arXiv subjects

Ariful Azad

Publications and source records attributed to Ariful Azad.

At least 37 records · Page 2Linked to original sources

arXiv2022

MarkovGNN: Graph Neural Networks on Markov Diffusion

Most real-world networks contain well-defined community structures where nodes are densely connected internally within communities. To learn from these networks, we develop MarkovGNN that captures the formation and evolution of communities directly in different convolutional layers. Unlike most Graph Neural Networks (GNNs) that consider a static graph at every layer, MarkovGNN generates different stochastic matrices using a Markov process and then uses these community-capturing matrices in different layers. MarkovGNN is a general approach that could be used with most existing GNNs. We experimentally show that MarkovGNN outperforms other GNNs for clustering, node classification, and visualization tasks. The source code of MarkovGNN is publicly available at \url{https://github.com/HipGraph/MarkovGNN}.

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arXiv2021

A Comprehensive Analytical Survey on Unsupervised and Semi-Supervised Graph Representation Learning Methods

Graph representation learning is a fast-growing field where one of the main objectives is to generate meaningful representations of graphs in lower-dimensional spaces. The learned embeddings have been successfully applied to perform various prediction tasks, such as link prediction, node classification, clustering, and visualization. The collective effort of the graph learning community has delivered hundreds of methods, but no single method excels under all evaluation metrics such as prediction accuracy, running time, scalability, etc. This survey aims to evaluate all major classes of graph embedding methods by considering algorithmic variations, parameter selections, scalability, hardware and software platforms, downstream ML tasks, and diverse datasets. We organized graph embedding techniques using a taxonomy that includes methods from manual feature engineering, matrix factorization, shallow neural networks, and deep graph convolutional networks. We evaluated these classes of algorithms for node classification, link prediction, clustering, and visualization tasks using widely used benchmark graphs. We designed our experiments on top of PyTorch Geometric and DGL libraries and run experiments on different multicore CPU and GPU platforms. We rigorously scrutinize the performance of embedding methods under various performance metrics and summarize the results. Thus, this paper may serve as a comparative guide to help users select methods that are most suitable for their tasks.

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arXiv2021

Parallel Algorithms for Adding a Collection of Sparse Matrices

We develop a family of parallel algorithms for the SpKAdd operation that adds a collection of k sparse matrices. SpKAdd is a much needed operation in many applications including distributed memory sparse matrix-matrix multiplication (SpGEMM), streaming accumulations of graphs, and algorithmic sparsification of the gradient updates in deep learning. While adding two sparse matrices is a common operation in Matlab, Python, Intel MKL, and various GraphBLAS libraries, these implementations do not perform well when adding a large collection of sparse matrices. We develop a series of algorithms using tree merging, heap, sparse accumulator, hash table, and sliding hash table data structures. Among them, hash-based algorithms attain the theoretical lower bounds both on the computational and I/O complexities and perform the best in practice. The newly-developed hash SpKAdd makes the computation of a distributed-memory SpGEMM algorithm at least 2x faster than that the previous state-of-the-art algorithms.

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arXiv2021

FusedMM: A Unified SDDMM-SpMM Kernel for Graph Embedding and Graph Neural Networks

We develop a fused matrix multiplication kernel that unifies sampled dense-dense matrix multiplication and sparse-dense matrix multiplication under a single operation called FusedMM. By using user-defined functions, FusedMM can capture almost all computational patterns needed by popular graph embedding and GNN approaches. FusedMM is an order of magnitude faster than its equivalent kernels in Deep Graph Library. The superior performance of FusedMM comes from the low-level vectorized kernels, a suitable load balancing scheme and an efficient utilization of the memory bandwidth. FusedMM can tune its performance using a code generator and perform equally well on Intel, AMD and ARM processors. FusedMM speeds up an end-to-end graph embedding algorithm by up to 28x on different processors.

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arXiv2021

Combinatorial BLAS 2.0: Scaling combinatorial algorithms on distributed-memory systems

Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for rapid development of combinatorial algorithms in distributed-memory systems. During the decade since its first introduction, the Combinatorial BLAS library has evolved and expanded significantly. This paper details many of the key technical features of Combinatorial BLAS version 2.0, such as communication avoidance, hierarchical parallelism via in-node multithreading, accelerator support via GPU kernels, generalized semiring support, implementations of key data structures and functions, and scalable distributed I/O operations for human-readable files. Our paper also presents several rules of thumb for choosing the right data structures and functions in Combinatorial BLAS 2.0, under various common application scenarios.

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arXiv2021

Inductive Predictions of Extreme Hydrologic Events in The Wabash River Watershed

We present a machine learning method to predict extreme hydrologic events from spatially and temporally varying hydrological and meteorological data. We used a timestep reduction technique to reduce the computational and memory requirements and trained a bidirection LSTM network to predict soil water and stream flow from time series data observed and simulated over eighty years in the Wabash River Watershed. We show that our simple model can be trained much faster than complex attention networks such as GeoMAN without sacrificing accuracy. Based on the predicted values of soil water and stream flow, we predict the occurrence and severity of extreme hydrologic events such as droughts. We also demonstrate that extreme events can be predicted in geographical locations separate from locations observed during the training process. This spatially-inductive setting enables us to predict extreme events in other areas in the US and other parts of the world using our model trained with the Wabash Basin data.

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arXiv2021

Bootstrapping Your Own Positive Sample: Contrastive Learning With Electronic Health Record Data

Electronic Health Record (EHR) data has been of tremendous utility in Artificial Intelligence (AI) for healthcare such as predicting future clinical events. These tasks, however, often come with many challenges when using classical machine learning models due to a myriad of factors including class imbalance and data heterogeneity (i.e., the complex intra-class variances). To address some of these research gaps, this paper leverages the exciting contrastive learning framework and proposes a novel contrastive regularized clinical classification model. The contrastive loss is found to substantially augment EHR-based prediction: it effectively characterizes the similar/dissimilar patterns (by its "push-and-pull" form), meanwhile mitigating the highly skewed class distribution by learning more balanced feature spaces (as also echoed by recent findings). In particular, when naively exporting the contrastive learning to the EHR data, one hurdle is in generating positive samples, since EHR data is not as amendable to data augmentation as image data. To this end, we have introduced two unique positive sampling strategies specifically tailored for EHR data: a feature-based positive sampling that exploits the feature space neighborhood structure to reinforce the feature learning; and an attribute-based positive sampling that incorporates pre-generated patient similarity metrics to define the sample proximity. Both sampling approaches are designed with an awareness of unique high intra-class variance in EHR data. Our overall framework yields highly competitive experimental results in predicting the mortality risk on real-world COVID-19 EHR data with a total of 5,712 patients admitted to a large, urban health system. Specifically, our method reaches a high AUROC prediction score of 0.959, which outperforms other baselines and alternatives: cross-entropy(0.873) and focal loss(0.931).

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arXiv2020

Deep Learning with Heterogeneous Graph Embeddings for Mortality Prediction from Electronic Health Records

Computational prediction of in-hospital mortality in the setting of an intensive care unit can help clinical practitioners to guide care and make early decisions for interventions. As clinical data are complex and varied in their structure and components, continued innovation of modeling strategies is required to identify architectures that can best model outcomes. In this work, we train a Heterogeneous Graph Model (HGM) on Electronic Health Record data and use the resulting embedding vector as additional information added to a Convolutional Neural Network (CNN) model for predicting in-hospital mortality. We show that the additional information provided by including time as a vector in the embedding captures the relationships between medical concepts, lab tests, and diagnoses, which enhances predictive performance. We find that adding HGM to a CNN model increases the mortality prediction accuracy up to 4\%. This framework serves as a foundation for future experiments involving different EHR data types on important healthcare prediction tasks.

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arXiv2020

Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale

Sparse matrix-matrix multiplication (SpGEMM) is a widely used kernel in various graph, scientific computing and machine learning algorithms. In this paper, we consider SpGEMMs performed on hundreds of thousands of processors generating trillions of nonzeros in the output matrix. Distributed SpGEMM at this extreme scale faces two key challenges: (1) high communication cost and (2) inadequate memory to generate the output. We address these challenges with an integrated communication-avoiding and memory-constrained SpGEMM algorithm that scales to 262,144 cores (more than 1 million hardware threads) and can multiply sparse matrices of any size as long as inputs and a fraction of output fit in the aggregated memory. As we go from 16,384 cores to 262,144 cores on a Cray XC40 supercomputer, the new SpGEMM algorithm runs 10x faster when multiplying large-scale protein-similarity matrices.

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arXiv2020

Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices

Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene location. Performance and scalability of protein similarity searches have proven to be a bottleneck in many bioinformatics pipelines due to increases in cheap and abundant sequencing data. This work presents a new distributed-memory software, PASTIS. PASTIS relies on sparse matrix computations for efficient identification of possibly similar proteins. We use distributed sparse matrices for scalability and show that the sparse matrix infrastructure is a great fit for protein similarity searches when coupled with a fully-distributed dictionary of sequences that allows remote sequence requests to be fulfilled. Our algorithm incorporates the unique bias in amino acid sequence substitution in searches without altering the basic sparse matrix model, and in turn, achieves ideal scaling up to millions of protein sequences.

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arXiv2020

SubGraph2Vec: Highly-Vectorized Tree-likeSubgraph Counting

Subgraph counting aims to count occurrences of a template T in a given network G(V, E). It is a powerful graph analysis tool and has found real-world applications in diverse domains. Scaling subgraph counting problems is known to be memory bounded and computationally challenging with exponential complexity. Although scalable parallel algorithms are known for several graph problems such as Triangle Counting and PageRank, this is not common for counting complex subgraphs. Here we address this challenge and study connected acyclic graphs or trees. We propose a novel vectorized subgraph counting algorithm, named Subgraph2Vec, as well as both shared memory and distributed implementations: 1) reducing algorithmic complexity by minimizing neighbor traversal; 2) achieving a highly-vectorized implementation upon linear algebra kernels to significantly improve performance and hardware utilization. 3) Subgraph2Vec improves the overall performance over the state-of-the-art work by orders of magnitude and up to 660x on a single node. 4) Subgraph2Vec in distributed mode can scale up the template size to 20 and maintain good strong scalability. 5) enabling portability to both CPU and GPU.

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arXiv2020

Force2Vec: Parallel force-directed graph embedding

A graph embedding algorithm embeds a graph into a low-dimensional space such that the embedding preserves the inherent properties of the graph. While graph embedding is fundamentally related to graph visualization, prior work did not exploit this connection explicitly. We develop Force2Vec that uses force-directed graph layout models in a graph embedding setting with an aim to excel in both machine learning (ML) and visualization tasks. We make Force2Vec highly parallel by mapping its core computations to linear algebra and utilizing multiple levels of parallelism available in modern processors. The resultant algorithm is an order of magnitude faster than existing methods (43x faster than DeepWalk, on average) and can generate embeddings from graphs with billions of edges in a few hours. In comparison to existing methods, Force2Vec is better in graph visualization and performs comparably or better in ML tasks such as link prediction, node classification, and clustering. Source code is available at https://github.com/HipGraph/Force2Vec.

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arXiv2020

A Distributed-Memory Algorithm for Computing a Heavy-Weight Perfect Matching on Bipartite Graphs

We design and implement an efficient parallel algorithm for finding a perfect matching in a weighted bipartite graph such that weights on the edges of the matching are large. This problem differs from the maximum weight matching problem, for which scalable approximation algorithms are known. It is primarily motivated by finding good pivots in scalable sparse direct solvers before factorization. Due to the lack of scalable alternatives, distributed solvers use sequential implementations of maximum weight perfect matching algorithms, such as those available in MC64. To overcome this limitation, we propose a fully parallel distributed memory algorithm that first generates a perfect matching and then iteratively improves the weight of the perfect matching by searching for weight-increasing cycles of length four in parallel. For most practical problems the weights of the perfect matchings generated by our algorithm are very close to the optimum. An efficient implementation of the algorithm scales up to 256 nodes (17,408 cores) on a Cray XC40 supercomputer and can solve instances that are too large to be handled by a single node using the sequential algorithm.

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arXiv2020

Attribute2vec: Deep Network Embedding Through Multi-Filtering GCN

We present a multi-filtering Graph Convolution Neural Network (GCN) framework for network embedding task. It uses multiple local GCN filters to do feature extraction in every propagation layer. We show this approach could capture different important aspects of node features against the existing attribute embedding based method. We also show that with multi-filtering GCN approach, we can achieve significant improvement against baseline methods when training data is limited. We also perform many empirical experiments and demonstrate the benefit of using multiple filters against single filter as well as most current existing network embedding methods for both the link prediction and node classification tasks.

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arXiv2020

Bandwidth-Optimized Parallel Algorithms for Sparse Matrix-Matrix Multiplication using Propagation Blocking

Sparse matrix-matrix multiplication (SpGEMM) is a widely used kernel in various graph, scientific computing and machine learning algorithms. It is well known that SpGEMM is a memory-bound operation, and its peak performance is expected to be bound by the memory bandwidth. Yet, existing algorithms fail to saturate the memory bandwidth, resulting in suboptimal performance under the Roofline model. In this paper we characterize existing SpGEMM algorithms based on their memory access patterns and develop practical lower and upper bounds for SpGEMM performance. We then develop an SpGEMM algorithm based on outer product matrix multiplication. The newly developed algorithm called PB-SpGEMM saturates memory bandwidth by using the propagation blocking technique and by performing in-cache sorting and merging. For many practical matrices, PB-SpGEMM runs 20%-50% faster than the state-of-the-art heap and hash SpGEMM algorithms on modern multicore processors. Most importantly, PB-SpGEMM attains performance predicted by the Roofline model, and its performance remains stable with respect to matrix size and sparsity.

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arXiv2020

Optimizing High Performance Markov Clustering for Pre-Exascale Architectures

HipMCL is a high-performance distributed memory implementation of the popular Markov Cluster Algorithm (MCL) and can cluster large-scale networks within hours using a few thousand CPU-equipped nodes. It relies on sparse matrix computations and heavily makes use of the sparse matrix-sparse matrix multiplication kernel (SpGEMM). The existing parallel algorithms in HipMCL are not scalable to Exascale architectures, both due to their communication costs dominating the runtime at large concurrencies and also due to their inability to take advantage of accelerators that are increasingly popular. In this work, we systematically remove scalability and performance bottlenecks of HipMCL. We enable GPUs by performing the expensive expansion phase of the MCL algorithm on GPU. We propose a CPU-GPU joint distributed SpGEMM algorithm called pipelined Sparse SUMMA and integrate a probabilistic memory requirement estimator that is fast and accurate. We develop a new merging algorithm for the incremental processing of partial results produced by the GPUs, which improves the overlap efficiency and the peak memory usage. We also integrate a recent and faster algorithm for performing SpGEMM on CPUs. We validate our new algorithms and optimizations with extensive evaluations. With the enabling of the GPUs and integration of new algorithms, HipMCL is up to 12.4x faster, being able to cluster a network with 70 million proteins and 68 billion connections just under 15 minutes using 1024 nodes of ORNL's Summit supercomputer.

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arXiv2020

BatchLayout: A Batch-Parallel Force-Directed Graph Layout Algorithm in Shared Memory

Force-directed algorithms are widely used to generate aesthetically pleasing layouts of graphs or networks arisen in many scientific disciplines. To visualize large-scale graphs, several parallel algorithms have been discussed in the literature. However, existing parallel algorithms do not utilize memory hierarchy efficiently and often offer limited parallelism. This paper addresses these limitations with BatchLayout, an algorithm that groups vertices into minibatches and processes them in parallel. BatchLayout also employs cache blocking techniques to utilize memory hierarchy efficiently. More parallelism and improved memory accesses coupled with force approximating techniques, better initialization, and optimized learning rate make BatchLayout significantly faster than other state-of-the-art algorithms such as ForceAtlas2 and OpenOrd. The visualization quality of layouts from BatchLayout is comparable or better than similar visualization tools. All of our source code, links to datasets, results and log files are available at https://github.com/khaled-rahman/BatchLayout.

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arXiv2020

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing.

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