4 papers
Compiling Bioinformatics Recurrences
Bala Vinaithirthan, Shiv Sundram, Sneha Goenka +1
Many bioinformatics algorithms, such as sequence alignment and structure prediction, can be expressed as recurrence equations over a dynamic programming matrix. Efficient implement…
Dependencies and Dataflow in Seed-Filter-Extend Pipelines
Shiv Sundram
Comparing genomes is critical for discovering mutations, tracking evolutionary lineages, and advancing cross-species genomics. Fundamentally, this reduces to an O(n^2) string-match…
Cyclotron: Compilation of Recurrences to Distributed and Systolic Architectures
Shiv Sundram, Akhilesh Balasingam, Nathan Zhang +2
We present Cyclotron, a framework and compiler for using recurrence equations to express streaming dataflow algorithms, which then get portably compiled to distributed topologies o…
Composing Distributed Computations Through Task and Kernel Fusion
Rohan Yadav, Shiv Sundram, Wonchan Lee +4
We introduce Diffuse, a system that dynamically performs task and kernel fusion in distributed, task-based runtime systems. The key component of Diffuse is an intermediate represen…