Related papers: Fast sequence to graph alignment using the graph w…
Recently, Graph Convolutional Networks (GCNs) have proven to be a powerful mean for Computer Aided Diagnosis (CADx). This approach requires building a population graph to aggregate structural information, where the graph adjacency matrix…
Network alignment is the task of establishing one-to-one correspondences between the nodes of different graphs. Although finding a plethora of applications in high-impact domains, this task is known to be NP-hard in its general form.…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Gravitational-wave detection strategies are based on a signal analysis technique known as matched filtering. Despite the success of matched filtering, due to its computational cost, there has been recent interest in developing deep…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
A graph embedding is an emerging approach that can represent a graph structure with a fixed-length low-dimensional vector. node2vec is a well-known algorithm to obtain such a graph embedding by sampling neighboring nodes on a given graph…
Text-rich graphs, which exhibit rich textual information on nodes and edges, are prevalent across a wide range of real-world business applications. Large Language Models (LLMs) have demonstrated remarkable abilities in understanding text,…
The graph Fourier transform (GFT) is an important tool for graph signal processing, with applications ranging from graph-based image processing to spectral clustering. However, unlike the discrete Fourier transform, the GFT typically does…
This paper introduces a design method for densergraph-frequency graph Fourier frames (DGFFs) to enhance graph signal processing and analysis. The graph Fourier transform (GFT) enables us to analyze graph signals in the graph spectral domain…
Graph neural networks (GNNs) are emerging for machine learning research on graph-structured data. GNNs achieve state-of-the-art performance on many tasks, but they face scalability challenges when it comes to real-world applications that…
Vertex-frequency analysis, particularly the windowed graph Fourier transform (WGFT), is a significant challenge in graph signal processing. Tight frame theories is known for its low computational complexity in signal reconstruction, while…
Graphs are widely used to model complicated data semantics in many application domains. In this paper, two novel and efficient algorithms Fast-ON and Fast-P are proposed for solving the subgraph isomorphism problem. The two algorithms are…
Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…
Optimization of data placement in complex scientific workflows has become very crucial since the large amounts of data generated by these workflows significantly increases the turnaround time of the end-to-end application. It is almost…
Graph Convolutional Networks (GCNs) have proven to be successful tools for semi-supervised classification on graph-based datasets. We propose a new GCN variant whose three-part filter space is targeted at dense graphs. Examples include…
Due to the irregular nature of connections in most graph datasets, partitioning graph analysis algorithms across multiple computational nodes that do not share a common memory inevitably leads to large amounts of interconnect traffic.…
Existing machine learning literature lacks graph-based domain adaptation techniques capable of handling large distribution shifts, primarily due to the difficulty in simulating a coherent evolutionary path from source to target graph. To…
High-performance analysis of unstructured data like graphs now is critical for applications ranging from business intelligence to genome analysis. Towards this, data centers hold large graphs in memory to serve multiple concurrent queries…
Graph convolution networks (GCNs) are currently mainstream in learning with irregular data. These models rely on message passing and attention mechanisms that capture context and node-to-node relationships. With multi-head attention, GCNs…