19 citations · 54 across the 9 of their papers we have counts for
11 papers
Cheaper by the Batch: Shared Traversal for Genotype Graph Editing
Aaron Li, Yifan Li, Drew DeHaas +1
Updating a graph by inserting or replacing nodes while preserving semantics and reusing existing structure is a recurring computational problem. In population genetics, this proble…
Space Efficient Sequence Alignment for SRAM-Based Computing: X-Drop on the Graphcore IPU
Luk Burchard, Max Xiaohang Zhao, Johannes Langguth +2
Dedicated accelerator hardware has become essential for processing AI-based workloads, leading to the rise of novel accelerator architectures. Furthermore, fundamental differences…
Extreme-scale many-against-many protein similarity search
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi +7
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncoverin…
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
Giulia Guidi, Gabriel Raulet, Daniel Rokhsar +3
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomi…
BuDDI: A Declarative Bloom Language for CALM Programming
Rolando Garcia, Giulia Guidi
Coordination protocols help programmers of distributed systems reason about the effects of transactions on the state of the system, but they're not cheap. Coordination protocols ma…
10 Years Later: Cloud Computing is Closing the Performance Gap
Giulia Guidi, Marquita Ellis, Aydin Buluc +2
Can cloud computing infrastructures provide HPC-competitive performance for scientific applications broadly? Despite prolific related literature, this question remains open. Answer…