Engineering topics

Neff, Reece W.

Publications and source records attributed to Neff, Reece W..

5 records

DOE OSTI2026

Graph Identification of Proteins in Tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins

Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have difficulty interpreting density associated with small proteins/complexes. To explore alternate approaches for identifying proteins in cryo-ET data we pursued a Graph Network and topologically invariant approach. Here, we report on a fast algorithm that classifies particles by searching for nuances of evolutionarily conversed motifs and the geometrical characteristics of protein structure. GRIP-Tomo 2.0 is a machine-learning pipeline that extracts interpretable topological features of protein structures within noisy experimental backgrounds. Compared to version 1.0, the new pipeline includes three upgrades that significantly improve performance including synthetic tomogram generation simulating realistic noise, graph-based persistent feature extraction as protein fingerprints, and high-performance computing acceleration. GRIP-Tomo 2.0 achieves over 90% accuracy in classifying between proteins and noise using both real and synthetic datasets which represents a foundational step toward advancing cryo-ET workflows and empowering automated visual proteomics.

Li, Chengxuan↗

DOE OSTI2024

Picasso: Memory-Efficient Graph Coloring Using Palettes With Applications in Quantum Computing

A coloring of a graph is an assignment of colors to vertices such that no two neighboring vertices have the same color. The need for memory-efficient coloring algorithms is motivated by their application in computing clique partitions of graphs arising in quantum computations where the objective is to map a large set of Pauli strings into a compact set of unitaries. We present Picasso, a randomized memory-efficient iterative parallel graph coloring algorithm with theoretical sublinear space guarantees under practical assumptions. The parameters of our algorithm provide a trade-off between coloring quality and resource consumption. To assist the user, we also propose a machine learning model to predict the coloring algorithm’s parameters considering these trade-offs. We provide a sequential and a parallel implementation of the proposed algorithm. We perform an experimental evaluation on a 64-core AMD CPU equipped with 512 GB of memory and an Nvidia A100 GPU with 40GB of memory. For a small dataset where existing coloring algorithms can be executed within the 512 GB memory budget, we show up to 68× memory savings. On massive datasets we demonstrate that GPU-accelerated Picasso can process inputs with 49.5× more Pauli strings (vertex set in our graph) and 2,478× more edges than state-of-the-art parallel approaches.

artificial intelligence, quantum computing↗

DOE OSTI2024

FuseIM: Fusing Probabilistic Traversals for Influence Maximization on Exascale Systems

Probabilistic breadth-first traversals (BPTs) are used in many network science and graph machine learning applications. In this paper, we are motivated by the application of BPTs in stochastic diffusion-based graph problems such as influence maximization. These applications heavily rely on BPTs to implement a Monte-Carlo sampling step for their approximations. Given the large sampling complexity, stochasticity of the diffusion process, and the inherent irregularity in real-world graph topologies, efficiently parallelizing these BPTs remains significantly challenging. In this paper, we present a new algorithm to fuse massive number of concurrently executing BPTs with random starts on the input graph. Our algorithm is designed to fuse BPTs by combining separate traversals into a unified frontier on distributed multi-GPU systems. To show the general applicability of the fused BPT technique, we have incorporated it into two state-of-the-art influence maximization parallel implementations (gIM and Ripples). Our experiments on up to 4K nodes of the OLCF Frontier supercomputer (32,768 GPUs and 196K CPU cores) show strong scaling behavior, and that fused BPTs can improve the performance of these implementations up to 34x (for gIM) and ~360x (for Ripples).

Neff, Reece W.↗

DOE OSTI2023

High-Level Synthesis of Irregular Applications: A Case Study on Influence Maximization

The Influence Maximization problem is the problem of identifying a small cohort of actors from a broader population that, when initially activated in a diffusion process, are expected to result in a large number of activations in the population. While the problem is known to be NP-hard, several approximation algorithms have been devised by leveraging its submodular structure. While these algorithms are theoretically efficient, they are computationally very expensive in practice. This work advances the current state-of-the-art parallelization scheme for the IMM algorithm by devising the adoption of custom hardware accelerators implemented on FPGAs by leveraging High Level Synthesis from OpenCL. We study the performance of our proposed approach by exploring optimizations tailored at improving the parallel efficiency of the accelerators and highlight their effects and limitations in accelerating complex graph analytic applications. Our experimental evaluation shows that FPGA acceleration can improve the performance of the LT diffusion model up to 1.72x for the entire application and up to 2.90x for its most important kernel with respect to a CPU only parallel execution. The FPGA acceleration of the LT model shows also a 1.54x reduction in energy consumption when compared to a parallel CPU only run.

Neff, Reece W.↗

DOE OSTI2023

Accelerating Random Forest Classification on GPU and FPGA

Random Forests (RFs) are a commonly used machine learning method for classification and regression tasks spanning a variety of application domains, including bioinformatics, business analytics, and software optimization. While prior work has focused primarily on improving performance of the training of RFs, many applications, such as malware identification, cancer prediction, and banking fraud detection, require fast RF classification. In this work, we accelerate RF classification on GPU and FPGA. In order to provide efficient support for large datasets, we propose a hierarchical memory layout suitable to the GPU/FPGA memory hierarchy. We design three RF classification code variants based on that layout, and we investigate GPU- and FPGA-specific considerations for these kernels. Our experimental evaluation, performed on an Nvidia Xp GPU and on a Xilinx Alveo U250 FPGA accelerator card using publicly available datasets on the scale of millions of samples and tens of features, covers various aspects. First, we evaluate the performance benefits of our hierarchical data structure over the standard compressed sparse row (CSR) format. Second, we compare our GPU implementation with cuML, a machine learning library targeting Nvidia GPUs. Third, we explore the performance/accuracy tradeoff resulting from the use of different tree depths in the RF. Finally, we perform a comparative performance analysis of our GPU and FPGA implementations. Our evaluation shows that for high accuracy targets, our GPU implementation yields 5-9x speedup over CSR, and up to a 2x speedup over cuML.

FPGA, Xilinx FPGA, GPU, Random Forest classificati↗