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Graph neural architecture search has received a lot of attention as Graph Neural Networks (GNNs) has been successfully applied on the non-Euclidean data recently. However, exploring all possible GNNs architectures in the huge search space…

Simulation-based Inference (SBI) is a widely used set of algorithms to learn the parameters of complex scientific simulation models. While primarily run on CPUs in HPC clusters, these algorithms have been shown to scale in performance when…

Alternative splicing creates complex bubbles in splicing graphs where more than two transcript paths compete, challenging methods designed for simple binary events. We present a unified framework that compares paths using distinct exonic…

Community Search (CS) aims to identify densely interconnected subgraphs corresponding to query vertices within a graph. However, existing heterogeneous graph-based community search methods need help identifying cross-group communities and…

We present a parallelized bijective graph matching algorithm that leverages seeds and is designed to match very large graphs. Our algorithm combines spectral graph embedding with existing state-of-the-art seeded graph matching procedures.…

Machine learning (ML) approaches are increasingly being used to accelerate combinatorial optimization (CO) problems. We investigate the Set Cover Problem (SCP) and propose Graph-SCP, a graph neural network method that augments existing…

Graph clustering has many important applications in computing, but due to growing sizes of graphs, even traditionally fast clustering methods such as spectral partitioning can be computationally expensive for real-world graphs of interest.…

We initiate the study of graph algorithms in the streaming setting on massive distributed and parallel systems inspired by practical data processing systems. The objective is to design algorithms that can efficiently process evolving graphs…

Discovering causal relationships from data is the ultimate goal of many research areas. Constraint based causal exploration algorithms, such as PC, FCI, RFCI, PC-simple, IDA and Joint-IDA have achieved significant progress and have many…

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves…

Directed Acylic Graphs with a single entry vertex and a single exit vertex (st-DAGs) have many applications. For instance, they are frequently used for modelling flow problems or precedence conditions among tasks, work packages, etc.. This…

Nearest Neighbor Search (NNS) has recently drawn a rapid increase of interest due to its core role in managing high-dimensional vector data in data science and AI applications. The interest is fueled by the success of neural embedding,…

Important graph mining problems such as Clustering are computationally demanding. To significantly accelerate these problems, we propose ProbGraph: a graph representation that enables simple and fast approximate parallel graph mining with…

While there have been many studies on hardware acceleration for deep learning on images, there has been a rather limited focus on accelerating deep learning applications involving graphs. The unique characteristics of graphs, such as the…

De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…

Identifying the connected components of a graph, apart from being a fundamental problem with countless applications, is a key primitive for many other algorithms. In this paper, we consider this problem in parallel settings. Particularly,…

Graph Neural Networks (GNNs) have demonstrated their superiority in collaborative filtering, where the user-item (U-I) interaction bipartite graph serves as the fundamental data format. However, when graph-structured side information (e.g.,…

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…

More and more large data collections are gathered worldwide in various IT systems. Many of them possess the networked nature and need to be processed and analysed as graph structures. Due to their size they require very often usage of…

Edge-coloured directed graphs provide an essential structure for modelling and analysis of complex systems arising in many scientific disciplines (e.g. feature-oriented systems, gene regulatory networks, etc.). One of the fundamental…