FARKLI BAĞLANTI YÖNTEMLERİ İLE HİYERARŞİK KÜMELEME TOPLULUĞU

Kümeleme topluluğu, yüksek kümeleme performansı sağlaması nedeniyle son yıllarda tercih edilen bir teknik haline gelmiştir. Bu çalışmada, Bağlantı-tabanlı Hiyerarşik Kümeleme Topluluğu (BHKT) olarak isimlendirilen yeni bir yaklaşım önerilmektedir. Önerilen yaklaşımda, topluluk elemanları farklı bağlantı yöntemleri kullanarak hiyerarşik kümeleme yapmakta ve sonrasında çoğunluk oylaması ile ortak karar üretmektedir. Çalışmada kullanılan bağlantı yöntemleri: tek bağlantı, tam bağlantı, ortalama bağlantı, merkez bağlantı, Ward yöntemi, komşu birleştirme yöntemi ve ayarlı tam bağlantıdır. Ayrıca çalışmada, farklı boyutlardaki hiyerarşik kümeleme toplulukları incelenmiş ve birbiriyle karşılaştırılmıştır. Deneysel çalışmalarda, hiyerarşik kümeleme toplulukları 8 farklı veri setinde uygulanmış ve tek bir kümeleme algoritmasına göre daha iyi sonuçlar elde edilmiştir

A novel artificial bee colony based clustering algorithm for categorical data

Funding: This work was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. (21127010, 61202309, http://www.nsfc.gov.cn/), China Postdoctoral Science Foundation under Grant No. 2013M530956 (http://res.chinapostdoctor.org.cn), the UK Economic & Social Research Council (ESRC): award reference: ES/M001628/1 (http://www.esrc.ac.uk/), Science and Technology Development Plan of Jilin province under Grant No. 20140520068JH (http://www.jlkjt.gov.cn), Fundamental Research Funds for the Central Universities under No. 14QNJJ028 (http://www.nenu.edu.cn), the open project program of Key Laboratory of Symbolic Computation andKnowledge Engineering of Ministry of Education, Jilin University under Grant No. 93K172014K07 (http://www.jlu.edu.cn). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Hybrid-enhanced siamese similarity models in ligand-based virtual screen

Information technology has become an integral aspect of the drug development process. The virtual screening process (VS) is a computational technique for screening chemical compounds in a reasonable amount of time and cost. The similarity search is one of the primary tasks in VS that estimates a molecule's similarity. It is predicated on the idea that molecules with similar structures may also have similar activities. Many techniques for comparing the biological similarity between a target compound and each compound in the database have been established. Although the approaches have a strong performance, particularly when dealing with molecules with homogenous active structural, they are not enough good when dealing with structurally heterogeneous compounds. The previous works examined many deep learning methods in the enhanced Siamese similarity model and demonstrated that the Enhanced Siamese Multi-Layer Perceptron similarity model (SMLP) and the Siamese Convolutional Neural Network-one dimension similarity model (SCNN1D) have good outcomes when dealing with structurally heterogeneous molecules. To further improve the retrieval effectiveness of the similarity model, we incorporate the best two models in one hybrid model. The reason is that each method gives good results in some classes, so combining them in one hybrid model may improve the retrieval recall. Many designs of the hybrid models will be tested in this study. Several experiments on real-world data sets were conducted, and the findings demonstrated that the new approaches outperformed the previous method

Voting-based consensus clustering for combining multiple clusterings of chemical structures

<p>Abstract</p> <p>Background</p> <p>Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster.</p> <p>Results</p> <p>The cumulative voting-based aggregation algorithm (CVAA), cluster-based similarity partitioning algorithm (CSPA) and hyper-graph partitioning algorithm (HGPA) were examined. The F-measure and Quality Partition Index method (QPI) were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR) dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria.</p> <p>Conclusions</p> <p>The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA) was the method of choice among consensus clustering methods.</p