5 papers
GRAINS: Storage-Aware Algorithm-Architecture Co-Design Enabling High-Performance and Low-Cost Graph-Based Genome Analysis
Nika Mansouri Ghiasi, Harun Mustafa, Talu Güloglu +8
Graph-based representations of genome sequences have emerged as a powerful approach for representing massive genomic databases in an expressive and efficient way. Despite their ben…
ASTRA-sim 3.0: Next-Level Distributed Machine Learning Simulations via High-Fidelity GPU and Infrastructure Modeling
William Won, Jinsun Yoo, Tuan Ta +16
Distributed machine learning (ML) is a key paradigm for today's large-scale artificial intelligence applications. As model inference arises as an important use case, faithful model…
Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
Can Firtina, Maximilian Mordig, Harun Mustafa +7
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling).…
No Generation without Representation: Efficient Causal Protein Language Models Enable Zero-Shot Fitness Estimation
Furkan Eris
Protein language models (PLMs) face a fundamental divide: masked language models (MLMs) excel at fitness prediction while causal models enable generation, forcing practitioners to…
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
Furkan Eris, Ulysse McConnell, Can Firtina +1
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to mil…