Concept embedding-based weighting scheme for biomedical text clustering and visualization

Biomedical text clustering is a text mining technique used to provide better document search, browsing, and retrieval in biomedical and clinical text collections. In this research, the document representation based on the concept embedding along with the proposed weighting scheme is explored. The concept embedding is learned through the neural networks to capture the associations between the concepts. The proposed weighting scheme makes use of the concept associations to build document vectors for clustering. We evaluate two types of concept embedding and new weighting scheme for text clustering and visualization on two different biomedical text collections. The returned results demonstrate that the concept embedding along with the new weighting scheme performs better than the baseline tf–idf for clustering and visualization. Based on the internal clustering evaluation metric-Davies–Bouldin index and the visualization, the concept embedding generated from aggregated word embedding can form well-separated clusters, whereas the intact concept embedding can better identify more clusters of specific diseases and gain better F-measure

Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme

<p>Abstract</p> <p>Background</p> <p>Recent technological advances applied to biology such as yeast-two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of protein interaction networks. These interaction networks represent a rich, yet noisy, source of data that could be used to extract meaningful information, such as protein complexes. Several interaction network weighting schemes have been proposed so far in the literature in order to eliminate the noise inherent in interactome data. In this paper, we propose a novel weighting scheme and apply it to the <it>S. cerevisiae </it>interactome. Complex prediction rates are improved by up to 39%, depending on the clustering algorithm applied.</p> <p>Results</p> <p>We adopt a two step procedure. During the first step, by applying both novel and well established protein-protein interaction (PPI) weighting methods, weights are introduced to the original interactome graph based on the confidence level that a given interaction is a true-positive one. The second step applies clustering using established algorithms in the field of graph theory, as well as two variations of Spectral clustering. The clustered interactome networks are also cross-validated against the confirmed protein complexes present in the MIPS database.</p> <p>Conclusions</p> <p>The results of our experimental work demonstrate that interactome graph weighting methods clearly improve the clustering results of several clustering algorithms. Moreover, our proposed weighting scheme outperforms other approaches of PPI graph weighting.</p

On Instance Weighted Clustering Ensembles

© ESANN, 2023. This is the accepted manuscript version of an article which has been published in final form at: www.esann.org/proceedings/2023Ensemble clustering is a technique which combines multipleclustering results, and instance weighting is a technique which highlightsimportant instances in a dataset. Both techniques are known to enhanceclustering performance and robustness. In this research, ensembles andinstance weighting are integrated with the spectral clustering algorithm.We believe this is the first attempt at creating diversity in the generativemechanism using density based instance weighting for a spectral ensemble.The proposed approach is empirically validated using synthetic datasetscomparing against spectral and a spectral ensemble with random instanceweighting. Results show that using the instance weighted sub-samplingapproach as the generative mechanism for an ensemble of spectral cluster-ing leads to improved clustering performance on datasets with imbalancedclusters.Peer reviewe

Fast Color Quantization Using Weighted Sort-Means Clustering

Color quantization is an important operation with numerous applications in graphics and image processing. Most quantization methods are essentially based on data clustering algorithms. However, despite its popularity as a general purpose clustering algorithm, k-means has not received much respect in the color quantization literature because of its high computational requirements and sensitivity to initialization. In this paper, a fast color quantization method based on k-means is presented. The method involves several modifications to the conventional (batch) k-means algorithm including data reduction, sample weighting, and the use of triangle inequality to speed up the nearest neighbor search. Experiments on a diverse set of images demonstrate that, with the proposed modifications, k-means becomes very competitive with state-of-the-art color quantization methods in terms of both effectiveness and efficiency.Comment: 30 pages, 2 figures, 4 table