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This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…

Many discrete optimization problems amount to selecting a feasible set of edges of least weight. We consider in this paper the context of spatial graphs where the positions of the vertices are uncertain and belong to known uncertainty sets.…

The phenomenon of self-organization has been of special interest to the neural network community for decades. In this paper, we study a variant of the Self-Organizing Map (SOM) that models the phenomenon of self-organization of the…

Retrieving occlusion relation among objects in a single image is challenging due to sparsity of boundaries in image. We observe two key issues in existing works: firstly, lack of an architecture which can exploit the limited amount of…

Many applications in graph theory are motivated by routing or flow problems. Among these problems is Steiner Orientation: given a mixed graph G (having directed and undirected edges) and a set T of k terminal pairs in G, is there an…

There has recently been great progress in automatic segmentation of medical images with deep learning algorithms. In most works observer variation is acknowledged to be a problem as it makes training data heterogeneous but so far no…

A frame is a generalization of a basis of a vector space to a redundant overspanning set whose vectors are linearly dependent. Frames find applications in signal processing and quantum information theory. We present a genetic algorithm that…

We consider the problem of finding a Hamiltonian path with precedence constraints in the form of a partial order on the vertex set. This problem is known as Partially Ordered Hamiltonian Path Problem (POHPP). Here, we study the complexity…

We initiate a general study of what we call orientation completion problems. For a fixed class C of oriented graphs, the orientation completion problem asks whether a given partially oriented graph P can be completed to an oriented graph in…

We consider the following problem: Given an undirected (mixed) network and a set of ordered source-target, or cause-effect pairs, direct all edges so as to maximize the number of pairs that admit a directed source-target path. This is…

Operational Neural Networks (ONNs) have recently been proposed to address the well-known limitations and drawbacks of conventional Convolutional Neural Networks (CNNs) such as network homogeneity with the sole linear neuron model. ONNs are…

Routing and scheduling problems are fundamental problems in combinatorial optimization, and also have many applications. Most variations of these problems are NP-Hard, so we need to use heuristics to solve these problems on large instances,…

The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…

This paper presents a neural network approach for solving two-dimensional optical tomography (OT) problems based on the radiative transfer equation. The mathematical problem of OT is to recover the optical properties of an object based on…

The Multi-Objective Shortest-Path (MOS) problem finds a set of Pareto-optimal solutions from a start node to a destination node in a multi-attribute graph. The literature explores multi-objective A*-style algorithmic approaches to solving…

Modern computer networks support interesting new routing models in which traffic flows from a source s to a destination t can be flexibly steered through a sequence of waypoints, such as (hardware) middleboxes or (virtualized) network…

Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of…

Classical problems of sorting and searching assume an underlying linear ordering of the objects being compared. In this paper, we study a more general setting, in which some pairs of objects are incomparable. This generalization is relevant…

Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…

The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…