9 citations · 13 across the 11 of their papers we have counts for
13 papers
HDLouvain: High-Throughput Incremental Clustering for Hyperdimensional Data
Beenish Gul, Mahbod Afarin, Farhat Ahmed +4
Modern shotgun proteomics generates tens of thousands of tandem mass spectra per hour, producing hundreds of gigabytes of data that strain conventional clustering pipelines. DBSCAN…
Multi-bit Ferroelectric-NAND for High-throughput Massive Database Search
Prasanna Venkatesan, Tanvir H. Pantha, Po-Kai Hsu +28
The growing demand for large-scale database search in data-intensive applications, ranging from proteomics to autonomous systems, has exposed fundamental limitations in von Neumann…
Cross-Domain Acceleration of Open Modification Search: From Commodity Platforms to Emerging Memory and Storage Devices
Sumukh Pinge, Chang Eun Song, Po-Kai Hsu +10
Open modification search (OMS) in mass spectrometry (MS) is a data-intensive workload whose performance is dominantly limited by reference data movement rather than computation. Pr…
D-NOVA: In-Storage Retrieval Accelerator via Dual-Bound 3D NAND-Optimized Similarity Search with Vector Adaptation
Chang Eun Song, Sumukh Pinge, Tianqi Zhang +3
Retrieval-Augmented Generation (RAG) enhances the factual grounding of large language model (LLM) inference by retrieving relevant information from external knowledge bases. Howeve…
HDDB: Efficient In-Storage SQL Database Search Using Hyperdimensional Computing on Ferroelectric NAND Flash
Quanling Zhao, Yanru Chen, Runyang Tian +6
Hyperdimensional Computing (HDC) encodes information and data into high-dimensional distributed vectors that can be manipulated using simple bitwise operations and similarity searc…
Cross-Layer Co-Designed In-Memory Hyperdimensional Computing Accelerator for Proteomics at the Edge
Md Mizanur Rahaman Nayan, Zheyu Li, Flavio Ponzina +4
Database (DB) search and clustering are fundamental to data-analytics workloads such as mass spectrometry-driven proteomics. Current workflows rely on resource-intensive search and…
FeNOMS: Enhancing Open Modification Spectral Library Search with In-Storage Processing on Ferroelectric NAND (FeNAND) Flash
Sumukh Pinge, Ashkan Moradifirouzabadi, Keming Fan +29
The rapid expansion of mass spectrometry (MS) data, now exceeding hundreds of terabytes, poses significant challenges for efficient, large-scale library search - a critical compone…
HPVM-HDC: A Heterogeneous Programming System for Accelerating Hyperdimensional Computing
Russel Arbore, Xavier Routh, Abdul Rafae Noor +7
Hyperdimensional Computing (HDC), a technique inspired by cognitive models of computation, has been proposed as an efficient and robust alternative basis for machine learning. HDC…
RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing
Sumukh Pinge, Weihong Xu, Wout Bittremieux +3
Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in difficultie…
Efficient Open Modification Spectral Library Searching in High-Dimensional Space with Multi-Level-Cell Memory
Keming Fan, Wei-Chen Chen, Sumukh Pinge +2
Open Modification Search (OMS) is a promising algorithm for mass spectrometry analysis that enables the discovery of modified peptides. However, OMS encounters challenges as it exp…
Proxima: Near-storage Acceleration for Graph-based Approximate Nearest Neighbor Search in 3D NAND
Weihong Xu, Junwei Chen, Po-Kai Hsu +5
Approximate nearest neighbor search (ANNS) plays an indispensable role in a wide variety of applications, including recommendation systems, information retrieval, and semantic sear…
SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering
Sumukh Pinge, Weihong Xu, Jaeyoung Kang +4
Mass spectrometry-based proteomics is a key enabler for personalized healthcare, providing a deep dive into the complex protein compositions of biological systems. This technology…
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations
Derek Jones, Jonathan E. Allen, Xiaohua Zhang +5
Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional m…