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Do graph neural networks learn traditional jet substructure?

At the CERN LHC, the task of jet tagging, whose goal is to infer the origin of a jet given a set of final-state particles, is dominated by machine learning methods. Graph neural networks have been used to address this task by treating jets as point clouds with underlying, learnable, edge connections between the particles inside. We explore the decision-making process for one such state-of-the-art network, ParticleNet, by looking for relevant edge connections identified using the layerwise-relevance propagation technique. As the model is trained, we observe changes in the distribution of relevant edges connecting different intermediate clusters of particles, known as subjets. The resulting distribution of subjet connections is different for signal jets originating from top quarks, whose subjets typically correspond to its three decay products, and background jets originating from lighter quarks and gluons. This behavior indicates that the model is using traditional jet substructure observables, such as the number of prongs -- energetic particle clusters -- within a jet, when identifying jets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Rare Higgs Processes at CMS and Precision Timing Detector Studies for HL-LHC CMS Upgrade

This thesis describes the search for two rare Higgs processes. The first analysis describes the CMS Run 2 search for $H$ $\rightarrow$ $\mu$$\mu$ decays, with 137.3 fb$^{-1}$ of data at $\sqrt{s}$ = 13 TeV. The analysis targeted four different Higgs production modes: the gluon fusion (ggH), the vector boson fusion (VBF), the Higgs-strahlung process (VH), and the production in association with a pair of top quarks (ttH). Each category used a dedicated machine learning based classifier to separate the signal from the background processes. A combined fit from all these categories saw a slight excess in the data corresponding to 3.0 standard deviations at $M$$_{H}$ = 125.38 GeV, and gave the first evidence for the Higgs boson decay to second-generation fermions. The best-fit signal strength and the corresponding 68% CL interval was found to be +0.17?????? = 1.19 $_{-0.39}^{+0.41}$ (stat)$_{-0.16}^{+0.17}$(syst) at $M$$_{H}$ = 125.38 GeV. The second analysis describes the CMS Run 2 search for 𝐻𝐻 → 𝑏𝑏𝑏𝑏 with highly boosted Higgs bosons. This analysis used a dedicated jet identification algorithm based on graph neural networks (ParticleNet) to identify boosted H→ bb jets. This search targeted the gluon fusion and the vector boson fusion HH production modes, and put constraints on the allowed values of the various Higgs couplings as: 𝜅𝜆 ∈ [−9.9, 16.9] when 𝜅𝑉 = 1, 𝜅2𝑉 = 1; 𝜅𝑉 ∈ [−1.17, −0.79] ∪ [0.81, 1.18] when 𝜅𝜆 = 1, 𝜅2𝑉 = 1; 𝜅2𝑉 ∈ [0.62, 1.41] when 𝜅𝜆 = 1, 𝜅𝑉 = 1. A scenario with 𝜅2𝑉 = 0 was excluded with a significance of 6.3 standard deviations for the first time, when other H couplings are fixed to their SM values. The combined observed (expected) 95% upper limit on the HH production cross section was found to be 9.9 (5.1) × SM. Finally, this thesis also discusses the planned MIP Timing Detector (MTD) upgrade for CMS at the HL-LHC. The MTD will be a time-of-flight (TOF) detector, designed to provide a precision timing information for charged particles using SiPMs + LYSO scintillating crystals, with a time resolution of ∼30 ps. This thesis describes several R&D tests that have been performed for characterizing the sensor properties (time resolution, light yield, etc.) and optimizing the sensor design geometry. This thesis also contains a description of mock test setups for cooling the sensors, since it is known to be an effective way of mitigating the increased dark current rates in the sensors due to radiation damage.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

High performance FPGA embedded system for machine learning based tracking and trigger in sPhenix and EIC

We present a comprehensive end-to-end pipeline to classify triggers versus background events in this paper. This pipeline makes online decisions to select signal data and enables the intelligent trigger system for efficient data collection in the Data Acquisition System (DAQ) of the upcoming sPHENIX and future EIC (Electron-Ion Collider) experiments. Starting from the coordinates of pixel hits that are lightened by passing particles in the detector, the pipeline applies three-stage of event processing (hits clustering, track reconstruction, and trigger detection) and labels all processed events with the binary tag of trigger versus background events. The pipeline consists of deterministic algorithms such as clustering pixels to reduce event size, tracking reconstruction to predict candidate edges, and advanced graph neural network-based models for recognizing the entire jet pattern. In particular, we apply the message-passing graph neural network to predict links between hits and reconstruct tracks and a hierarchical pooling algorithm (DiffPool) to make the graph-level trigger detection. We obtain an impressive performance (≥70% accuracy) for trigger detection with only 3200 neuron weights in the end-to-end pipeline. We deploy the end-to-end pipeline into a field-programmable gate array (FPGA) and accelerate the three stages with speedup factors of 1152, 280, and 21, respectively.

Instruments & Instrumentation↗

Brain segmentation and the generation of cortical surfaces

This paper describes methods for white matter segmentation in brain images and the generation of cortical surfaces from the segmentations. We have developed a system that allows a user to start with a brain volume, obtained by modalities such as MRI or cryosection, and constructs a complete digital representation of the cortical surface. The methodology consists of three basic components: local parametric modeling and Bayesian segmentation; surface generation and local quadratic coordinate fitting; and surface editing. Segmentations are computed by parametrically fitting known density functions to the histogram of the image using the expectation maximization algorithm [DLR77]. The parametric fits are obtained locally rather than globally over the whole volume to overcome local variations in gray levels. To represent the boundary of the gray and white matter we use triangulated meshes generated using isosurface generation algorithms [GH95]. A complete system of local parametric quadratic charts [JWM+95] is superimposed on the triangulated graph to facilitate smoothing and geodesic curve tracking. Algorithms for surface editing include extraction of the largest closed surface. Results for several macaque brains are presented comparing automated and hand surface generation. Copyright 1999 Academic Press.

NASA Discipline Neuroscience↗

Intelligent Experiments through Real-Time AI: Fast Data Processing and Autonomous Detector Control for High-Energy Nuclear Experiments

The aim of this project is to develop software and hardware for fast real-time data processing and autonomous detector control and calibration for the sPHENIX and the future EIC experiments. Below summarizes Georgia Tech team efforts in the past year: 1. We developed a real-time clustering algorithm and FPGA-based pipeline architecture for processing fired pixel data from ALPIDE sensors in sPHENIX experiments. Our Columnar Clustering Co-Design introduces a hardware-aware, stream-friendly approach that segments pixel data by column pairs using a Column Pair Clustering (CPC) strategy, followed by Cluster Stitching to merge adjacent subclusters. Implemented in Vitis HLS, the pipeline comprises five stages—read-in, subclustering, stitching, analysis, and write-out—connected by tagged HLS streams with custom end-of-event signaling for robust synchronization. We designed a pipelined dataflow model optimized for throughput, low latency, and minimal buffering, enabling scalable clustering across events of arbitrary size. Our system maintains spatial precision via center-of-mass and shape key extraction and efficiently handles edge cases such as fragmented or nested clusters. Compared against DBSCAN in both software and hardware, our approach demonstrates competitive performance under FPGA constraints. 2. We also conducted a comprehensive algorithm-to-hardware co-design of connected component analysis tailored for sPHENIX experiments, focusing on real-time, low-latency processing using FPGAs and High-Level Synthesis (HLS). Starting from a Python-based particle tracking pipeline, the team translated the core logic—graph traversal via DFS and Union-Find—into an HLS-compatible C++ model, replacing dynamic memory and recursion with static arrays and pipelined control flow. The final design includes a fully streamed and dataflow-compatible Union-Find kernel optimized across five iterations, incorporating loop pipelining, array partitioning, AXI/FIFO interface tuning, and function flattening. Experimental results show up to 14.8× speedup over the CPU baseline, reducing per-graph latency to 1.58 μs and demonstrating strong resource efficiency with only ~7k LUTs and zero BRAM usage. The design maintains functional correctness against the Python reference using a Python-based C-simulation framework and Mean Squared Error metrics. This work validates the potential of HLS-driven FPGA designs for edge-level HEP data acquisition, laying a scalable foundation for future integration with real-time detector pipelines and multi-graph processing systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Wavelet Methods Developed to Detect and Control Compressor Stall

A "wavelet" is, by definition, an amplitude-varying, short waveform with a finite bandwidth (e.g., that shown in the first two graphs). Naturally, wavelets are more effective than the sinusoids of Fourier analysis for matching and reconstructing signal features. In wavelet transformation and inversion, all transient or periodic data features (as in compressor-inlet pressures) can be detected and reconstructed by stretching or contracting a single wavelet to generate the matching building blocks. Consequently, wavelet analysis provides many flexible and effective ways to reduce noise and extract signals which surpass classical techniques - making it very attractive for data analysis, modeling, and active control of stall and surge in high-speed turbojet compressors. Therefore, fast and practical wavelet methods are being developed in-house at the NASA Lewis Research Center to assist in these tasks. This includes establishing user-friendly links between some fundamental wavelet analysis ideas and the classical theories (or practices) of system identification, data analysis, and processing.

Le, Dzu K.↗

Planar Particle Imaging Doppler Velocimetry Developed

Two current techniques exist for the measurement of planar, three-component velocity fields. Both techniques require multiple views of the illumination plane in order to extract all three velocity components. Particle image velocimetry (PIV) is a high-resolution, high accuracy, planar velocimetry technique that provides valuable instantaneous velocity information in aeropropulsion test facilities. PIV can provide three-component flow-field measurements using a two-camera, stereo viewing configuration. Doppler global velocimetry (DGV) is another planar velocimetry technique that can provide three component flow-field measurements; however, it requires three detector systems that must be located at oblique angles from the measurement plane. The three-dimensional configurations of either technique require multiple (DGV) or at least large (stereo PIV) optical access ports in the facility in which the measurements are being conducted. Optical access is extremely limited in aeropropulsion test facilities. In many cases, only one optical access port is available. A hybrid measurement technique has been developed at the NASA Glenn Research Center, planar particle image and Doppler velocimetry (PPIDV), which combines elements from both the PIV and DGV techniques into a single detection system that can measure all three components of velocity across a planar region of a flow field through a single optical access port. In the standard PIV technique, a pulsed laser is used to illuminate the flow field at two closely spaced instances in time, which are recorded on a "frame-straddling" camera, yielding a pair of single-exposure image frames. The PIV camera is oriented perpendicular to the light sheet, and the processed PIV data yield the two-component velocity field in the plane of the light sheet. In the standard DGV technique, an injection-seeded Nd:YAG pulsed laser light sheet illuminates the seeded flow field, and three receiver systems are used to measure three components of velocity. The receiver systems are oriented at oblique angles to the light sheet in order to accurately resolve the three-component velocity. Each DGV receiver system contains two cameras, which share a common view of the illuminated flow through a beam-splitting cube. One camera views the illuminated flow directly (reference camera) and the second camera images the illuminated flow through an iodine vapor cell (signal camera). The laser frequency (wavelength) is adjusted so that the Doppler-shifted light from particles in the flow falls on an iodine absorption feature, see the following graph. The iodine vapor cell acts as a frequency-to-velocity filter by modulating the intensity of the transmitted light as a function of the flow velocity (Doppler shift). The ratio of the signal and reference images yields the component of the flow velocity along the bisector of the laser sheet propagation direction and the receiver system observation direction. The hybrid system employs a single-component DGV receiver system configured to simultaneously acquire PIV image data, as shown in the following diagram. The cameras used in the DGV receiver are replaced with PIV frame-straddling cameras, and the receiver system views the illuminated light sheet plane at 90 (as in the standard PIV configuration).

Wernet, Mark P.↗

Using LDPC Code Constraints to Aid Recovery of Symbol Timing

A method of utilizing information available in the constraints imposed by a low-density parity-check (LDPC) code has been proposed as a means of aiding the recovery of symbol timing in the reception of a binary-phase-shift-keying (BPSK) signal representing such a code in the presence of noise, timing error, and/or Doppler shift between the transmitter and the receiver. This method and the receiver architecture in which it would be implemented belong to a class of timing-recovery methods and corresponding receiver architectures characterized as pilotless in that they do not require transmission and reception of pilot signals. Acquisition and tracking of a signal of the type described above have traditionally been performed upstream of, and independently of, decoding and have typically involved utilization of a phase-locked loop (PLL). However, the LDPC decoding process, which is iterative, provides information that can be fed back to the timing-recovery receiver circuits to improve performance significantly over that attainable in the absence of such feedback. Prior methods of coupling LDPC decoding with timing recovery had focused on the use of output code words produced as the iterations progress. In contrast, in the present method, one exploits the information available from the metrics computed for the constraint nodes of an LDPC code during the decoding process. In addition, the method involves the use of a waveform model that captures, better than do the waveform models of the prior methods, distortions introduced by receiver timing errors and transmitter/ receiver motions. An LDPC code is commonly represented by use of a bipartite graph containing two sets of nodes. In the graph corresponding to an (n,k) code, the n variable nodes correspond to the code word symbols and the n-k constraint nodes represent the constraints that the code places on the variable nodes in order for them to form a valid code word. The decoding procedure involves iterative computation of values associated with these nodes. A constraint node represents a parity-check equation using a set of variable nodes as inputs. A valid decoded code word is obtained if all parity-check equations are satisfied. After each iteration, the metrics associated with each constraint node can be evaluated to determine the status of the associated parity check. Heretofore, normally, these metrics would be utilized only within the LDPC decoding process to assess whether or not variable nodes had converged to a codeword. In the present method, it is recognized that these metrics can be used to determine accuracy of the timing estimates used in acquiring the sampled data that constitute the input to the LDPC decoder. In fact, the number of constraints that are satisfied exhibits a peak near the optimal timing estimate. Coarse timing estimation (or first-stage estimation as described below) is found via a parametric search for this peak. The present method calls for a two-stage receiver architecture illustrated in the figure. The first stage would correct large time delays and frequency offsets; the second stage would track random walks and correct residual time and frequency offsets. In the first stage, constraint-node feedback from the LDPC decoder would be employed in a search algorithm in which the searches would be performed in successively narrower windows to find the correct time delay and/or frequency offset. The second stage would include a conventional first-order PLL with a decision-aided timing-error detector that would utilize, as its decision aid, decoded symbols from the LDPC decoder. The method has been tested by means of computational simulations in cases involving various timing and frequency errors. The results of the simulations ined in the ideal case of perfect timing in the receiver.

Jones, Christopher↗

Graph Neural Networks for low-energy event classification & reconstruction in IceCube

IceCube, a cubic-kilometer array of optical sensors built to detect atmospheric and astrophysical neutrinos between 1 GeV and 1 PeV, is deployed 1.45 km to 2.45 km below the surface of the ice sheet at the South Pole. The classification and reconstruction of events from the in-ice detectors play a central role in the analysis of data from IceCube. Reconstructing and classifying events is a challenge due to the irregular detector geometry, inhomogeneous scattering and absorption of light in the ice and, below 100 GeV, the relatively low number of signal photons produced per event. To address this challenge, it is possible to represent IceCube events as point cloud graphs and use a Graph Neural Network (GNN) as the classification and reconstruction method. The GNN is capable of distinguishing neutrino events from cosmic-ray backgrounds, classifying different neutrino event types, and reconstructing the deposited energy, direction and interaction vertex. Based on simulation, we provide a comparison in the 1 GeV–100 GeV energy range to the current state-of-the-art maximum likelihood techniques used in current IceCube analyses, including the effects of known systematic uncertainties. For neutrino event classification, the GNN increases the signal efficiency by 18% at a fixed background rate, compared to current IceCube methods. Alternatively, the GNN offers a reduction of the background (i.e. false positive) rate by over a factor 8 (to below half a percent) at a fixed signal efficiency. For the reconstruction of energy, direction, and interaction vertex, the resolution improves by an average of 13%–20% compared to current maximum likelihood techniques in the energy range of 1 GeV–30 GeV. The GNN, when run on a GPU, is capable of processing IceCube events at a rate nearly double of the median IceCube trigger rate of 2.7 kHz, which opens the possibility of using low energy neutrinos in online searches for transient events.

47 OTHER INSTRUMENTATION↗

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations that can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.

Non-NASA Center↗

Oxidation States of Grim Glasses in EET79001 Based on Vanadium Valence

Gas-rich impact-melt (GRIM) glasses in SNC meteorites are very rich in Martian atmospheric noble gases and sulfur suggesting a possible occurrence of regolith-derived secondary mineral assemblages in these samples. Previously, we have studied two GRIM glasses, 506 and 507, from EET79001 Lith A and Lith B, respectively, for elemental abundances and spatial distribution of sulfur using EMPA (WDS) and FE-SEM (EDS) techniques and for sulfur-speciation using K-edge XANES techniques. These elemental and FE-SEM micro-graph data at several locations in the GRIM glasses from Shergotty (DBS), Zagami 994 and EET79001, Lith B showed that FeO and SO3 are positively correlated (SO3 represents a mixture of sulfide and sulfate). FE-SEM (EDS) study revealed that the sulfur-rich pockets in these glasses contain numerous micron-sized iron-sulfide (Fe-S) globules sequestered throughout the volume. However, in some areas (though less frequently), we detected significant Fe-S-O signals suggesting the occurrence of iron sulfate. These GRIM glasses were studied by K-edge microXANES techniques for sulfur speciation in association with iron in sulfur-rich areas. In both samples, we found the sulfur speciation dominated by sulfide with minor oxidized sulfur mixed in with various proportions. The abundance of oxidized sulfur was greater in 506 than in 507. Based on these results, we hypothesize that sulfur initially existed as sulfate in the glass precursor materials and, on shock-impact melting of the precursor materials producing these glasses, the oxidized sulfur was reduced to predominately sulfide. In order to further test this hypothesis, we have used microXANES to measure the valence states of vanadium in GRIM glasses from Lith A and Lith B to complement and compare with previous analogous measurements on Lith C (note: 506 and 507 contain the largest amounts of martian atmospheric gases but the gas-contents in Lith C measured by are unknown). Vanadium is ideal for addressing this re-dox issue because it has multiple valence states and is a well-studied element. Ferrous-dominated iron valences determined by microXANES on the Lith A and Lith B glasses provide little redox sensitivity. Vanadium valence measurements for impact glass in Lith C at three different locations yielded valence values of 3.1, 3.2 and 3.4 with inferred fO2 values of IW-0.7, IW-0.1 and IW+0.7, respectively. This range of oxygen-fugacity values is understandable because the glasses are shock-molten impact glasses which are heterogeneous in nature. Oxygen fugacity values obtained from the analysis of Fe-Ti oxides and Eu partitioning in pyroxenes from EET79001 Lith A and Lith B (host lithologies) were in the range of IW+0.3 to IW+1.9 suggesting that V in the Lith C impact glass was reduced in the impact process. Here, we examine whether the 506 from Lith A and 507 from Lith B GRIM glasses yield similar or different fO2 values from those of Lith C using the vanadium K-edge microXANES technique.

Sutton, S. R.↗

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗