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Node embedding learns low-dimensional vectors for nodes in the graph. Recent state-of-the-art embedding approaches take Personalized PageRank (PPR) as the proximity measure and factorize the PPR matrix or its adaptation to generate…
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic,…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
During the last 3 years, our group has investigated extensively the complexation mechanism between neutral-polyelectrolyte block copolymers with oppositely charged species. These species are surfactant micelles, multivalent counterions and…
$\renewcommand{\Re}{\mathbb{R}}$Given a set $P$ of $n$ points in $\Re^d$, and a parameter $\varepsilon \in (0,1)$, we present a new construction of a directed graph $G$, of size $O(n/\varepsilon^d)$, such that $(1+\varepsilon)$-ANN queries…
Graphene nanogaps and nanopores show potential for the purpose of electrical DNA sequencing, in particular because single-base resolution appears to be readily achievable. Here, we evaluated from first principles the advantages of a nanogap…
The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of amorphous…
We initiate the study of the parameterized complexity of the {\sc Collective Graph Exploration} ({\sc CGE}) problem. In {\sc CGE}, the input consists of an undirected connected graph $G$ and a collection of $k$ robots, initially placed at…
We consider the problem of reconstructing an undirected graph $G$ on $n$ vertices given multiple random noisy subgraphs or "traces". Specifically, a trace is generated by sampling each vertex with probability $p_v$, then taking the…
The approximate single-source shortest-path problem is as follows: given a graph with nonnegative edge weights and a designated source vertex $s$, return estimates of the distances from~$s$ to each other vertex such that the estimate falls…
The main paradigm of smoothed analysis on graphs suggests that for any large graph $G$ in a certain class of graphs, perturbing slightly the edges of $G$ at random (usually adding few random edges to $G$) typically results in a graph having…
We present algorithmic results for the parallel assembly of many micro-scale objects in two and three dimensions from tiny particles, which has been proposed in the context of programmable matter and self-assembly for building high-yield…
Graph embedding has been proven to be efficient and effective in facilitating graph analysis. In this paper, we present a novel spectral framework called NOn-Backtracking Embedding (NOBE), which offers a new perspective that organizes graph…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
The discovery and analysis of network patterns are central to the scientific enterprise. In the present work, we developed and evaluated a new approach that learns the building blocks of graphs that can be used to understand and generate…
The classic problem of exact subgraph matching returns those subgraphs in a large-scale data graph that are isomorphic to a given query graph, which has gained increasing importance in many real-world applications. In this paper, we propose…
Hypergraphs provide a fundamental framework for representing complex systems involving interactions among three or more entities. As empirical hypergraphs grow in size, characterizing their structural properties becomes increasingly…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
Developing graphene-based nanoelectronics hinges on opening a band gap in the electronic structure of graphene, which is commonly achieved by breaking the inversion symmetry of the graphene lattice via an electric field (gate bias) or…