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Multi-assembly methods rely at their core on a flow decomposition problem, namely, decomposing a weighted graph into weighted paths or walks. However, most results over the past decade have focused on decompositions over directed acyclic…
Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausible matches between substrings of a read to subpaths of the…
The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In…
The Minimum Path Cover (MPC) problem consists of finding a minimum-cardinality set of node-disjoint paths that cover all nodes in a given graph. We explore a variant of the MPC problem on acyclic digraphs (DAGs) where, given a subset of…
Network flow is one of the most studied combinatorial optimization problems having innumerable applications. Any flow on a directed acyclic graph $G$ having $n$ vertices and $m$ edges can be decomposed into a set of $O(m)$ paths. In some…
We present practical linear and almost linear-time algorithms to compute a chain decomposition of a directed acyclic graph (DAG), $G=(V,E)$. The number of vertex-disjoint chains computed is very close to the minimum. The time complexity of…
Many important problems in Bioinformatics (e.g., assembly or multi-assembly) admit multiple solutions, while the final objective is to report only one. A common approach to deal with this uncertainty is finding safe partial solutions (e.g.,…
Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph nodes. A recent breakthrough…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
We define and study analogs of probabilistic tree embedding and tree cover for directed graphs. We define the notion of a DAG cover of a general directed graph $G$: a small collection $D_1,\dots D_g$ of DAGs so that for all pairs of…
In this article, the optimal sample complexity of learning the underlying interactions or dependencies of a Linear Dynamical System (LDS) over a Directed Acyclic Graph (DAG) is studied. We call such a DAG underlying an LDS as dynamical DAG…
We show that every directed graph $G$ with $n$ vertices and $m$ edges admits a directed acyclic graph (DAG) with $m^{1+o(1)}$ edges, called a DAG projection, that can either $(1+1/\text{polylog} (n))$-approximate distances between all pairs…
Parallel real-time systems (e.g., autonomous driving systems) often contain functionalities with complex dependencies and execution uncertainties, leading to significant timing variability which can be represented as a probabilistic…
Computing a minimum path cover (MPC) of a directed acyclic graph (DAG) is a fundamental problem with a myriad of applications, including reachability. Although it is known how to solve the problem by a simple reduction to minimum flow,…
Given a flow network, the Minimum Flow Decomposition (MFD) problem is finding the smallest possible set of weighted paths whose superposition equals the flow. It is a classical, strongly NP-hard problem that is proven to be useful in RNA…
Optimization of directed acyclic graph (DAG) structures has many applications, such as neural architecture search (NAS) and probabilistic graphical model learning. Encoding DAGs into real vectors is a dominant component in most…
We consider the problem of designing succinct data structures for interval graphs with $n$ vertices while supporting degree, adjacency, neighborhood and shortest path queries in optimal time in the $\Theta(\log n)$-bit word RAM model. The…
A minimum path cover (MPC) of a directed acyclic graph (DAG) $G = (V,E)$ is a minimum-size set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic polynomial problem, dating back to Dilworth's and…
We show how to chain maximal exact matches (MEMs) between a query string $Q$ and a labeled directed acyclic graph (DAG) $G=(V,E)$ to solve the longest common subsequence (LCS) problem between $Q$ and $G$. We obtain our result via a new…
We consider the problem of designing a succinct data structure for {\it path graphs} (which are a proper subclass of chordal graphs and a proper superclass of interval graphs) on $n$ vertices while supporting degree, adjacency, and…