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Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genomes. Sequence-to-graph alignment is an essential step for the…
The Partially Ordered Workflow Language (POWL) has recently emerged as a process modeling notation, offering strong quality guarantees and high expressiveness. While early versions of POWL relied on strict block-structured operators for…
Neural table-to-text generation approaches are data-hungry, limiting their adaptation for low-resource real-world applications. Previous works mostly resort to Pre-trained Language Models (PLMs) to generate fluent summaries of a table.…
We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…
In this paper, we propose a new, combined Zero-Forcing Per-Group Precoding (ZF-PGP) method that achieves very high gains in comparison to ZF Precoding techniques, while it simultaneously offers individually separate streams to reach…
Shortest path (SP) computation is the building block for many location-based services, and achieving high throughput SP query processing with real-time response is crucial for those services. However, existing solutions can hardly handle…
In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…
We propose a new nonlinear factorization model for graphs that are with topological structures, and optionally, node attributes. This model is based on a pseudometric called Gromov-Wasserstein (GW) discrepancy, which compares graphs in a…
Recent results show that modern Large Language Models (LLM) are indeed capable of understanding and answering questions about structured data such as graphs. This new paradigm can lead to solutions that require less supervision while, at…
Feature pyramid networks have been widely adopted in the object detection literature to improve feature representations for better handling of variations in scale. In this paper, we present Feature Pyramid Grids (FPG), a deep multi-pathway…
This paper presents the Persistent Weisfeiler-Lehman Random walk scheme (abbreviated as PWLR) for graph representations, a novel mathematical framework which produces a collection of explainable low-dimensional representations of graphs…
In this paper, we propose a method to generate personalized filled pauses (FPs) with group-wise prediction models. Compared with fluent text generation, disfluent text generation has not been widely explored. To generate more human-like…
Gaussian processes (GPs) are crucial in machine learning for quantifying uncertainty in predictions. However, their associated covariance matrices, defined by kernel functions, are typically dense and large-scale, posing significant…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this paper, we explore a novel approach to compute…
Analyzing massive complex networks yields promising insights about our everyday lives. Building scalable algorithms to do so is a challenging task that requires a careful analysis and an extensive evaluation. However, engineering such…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Linearization is a widely used method for solving polynomial eigenvalue problems (PEPs) and rational eigenvalue problem (REPs) in which the PEP/REP is transformed to a generalized eigenproblem and then solve this generalized eigenproblem…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
In real-world applications of large language models, outputs are often required to be confined: selecting items from predefined product or document sets, generating phrases that comply with safety standards, or conforming to specialized…