Related papers: On the Border Length Minimization Problem (BLMP) o…
Computing supertrees is a central problem in phylogenetics. The supertree method that is by far the most widely used today was introduced in 1992 and is called Matrix Representation with Parsimony analysis (MRP). Matrix Representation using…
Accuracy at the top is a special class of binary classification problems where the performance is evaluated only on a small number of relevant (top) samples. Applications include information retrieval systems or processes with manual…
This article presents the first mixed-integer linear programming (MILP)-based iterative algorithm to solve factorable mixed-integer nonlinear programs (MINLPs) with bounded, differentiable periodic functions to global optimality with an…
Hyperparameter tuning is an important task of machine learning, which can be formulated as a bilevel program (BLP). However, most existing algorithms are not applicable for BLP with non-smooth lower-level problems. To address this, we…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
We provide a number of algorithmic results for the following family of problems: For a given binary m\times n matrix A and integer k, decide whether there is a "simple" binary matrix B which differs from A in at most k entries. For an…
The Maximum s-Bundle Problem (MBP) addresses the task of identifying a maximum s-bundle in a given graph. A graph G=(V, E) is called an s-bundle if its vertex connectivity is at least |V|-s, where the vertex connectivity equals the minimum…
In metabolomics, small molecules are structurally elucidated using tandem mass spectrometry (MS/MS); this resulted in the computational Maximum Colorful Subtree problem, which is NP-hard. Unfortunately, data from a single metabolite…
Neural networks have recently been proposed for multi-label classification because they are able to capture and model label dependencies in the output layer. In this work, we investigate limitations of BP-MLL, a neural network (NN)…
Estimating a constrained relation is a fundamental problem in machine learning. Special cases are classification (the problem of estimating a map from a set of to-be-classified elements to a set of labels), clustering (the problem of…
We propose a novel Riemannian method for solving the Extreme multi-label classification problem that exploits the geometric structure of the sparse low-dimensional local embedding models. A constrained optimization problem is formulated as…
Optimization problems, particularly NP-Hard Combinatorial Optimization problems, are some of the hardest computing problems with no known polynomial time algorithm existing. Recently there has been interest in using dedicated hardware to…
Detectability of failures of linear programming (LP) decoding and the potential for improvement by adding new constraints motivate the use of an adaptive approach in selecting the constraints for the underlying LP problem. In this paper, we…
The Partitioning Min-Max Weighted Matching (PMMWM) problem is an NP-hard problem that combines the problem of partitioning a group of vertices of a bipartite graph into disjoint subsets with limited size and the classical Min-Max Weighted…
The linearly constrained matrix rank minimization problem is widely applicable in many fields such as control, signal processing and system identification. The tightest convex relaxation of this problem is the linearly constrained nuclear…
We consider the general problem of finding the minimum weight $\bm$-matching on arbitrary graphs. We prove that, whenever the linear programming (LP) relaxation of the problem has no fractional solutions, then the belief propagation (BP)…
The A* algorithm is commonly used to solve NP-hard combinatorial optimization problems. When provided with a completely informed heuristic function, A* solves many NP-hard minimum-cost path problems in time polynomial in the branching…
The minimum common string partition problem is an NP-hard combinatorial optimization problem with applications in computational biology. In this work we propose the first integer linear programming model for solving this problem. Moreover,…
Enumerating maximal $k$-biplexes (MBPs) of a bipartite graph has been used for applications such as fraud detection. Nevertheless, there usually exists an exponential number of MBPs, which brings up two issues when enumerating MBPs, namely…
Minimizing the number of reshuffling operations at maritime container terminals incorporates the Pre-Marshalling Problem (PMP) as an important problem. Based on an analysis of existing solution approaches we develop new heuristics utilizing…