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In this paper, we present a new method for detecting overlapping communities in networks with a predefined number of clusters called LPAM (Link Partitioning Around Medoids). The overlapping communities in the graph are obtained by detecting the disjoint communities in the associated line graph employing link partitioning and partitioning around medoids which are done through the use of a distance function defined on the set of nodes. We consider both the commute distance and amplified commute distance as distance functions. The performance of the LPAM method is evaluated with computational experiments on real life instances, as well as synthetic network benchmarks. For small and medium-size networks, the exact solution was found, while for large networks we found solutions with a heuristic version of the LPAM method.

The use of mobile communication devices in health care is spreading worldwide. A huge amount of health data collected by these devices (mobile health data) is nowadays available. Mobile health data may allow for real-time monitoring of patients and delivering ad-hoc treatment recommendations. This paper aims at showing how this may be done by exploiting the potentialities of fuzzy clustering techniques. In fact, such techniques can be fruitfully applied to mobile health data in order to identify clusters of patients for diagnostic classification and cluster-specific therapies. However, since mobile health data are full of noise, fuzzy clustering methods cannot be directly applied to mobile health data. Such data must be denoised prior to analyzing them. When longitudinal mobile health data are available, functional data analysis represents a powerful tool for filtering out the noise in the data. Fuzzy clustering methods for functional data can then be used to determine groups of patients. In this work we develop a fuzzy clustering method, based on the concept of medoid, for functional data and we apply it to longitudinal mHealth data on daily symptoms and consumptions of anti-symptomatic drugs collected by two sets of patients in Berlin (Germany) and Ascoli Piceno (Italy) suffering from allergic rhinoconjunctivitis. The studies showed that clusters of patients with similar changes in symptoms were identified opening the possibility of precision medicine.

Clustering time series data is of great significance since it could extract meaningful statistics and other characteristics. Especially in biomedical engineering, outstanding clustering algorithms for time series may help improve the health level of people. Considering data scale and time shifts of time series, in this paper, we introduce two incremental fuzzy clustering algorithms based on a Dynamic Time Warping (DTW) distance. For recruiting Single-Pass and Online patterns, our algorithms could handle large-scale time series data by splitting it into a set of chunks which are processed sequentially. Besides, our algorithms select DTW to measure distance of pair-wise time series and encourage higher clustering accuracy because DTW could determine an optimal match between any two time series by stretching or compressing segments of temporal data. Our new algorithms are compared to some existing prominent incremental fuzzy clustering algorithms on 12 benchmark time series datasets. The experimental results show that the proposed approaches could yield high quality clusters and were better than all the competitors in terms of clustering accuracy.

Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD) values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids) and four agglomerative hierarchical methods (Complete linkage, Ward’s, Unweighted Pair Group Method and Weighted Pair Group Method) to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to distill biologically relevant information from MD trajectories, especially for docking purposes.

PurposeTo cluster test points in glaucoma patients' 30-2 and 10-2 visual field (VF) (Humphrey Field Analyzer: HFA, Carl Zeiss Meditec, Dublin, CA) in order to map the different regions damaged by the disease.MethodThis retrospective study included 128 eyes from 128 patients. 142 total deviation (TD) values (74 from the 30-2 VF and 68 from the 10-2 VF) were clustered using the 'Hierarchical Ordered Partitioning And Collapsing Hybrid-Partitioning Around Medoids' algorithm. The stability of the identified clusters was evaluated using bootstrapping.Results65 sectors were identified in total: 38 sectors were located outside the 10-2 VF whereas 29 sectors were located inside the 10-2 VF (two sectors overlap in both grids). The mapping of many sectors appeared to follow the distribution of retinal nerve fiber bundles. The results of bootstrapping suggested clusters were stable whether they were outside or inside the 10-2 VF.ConclusionA considerable number of sectors were identified in the 10-2 VF area, despite the fact that clustering was carried out on all points in both the 30-2 VF and 10-2 VF simultaneously. These findings suggest that glaucomatous central VF deterioration cannot be picked up by the 30-2 test grid alone, because of poor spatial sampling; denser estimation of the central ten degrees, than offered by the 30-2 test grid alone, is needed. It may be beneficial to develop a new VF test grid that combines test points from 30-2 and 10-2 VFs--the results of this study could help to devise this test grid.

A large number of nucleotide sequences of various pathogens are available in public databases. The growth of the datasets has resulted in an enormous increase in computational costs. Moreover, due to differences in surveillance activities, the number of sequences found in databases varies from one country to another and from year to year. Therefore, it is important to study resampling methods to reduce the sampling bias. A novel algorithm-called the closest-neighbor trimming method-that resamples a given number of sequences from a large nucleotide sequence dataset was proposed. The performance of the proposed algorithm was compared with other algorithms by using the nucleotide sequences of human H3N2 influenza viruses. We compared the closest-neighbor trimming method with the naive hierarchical clustering algorithm and [Formula: see text]-medoids clustering algorithm. Genetic information accumulated in public databases contains sampling bias. The closest-neighbor trimming method can thin out densely sampled sequences from a given dataset. Since nucleotide sequences are among the most widely used materials for life sciences, we anticipate that our algorithm to various datasets will result in reducing sampling bias.