Pathway-Based Genomics Prediction using Generalized Elastic Net.

We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection. The proposed formulation is applicable to a wide variety of problems in which the interpretation of predictive features using known molecular interactions is desired. The method naturally steers solutions toward sets of mechanistically interlinked genes. Using experiments on synthetic data, we demonstrate that pathway-guided results maintain, and often improve, the accuracy of predictors even in cases where the full gene network is unknown. We apply the method to predict the drug response of breast cancer cell lines. GELnet is able to reveal genetic determinants of sensitivity and resistance for several compounds. In particular, for an EGFR/HER2 inhibitor, it finds a possible trans-differentiation resistance mechanism missed by the corresponding pathway agnostic approach

Determination of normalized electric eigenfields in microwave cavities with sharp edges

The magnetic field integral equation for axially symmetric cavities with perfectly conducting piecewise smooth surfaces is discretized according to a high-order convergent Fourier--Nystr\"om scheme. The resulting solver is used to accurately determine eigenwavenumbers and normalized electric eigenfields in the entire computational domain.Comment: 34 pages, 6 figure

A Step Towards QC Blind Signatures

In this paper we propose a conversion from signature schemes connected to coding theory into blind signature schemes. We give formal security reductions to combinatorial problems not connected to number theory. This is the first blind signature scheme which can not be broken by quantum computers via cryptanalyzing the underlying signature scheme employing Shor’s algorithms. We thus present a step towards diversifying computational assumptions on which blind signatures can be based. We achieve blind signatures by a different concept of blinding: Instead of blinding the message, we blind the public key, such that generating a (blind) signature for the blinded key requires the interaction of the holder of the original secret key. To verify the blind signature, the connection between the original and the blinded key is proven by a static ZK proof. The major ingredient for our conversion is the PKP protocol by Shamir

Sampling and Reconstruction of Sparse Signals on Circulant Graphs - An Introduction to Graph-FRI

With the objective of employing graphs toward a more generalized theory of signal processing, we present a novel sampling framework for (wavelet-)sparse signals defined on circulant graphs which extends basic properties of Finite Rate of Innovation (FRI) theory to the graph domain, and can be applied to arbitrary graphs via suitable approximation schemes. At its core, the introduced Graph-FRI-framework states that any K-sparse signal on the vertices of a circulant graph can be perfectly reconstructed from its dimensionality-reduced representation in the graph spectral domain, the Graph Fourier Transform (GFT), of minimum size 2K. By leveraging the recently developed theory of e-splines and e-spline wavelets on graphs, one can decompose this graph spectral transformation into the multiresolution low-pass filtering operation with a graph e-spline filter, and subsequent transformation to the spectral graph domain; this allows to infer a distinct sampling pattern, and, ultimately, the structure of an associated coarsened graph, which preserves essential properties of the original, including circularity and, where applicable, the graph generating set.Comment: To appear in Appl. Comput. Harmon. Anal. (2017

Task-Driven Dictionary Learning

Modeling data with linear combinations of a few elements from a learned dictionary has been the focus of much recent research in machine learning, neuroscience and signal processing. For signals such as natural images that admit such sparse representations, it is now well established that these models are well suited to restoration tasks. In this context, learning the dictionary amounts to solving a large-scale matrix factorization problem, which can be done efficiently with classical optimization tools. The same approach has also been used for learning features from data for other purposes, e.g., image classification, but tuning the dictionary in a supervised way for these tasks has proven to be more difficult. In this paper, we present a general formulation for supervised dictionary learning adapted to a wide variety of tasks, and present an efficient algorithm for solving the corresponding optimization problem. Experiments on handwritten digit classification, digital art identification, nonlinear inverse image problems, and compressed sensing demonstrate that our approach is effective in large-scale settings, and is well suited to supervised and semi-supervised classification, as well as regression tasks for data that admit sparse representations.Comment: final draft post-refereein

Many-to-Many Graph Matching: a Continuous Relaxation Approach

Graphs provide an efficient tool for object representation in various computer vision applications. Once graph-based representations are constructed, an important question is how to compare graphs. This problem is often formulated as a graph matching problem where one seeks a mapping between vertices of two graphs which optimally aligns their structure. In the classical formulation of graph matching, only one-to-one correspondences between vertices are considered. However, in many applications, graphs cannot be matched perfectly and it is more interesting to consider many-to-many correspondences where clusters of vertices in one graph are matched to clusters of vertices in the other graph. In this paper, we formulate the many-to-many graph matching problem as a discrete optimization problem and propose an approximate algorithm based on a continuous relaxation of the combinatorial problem. We compare our method with other existing methods on several benchmark computer vision datasets.Comment: 1