Data clustering by minimizing disconnectivity

SCMDOT: Spatial Clustering with Multiple Density-Ordered Trees

With the rapid explosion of information based on location, spatial clustering plays an increasingly significant role in this day and age as an important technique in geographical data analysis. Most existing spatial clustering algorithms are limited by complicated spatial patterns, which have difficulty in discovering clusters with arbitrary shapes and uneven density. In order to overcome such limitations, we propose a novel clustering method called Spatial Clustering with Multiple Density-Ordered Trees (SCMDOT). Motivated by the idea of the Density-Ordered Tree (DOT), we firstly represent the original dataset by the means of constructing Multiple Density-Ordered Trees (MDOT). In the constructing process, we impose additional constraints to control the growth of each Density-Ordered Tree, ensuring that they all have high spatial similarity. Furthermore, a series of MDOT can be successively generated from regions of sparse areas to the dense areas, where each Density-Ordered Tree, also treated as a sub-tree, represents a cluster. In the merging process, the final clusters are obtained by repeatedly merging a suitable pair of clusters until they satisfy the expected clustering result. In addition, a heuristic strategy is applied during the process of our algorithm for suitability for special applications. The experiments on synthetic and real-world spatial databases are utilised to demonstrate the performance of our proposed method.

An in silico model to demonstrate the effects of Maspin on cancer cell dynamics

Most cancer treatments efficacy depends on tumor metastasis suppression, where tumor suppressor genes play an important role. Maspin (Mammary Serine Protease Inhibitor), an non-inhibitory serpin has been reported as a potential tumor suppressor to influence cell migration, adhesion, proliferation and apoptosis in in vitro and in vivo experiments in last two decades. Lack of computational investigations hinders its ability to go through clinical trials. Previously, we reported first computational model for maspin effects on tumor growth using artificial neural network and cellular automata paradigm with in vitro data support. This paper extends the previous in silico model by encompassing how maspin influences cell migration and the cell-extracellular matrix interaction in subcellular level. A feedforward neural network was used to define each cell behavior (proliferation, quiescence, apoptosis) which followed a cell-cycle algorithm to show the microenvironment impacts over tumor growth. Furthermore, the model concentrates how the in silico experiments results can further confirm the fact that maspin reduces cell migration using specific in vitro data verification method. The data collected from in vitro and in silico experiments formulates an unsupervised learning problem which can be solved by using different clustering algorithms. A density based clustering technique was developed to measure the similarity between two datasets based on the number of links between instances. Our proposed clustering algorithm first finds the nearest neighbors of each instance, and then redefines the similarity between pairs of instances in terms of how many nearest neighbors share the two instances. The number of links between two instances is defined as the number of common neighbors they have. The results showed significant resemblances with in vitro experimental data. The results also offer a new insight into the dynamics of maspin and establish as a metastasis suppressor gene for further molecular research.