Research
Publications
Journal and conference papers, chapters, reports, and preprints.
153 publications
2026
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Fast Algorithms for Scheduling Many-body Correlation Functions on Accelerators
IEEE International Parallel and Distributed Processing Symposium (IPDPS), 307–320
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metagRoot: a comprehensive database of protein families associated with plant root microbiomes
Nucleic Acids Research 54 (D1), D1733–D1742; first published online September 2025
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Tackling Parallelization Challenges of Randomized Preconditioners with Dependency Tracking
SC26 — forthcoming
2025
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A Partition Function Algorithm to Evaluate Inferred Subclonal Structures in Single-Cell Sequencing Data
Research in Computational Molecular Biology (RECOMB), 409–413
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An Efficient Sparse Kernel Generator for O(3)-Equivariant Deep Networks
SIAM Conference on Applied and Computational Discrete Algorithms (ACDA)
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Distributed-Memory Parallel Algorithms for Fixed-Radius Near Neighbor Graph Construction
arXiv:2510.14147
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DyG-DPCD: A Distributed Parallel Community Detection Algorithm for Large-Scale Dynamic Graphs
International Journal of Parallel Programming 53 (1), article 4
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Improving SpGEMM Performance Through Matrix Reordering and Cluster-wise Computation
International Conference for High Performance Computing, Networking, Storage and Analysis (SC25)
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Parallelizing the Approximate Minimum Degree Ordering Algorithm: Strategies and Evaluation
arXiv:2504.17097
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Performance-Portable Symbolic Factorization through Common Graph Operations
SC Workshops, 804–812
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Scaling Graph Neural Networks for Particle Track Reconstruction
GrAPL, IEEE IPDPS Workshops, 772–776
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Sempervirens: A Fast Reconstruction Algorithm for Noisy and Incomplete Binary Matrix Representations of Trees
INFORMS Journal on Computing
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The Ubiquitous Sparse Matrix-Matrix Products
arXiv:2508.04077
2024
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A sparsity-aware distributed-memory algorithm for sparse-sparse matrix multiplication
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'24)
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Accelerating Multi-GPU Embedding Retrieval with PGAS-Style Communication for Deep Learning Recommendation Systems
SC Workshops, 1262–1273
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Anonymized Network Sensing Graph Challenge
IEEE High Performance Extreme Computing Conference (HPEC)
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CPMA: An Efficient Batch-Parallel Compressed Set Without Pointers
ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPOPP)
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Distributed Matrix-Based Sampling for Graph Neural Network Training
Proceedings of Machine Learning and Systems 6 (MLSys 2024)
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Distributed-Memory Randomized Algorithms for Sparse Tensor CP Decomposition
SPAA '24: Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures
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Exabiome: Advancing Microbial Science through Exascale Computing
Computing in Science & Engineering
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Fast multiplication of random dense matrices with fixed sparse matrices
International Parallel and Distributed Processing Symposium (IPDPS)
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GenomeFace: a deep learning-based metagenome binner trained on 43,000 microbial genomes
bioRxiv
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Interface for Sparse Linear Algebra Operations
arXiv:2411.13259
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RDMA-Based Algorithms for Sparse Matrix Multiplication on GPUs
ICS '24: Proceedings of the 38th ACM International Conference on Supercomputing, 225–235
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Sparsity-aware communication for distributed graph neural network training
Proceedings of the 53rd International Conference on Parallel Processing (ICPP), 117–126
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What Is Normal? A Big Data Observational Science Model of Anonymized Internet Traffic
IEEE High Performance Extreme Computing Conference (HPEC)
2023
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Exploring temporal community evolution: algorithmic approaches and parallel optimization for dynamic community detection
Applied Network Science 8 (1), 64
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Fast Exact Leverage Score Sampling from Khatri-Rao Products with Applications to Tensor Decomposition
Thirty-seventh Conference on Neural Information Processing Systems (NeurIPS)
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Optimizing Search Layouts in Packed Memory Arrays
Proceedings of the Symposium on Algorithm Engineering and Experiments (ALENEX), 148–161
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Space Efficient Sequence Alignment for SRAM-Based Computing: X-Drop on the Graphcore IPU
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
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Unraveling the functional dark matter through global metagenomics
Nature 622 (7983), 594–602
2022
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Atos: A task-parallel GPU scheduler for graph analytics
Proceedings of the 51st International Conference on Parallel Processing, 1–11
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Critical Assessment of Metagenome Interpretation: the second round of challenges
Nature Methods 19 (4), 429–440
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Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
Proceedings of the 51st International Conference on Parallel Processing, 1–11
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Distributed-Memory Sparse Kernels for Machine Learning
International Parallel and Distributed Processing Symposium (IPDPS), 47–58
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Extreme-scale many-against-many protein similarity search
International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 1–12
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Fast intratumor heterogeneity inference from single-cell sequencing data
Nature Computational Science 2 (9), 577–583
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GraphBLAS on the Edge: Anonymized High Performance Streaming of Network Traffic
2022 IEEE High Performance Extreme Computing Conference (HPEC), 1–8
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GraphBLAS: C++ Iterators for Sparse Matrices
International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 238–246
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GraphBLAST: A high-performance linear algebra-based graph framework on the GPU
ACM Transactions on Mathematical Software 48 (1), 1–51
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Large Scale Enrichment and Statistical Cyber Characterization of Network Traffic
High Performance Extreme Computing Conference (HPEC), 1–7
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Parallel Algorithms for Adding a Collection of Sparse Matrices
International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 285–294
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Parallel algorithms for masked sparse matrix-matrix products
Proceedings of the 51st International Conference on Parallel Processing, 1–11
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POSTER: Parallel Algorithms for Masked Sparse Matrix-Matrix Products
ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP), 453–454
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Scalable irregular parallelism with GPUs: getting CPUs out of the way
International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 708–723
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Sparse Matrices Powering Three Pillars of Science: Simulation, Data, and Learning
Proceedings of the International Symposium on Symbolic and Algebraic Computation, 31–31
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Temporal Correlation of Internet Observatories and Outposts
International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 247–254
2021
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10 years later: Cloud computing is closing the performance gap
Companion of the ACM/SPEC International Conference on Performance Engineering, 41–48
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Accelerating large scale de novo metagenome assembly using GPUs
International Conference for High Performance Computing, Networking, Storage and Analysis
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Asynchrony versus bulk-synchrony for a generalized N-body problem from genomics
Proceedings of the 26th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPOPP), 465–466
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BELLA: Berkeley efficient long-read to long-read aligner and overlapper
SIAM Conference on Applied and Computational Discrete Algorithms (ACDA21), 123–134
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Combinatorial BLAS 2.0: Scaling combinatorial algorithms on distributed-memory systems
IEEE Transactions on Parallel and Distributed Systems 33 (4), 989–1001
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Communication-Avoiding and Memory-Constrained Sparse Matrix-Matrix Multiplication at Extreme Scale
International Parallel and Distributed Processing Symposium (IPDPS), 90–100
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Distributed-Memory k-mer Counting on GPUs
International Parallel and Distributed Processing Symposium (IPDPS), 527–536
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Distributed-memory parallel algorithms for sparse times tall-skinny-dense matrix multiplication
Proceedings of the ACM International Conference on Supercomputing (ICS), 431–442
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EXAGRAPH: Graph and Combinatorial Methods for Enabling Exascale Applications
International Journal of High Performance Computing Applications (IJHPCA) 35 (6), 553–571
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Introduction to GraphBLAS 2.0
International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 253–262
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Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
International Parallel and Distributed Processing Symposium (IPDPS), 517–526
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Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity
bioRxiv
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Randomized algorithms for scientific computing (RASC)
DOE report: Randomized Algorithms for Scientific Computing (RASC)
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Scaling Generalized N-Body Problems, A Case Study from Genomics
50th International Conference on Parallel Processing (ICPP)
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Spatial temporal analysis of 40,000,000,000,000 internet darkspace packets
2021 IEEE High Performance Extreme Computing Conference (HPEC), 1–8
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Terrace: A Hierarchical Graph Container for Skewed Dynamic Graphs
Proceedings of the 2021 International Conference on Management of Data (SIGMOD), 1372–1385
2020
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A Distributed-Memory Algorithm for Computing a Heavy-Weight Perfect Matching on Bipartite Graphs
SIAM Journal on Scientific Computing 42 (4), C143–C168
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A High-Throughput Solver for Marginalized Graph Kernels on GPU
Proceedings of the IPDPS
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A Roadmap for the GraphBLAS C++ API
GrAPL: Workshop on Graphs, Architectures, Programming, and Learning (IPDPSW)
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ADEPT: a domain independent sequence alignment strategy for gpu architectures
BMC bioinformatics 21 (1), 1–29
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Considerations for a Distributed GraphBLAS API
GrAPL: Workshop on Graphs, Architectures, Programming, and Learning (IPDPSW)
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Distributed Many-to-Many Protein Sequence Alignment Using Sparse Matrices
International Conference for High Performance Computing, Networking, Storage and Analysis
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GPU accelerated partial order multiple sequence alignment for long reads self-correction
IEEE International Workshop on High Performance Computational Biology (HiCOMB)
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LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment
Proceedings of the IPDPS
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Optimizing High Performance Markov Clustering for Pre-Exascale Architectures
Proceedings of the IPDPS
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Parallel algorithms for finding connected components using linear algebra
Journal of Parallel and Distributed Computing
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PersGNN: Applying topological data analysis and geometric deep learning to structure-based protein function prediction
arXiv preprint arXiv:2010.16027
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Reducing Communication in Graph Neural Network Training
International Conference for High Performance Computing, Networking, Storage and Analysis
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Terabase-scale metagenome coassembly with MetaHipMer
Scientific reports
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The parallelism motifs of genomic data analysis
Philosophical Transactions of the Royal Society A 378 (2166), 20190394
2019
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BCL: A Cross-Platform Distributed Data Structures Library
48th International Conference on Parallel Processing (ICPP)
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diBELLA: Distributed Long Read to Long Read Alignment
48th International Conference on Parallel Processing (ICPP)
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Graph Coloring on the GPU
GrAPL: Workshop on Graphs, Architectures, Programming, and Learning (IPDPSW)
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H-INDEX: Hash-Indexing for Parallel Triangle Counting on GPUs
IEEE High Performance Extreme Computing Conference (HPEC), 1–7
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LACC: A Linear-Algebraic Algorithm for Finding Connected Components in Distributed Memory
Proceedings of the IPDPS
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LAGraph: A Community Effort to Collect Graph Algorithms Built on Top of the GraphBLAS
GrAPL: Workshop on Graphs, Architectures, Programming, and Learning (IPDPSW)
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Performance optimization, modeling and analysis of sparse matrix-matrix products on multi-core and many-core processors
Parallel Computing 90, 102545
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RDMA vs. RPC for Implementing Distributed Data Structures
IEEE/ACM 9th Workshop on Irregular Applications: Architectures and Algorithms (IA3)
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The GraphBLAS C API Specification, version 1.3.0
The GraphBLAS Signatures Subgroup, September 2019
2018
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Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation
The 21st International Conference on Artificial Intelligence and Statistics (AISTATS)
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Design Principles for Sparse Matrix Multiplication on the GPU
24th International European Conference on Parallel and Distributed Computing (Euro-Par)
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Extreme scale de novo metagenome assembly
Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC), 10
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High-performance sparse matrix-matrix products on Intel KNL and multicore architectures
47th International Conference on Parallel Processing Workshops (ICPPW)
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HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks
Nucleic Acids Research (NAR)
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Implementing Push-Pull Efficiently in GraphBLAS
47th International Conference on Parallel Processing (ICPP)
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Integrated Model, Batch, and Domain Parallelism in Training Neural Networks
SPAA'18: 30th ACM Symposium on Parallelism in Algorithms and Architectures
2017
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A High Performance Block Eigensolver for Nuclear Configuration Interaction Calculations
IEEE Transactions on Parallel and Distributed Systems (TPDS))
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A work-efficient parallel sparse matrix-sparse vector multiplication algorithm
Proceedings of the IPDPS
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Communication Analysis of Hybrid Model and Data Parallelism in Training Neural Networks
NIPS Workshop on Deep Learning at Supercomputer Scale
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Computing Maximum Cardinality Matchings in Parallel on Bipartite Graphs via Tree-Grafting
IEEE Transactions on Parallel and Distributed Systems (TPDS)) 28 (1), 44–59
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Design of the GraphBLAS API for C
IEEE Workshop on Graph Algorithm Building Blocks, IPDPSW
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Distributed-Memory Breadth-First Search on Massive Graphs
arXiv:1705.04590
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Extreme-Scale De Novo Genome Assembly
To appear as a chapter in Exascale Scientific Applications: Programming Approaches for Scalability, Performance, and Portability (CRC Press)
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GraphBLAS C API: Ideas for future versions of the specification
IEEE High Performance Extreme Computing Conference (HPEC)
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MerBench: PGAS Benchmarks for High Performance Genome Assembly
Proceedings of the Second Annual PGAS Applications Workshop, 5
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Performance Characterization of De Novo Genome Assembly on Leading Parallel Systems
Europar - International European Conference on Parallel and Distributed Computing
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Scaling Deep Learning on GPU and Knights Landing Clusters
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'17)
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The Reverse Cuthill-McKee Algorithm in Distributed-Memory
Proceedings of the IPDPS
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Towards a GraphBLAS Library in Chapel
Intl. Parallel & Distributed Processing Symposium Workshops (IPDPSW)
2016
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A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs
Parallel Computing
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Communication-Avoiding Parallel Sparse-Dense Matrix-Matrix Multiplication
Proceedings of the IPDPS
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Distributed-Memory Algorithms for Maximum Cardinality Matching in Bipartite Graphs
Proceedings of the IPDPS
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Exploiting Multiple Levels of Parallelism in Sparse Matrix-Matrix Multiplication
SIAM Journal on Scientific Computing (SISC) 38 (6), C624-C651
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LiRa: A New Likelihood-Based Similarity Score for Collaborative Filtering
arXiv preprint arXiv:1608.08646
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Mathematical Foundations of the GraphBLAS
IEEE High Performance Extreme Computing (HPEC)
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Recent Advances in Graph Partitioning
Algorithm Engineering - Selected Results and Surveys 9220
2015
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A Parallel Tree Grafting Algorithm for Maximum Cardinality Matching in Bipartite Graphs
Proceedings of the IPDPS
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A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Genome Biology 16 (26)
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Distributed-Memory Algorithms for Maximal Cardinality Matching using Matrix Algebra
IEEE International Conference on Cluster Computing (CLUSTER)
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Efficient Data Reduction for Large-Scale Genetic Mapping
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB)
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Graphs, Matrices, and the GraphBLAS: Seven Good Reasons
The International Conference on Computational Science (ICCS)
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HipMer: An Extreme-Scale De Novo Genome Assembler
International Conference for High Performance Computing, Networking, Storage and Analysis (SC'15)
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merAligner: A Fully Parallel Sequence Aligner
Proceedings of the IPDPS
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Parallel Processing of Filtered Queries in Attributed Semantic Graphs
Journal of Parallel and Distributed Computing (JPDC)) 79-80, 115-131
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Parallel Triangle Counting and Enumeration using Matrix Algebra
Proceedings of the IPDPSW, Workshop on Graph Algorithm Building Blocks (GABB), 804 - 811
2014
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Computing Shortest Paths Using Sparse Gaussian Elimination
SIAM Workshop on Network Science (NS14)
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Efficient and Accurate Clustering for Large-Scale Genetic Mapping
The IEEE International Conference on Bioinformatics and Biomedicine (BIBM'14)
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Optimizing Sparse Matrix-Multiple Vectors Multiplication for Nuclear Configuration Interaction Calculations
Proceedings of the IPDPS
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Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'14)
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The Graph BLAS effort and its implications for Exascale
SIAM Workshop on Exascale Applied Mathematics Challenges and Opportunities (EX14)
2013
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Communication Optimal Parallel Multiplication of Sparse Random Matrices
SPAA 2013: The 25th ACM Symposium on Parallelism in Algorithms and Architectures
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Distributed Memory Breadth-First Search Revisited: Enabling Bottom-Up Search
Workshop on Multithreaded Architectures and Applications (MTAAP), in conjunction with IPDPS
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Graph Partitioning for Scalable Distributed Graph Computations
Graph Partitioning and Graph Clustering (Proc. 10th DIMACS Implementation Challenge) 588, 83-101
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High-Productivity and High-Performance Analysis of Filtered Semantic Graphs
Proceedings of the IPDPS
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Minimizing communication in all-pairs shortest paths
Proceedings of the IPDPS
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Standards for Graph Algorithm Primitives
High Performance Extreme Computing Conference (HPEC '13)
2012
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A Flexible Open-Source Toolbox for Scalable Complex Graph Analysis
SIAM Conference on Data Mining (SDM)
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Can Network-Offload based Non-Blocking Neighborhood MPI Collectives Improve Communication Overheads of Irregular Graph Algorithms?
IEEE International Conference on Cluster Computing Workshops, 222–230
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High-Performance Analysis of Filtered Semantic Graphs
International Conference on Parallel Architectures and Compilation Techniques (PACT)
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Parallel Sparse Matrix-Matrix Multiplication and Indexing: Implementation and Experiments
SIAM Journal of Scientific Computing (SISC) 34 (4), 170 - 191
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Scalable Complex Graph Analysis with the Knowledge Discovery Toolbox
ICASSP, Special session on “Big Data”
2011
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Enabling Non-Graph-Expert Use of Very-Large-Scale Graph Analysis
SIAM Workshop on Combinatorial Scientific Computing (CSC)
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Implementing Sparse Matrices for Graph Algorithms
Graph Algorithms in the Language of Linear Algebra
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New Ideas in Sparse Matrix-Matrix Multiplication
Graph Algorithms in the Language of Linear Algebra
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Parallel Breadth-First Search on Distributed Memory Systems
International Conference for High Performance Computing, Networking, Storage and Analysis (SC'11)
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Parallel Sparse Matrix Indexing and Assignment
SIAM Workshop on Combinatorial Scientific Computing (CSC)
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Reduced-Bandwidth Multithreaded Algorithms for Sparse Matrix-Vector Multiplication
Proc. IPDPS
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The Combinatorial BLAS: Design, Implementation, and Applications
The International Journal of High Performance Computing Applications 25 (4), 496 - 509
2010
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Highly Parallel Sparse Matrix-Matrix Multiplication
UCSB CS Department (UCSB-CS-2010-10)
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Linear Algebraic Primitives for Parallel Computing on Large Graphs
University of California
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Solving path problems on the GPU
Parallel Computing 36 (5-6), 241 - 253
2009
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Parallel Primitives for Computation with Large Graphs
TCPP Ph.D. Forum, IEEE IPDPS
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Parallel Sparse Matrix-Vector and Matrix-Transpose-Vector Multiplication Using Compressed Sparse Blocks
Proc. SPAA
2008
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Challenges and Advances in Parallel Sparse Matrix-Matrix Multiplication
The 37th International Conference on Parallel Processing (ICPP'08), 503-510
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On the Representation and Multiplication of Hypersparse Matrices
Proc. IPDPS
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Towards Scalable Parallel Hypergraph Partitioning
CSRI Summer Proceedings
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