Related papers: New error measures and methods for realizing prote…
In this paper, we present a novel method for solving multiobjective linear programming problems (MOLPP) that overcomes the need to calculate the optimal value of each objective function. This method is a follow-up to our previous work on…
Graph modification problems, which aim to find a small set of modifications to a graph so that it satisfies a desired property, have been studied for several special graph classes. The literature is rather rich in NP-completeness results…
We present self-supervised geometric perception (SGP), the first general framework to learn a feature descriptor for correspondence matching without any ground-truth geometric model labels (e.g., camera poses, rigid transformations). Our…
This paper proposes and analyzes a gradient-type algorithm based on Burer-Monteiro factorization, called the Asymmetric Projected Gradient Descent (APGD), for reconstructing the point set configuration from partial Euclidean distance…
We introduce and study conic geometric programs (CGPs), which are convex optimization problems that unify geometric programs (GPs) and conic optimization problems such as semidefinite programs (SDPs). A CGP consists of a linear objective…
An increasingly common viewpoint is that protein dynamics data sets reside in a non-linear subspace of low conformational energy. Ideal data analysis tools for such data sets should therefore account for such non-linear geometry. The…
Determining what to eat to satisfy nutritional requirements is one of the oldest optimization problems in operations research, yet existing formulations have two persistent limitations: continuous variables produce impractical fractional…
Computing efficiently a robust measure of similarity or dissimilarity between graphs is a major challenge in Pattern Recognition. The Graph Edit Distance (GED) is a flexible measure of dissimilarity between graphs which arises in…
This paper presents a spectral framework for quantifying the differentiation between graph data samples by introducing a novel metric named Graph Geodesic Distance (GGD). For two different graphs with the same number of nodes, our framework…
Graph matching aims to establish correspondences between vertices of graphs such that both the node and edge attributes agree. Various learning-based methods were recently proposed for finding correspondences between image key points based…
Calibration, the practice of choosing the parameters of a structural model to match certain empirical moments, can be viewed as minimum distance estimation. Existing standard error formulas for such estimators require a consistent estimate…
The Discretizable Molecular Distance Geometry Problem (DMDGP) consists in a subclass of the Molecular Distance Geometry Problem for which an embedding in ${\mathbb{R}^3}$ can be found using a Branch & Prune (BP) algorithm in a discrete…
Fitting concentric geometric objects to digitized data is an important problem in many areas such as iris detection, autonomous navigation, and industrial robotics operations. There are two common approaches to fitting geometric shapes to…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Protein function is executed at the molecular surface, where shape and chemistry act together to govern interaction. Yet most comparison methods treat these aspects separately, privileging either global fold or local descriptors and missing…
We propose and analyze a numerical method to solve an elliptic transmission problem in full space. The method consists of a variational formulation involving standard boundary integral operators on the coupling interface and an ultra-weak…
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running…
Motivated by an open problem of validating protein identities in label-free shotgun proteomics work-flows, we present a testing procedure to validate class/protein labels using available measurements across instances/peptides. More…
Computing the diameter of the intersection graphs of objects is a basic problem in computational geometry. Previous works showed that the complexity of computing the diameter mainly depends on the object types: for unit disks and squares in…
The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend on previous work and propose the…