Biomedical subjects

Ronen Basri

Publications and source records attributed to Ronen Basri.

3 recordsLinked to original sources

PubMed2006

Hierarchy and adaptivity in segmenting visual scenes.

Finding salient, coherent regions in images is the basis for many visual tasks, and is especially important for object recognition. Human observers perform this task with ease, relying on a system in which hierarchical processing seems to have a critical role. Despite many attempts, computerized algorithms have so far not demonstrated robust segmentation capabilities under general viewing conditions. Here we describe a new, highly efficient approach that determines all salient regions of an image and builds them into a hierarchical structure. Our algorithm, segmentation by weighted aggregation, is derived from algebraic multigrid solvers for physical systems, and consists of fine-to-coarse pixel aggregation. Aggregates of various sizes, which may or may not overlap, are revealed as salient, without predetermining their number or scale. Results using this algorithm are markedly more accurate and significantly faster (linear in data size) than previous approaches.

Adaptation, Physiological↗

PubMed2006

Shape representation and classification using the poisson equation.

We present a novel approach that allows us to reliably compute many useful properties of a silhouette. Our approach assigns, for every internal point of the silhouette, a value reflecting the mean time required for a random walk beginning at the point to hit the boundaries. This function can be computed by solving Poisson's equation, with the silhouette contours providing boundary conditions. We show how this function can be used to reliably extract various shape properties including part structure and rough skeleton, local orientation and aspect ratio of different parts, and convex and concave sections of the boundaries. In addition to this, we discuss properties of the solution and show how to efficiently compute this solution using multigrid algorithms. We demonstrate the utility of the extracted properties by using them for shape classification and retrieval.

Algorithms↗

PubMed2003

Spectral biclustering of microarray data: coclustering genes and conditions.

Global analyses of RNA expression levels are useful for classifying genes and overall phenotypes. Often these classification problems are linked, and one wants to find "marker genes" that are differentially expressed in particular sets of "conditions." We have developed a method that simultaneously clusters genes and conditions, finding distinctive "checkerboard" patterns in matrices of gene expression data, if they exist. In a cancer context, these checkerboards correspond to genes that are markedly up- or downregulated in patients with particular types of tumors. Our method, spectral biclustering, is based on the observation that checkerboard structures in matrices of expression data can be found in eigenvectors corresponding to characteristic expression patterns across genes or conditions. In addition, these eigenvectors can be readily identified by commonly used linear algebra approaches, in particular the singular value decomposition (SVD), coupled with closely integrated normalization steps. We present a number of variants of the approach, depending on whether the normalization over genes and conditions is done independently or in a coupled fashion. We then apply spectral biclustering to a selection of publicly available cancer expression data sets, and examine the degree to which the approach is able to identify checkerboard structures. Furthermore, we compare the performance of our biclustering methods against a number of reasonable benchmarks (e.g., direct application of SVD or normalized cuts to raw data).

Breast Neoplasms↗