particles in such a manner that every cluster move is accepted, irrespective of the nature of the pair interactions. The rejection-free and nonlocal nature of the algorithm make it particularly suitable for the efficient simulation of complex fluids with components of widely varying size, such as colloidal mixtures. Compared to conventional simulation algorithms, typical efficiency improvements amount to several orders of magnitude.

Journal Article↗
PubMed2005

GenClust: a genetic algorithm for clustering gene expression data.

BACKGROUND: Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the widespread use of artificial intelligence techniques in bioinformatics and, more generally, data analysis, there are very few clustering algorithms based on the genetic paradigm, yet that paradigm has great potential in finding good heuristic solutions to a difficult optimization problem such as clustering. RESULTS: GenClust is a new genetic algorithm for clustering gene expression data. It has two key features: (a) a novel coding of the search space that is simple, compact and easy to update; (b) it can be used naturally in conjunction with data driven internal validation methods. We have experimented with the FOM methodology, specifically conceived for validating clusters of gene expression data. The validity of GenClust has been assessed experimentally on real data sets, both with the use of validation measures and in comparison with other algorithms, i.e., Average Link, Cast, Click and K-means. CONCLUSION: Experiments show that none of the algorithms we have used is markedly superior to the others across data sets and validation measures; i.e., in many cases the observed differences between the worst and best performing algorithm may be statistically insignificant and they could be considered equivalent. However, there are cases in which an algorithm may be better than others and therefore worthwhile. In particular, experiments for GenClust show that, although simple in its data representation, it converges very rapidly to a local optimum and that its ability to identify meaningful clusters is comparable, and sometimes superior, to that of more sophisticated algorithms. In addition, it is well suited for use in conjunction with data driven internal validation measures and, in particular, the FOM methodology.

Algorithms↗
PubMed2002

The metric space of proteins-comparative study of clustering algorithms.

MOTIVATION: A large fraction of biological research concentrates on individual proteins and on small families of proteins. One of the current major challenges in bioinformatics is to extend our knowledge to very large sets of proteins. Several major projects have tackled this problem. Such undertakings usually start with a process that clusters all known proteins or large subsets of this space. Some work in this area is carried out automatically, while other attempts incorporate expert advice and annotation. RESULTS: We propose a novel technique that automatically clusters protein sequences. We consider all proteins in SWISSPROT, and carry out an all-against-all BLAST similarity test among them. With this similarity measure in hand we proceed to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. Here we compare the clusters that result from alternative merging rules, and validate the results against InterPro. Our preliminary results show that clusters that are consistent with several rather than a single merging rule tend to comply with InterPro annotation. This is an affirmation of the view that the protein space consists of families that differ markedly in their evolutionary conservation.

Algorithms↗
PubMed2003

CASTOR: clustering algorithm for sequence taxonomical organization and relationships.

Given a set of related proteins, two important problems in biology are the inference of protein subsets such that members of one subset share a common function and the identification of protein regions that possess functional significance. The former is typically approached by hierarchical bottom-up clustering based on pairwise sequence similarity and various linkage rules. The latter is typically approached in a supervised manner, based on global multiple sequence alignment. However, the two problems are inextricably linked, since functional subsets are usually characterized by distinctive functional regions. This paper introduces CASTOR, an automatic and unsupervised system that addresses both problems simultaneously and efficiently. It identifies protein regions that are likely to have functional significance by discovering and refining statistically significant motifs. It infers likely functional protein subsets and their relationships based on the presence of the discovered motifs in a top-down and recursive manner, allowing the identification of both hierarchical and nonhierarchical subset relationships. This is, to our knowledge, the first system that approaches both problems simultaneously in a top-down, systematic manner. CASTOR's performance is evaluated against the G-protein coupled receptor superfamily. The identified protein regions lead to a taxonomical organization of this superfamily that is in remarkable agreement with a biologically motivated one and which outperforms those produced by bottom-up clustering methods. We also find that conventional hierarchical representations may fail to accurately describe the complexity of evolutionary development responsible for the final organization of a complex protein family. In particular, many functional relationships governing distant subfamilies of such a protein family may not be represented hierarchically.

Algorithms↗
PubMed2005

Precipitation, pH and metal load in AMD river basins: an application of fuzzy clustering algorithms to the process characterization.

In the present work, Acid Mine Drainage (AMD) processes in the Chorrito Stream, which flows into the Cobica River (Iberian Pyrite Belt, Southwest Spain) are characterized by means of clustering techniques based on fuzzy logic. Also, pH behavior in contrast to precipitation is clearly explained, proving that the influence of rainfall inputs on the acidity and, as a result, on the metal load of a riverbed undergoing AMD processes highly depends on the moment when it occurs. In general, the riverbed dynamic behavior is the response to the sum of instant stimuli produced by isolated rainfall, the seasonal memory depending on the moment of the target hydrological year and, finally, the own inertia of the river basin, as a result of an accumulation process caused by age-long mining activity.

Environmental Monitoring↗
PubMed1999

A modified fuzzy clustering algorithm for operator independent brain tissue classification of dual echo MR images.

Methods for brain tissue classification or segmentation of structural magnetic resonance imaging (MRI) data should ideally be independent of human operators for reasons of reliability and tractability. An algorithm is described for fully automated segmentation of dual echo, fast spin-echo MRI data. The method is used to assign fuzzy-membership values for each of four tissue classes (gray matter, white matter, cerebrospinal fluid and dura) to each voxel based on partition of a two dimensional feature space. Fuzzy clustering is modified for this application in two ways. First, a two component normal mixture model is initially fitted to the thresholded feature space to identify exemplary gray and white matter voxels. These exemplary data protect subsequently estimated cluster means against the tendency of unmodified fuzzy clustering to equalize the number of voxels in each class. Second, fuzzy clustering is implemented in a moving window scheme that accommodates reduced image contrast at the axial extremes of the transmitting/receiving coil. MRI data acquired from 5 normal volunteers were used to identify stable values for three arbitrary parameters of the algorithm: feature space threshold, relative weight of exemplary gray and white matter voxels, and moving window size. The modified algorithm incorporating these parameter values was then used to classify data from simulated images of the brain, validating the use of fuzzy-membership values as estimates of partial volume. Gray:white matter ratios were estimated from 20 twenty normal volunteers (mean age 32.8 years). Processing time for each three-dimensional image was approximately 30 min on a 170 MHz workstation. Mean cerebral gray and white matter volumes estimated from these automatically segmented images were very similar to comparable results previously obtained by operator dependent methods, but without their inherent unreliability.

Adult↗
PubMed2004

Falcon: neural fuzzy control and decision systems using FKP and PFKP clustering algorithms.

Neural fuzzy networks proposed in the literature can be broadly classified into two groups. The first group is essentially fuzzy systems with self-tuning capabilities and requires an initial rule base to be specified prior to training. The second group of neural fuzzy networks, on the other hand, is able to automatically formulate the fuzzy rules from the numerical training data. Examples are the Falcon-ART, and the POPFNN family of networks. A cluster analysis is first performed on the training data and the fuzzy rules are subsequently derived through the proper connections of these computed clusters. This correspondence proposes two new networks: Falcon-FKP and Falcon-PFKP. They are extensions of the Falcon-ART network, and aimed to overcome the shortcomings faced by the Falcon-ART network itself, i.e., poor classification ability when the classes of input data are very similar to each other, termination of training cycle depends heavily on a preset error parameter, the fuzzy rule base of the Falcon-ART network may not be consistent Nauck, there is no control over the number of fuzzy rules generated, and learning efficiency may deteriorate by using complementarily coded training data. These deficiencies are essentially inherent to the fuzzy ART, clustering technique employed by the Falcon-ART network. Hence, two clustering techniques--Fuzzy Kohonen Partitioning (FKP) and its pseudo variant PFKP, are synthesized with the basic Falcon structure to compute the fuzzy sets and to automatically derive the fuzzy rules from the training data. The resultant neural fuzzy networks are Falcon-FKP and Falcon-PFKP, respectively. These two proposed networks have a lean and efficient training algorithm and consistent fuzzy rule bases. Extensive simulations are conducted using the two networks and their performances are encouraging when benchmarked against other neural and neural fuzzy systems.

Journal Article↗
PubMed1996

Sequential Competitive Learning and the Fuzzy c-Means Clustering Algorithms.

Several recent papers have described sequential competitive learning algorithms that are curious hybrids of algorithms used to optimize the fuzzy c-means (FCM) and learning vector quantization (LVQ) models. First, we show that these hybrids do not optimize the FCM functional. Then we show that the gradient descent conditions they use are not necessary conditions for optimization of a sequential version of the FCM functional. We give a numerical example that demonstrates some weaknesses of the sequential scheme proposed by Chung and Lee. And finally, we explain why these algorithms may work at times, by exhibiting the stochastic approximation problem that they unknowingly attempt to solve. Copyright 1996 Published by Elsevier Science Ltd

Journal Article↗
PubMed2006

Segmentation of thalamic nuclei using a modified k-means clustering algorithm and high-resolution quantitative magnetic resonance imaging at 1.5 T.

Patient outcome in minimally invasive stereotactic neurosurgical procedures depends on the ability to accurately locate the desired functional region within the deep brain while avoiding the surrounding anatomy. Due to the lack of sufficient contrast within this region in pre-operatively acquired MR images, electrophysiological exploration and histological atlases are currently required to define the surgical target within the thalamus in the treatment of many motor-control disorders. In this paper we introduce a method for segmenting the individual thalamic nuclei based on high-resolution quantitative magnetic resonance images, providing improved target visualization. The method was tested using whole-brain T1 and T2 data acquired from four healthy individuals. Accuracy of the segmentation results was assessed by comparing the center-of-mass coordinates of the segmented nuclei, with coordinates obtained from a classic histological atlas registered to these images. Strong agreement was found, with an average Euclidean distance difference of less than 4.5 mm averaged across all nuclei and all individuals. Reproducibility of the method, determined by calculating the percent similarity of segmentation results derived from data acquired from repeated scan sessions, was greater than 85%. These results illustrate the ability to accurately and reliably segment the primary nuclei of the thalamus and suggest that the method may have utility in the study of individual nuclear regions in disease state as well as for planning deep-brain surgical procedures.

Adult↗