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Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
We introduce models and algorithmic foundations for graph watermarking. Our frameworks include security definitions and proofs, as well as characterizations when graph watermarking is algorithmically feasible, in spite of the fact that the…
Many computational problems admit fast algorithms on special inputs, however, the required properties might be quite restrictive. E.g., many graph problems can be solved much faster on interval or cographs, or on graphs of small…
Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain minimal hyperpaths in B-hypergraphs. This makes it possible to…
Assembly planning is the core of automating product assembly, maintenance, and recycling for modern industrial manufacturing. Despite its importance and long history of research, planning for mechanical assemblies when given the final…
We study methods for finding the solution set of a generic system in a family of polynomial systems with parametric coefficients. We present a framework for describing monodromy based solvers in terms of decorated graphs. Under the…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium…
Fully Homomorphic Encryption (FHE) provides a powerful paradigm for secure computation, but its practical adoption is severely hindered by the prohibitive computational cost of its bootstrapping procedure. The complexity of all current…
Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Capturing structural similarity has been a hot topic in the field of network embedding recently due to its great help in understanding the node functions and behaviors. However, existing works have paid very much attention to learning…
In this work, we analyze an efficient sampling-based algorithm for general-purpose reachability analysis, which remains a notoriously challenging problem with applications ranging from neural network verification to safety analysis of…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Subgraph matching, a cornerstone of relational pattern detection in domains ranging from biochemical systems to social network analysis, faces significant computational challenges due to the dramatically growing search space. Existing…
Graph embedding based on random-walks supports effective solutions for many graph-related downstream tasks. However, the abundance of embedding literature has made it increasingly difficult to compare existing methods and to identify…