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Linear systems and eigen-calculations on symmetric diagonally dominant matrices (SDDs) occur ubiquitously in computer vision, computer graphics, and machine learning. In the past decade a multitude of specialized solvers have been developed to tackle restricted instances of SDD systems for a diverse collection of problems including segmentation, gradient inpainting and total variation. In this paper we explain and apply the support theory of graphs, a set of of techniques developed by the computer science theory community, to construct SDD solvers with provable properties. To demonstrate the power of these techniques, we describe an efficient multigrid-like solver which is based on support theory principles. The solver tackles problems in fairly general and arbitrarily weighted topologies not supported by prior solvers. It achieves state of the art empirical results while providing robust guarantees on the speed of convergence. The method is evaluated on a variety of vision applications.

Motivation: Tumorigenesis is an evolutionary process by which tumor cells acquire sequences of mutations leading to increased growth, invasiveness and eventually metastasis. It is hoped that by identifying the common patterns of mutations underlying major cancer sub-types, we can better understand the molecular basis of tumor development and identify new diagnostics and therapeutic targets. This goal has motivated several attempts to apply evolutionary tree reconstruction methods to assays of tumor state. Inference of tumor evolution is in principle aided by the fact that tumors are heterogeneous, retaining remnant populations of different stages along their development along with contaminating healthy cell populations. In practice, though, this heterogeneity complicates interpretation of tumor data because distinct cell types are conflated by common methods for assaying the tumor state. We previously proposed a method to computationally infer cell populations from measures of tumor-wide gene expression through a geometric interpretation of mixture type separation, but this approach deals poorly with noisy and outlier data.Results: In the present work, we propose a new method to perform tumor mixture separation efficiently and robustly to an experimental error. The method builds on the prior geometric approach but uses a novel objective function allowing for robust fits that greatly reduces the sensitivity to noise and outliers. We further develop an efficient gradient optimization method to optimize this ‘soft geometric unmixing’ objective for measurements of tumor DNA copy numbers assessed by array comparative genomic hybridization (aCGH) data. We show, on a combination of semi-synthetic and real data, that the method yields fast and accurate separation of tumor states.Conclusions: We have shown a novel objective function and optimization method for the robust separation of tumor sub-types from aCGH data and have shown that the method provides fast, accurate reconstruction of tumor states from mixed samples. Better solutions to this problem can be expected to improve our ability to accurately identify genetic abnormalities in primary tumor samples and to infer patterns of tumor evolution.Contact: tolliver@cs.cmu.eduSupplementary information:Supplementary data are available at Bioinformatics online.

Linear systems and eigen-calculations on symmetric diagonally dominant matrices (SDDs) occur ubiquitously in computer vision, computer graphics, and machine learning. In the past decade a multitude of specialized solvers have been developed to tackle restricted instances of SDD systems for a diverse collection of problems including segmentation, gradient inpainting and total variation. In this paper we explain and apply the support theory of graphs, a set of of techniques developed by the computer science theory community, to construct SDD solvers with provable properties. To demonstrate the power of these techniques, we describe an efficient multigrid-like solver which is based on support theory principles. The solver tackles problems in fairly general and arbitrarily weighted topologies not supported by prior solvers. It achieves state of the art empirical results while providing robust guarantees on the speed of convergence. The method is evaluated on a variety of vision applications.