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At least 163 records · Page 9

HOP and Cybersecurity: Leveraging safety and reliability experience to improve digital security culture

This presentation will introduce participants to key mental models on how to think about and understand safety and the organizational attributes that support it from three of the leading voices in the discipline – David Marx, Dr. Erik Hollnagel and Dr. Todd Conklin – and from there we ask the simple question of “how can we apply this to cybersecurity?” Opportunities, similarities, and differences from the history of accomplishment applying human and organizational performance principles to safety and reliability can be collectively leveraged to the meet the challenge of cybersecurity for OT/ICS/cyber-physical systems. This is the same intent as the "Cybersecurity Culture" principle of Cyber-Informed Engineering (CIE).

42 ENGINEERING↗

Theory of the effect of external stress on the activated dynamics and transport of dilute penetrants in supercooled liquids and glasses

We generalize the self-consistent cooperative hopping theory for a dilute spherical penetrant or tracer activated dynamics in dense metastable hard sphere fluids and glasses to address the effect of external stress, the consequences of which are systematically established as a function of matrix packing fraction and penetrant-to-matrix size ratio. All relaxation processes speed up under stress, but the difference between the penetrant and matrix hopping (alpha relaxation) times decreases significantly with stress corresponding to less time scale decoupling. A dynamic crossover occurs at a critical “slaving onset” stress beyond which the matrix activated hopping relaxation time controls the penetrant hopping time. This characteristic stress increases (decreases) exponentially with packing fraction (size ratio) and can be well below the absolute yield stress of the matrix. Below the slaving onset, the penetrant hopping time is predicted to vary exponentially with stress, differing from the power law dependence of the pure matrix alpha time due to system-specificity of the stress-induced changes in the penetrant local cage and elastic barriers. An exponential growth of the penetrant alpha relaxation time with size ratio under stress is predicted, and at a fixed matrix packing fraction, the exponential relation between penetrant hopping time and stress for different size ratios can be collapsed onto a master curve. Direct connections between the short- and long-time activated penetrant dynamics and between the penetrant (or matrix) alpha relaxation time and matrix thermodynamic dimensionless compressibility are also predicted. The presented results should be testable in future experiments and simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Higher-order Van Hove singularities in kagome topological bands

Motivated by the growing interest in band structures featuring higher-order Van Hove singularities (HOVHS), we investigate a spinless fermion kagome system characterized by nearest-neighbor (NN) and next-nearest-neighbor (NNN) hopping amplitudes. While NN hopping preserves time-reversal symmetry, NNN hopping, akin to chiral hopping on the Haldane lattice, breaks time-reversal symmetry and leads to the formation of topological bands with Chern numbers ranging from 𝐶 = ±1 to ±4. We perform analytical and numerical analysis of the energy bands near the high-symmetry points Γ, ±𝐊, and 𝐌 𝑖 (𝑖 = 1, 2, and 3), which uncover a rich and complex landscape of HOVHS, controlled by the magnitude and phase of the NNN hopping. We observe power-law divergences in the density of states (DOS), 𝜌⁡(𝜀)∼|𝜀| −𝜈 , with exponents 𝜈 = 1/2, 1/3, 1/4, which can significantly affect the anomalous Hall response at low temperatures when the Fermi level crosses the HOVHS. Additionally, the NNN hopping induces the formation of higher Chern number bands 𝐶 = ±2, ±4 in the middle of the spectrum obeying a sublattice interference whereupon electronic states are maximally localized in each of the sublattices when the momentum approaches the three high-symmetry points 𝐌 𝑖 (𝑖 = 1, 2, and 3) on the Brillouin zone boundary. Finally, this classification of HOVHS in kagome systems provides a platform to explore unconventional electronic orders induced by electronic correlations.

Chern insulators↗

High-Speed On-Board Data Processing for Science Instruments

A new development of on-board data processing platform has been in progress at NASA Langley Research Center since April, 2012, and the overall review of such work is presented in this paper. The project is called High-Speed On-Board Data Processing for Science Instruments (HOPS) and focuses on a high-speed scalable data processing platform for three particular National Research Council's Decadal Survey missions such as Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS), Aerosol-Cloud-Ecosystems (ACE), and Doppler Aerosol Wind Lidar (DAWN) 3-D Winds. HOPS utilizes advanced general purpose computing with Field Programmable Gate Array (FPGA) based algorithm implementation techniques. The significance of HOPS is to enable high speed on-board data processing for current and future science missions with its reconfigurable and scalable data processing platform. A single HOPS processing board is expected to provide approximately 66 times faster data processing speed for ASCENDS, more than 70% reduction in both power and weight, and about two orders of cost reduction compared to the state-of-the-art (SOA) on-board data processing system. Such benchmark predictions are based on the data when HOPS was originally proposed in August, 2011. The details of these improvement measures are also presented. The two facets of HOPS development are identifying the most computationally intensive algorithm segments of each mission and implementing them in a FPGA-based data processing board. A general introduction of such facets is also the purpose of this paper.

Beyon, Jeffrey Y.↗

Charge Transport in Zirconium-Based Metal–Organic Frameworks

Metal–organic frameworks (MOFs) are a class of crystalline porous materials characterized by inorganic nodes and multitopic organic linkers. Because of their molecular-scale porosity and periodic intraframework chemical functionality, MOFs are attractive scaffolds for supporting and/or organizing catalysts, photocatalysts, chemical-sensing elements, small enzymes, and numerous other functional-property-imparting, nanometer-scale objects. Notably, these objects can be installed after the synthesis of the MOF, eliminating the need for chemical and thermal compatibility of the objects with the synthesis milieu. Thus, postsynthetically functionalized MOFs can present three-dimensional arrays of high-density, yet well-separated, active sites. Depending on the application and corresponding morphological requirements, MOF materials can be prepared in thin-film form, pelletized form, isolated single-crystal form, polycrystalline powder form, mixed-matrix membrane form, or other forms. For certain applications, most obviously catalytic hydrolysis and electro- or photocatalytic water splitting, but also many others, an additional requirement is water stability. MOFs featuring hexa-zirconium(IV)-oxy nodes satisfy this requirement. For applications involving electrocatalysis, charge storage, photoelectrochemical energy conversion, and chemiresistive sensing, a further requirement is electrical conductivity, as embodied in electron or hole transport. As most MOFs, under most conditions, are electrically insulating, imparting controllable charge-transport behavior is both a chemically intriguing and chemically compelling challenge. Herein, we describe three strategies to render zirconium-based metal–organic frameworks (MOFs) tunably electrically conductive and, therefore, capable of transporting charge on the few nanometers (i.e., several molecular units) to few micrometers (i.e., typical dimensions for MOF microcrystallites) scale. The first strategy centers on redox-hopping between periodically arranged, chemically equivalent sites, essentially repetitive electron (or hole) self-exchange. Zirconium nodes are electrically insulating, but they can function as grafting sites for (a) redox-active inorganic clusters or (b) molecular redox couples. Alternatively, charge hopping based on linker redox properties can be exploited. Marcus’s theory of electron transfer has proven useful for understanding/predicting trends in redox-hopping based conductivity, most notably, in accounting for variations as great as 3000-fold depending on the direction of charge propagation through structurally anisotropic MOFs. In MOF environments, propagation of electronic charge via redox hopping is necessarily accompanied by movement of charge-compensating ions. Consequently, rates of redox hopping can depend on both the identity and concentration of ions permeating the MOF. In the context of electrocatalysis, an important goal is to transport electronic charge fast enough to match or exceed the inherent activity of MOF-based or MOF-immobilized catalysts. Bandlike electronic conductivity is the focus of an alternative strategy: one based on the introduction of molecular guests capable of forming donor–acceptor charge transfer complexes with the host framework. Theory again can be applied predictively to alter conductivity. A third strategy similarly emphasizes electronic conductivity, but it makes use of added bridges in the form of molecular oligomers or inorganic clusters that can then be linked to span the length of a MOF crystallite. For all strategies, retention of molecular-scale porosity is emphasized, as this property is key to many applications. Lastly, while our focus is on Zr-MOFs, the described approaches clearly are extendable to other MOF compositions, as has already been demonstrated, in part, in studies by others.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The persistence of memory in ionic conduction probed by nonlinear optics

Predicting practical rates of transport in condensed phases enables the rational design of materials, devices and processes. This is especially critical to developing low-carbon energy technologies such as rechargeable batteries. For ionic conduction, the collective mechanisms, variation of conductivity with timescales and confinement, and ambiguity in the phononic origin of translation, call for a direct probe of the fundamental steps of ionic diffusion: ion hops. However, such hops are rare-event large-amplitude translations, and are challenging to excite and detect. Here we use single-cycle terahertz pumps to impulsively trigger ionic hopping in battery solid electrolytes. This is visualized by an induced transient birefringence, enabling direct probing of anisotropy in ionic hopping on the picosecond timescale. The relaxation of the transient signal measures the decay of orientational memory, and the production of entropy in diffusion. We extend experimental results using in silico transient birefringence to identify vibrational attempt frequencies for ion hopping. Using nonlinear optical methods, we probe ion transport at its fastest limit, distinguish correlated conduction mechanisms from a true random walk at the atomic scale, and demonstrate the connection between activated transport and the thermodynamics of information.

25 ENERGY STORAGE↗

Charge density waves on a half-filled decorated honeycomb lattice

Tight binding models like the Hubbard Hamiltonian are most often explored in the context of uniform intersite hopping $\textit{t}$. The electron-electron interactions, if sufficiently large compared to this translationally invariant $\textit{t}$, can give rise to ordered magnetic phases and Mott insulator transitions, especially at commensurate filling. The more complex situation of nonuniform $\textit{t}$ has been studied within a number of situations, perhaps most prominently in multiband geometries where there is a natural distinction of hopping between orbitals of different degree of overlap. In this paper we explore related questions arising from the interplay of multiple kinetic energy scales and electron-phonon interactions. Specifically, we use determinant quantum Monte Carlo (DQMC) to solve the half-filled Holstein Hamiltonian on a “decorated honeycomb lattice,” consisting of hexagons with internal hopping $\textit{t}$ coupled together by $\textit{t'}$. This modulation of the hopping introduces a gap in the Dirac spectrum and affects the nature of the topological phases. Here, we determine the range of $\textit{t/t'}$ values which support a charge density wave phase about the Dirac point of uniform hopping $\textit{t = t'}$, as well as the critical transition temperature $T_c$. The QMC simulations are compared with the results of mean field theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Investigation of the electrical conduction mechanisms in P-type amorphous germanium electrical contacts for germanium detectors in searching for rare-event physics

For the first time, electrical conduction mechanisms in the disordered material system is experimentally studied for p-type amorphous germanium (a-Ge) used for high-purity Ge detector contacts. The localization length and the hopping parameters in a-Ge are determined using the surface leakage current measured from three high-purity planar Ge detectors. The temperature dependent hopping distance and hopping energy are obtained for a-Ge fabricated as the electrical contact materials for high-purity Ge planar detectors. As a result, we find that the hopping energy in a-Ge increases as temperature increases while the hopping distance in a-Ge decreases as temperature increases. The localization length of a-Ge is on the order of 2.13$^{-0.05}_{+0.07}$A° to 5.07$^{0.83}_{+2.58}$A°,depending on the density of states near the Fermi energy level within bandgap. Using these parameters, we predict that the surface leakage current from a Ge detector with a-Ge contacts can be much smaller than one yocto amp (yA) at helium temperature, suitable for rare-event physics searches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Design of a Radioisotope Heat Exchanger Rocket

The state of planetary exploration vehicle technology has become increasingly more advanced over its long history. Better technologies enable more detailed scientific research to be conducted during the vehicle’s life, while advanced manufacturing strategies allow the vehicles to operate for greater lengths of time. However, one aspect of these vehicles has remained constant: the means of exploration. Previous vehicles have all relied on wheels to traverse the surface of the explored planet, limiting their range. The Mars Opportunity Rover, the longest operating rover, only traveled 45.15 km over its life. The radioisotope heat exchanger rocket is a new vehicle concept, designed to use heated gas as a means of propellant. The vehicle collects gas from the surface of a body, stores it in a heated tank, and passes it through a heat exchanger. This process significantly increases the temperature of the collected gas, allowing it to exit through a nozzle with high velocity and efficiency. This process will enable the vehicle to hop across the surface of the body and repeatedly refuel, with the potential of travelling thousands of kilometers during its lifetime. A computer model was constructed to simulate the heat exchanger and nozzle of this proposed system. This simulation allowed the heat exchanger and propellant tank properties to be optimized for the current mission parameters: the exploration of Triton. The nitrogen flows through a 25 kg lithium heat exchanger, consisting of 540, 1.5-mm diameter, 40-cm long Titanium Zirconium Molybdenum pipes, to three operating nozzles. Once landed, the vehicle will conduct science and refueling operations for six days before hopping again. With the optimized design determined from the simulations conducted in this paper, 235.26 kg of nitrogen is collected and stored in a 300 K, 3000 psia tank. With these parameters, a potential hop distance of 39 km with an average specific impulse of 127.5 s is attained. A previous iteration of this vehicle did not include a heat exchanger, instead heating 100 kg of nitrogen to 300 K, only allowing the vehicle to hop 5 km and with a low specific impulse of 60 s. Thus, the addition of the heat exchanger component of the vehicle is shown to potentially double the specific impulse and quadruple the hop distance compared to the previous design.

Thomas E. O'Brien↗

Two-terminal electronic charge resistance switching device

A two-terminal memory device and methods for its use are provided. In the device, a bottom electrode is electrically continuous with a first operating terminal, and a control gate electrode is electrically continuous with a second operating terminal. A stack of insulator layers comprising a hopping conduction layer and a tunnel layer is contactingly interposed between the bottom electrode and the control gate electrode. The tunnel layer is thinner than the hopping conduction layer, and it has a wider bandgap than the hopping conduction layer. The hopping conduction layer consists of a material that supports electron hopping transport.

Marinella, Matthew↗

Structure–Activity Relationships in Ether-Functionalized Solid-State Metal–Organic Framework Electrolytes

The structure–property relationships of metal–organic framework (MOF)-based solid-state electrolytes are not well understood. Herein, a systematic investigation of 12 Zr(IV)-based UiO-66 MOFs with varying ether-chain functional groups was carried out to elucidate the critical microscopic interactions that facilitate improved solid-state electrolyte performance. Enhanced sampling molecular dynamics (MD) simulations were employed and revealed a three-tier ion hopping mechanism: linker–linker hopping, linker-counterion hopping, and counterion-counterion hopping. Detailed structural analysis of the MD trajectories revealed that the chemistry and morphology of the linker groups affect the relative stability and population distribution of the electrolyte components, such that crown-ether-based linker groups enhance the probability of extended, low-barrier ion percolation pathways. As a result, we were able to tune the ionic conductivities by rationally manipulating the counterion distributions, linker binding strengths, and the configurational entropy (multivariability of the linkers). The resulting performance of these MOF-based solid-state electrolytes was significantly enhanced, with a methoxy-functionalized framework (UiO-66-L1 100 ) achieving high ionic conductivities of 2.32 × 10 –4 S/cm and 2.07 × 10 –3 S/cm at 30 °C and 90 °C, respectively, an order of magnitude greater than other all-solid-state MOF electrolyte systems. The electrolyte stability was evaluated with LiIn|LPSCl|MOF:LiTFSI|LPSCl|LiIn symmetric cells, showing excellent Li plating/stripping processes for over 2 months.

36 MATERIALS SCIENCE↗

Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles

Transport mechanisms of solvated protons of 1 M HCl acid pools, confined within reverse micelles (RMs) containing the negatively charged surfactant sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) or the positively charged cetyltrimethylammonium bromide (CTABr), are analyzed with reactive force field simulations to interpret dynamical signatures from TeraHertz absorption and dielectric relaxation spectroscopy. We find that the forward proton hopping events for NaAOT are further suppressed compared to a nonionic RM, while the Grotthuss mechanism ceases altogether for CTABr. We attribute the sluggish proton dynamics for both charged RMs as due to headgroup and counterion charges that expel hydronium and chloride ions from the interface and into the bulk interior, thereby increasing the pH of the acid pools relative to the nonionic RM. For charged NaAOT and CTABr RMs, the localization of hydronium near a counterion or conjugate base reduces the Eigen and Zundel configurations that enable forward hopping. Thus, localized oscillatory hopping dominates, an effect that is most extreme for CTABr in which the proton residence time increases dramatically such that even oscillatory hopping is slow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Activated penetrant dynamics in glass forming liquids: size effects, decoupling, slaving, collective elasticity and correlation with matrix compressibility

In this work, we employ the microscopic self-consistent cooperative hopping theory of penetrant activated dynamics in glass forming viscous liquids and colloidal suspensions to address new questions over a wide range of high matrix packing fractions and penetrant-to-matrix particle size ratios. The focus is on the mean activated relaxation time of smaller tracers in a hard sphere fluid of larger particle matrices. This quantity also determines the penetrant diffusion constant and connects directly with the structural relaxation time probed in an incoherent dynamic structure factor measurement. The timescale of the non-activated fast dissipative process is also studied and is predicted to follow power laws with the contact value of the penetrant–matrix pair correlation function and the penetrant–matrix size ratio. For long time penetrant relaxation, in the relatively lower packing fraction metastable regime the local cage barriers are dominant and matrix collective elasticity effects unimportant. As packing fraction and/or penetrant size grows, much higher barriers emerge and the collective elasticity associated with the correlated matrix dynamic displacement that facilitates penetrant hopping becomes important. This results in a non-monotonic variation with packing fraction of the degree of decoupling between the matrix and penetrant alpha relaxation times. The conditions required for penetrant hopping to become slaved to the matrix alpha process are determined, which depend mainly on the penetrant to matrix particle size ratio. By analyzing the absolute and relative importance of the cage and elastic barriers we establish a mechanistic understanding of the origin of the predicted exponential growth of the penetrant hopping time with size ratio predicted at very high packing fractions. A dynamics-thermodynamics power law connection between the penetrant activation barrier and the matrix dimensionless compressibility is established as a prediction of theory, with different scaling exponents depending on whether matrix collective elasticity effects are important. Quantitative comparisons with simulations of the penetrant relaxation time, diffusion constant, and transient localization length of tracers in dense colloidal suspensions and cold viscous liquids reveal good agreements. Multiple new predictions are made that are testable via future experiments and simulations. Extension of the theoretical approach to more complex systems of high experimental interest (nonspherical molecules, semiflexible polymers, crosslinked networks) interacting via variable hard or soft repulsions and/or short range attractions is possible, including under external deformation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Field-dependent carrier transport in implanted isolation region of GaN lateral power devices

Among GaN lateral power devices, with proper E-field management, the breakdown occurs in the device isolation region rather than the active region. In this paper, we investigate field-dependent carrier transport in the isolation structures. Isolation test structures with variations in buffer doping, un-intentionally doped (UID) GaN thickness, and implantation conditions were fabricated. Electrical characterization was performed over a wide range of voltage and temperature. With varying UID GaN thickness and buffer doping, the leakage current and breakdown characteristics remain the same for a specific implantation condition, indicating that the leakage conduction and breakdown are governed by the implanted GaN region. Analysis of the temperature-dependent I–V reveals that carrier transport in the implanted GaN can be well explained by hopping conduction, involving three distinctive regions of operation depending on the E-field. At low E-field, carrier transport is ohmic, consistent with variable range hopping, driven by thermal activation. At medium E-field, a field enhanced thermally activated hopping is observed, following σ ∼ σ(T)exp(E). At high E-field, activation-less hopping is visible, following σ ∼ exp(−1/E), which occurs above a critical E-field limited by localization length.

Sadek, Mansura (ORCID:0000000322588338)↗

Magic-angle semimetals with chiral symmetry

Here, we construct and solve a two-dimensional, chirally symmetric model of Dirac cones subjected to a quasiperiodic modulation. In real space, this is realized with a quasiperiodic hopping term. This hopping model, as we show, at the Dirac node energy has a rich phase diagram with a semimetal-to-metal phase transition at intermediate amplitude of the quasiperiodic modulation, and a transition to a phase with a diverging density of states (DOS) and subdiffusive transport when the quasiperiodic hopping is strongest. We further demonstrate that the semimetal-to-metal phase transition can be characterized by the multifractal structure of eigenstates in momentum space and can be considered as a unique “unfreezing” transition. This unfreezing transition in momentum space generates flat bands with a dramatically renormalized bandwidth in the metallic phase similar to the phenomena of the band structure of twisted bilayer graphene at the magic angle. We characterize the nature of this transition numerically as well as analytically in terms of the formation of a band of topological zero modes. For pure quasiperiodic hopping, we provide strong numerical evidence that the low-energy DOS develops a divergence and the eigenstates exhibit Chalker (quantum-critical) scaling despite the model not being random. At particular commensurate limits the model realizes higher-order topological insulating phases. We discuss how these systems can be realized in experiments on ultracold atoms and metamaterials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum/AI Topology-Aware Latency-Adaptive HPC Workflow Scheduling Optimization

The growing demand for more powerful high-performance computing (HPC) systems has led to a steady rise in energy consumption by supercomputing worldwide. This study is focused on comparing our Application-Topology Mapper (ATMapper) to the popular Simple Linux Utility for Resource Management (SLURM) for the purpose of exploring methods that can further optimize job-scheduling within HPC systems. ATMapper is an Artificial-Intelligence based approach to job-scheduling that is currently being enhanced with quantum annealing (QA) to generate optimal schedules faster. We are applying QA to speedup our ATMapper process to achieve higher computing efficiency, thereby reducing HPC energy consumption. Here, we examine how four job-scheduling approaches perform in processor node assignment when using an example network architecture of 4 interconnected nodes. Using a specialized script, we are assessing the schedule of a computation flow with 11 interdependent tasks. The data movements among nodes were tracked to count for the number of interactions (network hops) between nodes needed to complete the tasks. The total number of hops and the job completion time were then used to quantify the efficiency of the different mapping approaches. In addition to SLURM, we also compare our ATMapper to the QA-enabled LBNL TIGER and the D-Wave Distributed Computing processor assignment approaches. The preliminary results showed that our topology-aware, latency-adaptive ATMapper is significantly more efficient when compared to the other scheduling approaches due to its load-imbalance network allocation. The scheduler displayed a computing efficiency of 53% by performing significantly fewer network hops than its alternatives. By reducing the number of hops, ATMapper was able to perform all 11 tasks by using only 3 nodes out of given 4. This research indicates the potential to use QA/AI for HPC job-scheduling. Later, we will test a SLURM simulator program to draw further comparisons on the effectiveness of ATMapper's scheduling approach. The results of this comparison will serve as a baseline for later improving SLURM's performance using a QA-enhanced ATMapper approach.

Caraveo, Braulio [University of Huston - Clear Lak↗

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗