Identification of Topological Features in Renal Tumor Microenvironment Associated with Patient Survival

Motivation As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However, traditional qualitative and/or semi-quantitative parameters obtained by pathologist’s visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem. Results We propose a novel bioimage informatics pipeline for automatically characterizing the topological organization of different cell patterns in the tumor microenvironment. We apply this pipeline to the only publicly available large histopathology image dataset for a cohort of 190 patients with papillary renal cell carcinoma obtained from The Cancer Genome Atlas project. Experimental results show that the proposed topological features can successfully stratify early- and middle-stage patients with distinct survival, and show superior performance to traditional clinical features and cellular morphological and intensity features. The proposed features not only provide new insights into the topological organizations of cancers, but also can be integrated with genomic data in future studies to develop new integrative biomarkers

Spatially Coherent RANSAC for Multi-Model Fitting

RANSAC [15, 38, 1] is a reliable method for fitting parametric models to sparse data with many outliers. Originally designed for extracting a single model, RANSAC also has variants for fitting multiple models when supported by data. Our main insight is that, in practice, inliers for each model are often spatially coherent — all previous RANSAC-based methods ignore this. Our new method fits an unspecified number of models to data by combining ideas of random sampling and spatial regularization. As in basic RANSAC, we randomly sample data points to generate a set of proposed models (labels). We formulate model selection and inlier classification as a single problem — labeling of triangulated data points. Geometric fit errors and spatial coherence are combined in one MRF-based energy. In contrast to basic RANSAC, inlier classification does not depend on a fixed threshold. Moreover, our optimization framework allows iterative re-estimation of models/inliers with a clear stopping criteria and convergence guarantees. We show that our new method, SCO- RANSAC, can significantly improve results on synthetic and real data supporting multiple linear, affine, and homographic models

Data Clustering Using Wave Atom

Clustering of huge spatial databases is an important issue which tries to track the densely regions in the feature space to be used in data mining, knowledge discovery, or efficient information retrieval. Clustering approach should be efficient and can detect clusters of arbitrary shapes because spatial objects cannot be simply abstracted as isolated points they have different boundary, size, volume, and location. In this paper we use discrete wave atom transformation technique in clustering to achieve more accurate result. By using multi-resolution transformation like wavelet and wave atom we can effectively identify arbitrary shape clusters at different degrees of accuracy. Experimental results on very large data sets show the efficiency and effectiveness of the proposed wave atom bases clustering approach compared to other recent clustering methods. Experimental result shows that we get more accurate result and denoised output than others