Related papers: LCPan: efficient variation graph construction usin…

A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…

The graph coloring problem (GCP) is a classic combinatorial optimization problem that aims to find the minimum number of colors assigned to vertices of a graph such that no two adjacent vertices receive the same color. GCP has been…

As large graph processing emerges, we observe a costly fork-processing pattern (FPP) that is common in many graph algorithms. The unique feature of the FPP is that it launches many independent queries from different source vertices on the…

In this paper, we construct protograph-based spatially coupled low-density parity-check (SC-LDPC) codes by coupling together a series of L disjoint, or uncoupled, LDPC code Tanner graphs into a single coupled chain. By varying L, we obtain…

Low-density parity-check (LDPC) convolutional codes are capable of achieving excellent performance with low encoding and decoding complexity. In this paper we discuss several graph-cover-based methods for deriving families of time-invariant…

Over the years, Principal Component Analysis (PCA) has served as the baseline approach for dimensionality reduction in gene expression data analysis. It primary objective is to identify a subset of disease-causing genes from a vast pool of…

We present a new family of low-density parity-check (LDPC) convolutional codes that can be designed using ordered sets of progressive differences. We study their properties and define a subset of codes in this class that have some desirable…

Graph Convolutional Networks (GCNs) are widely used in graph-based applications, such as social networks and recommendation systems. Nevertheless, large-scale graphs or deep aggregation layers in full-batch GCNs consume significant GPU…

For a deep learning model, efficient execution of its computation graph is key to achieving high performance. Previous work has focused on improving the performance for individual nodes of the computation graph, while ignoring the…

In this paper we propose a new efficient message passing algorithm for decoding LDPC transmitted over a channel with strong phase noise. The algorithm performs approximate bayesian inference on a factor graph representation of the channel…

We present Locality-aware Parallel Decoding (LPD) to accelerate autoregressive image generation. Traditional autoregressive image generation relies on next-patch prediction, a memory-bound process that leads to high latency. Existing works…

Conductance-based graph clustering has been recognized as a fundamental operator in numerous graph analysis applications. Despite the significant success of conductance-based graph clustering, existing algorithms are either hard to obtain…

Lateral predictive coding (LPC) is a simple theoretical framework to appreciate feature detection in biological neural circuits. Recent theoretical work [Huang et al., Phys.Rev.E 112, 034304 (2025)] has successfully constructed optimal LPC…

This paper investigates the application of low-density parity-check (LDPC) codes to Flash memories. Multiple cell reads with distinct word-line voltages provide limited-precision soft information for the LDPC decoder. The values of the…

We introduce a decoding framework for correlated errors in quantum LDPC codes under circuit-level noise. The core of our approach is a graph augmentation and rewiring for interference (GARI) method, which modifies the correlated detector…

This paper studies the problem of graph-level clustering, which is a novel yet challenging task. This problem is critical in a variety of real-world applications such as protein clustering and genome analysis in bioinformatics. Recent years…

Recently, machine learning has been successfully applied to model-based left ventricle (LV) segmentation. The general framework involves two stages, which starts with LV localization and is followed by boundary delineation. Both are driven…

Personalized PageRank (PPR) is a graph algorithm that evaluates the importance of the surrounding nodes from a source node. Widely used in social network related applications such as recommender systems, PPR requires real-time responses…

For graph learning tasks, many existing methods utilize a message-passing mechanism where vertex features are updated iteratively by aggregation of neighbor information. This strategy provides an efficient means for graph features…

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…