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HDBind: encoding of molecular structure with hyperdimensional binary representations

Traditional methods for identifying “hit” molecules from a large collection of potential drug-like candidates rely on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have a significant limitation in that they require exceptional computing capabilities for even relatively small collections of molecules. Increasingly large and complex state-of-the-art deep learning approaches have gained popularity with the promise to improve the productivity of drug design, notorious for its numerous failures. However, as deep learning models increase in their size and complexity, their acceleration at the hardware level becomes more challenging. Hyperdimensional Computing (HDC) has recently gained attention in the computer hardware community due to its algorithmic simplicity relative to deep learning approaches. The HDC learning paradigm, which represents data with high-dimension binary vectors, allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas (computer vision, bioinformatics, mass spectrometery, remote sensing, edge devices, etc.). To the best of our knowledge, our work is the first to consider HDC for the task of fast and efficient screening of modern drug-like compound libraries. We also propose the first HDC graph-based encoding methods for molecular data, demonstrating consistent and substantial improvement over previous work. We compare our approaches to alternative approaches on the well-studied MoleculeNet dataset and the recently proposed LIT-PCBA dataset derived from high quality PubChem assays. We demonstrate our methods on multiple target hardware platforms, including Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs), showing at least an order of magnitude improvement in energy efficiency versus even our smallest neural network baseline model with a single hidden layer. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools. We make our code publicly available at https://github.com/LLNL/hdbind.

59 BASIC BIOLOGICAL SCIENCES

Even Higher-Level Synthesis: An Exploration of AI Hardware Accelerators using HLS4ML

With the rise of artificial intelligence, the popularization of deep learning, and a constantly evolving industry, the demand for flexible and efficient tools has never been greater. As algorithms grow more complex, their runtime and energy consumption increase exponentially. Customized hardware accelerators, long used for specific mathematical operations, remain essential for managing modern applications' computational and power demands. Hardware accelerators can speed up complex computations by orders of magnitude, but their manual design and verification processes are often challenging and time-consuming. High-Level Synthesis (HLS) provides a solution by transforming high-level algorithm descriptions, typically written in C++ or SystemC, into synthesizable RTL suitable for hardware implementation. This approach reduces development time for RTL engineers while offering flexibility beyond what traditional handwritten RTL can provide. We extended this capability to the machine-learning domain with the open-source framework hls4ml, which allows neural networks trained in Python frameworks like Tensorflow or PyTorch to be synthesized into efficient hardware representations for the traditional FPGA and ASIC flows. This breakthrough addresses the growing need for reduced design turnaround and easy verification of ML hardware accelerators with low latency and power efficiency constraints. During this tutorial, we will demonstrate how Python complements HLS by simplifying the ML design process, bridging the gap between software and hardware development. Attendees will explore how we translate neural networks modeled in Python into fixed-point C++ models suitable for HLS workflows. We will dive into strategies like Value-Range Analysis and Quantization-Aware Training, which optimize these designs for deployment and evaluate their accuracy, power consumption, and energy efficiency. To exemplify these concepts, experts from Fermilab will share their experiences applying this technology to high-energy physics experiments, where real-time, low-latency processing is critical. Over the years, Fermilab engineers have demonstrated how deep neural networks, optimized for hardware using hls4ml, can meet the stringent requirements of trigger systems at the CERN Large Hadron Collider. These systems rely on rapid decision-making to process immense data volumes while retaining only the most relevant events for further analysis. The application of hls4ml has also been extended to innovative technologies like smart pixel arrays. These smart pixels integrate ML inference capabilities directly into sensor devices, enabling localized data processing at the pixel level. This approach drastically reduces the need to transmit raw data to external processing units, significantly decreasing power consumption and latency. By embedding neural networks within the pixel architecture, the smart pixels can identify and prioritize relevant data in real time, providing a highly efficient solution for edge computing in scenarios such as particle detectors and imaging systems. Fermilab's work highlights the potential of hardware-accelerated ML in scenarios where both speed and power efficiency are mission-critical. Through this tutorial, attendees will gain valuable insights into the challenges and solutions of deploying ML in hardware. Understanding how HLS and hls4ml streamline the development of neural network-based hardware accelerators is fundamental for the industry's future. Participants will learn how these technologies are shaping the future of AI and scientific computing.

Di Guglielmo, Giuseppe [Fermilab]

SECURED: Simulator-Enhanced Control and Understanding of Reactor systems for cyber-Event Defense

The study discusses a learning approach for analyzing cyber-events in reactor systems using integrated hardware and personal computer simulator models. Key points include the rise in cyber-attacks and their sophistication in industrial control systems (ICS), the necessity for awareness, understanding, resource allocation, and preparation to combat these threats, and the digital transformation of old and new nuclear plants, increasing their exposure to cyber threats. It highlights the cyber vulnerabilities of advanced reactor systems, which rely on digital instrumentation and control for operations and safety functions, making them susceptible to cyber-attacks. The approach involves demonstrating reactor system plant ICS cyber-attacks under various operational conditions utilizing tools like simulator models and hardware-based kits. A strategic solution approach tailored to critical infrastructure is emphasized, along with community engagement for public and government support, adopting effective learning approaches, and the preparation for anticipated future challenges. The presentation concludes with a call to action to address challenges, leverage opportunities, and advance through lesson learning in cybersecurity for nuclear energy systems.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS

Surrogate Neural Architecture Codesign Package (SNAC-Pack)

Neural architecture search (NAS) is a powerful approach for automating model design, but existing methods often optimize for accuracy alone or rely on proxy metrics such as bit operations (BOPs) that correlate poorly with hardware cost. This gap is particularly large for FPGA deployment, where cost is dominated by a multi-dimensional budget of lookup tables, DSPs, flip-flops, BRAM, and latency. We present the Surrogate Neural Architecture Codesign Package (SNAC-Pack), an open-source AutoML framework for hardware-aware neural architecture codesign and end-to-end FPGA deployment. SNAC-Pack runs a multi-objective global search with Optuna and NSGA-II, loading trials to a shared SQLite store that enables parallel workers across compute nodes. A hardware surrogate model outputs per-trial resource and latency estimates, avoiding the synthesis cost that would otherwise dominate the search loop. A local search stage then applies quantization-aware training (QAT) together with iterative magnitude pruning in a combined compression loop, after which the final model is synthesized to FPGA firmware via the hls4ml Python library. A YAML configuration and an optional agentic frontend let users run the pipeline on new datasets without modifying the framework. We demonstrate SNAC-Pack on jet classification at the Large Hadron Collider and superconducting qubit readout, discovering compact architectures that match or exceed strong baselines on the task metric while reducing FPGA resource utilization and, in the qubit readout case, reducing the design space exploration process from months of manual fine-tuning to hours of automated search.

Weitz, Jason [UC, San Diego]

Sentinel

Network intrusion detection systems (NIDS) are commonplace in network security but they frequently employ algorithms that are computational demanding requiring hardware and software with significant power requirements. Two examples of such resource-intensive algorithms used for network security are regular expression matching and broader signature pattern matching which are commonly used in deep packet inspection (DPI). Network security algorithms that have large power requirements may be a challenge for low-power internet-of-things (IoT) environments, which generally lack the power resources to implement complex security measures like computationally expensive DPI at the edge. Furthermore, IoT environments incorporating 5G standalone networks have network latency constraints beyond just power that make DPI at the edge even more difficult. Programmable logic is ideally suited for machine learning inference for DPI because of its deep instruction level parallelism and single-cycle memory access. Machine learning approaches for DPI have been explored before using the programmable logic of field programmable gate arrays (FPGA) as a potential solution for NIDS approaches that would be power-suitable for IoT. However, those previous programmable logic NIDS approaches utilize either a supervised or unsupervised learning model. Sentinel utilizes the ensemble of these two machine learning approaches known as a semi-supervised approach which has shown promise in NIDS implementations. Sentinel provides a programmable logic implementation of a semi-supervised approach for DPI which operates at much lower power and latency than a GPU implementation with negligible loss of accuracy due to quantization through a logistic regressor.

Anderson, MatthewW [Idaho National Laboratory (INL

LuGo: An enhanced quantum phase estimation implementation

Quantum Phase Estimation (QPE) is a cardinal algorithm in quantum computing that plays a crucial role in various applications, including cryptography, molecular simulation, and solving systems of linear equations. However, the standard implementation of QPE faces challenges related to time complexity and circuit depth, which limit its practicality for large-scale computations. We introduce LuGo, a novel framework designed to enhance the performance of QPE by reducing circuit duplication, as well as using parallelization techniques to achieve faster generation of the QPE circuit and gate reduction. We validate the effectiveness of our framework by generating quantum linear solver circuits, which require both QPE and inverse QPE, to solve linear systems of equations. LuGo achieves significant improvements in both computational efficiency and hardware requirements without compromising on accuracy. Compared to a standard QPE implementation, LuGo reduces time consumption to generate a circuit that solves a 2 6 × 2 6 system matrix by a factor of 50.68 and over 31× reduction of quantum gates and circuit depth, with no fidelity loss on an ideal quantum simulator. Furthermore, we demonstrated the versatility and scalability of LuGo enabled HHL algorithm by simulating a canonical Hele-Shaw fluid problem using a quantum simulator. With these advantages, LuGo paves the way for more efficient implementations of QPE, enabling broader applications across several quantum computing domains.

Quantum algorithm

Syncopated dynamical decoupling to suppress crosstalk in quantum circuits

Theoretically understanding and experimentally characterizing and modifying the underlying Hamiltonian of a quantum system is of utmost importance in achieving high-fidelity quantum gates for quantum computing. Here, in this work, we explore the use of dynamical decoupling (DD) in characterizing and suppressing undesired two-qubit couplings as well as the underlying single-qubit decoherence, both significant hurdles to achieving precise quantum control and realizing quantum computing on many hardware prototypes. Through discrete search of DD sequences, we identify sequences that protect against decoherence and selectively target unwanted two-qubit interactions of general form. On a transmon-qubit-based superconducting quantum device, we identify separate white and 1/𝑓 noise components underlying the single-qubit decoherence and a static ZZ coupling between pairs of qubits. A family of syncopated DD sequences is found and their efficiency is demonstrated in two-qubit benchmarking experiments. The syncopated decoupling technique significantly boosts performance in a realistic algorithmic quantum circuit.

97 MATHEMATICS AND COMPUTING

Advantages of imperfect dice rolls over coin flips for random number generation

With an eye toward neural-inspired probabilistic computation, recent work has examined the development of true random number generators via stochastic devices. Typically, these devices are operated in a two-state regime to produce a sequence of binary outcomes (i.e., coin flips). However, there is no guarantee that stochastic devices will infallibly produce fair outputs and small deviations from a uniform distribution may have unwanted complications in applications. Using mathematical analysis, we contend that opting instead for a multi-state device (i.e., a dice roll) has benefits in these unfair paradigms. To demonstrate these benefits, we apply this framework to the analysis of a tunnel diode operated in a stochastic regime. In particular, interpreting the binary stochastic output of the tunnel diode as a multi-state die roll output also sees advantages in remaining closer to uniform. Overall, our approach provides a compelling argument for mathematical driven co-design and development of novel probabilistic computing devices and hardware.

applied mathematics

Ultrasonic Resonance Techniques for Materials Research

Mechanical resonances are directly related to the physical behavior of a system at the bulk and microscopic levels. In materials science, resonant ultrasound spectroscopy (RUS) has long been a preferred nondestructive method to study mechanical resonances of solids and precisely measure quantitative material properties, namely elasticity. In recent years, advances in computational power and hardware have enabled RUS to be relevant for an increasing range of applications, such as advanced manufacturing. An extension of this technique, nonlinear RUS (NRUS), has been demonstrated to provide unmatched sensitivity to early-stage damage. NRUS was originally developed to probe geologic materials but has become a vital tool in nondestructive evaluation and materials research, offering a powerful means of quantifying and characterizing microstructural nonlinearity in a broad range of materials. This review summarizes recent developments and growth opportunities in RUS and NRUS techniques, modeling, and applications across a wide range of material systems including metals, composites, geomaterials, and explosives.

36 MATERIALS SCIENCE

Berkeley eXtensible Environment (BXE) v3

The Berkeley eXtensible Environment (BXE) provides a cloud environment for hardware designers and computer architects to design, build, and simulate their custom architectures on an on-premises FPGA cluster. Utilizing the Chipyard, MoSAIC, and FireSim frameworks, users are provided an environment where they can assemble SoC designs from an existing library of components or import their own source code. Once their designs are ready, they can utilize the FireSim framework provided by BXE to deploy and simulate their designs on the FPGA. Users aren't limited to a single FPGA; they can deploy multiple instances across multiple FPGAs, acting like a rack of servers, or partition their large design across multiple FPGAs, ganging multiple FPGAs into a single simulated system.

Fatollahi-Fard, Farzin

GPU-friendly surface model for Monte-Carlo detector simulations

The demands for Monte-Carlo simulation are drastically increasing with the Large Hadron Collider’s high-luminosity upgrade, and are expected to exceed the currently available compute resources. At the same time, modern high-performance computing has adopted powerful hardware accelerators, particularly GPUs. The AdePT and Celeritas projects aim to address the demanding computational needs by leveraging these heterogeneous computing architectures. While both have successfully ported realistic detector simulations to GPUs using the VecGeom library, the complexity of geometry modeling emerged as a bottleneck. Thread divergence and high register usage were degrading the GPU performance. Therefore, a new, GPU-friendly surface-based model has been introduced in the VecGeom library that decomposes the divergent code of the 3D primitive solids into simpler and more balanced surface algorithms. In this work, we present the latest developments, focusing on the additions required to efficiently model complex setups like the CMS Phase-2 geometry. This includes memory reduction techniques, and adding accelerating structures for faster traversal.

Diederichs, Severin [CERN]

Optical neural engine for solving scientific partial differential equations

Abstract Solving partial differential equations (PDEs) is the cornerstone of scientific research and development. Data-driven machine learning (ML) approaches are emerging to accelerate time-consuming and computation-intensive numerical simulations of PDEs. Although optical systems offer high-throughput and energy-efficient ML hardware, their demonstration for solving PDEs is limited. Here, we present an optical neural engine (ONE) architecture combining diffractive optical neural networks for Fourier space processing and optical crossbar structures for real space processing to solve time-dependent and time-independent PDEs in diverse disciplines, including Darcy flow equation, the magnetostatic Poisson’s equation in demagnetization, the Navier-Stokes equation in incompressible fluid, Maxwell’s equations in nanophotonic metasurfaces, and coupled PDEs in a multiphysics system. We numerically and experimentally demonstrate the capability of the ONE architecture, which not only leverages the advantages of high-performance dual-space processing for outperforming traditional PDE solvers and being comparable with state-of-the-art ML models but also can be implemented using optical computing hardware with unique features of low-energy and highly parallel constant-time processing irrespective of model scales and real-time reconfigurability for tackling multiple tasks with the same architecture. The demonstrated architecture offers a versatile and powerful platform for large-scale scientific and engineering computations.

Tang, Yingheng (ORCID:0009000153622546)

Neuromorphic intermediate representation: A unified instruction set for interoperable brain-inspired computing

Abstract Spiking neural networks and neuromorphic hardware platforms that simulate neuronal dynamics are getting wide attention and are being applied to many relevant problems using Machine Learning. Despite a well-established mathematical foundation for neural dynamics, there exists numerous software and hardware solutions and stacks whose variability makes it difficult to reproduce findings. Here, we establish a common reference frame for computations in digital neuromorphic systems, titled Neuromorphic Intermediate Representation (NIR). NIR defines a set of computational and composable model primitives as hybrid systems combining continuous-time dynamics and discrete events. By abstracting away assumptions around discretization and hardware constraints, NIR faithfully captures the computational model, while bridging differences between the evaluated implementation and the underlying mathematical formalism. NIR supports an unprecedented number of neuromorphic systems, which we demonstrate by reproducing three spiking neural network models of different complexity across 7 neuromorphic simulators and 4 digital hardware platforms. NIR decouples the development of neuromorphic hardware and software, enabling interoperability between platforms and improving accessibility to multiple neuromorphic technologies. We believe that NIR is a key next step in brain-inspired hardware-software co-evolution, enabling research towards the implementation of energy efficient computational principles of nervous systems. NIR is available atneuroir.org

Science & Technology - Other Topics

Dendritic Computing with Multigate Ferroelectric Field-Effect Transistors

Although inspired by neuronal systems in the brain, artificial neural networks generally employ point-neurons, which offer computational complexity far less than that of their biological counterparts. Neurons have dendritic arbors that connect to different sets of synapses and offer local nonlinear accumulation – playing a pivotal role in processing and learning. Inspired by this, we propose a novel neuron design based on a multigate ferroelectric field-effect transistor that mimics dendrites. It leverages ferroelectric nonlinearity for local computations within dendritic branches while utilizing the transistor action to generate the neuronal output. The branched architecture enables smaller crossbar arrays in hardware integration, improving efficiency. Using an experimentally calibrated device-circuit-algorithm cosimulation framework, we demonstrate that networks incorporating our dendritic neurons achieve superior performance compared to much larger networks without dendrites (∼ 17× fewer trainable weight parameters). These findings suggest that dendritic hardware can significantly improve computational efficiency and learning capacity of neuromorphic systems optimized for edge applications.

36 MATERIALS SCIENCE

SPARTAN (Scalable Probabilistic Application Reconfigurable Tensor Autonomous Network)

The technical founder of Ludwig Computing Inc has been competitively selected for support by Cyclotron Road, a U.S. Department of Energy (DOE) Advanced Manufacturing Office (AMO) Lab-Embedded Entrepreneurship Program (LEEP) through an approved merit review process. Ludwig Computing Inc, supported by the U.S. Department of Energy's Advanced Manufacturing Office through the Cyclotron Road program, has investigated the advantages of probabilistic computing for real-world compute-intensive applications. This research adds to the understanding of alternative computing paradigms by exploring a unique hardware-software co-design that integrates quantum computing methods with nature-inspired problem-solving techniques. The project's focus on areas such as combinatorial optimization, graph analytics, and machine learning demonstrates the potential for significant advancements in computational efficiency and performance. By harnessing natural randomness to streamline large circuits into fewer devices, Ludwig's approach enables massive parallelism, potentially offering higher throughput, speed, and energy efficiency compared to conventional hardware solutions. This work benefits the public by paving the way for more efficient computing solutions that could address complex real-world problems while potentially reducing energy consumption in data-intensive industries.

97 MATHEMATICS AND COMPUTING

Converged Computing: A Best of Both Worlds of High-Performance Computing and Cloud

Collaboration between Cloud and High Performance Computing (HPC) communities has accelerated in the last half decade. A common goal to run batch workloads combined with a desire for reproducibility, automation, and optimization has led to successful projects that range from container technologies to workload management and security. This span of current and future work defines a novel “Converged Computing” paradigm that aims to combine the best of both worlds, both from a technological and cultural standpoint. Furthermore, in this Special Issue, we review common themes in the space, showcasing current work and encouraging a continued effort toward innovative ideas that will enable the next generations of scientific discovery.

97 MATHEMATICS AND COMPUTING