Related papers: An External-Memory Algorithm for String Graph Cons…
Discovering the underlying structures present in large real world graphs is a fundamental scientific problem. Recent work at the intersection of formal language theory and graph theory has found that a Hyperedge Replacement Grammar (HRG)…
Neural networks powered with external memory simulate computer behaviors. These models, which use the memory to store data for a neural controller, can learn algorithms and other complex tasks. In this paper, we introduce a new memory to…
An \emph{outer-string representation} of a graph $G$ is an intersection representation of $G$ where vertices are represented by curves (strings) inside the unit disk and each curve has exactly one endpoint on the boundary of the unit disk…
We present an approach for agents to learn representations of a global map from sensor data, to aid their exploration in new environments. To achieve this, we embed procedures mimicking that of traditional Simultaneous Localization and…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
We present graph-based translation models which translate source graphs into target strings. Source graphs are constructed from dependency trees with extra links so that non-syntactic phrases are connected. Inspired by phrase-based models,…
Graph-based semantic representations are valuable in natural language processing, where it is often simple and effective to represent linguistic concepts as nodes, and relations as edges between them. Several attempts has been made to find…
Recent years has witnessed dramatic progress of neural machine translation (NMT), however, the method of manually guiding the translation procedure remains to be better explored. Previous works proposed to handle such problem through…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
The future of main memory appears to lie in the direction of new technologies that provide strong capacity-to-performance ratios, but have write operations that are much more expensive than reads in terms of latency, bandwidth, and energy.…
The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…
We consider the dictionary problem in external memory and improve the update time of the well-known buffer tree by roughly a logarithmic factor. For any \lambda >= max {lg lg n, log_{M/B} (n/B)}, we can support updates in time O(\lambda /…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
Breadth-first search (BFS) is known as a basic search strategy for learning graph properties. As the scales of graph databases have increased tremendously in recent years, large-scale graphs G are often disk-resident. Obtaining the BFS…
Many data structures support dictionaries, also known as maps or associative arrays, which store and manage a set of key-value pairs. A \emph{multimap} is generalization that allows multiple values to be associated with the same key. For…
Graph Signal Processing has become a very useful framework for signal operations and representations defined on irregular domains. Exploiting transformations that are defined on graph models can be highly beneficial when the graph encodes…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…
The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…
We present novel graph kernels for graphs with node and edge labels that have ordered neighborhoods, i.e. when neighbor nodes follow an order. Graphs with ordered neighborhoods are a natural data representation for evolving graphs where…