HPCA 2026
Sat 31 January - Wed 4 February 2026 Sydney, Australia
co-located with HPCA/CGO/PPoPP/CC 2026
Tue 3 Feb 2026 17:55 - 18:15 at Cronulla - Genomics and Bioinformatics Chair(s): Abdulaziz Tabbakh

The rapid advancement in genomic sequencing technologies has resulted in an explosion of data, creating substantial computational bottlenecks in DNA analysis workloads. Applications such as DNA classification are particularly impacted due to their reliance on intensive, large-scale pattern matching. Existing hardware accelerator and software solutions are increasingly unable to manage the scale and energy demands of these datasets, highlighting the need for architectures that can perform faster and more efficient pattern matching. To address these challenges, we propose NP-CAM: a data-optimized, CAM-based accelerator designed for parallel and energy-efficient DNA classification. NP-CAM harnesses a network-on-chip to implement a novel optimized indexing and CAM partitioning scheme that reduces the active search space, allowing significant scalability. We demonstrate results for NP-CAM on commodity 10T binary CAM cell designs. Our experimental evaluations show that NP-CAM achieves a simultaneous $65\times$ improvement in sequence throughput and an over $173\times$ improvement in energy efficiency over state-of-the-art hardware solutions on existing small viral workloads. We go on to demonstrate feasibility for larger bacterial and fungal workloads, enabling scalable DNA classification in the era of large-scale genomic data.

Tue 3 Feb

Displayed time zone: Hobart change

17:15 - 18:15
Genomics and BioinformaticsMain Conference at Cronulla
Chair(s): Abdulaziz Tabbakh King Fahd University of Petroleum and Minerals
17:15
20m
Talk
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
Main Conference
Julien Eudine Huawei Technologies Switzerland AG, Chu Li Huawei Zurich Research Center, Zhuo Cheng Huawei Zurich Research Center, Renzo Andri Huawei Technologies Switzerland AG, Onur Mutlu ETH Zurich, Can Firtina ETH Zurich and UMD, Mohammad Sadrosadati ETH Zürich, Nika Mansouri Ghiasi ETH Zurich, Konstantina Koliogeorgi ETH Zurich, Anirban Nag Huawei Zurich Research Center, Arash Tavakkol Huawei Zurich Research Center, Haiyu Mao King's College London, Shai Bergman Huawei Zurich Research Center, Ji Zhang Huawei Zurich Research Center
17:35
20m
Talk
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis
Main Conference
Nika Mansouri Ghiasi ETH Zurich, Talu Güloglu ETH Zurich, Harun Mustafa ETH Zurich and Johns Hopkins University, Can Firtina ETH Zurich and UMD, Konstantina Koliogeorgi ETH Zurich, Konstantinos Kanellopoulos ETH Zurich, Haiyu Mao King's College London, Rakesh Nadig ETH Zurich, Mohammad Sadrosadati ETH Zürich, Jisung Park POSTECH (Pohang University of Science and Technology), Onur Mutlu ETH Zurich
17:55
20m
Talk
NP-CAM: Efficient and Scalable DNA Classification using a NoC-Partitioned CAM Architecture
Main Conference
Benjamin F. Morris III Duke University, Tergel Molom-Ochir Duke University, Changchun Zhou Duke University, Yiran Chen Duke University, Alex Jones Syracuse University, Hai "Helen" Li Duke University