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At least 289 records · Page 16

Code for the manuscript titled "Blackout Diffusion: Generative Diffusion Models in Discrete-State Spaces"

We would like to disclose two scripts, written in Jupyter notebook, in which we implement the "Blackout Diffusion Process" described in the manuscript "Blackout Diffusion: Generative Diffusion Models in Discrete-State Spaces" (LA-UR-23-20509), to be submitted to the International Conference of Machine Learning (ICML). The abstract of the manuscript is append below. == Typical generative diffusion models rely on a Gaussian diffusion process for training the backward transformations, which can then be used generate samples from Gaussian noise. However, real world data often takes place in discrete-state spaces, which occur in many scientific applications. Here, we develop a theoretical formulation for arbitrary discrete-state Markov processes in the forward diffusion process. We relate the theory to the existing continuous-state Gaussian diffusion and identify the corresponding reverse-time stochastic process and score function in the continuous-time setting, and the reverse-time mapping in the discrete-time setting. As an example of this framework, we introduce "Blackout Diffusion", which learns to produce samples from an empty image instead of from noise. Numerical experiments on the CIFAR-10 dataset confirm the feasibility of generative diffusion modeling in a discrete space. Generalizing from specific (Gaussian) forward processes to a more general framework also sheds light on how to interpret generative diffusion models and their mathematical structure, which we comment on.

Lin, Yen Ting↗

Electron Beam Longitudinal Tracking (EBLT) v1.0

It is a serial/parallel code for fast electron beam longitudinal forward or backward tracking through an electron linear accelerator. This codes includes longitudinal space-charge effect, structure and resistive wall wakefields, and longitudinal coherent synchrotron radiation effect. To use it as a parallel code, please comment out the "use mpistub" in BeamBunch.f90, rename mpif.h as mpif.hh, and use the Makefile_parallel as Makefile.

Qiang, Ji↗

TReactMech v4.217

TReactMech couples geomechanical processes (poroelasticity, failure, and inelastic strain) with multiphase nonisothermal flow (derived from TOUGH2) and reactive geochemical transport. At its core is the reactive-transport code TOUGHREACT v4.13. TReactMech is an efficient hybrid parallel simulator, solving the geomechanics using finite elements and MPI/PetSc, the multiphase flow using integrated finite difference and MPI/PETSc, and the reactive chemistry using OpenMP. The advantages of TReactMech are in its multiphase flow capabilities (e.g., supercritical CO2, supercritical water, air) and parallel geomechanics including full 3-D stress tensor, shear and tensile failure, coupled to porosity and permeability changes. It is backwardly compatible with TOUGH2 and TOUGHREACT v4.13, allowing for easier transitions between the codes. TReactMech can be used to simulate many natural and engineered subsurface systems, including geothermal reservoirs, borehole heat exchangers, geologic carbon sequestration, geologic storage of nuclear waste, groundwater resources, weathering, sediment diagenesis, seafloor hydrothermal circulation, hydrofracturing in unconventional reservoirs, and injection/production-induced surface deformation.

Sonnenthal, Eric↗

PyTorch Circuit-Aware Bit-Cell Modeling

SAND2024-08549O PyTorch Circuit-Aware Bit-Cell Modeling, a Python library, demonstrates circuit-aware training for analog machine learning accelerators. Built upon PyTorch, this software provides hardware-aware versions of common neural network layers to mitigate non-ideal behavior from novel hardware. The software provides accurate forward and backward pass estimates for hardware-mapped neural networks that are implemented in crossbars (arrays) that contain a non-linear transistor selector device. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Bennett, Christopher↗

Optimization Layers for Pyomo [SWR-25-132]

Optimization Layers for Pyomo solves an optimization problem using Pyomo and IPOPT during the forward pass. It computes the gradient of the optimal solution with respect to the parameters based on the KKT conditions in the backward pass. It is a Python library for constructing differentiable optimization layers in PyTorch from Pyomo optimization models.

Chen, Kejun [National Laboratory of the Rockies (N↗

torch-einshard v1.0

torch-einshard is a Python library for describing local and distributed PyTorch tensor computations with compact, einsum-like notation. Its expressions name logical axes, specify how they are sharded across a PyTorch DeviceMesh, and represent partial reductions. The library automatically performs contractions, permutations, reshaping, splitting, gathering, reduction, reduce-scatter, and repartitioning while preserving autograd. Additional features include sharding-aware FFTs, tensor rolls, halo exchange, sliding windows, 1D–3D convolutions, uneven-shard handling, parameter initialization and gradient management, and cost-based execution planning. It is designed for scientific machine learning and large-model workloads, including tensor-, sequence-, and spatial-parallel MLPs, attention, convolutions, and spectral operations. Compared with manually combining torch.einsum and distributed collectives, torch-einshard expresses both the mathematical operation and data placement in one readable formula. This reduces boilerplate and synchronization errors, keeps forward and backward communication consistent, and allows the library to select optimized collective strategies without changing model code.

Morozov, Dmitriy [Lawrence Berkeley National Labor↗

Data-Driven Transition Path Analysis Yields a Statistical Understanding of Sudden Stratospheric Warming Events in an Idealized Model

Abstract Atmospheric regime transitions are highly impactful as drivers of extreme weather events, but pose two formidable modeling challenges: predicting the next event (weather forecasting) and characterizing the statistics of events of a given severity (the risk climatology). Each event has a different duration and spatial structure, making it hard to define an objective “average event.” We argue here that transition path theory (TPT), a stochastic process framework, is an appropriate tool for the task. We demonstrate TPT’s capacities on a wave–mean flow model of sudden stratospheric warmings (SSWs) developed by Holton and Mass, which is idealized enough for transparent TPT analysis but complex enough to demonstrate computational scalability. Whereas a recent article (Finkel et al. 2021) studied near-term SSW predictability, the present article uses TPT to link predictability to long-term SSW frequency. This requires not only forecasting forward in time from an initial condition, but also backward in time to assess the probability of the initial conditions themselves. TPT enables one to condition the dynamics on the regime transition occurring, and thus visualize its physical drivers with a vector field called the reactive current . The reactive current shows that before an SSW, dissipation and stochastic forcing drive a slow decay of vortex strength at lower altitudes. The response of upper-level winds is late and sudden, occurring only after the transition is almost complete from a probabilistic point of view. This case study demonstrates that TPT quantities, visualized in a space of physically meaningful variables, can help one understand the dynamics of regime transitions.

Meteorology & Atmospheric Sciences↗

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗

Exponential time differencing scheme for mass transport and depletion in molten salt reactors

This work extends the capability previously shown for addressing the problem of computing depletion and mass transport calculations in molten salt reactors (MSRs) by calculating matrix exponentials. Additional algorithms are implemented to compute the matrix exponential and the action of the matrix exponential on a matrix. These algorithms include two methods based on the Pade approximation, a Taylor series method, and three methods based on Cauchy's integral formula. In addition to the added matrix exponential solvers, a variable-order total variation diminishing scheme is applied to the convective flux approximation to provide enhanced accuracy. Finally, a simplified MSR problem is shown for each of the exponential time differencing solvers along with classical backwards differencing integrators. The results show excellent convergence for exponential time differencing methods. Computation time is a key element for selecting the optimal solver in these problems, and this work shows that Pade and Cauchy-based solvers may provided the fastest and most accurate solutions. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

SSA Monte Carlo and Master Equation Modeling of Neutron Leakage Distributions

Strongly stochastic neutron populations in highly subcritical multiplying media containing weak spontaneous fission sources are unique indicators of the presence of SNM. For instance, in neutron multiplicity counting, an extended tail in the count number probability distribution is observed that is a characteristic of and sensitive to the amount of SNM present. Theoretical modeling and efficient computation of stochastic neutron distributions are complementary to experimental measurements and moreover shed light on the fundamental interactions and transport processes that underlie nuclear signatures. Modeling approaches that are intermediate between gross-system level models and high-fidelity but computationally demanding Monte Carlo simulations are of particular interest in this regard. Furthermore we present three advances on existing work in point kinetic or lumped geometry: (i) implementation of the Stochastic Simulation Algorithm (SSA), a system state-updating Monte Carlo method that is more e cient than single-event Monte Carlo in lumped geometries, (ii) application of the backward Master equation to obtain time-gated count moments, and (iii) reconstructing the count number distribution from the deterministically computed moments using a generalized Laguerre polynomial expansion.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

EXPLAINABLE AND TRUSTWORTHY DIAGNOSTICS ACHIEVABLE THROUGH PROCESS-BASED AUTOMATED REASONING

An approach has been developed that incorporates domain knowledge to obtain a more explainable and trustworthy equipment health monitoring diagnosis than might otherwise be obtained from a purely data-driven method. Physics-based models serve to constrain the realizable solution space and render a more trusted diagnosis. An automated reasoning algorithm performs backward chaining to infer a diagnosis that is consistent with logic statements that have been evaluated as true. This diagnosis is made explainable to an operator by providing the forward chaining path that elucidates for inspection and validity testing those truths implied by the diagnosis.

automated reasoning↗

Infrared all-dielectric Kerker metasurfaces

The unidirectional scattering of electromagnetic waves in the backward and forward direction, termed Kerkers’ first and second conditions, respectively, is a prominent feature of sub-wavelength particles, which also has been found recently in all-dielectric metasurfaces. Here we formulate the exact polarizability requirements necessary to achieve both Kerker conditions simultaneously with dipole terms only and demonstrate its equivalence to so-called “invisible metasurfaces”. We further describe the perfect absorption mechanism in all-dielectric metasurfaces through development of an extended Kerker formalism. The phenomena of both invisibility and perfect absorption is shown in a 2D hexagonal array of cylindrical resonators, where only the resonator height is modified to switch between the two states. The developed framework provides critical insight into the range of scattering response possible with all-dielectric metasurfaces, providing a methodology for studying exotic electromagnetic phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Symmetric second-harmonic generation in sub-wavelength periodically poled thin film lithium niobate

Second-harmonic generation (SHG) extensively employs periodically poled nonlinear crystals through forward quasi-phase-matching to achieve efficient frequency conversion. As poling periods approach sub-micrometers, backward quasi-phase-matching has also been demonstrated, albeit by utilizing pulsed laser drives. The realization of symmetric second-harmonic generation, characterized by counterpropagating pumps, however, has remained elusive despite theoretical predictions. The main challenge lies in achieving strong nonlinear coupling with the poling period below half the wavelength of the second-harmonic light. The recent emergence of high-quality ferroelectric lithium niobate thin films provides an opportunity for achieving precise domain control at submicron dimensions. In this paper, we demonstrate reliable control of ferroelectric domains in a thin film lithium niobate waveguide with a poling period down to 370 nm, thereby realizing highly efficient continuous-wave pumped symmetric SHG. This demonstration not only validates the feasibility of achieving subwavelength periodic poling on waveguides but could also enable submicron ferrolectric domain structures to be leveraged in integrated photonics and nonlinear optics research.

Optics↗

Exceptional points in a passive strip waveguide

Abstract Exceptional points (EPs) in non‐Hermitian systems have attracted significant interest due to their unique behaviors, including novel wave propagation and radiation. While EPs have been explored in various photonic systems, their integration into standard photonic platforms can expand their applicability to broader technological domains. In this work, we propose and experimentally demonstrate EPs in an integrated photonic strip waveguide configuration, exhibiting unique deep wave penetration and uniform‐intensity radiation profiles. By introducing the second‐order grating on one side of the waveguide, forward and backward propagating modes are coupled both directly through second‐order coupling and indirectly through first‐order coupling via a radiative intermediate mode. To describe the EP behavior in a strip configuration, we introduce modified coupled‐mode equations that account for both transverse and longitudinal components. These coupled‐mode formulas reveal the formation of EPs in bandgap closure, achieved by numerically optimizing the grating’s duty cycle to manipulate the first‐ and second‐order couplings simultaneously. Experimental observations, consistent with simulations, confirm the EP behavior, with symmetric transmission spectra and constant radiation profiles at the EP wavelength, in contrast to conventional exponential decay observed at detuned wavelengths. These results demonstrate the realization of EPs in a widely applicable strip waveguide configuration, paving the way for advanced EP applications in nonlinear and ultrafast photonics, as well as advanced sensing technologies.

Materials Science↗

Downscaled precipitation and mean air temperature datasets; East-Taylor subbasin; 2008-2019; daily temporal resolution; 400 m spatial resolution

This dataset provides gridded meteorological forcing data (specifically, daily precipitation and daily mean air temperature). The dataset has been generated by downscaling the Parameter-elevation Regressions on Independent Slopes Model (PRISM) dataset from a spatial resolution of 800 m to 400 m. The time period is 2008-2019, and the mapped area is East Taylor subbasin in Upper Colorado. The data are in the form of NetCDF files, arranged by year. Compared to the PRISM dataset, the dates of the downscaled dataset are shifted backwards by one (e.g., downscaled data for May 25 corresponds to PRISM data for May 26). This temporal shifting makes the meteorological forcing correspond more closely to the prescribed date. The NetCDF format is a standard raster format that can be read using any Geographic Information System (GIS) software; plenty of modules exist in popular scripting languages (such as Python, R and Matlab) that can also be used to read NetCDF files.East_Taylor_Tavg_PRISM400 corresponds to mean air temperature.East_Taylor_Precip_PRISM400.zip corresponds to precipitation.The proprietary PRISM data (800 m resolution) were purchased with funding from the Watershed Function Scientific Focus Area supported by U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award no. DE-AC02-05CH11231.Dataset update on March 9, 2022:Uploaded new data files that are identical to the earlier files but are now in the NetCDF format, arranged by year. Earlier, the files were in the GeoTiff format, arranged by date.

54 ENVIRONMENTAL SCIENCES↗

IDAES-PSE 2.2.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. New features in the 2.2 release include: DiagnosticsToolbox DiagnosticsToolbox (idaes.core.util.model_diagnostics. DiagnosticsToolbox is a new self-guiding toolbox for assisting with diagnosing modeling issues. The toolbox contains a wide range of tools for identifying common modeling issues and conveying these to the user, and more features will be added in the coming months. To try the new toolbox, use the following steps: from idaes.core.util import DiagnosticsToolbox Build an instance of your model Ensure your models has zero degrees of freedom (as best you can) dt = DiagnosticsToolbox(model) dt.report_structural_issues() Follow the prompts Deprecations DegeneracyHunter is being deprecated in favor of the new DiagnosticsToolbox. The features and capabilities of DegeneracyHunter will be moved over to the DiagnositcsToolbox in the coming months. Removal of usage of Pyomo's expr.current due to deprecation upstream. Removed support for radial basis functions in ALAMOpy as these did not work in the current implementation. Those wishing to use radial basis functions should use Pysmo instead. New Capabilities MSContactor model for unit operations involving mass transfer between 2 or more streams, such as membrane, solvent extraction and solids leaching operations. Other Improvements Improved formulation for solubility products with additional parameters for better scaling of terms Better backward compatibility, verification and robustness testing of core models and APIs Added support for Separator models without energy balances

DiagnosticsToolbox↗

IDAES-PSE 2.1.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.1.0 Release Highlights New IDAES Examples Repository Starting with this release, the IDAES examples are developed in the new IDAES/examples repository. Along with many content and usability improvements, the most significant changes are: To install the examples, after installing IDAES, run pip install idaes-examples The idaes get-examples command, previously used for this, has been removed The HTML version is now available at https://idaes-examples.readthedocs.io The previous URL, https://idaes.github.io/examples-pse, will not be updated and may be removed at some point in the future For more details, refer to the resources available at IDAES/examples. Removal of Non-Functional Apps A review of the code in the idaes/apps and idaes/models_extra folders was undertaken, and a number of tools were identified as being outdated or non-functional and no longer supported by their development teams. Due to this, the following tools have been removed: idaes/apps/alamopy_depr (note that the new ALAMOpy interface remains avaialble in idaes/core/surrogates) idaes/apps/helmet idaes/apps/ripe idaes/apps/roundingRegression idaes/models_extra/carbon_capture Pyomo 6.6 This version of IDAES is the first requiring Pyomo 6.6. This version of Pyomo contains multiple internal improvements and refactorings. While for the majority of cases this should have positive or no impact on solvability of IDAES models, we are aware of a small number of models that have been affected as a result of these changes. For more information, refer to the Pyomo 6.6.1 release notes. Other highlights Model Initialization A prototype API for a new approach to initializing IDAES models is now available which makes available some new techniques for initializing models. This is documented in the Initializing Models Reference Guide Modular Properties Framework Support for some transport properties Helmholtz Equation of State properties Better error checking for case where unit models are set to include phase equilibrium but the property package is set to support only a single phase Multi-Stream Contactor model: a new base model for systems involving contacting of two or more streams with mass transfer. This model is intended to be used as the foundation for models such as membrane separators, solvent extraction and other similar processes. This is documented in the Multi-Stream Contactor Reference Guide idaes/models_extra/power_generation report() methods for unit models using Helmholtz equation of state General Code Maintenance Streamlining of dependencies and creation of new optional dependency groupings to support non-core tools General linting of codebase to ensure compliance with most pylint checks Spell checking of all code and doc strings Removal of backward compatibility code for Python 2

IDAES↗

IDAES-PSE 2.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications. IDAES-PSE 2.0.0 Release Highlights Removal of deprecated features from IDAES v1 Update to Pyomo v6.5 – this required a number of updates to support the new NL solver writer and to address some changes in Pyomo Creation of new testing suite for backward compatibility, model robustness and verification More general implementation of the Helmholtz EoS. This brings some new features like standard property diagrams, choice of mass or mole basis, and new state variable options Standardizing names in Heat Exchanger models (breaking change from v2.0.0a2): Control Volumes named hot_side and cold_side Ports names hot_side_inlet, hot_side_outlet, cold_side_inlet and cold_side_outlet Config Blocks names hot_side_config and cold_side_config Config arguments for user provided names for each side: hot_side_name and cold_side_name. Updating Keras surrogate tool to use v1.1 of OMLT New prototype API for model initialization (idaes.core.initialization) The new API uses "Model Initializer" objects instead of class methods, allowing for the definition of multiple initialization routines for a single model A number of common, model agnostic initialization routines have also been defined, including initialization from data, block-decomposition and a general hierarchical approach equivalent to the existing method for common unit models New metadata for thermophysical properties – valid_range This can be used to record the range of values over which a property value can be trusted, such as the range of experimental data used to regress parameters A number of new utility functions have been added to check for properties with values outside the valid range and to set bounds based on this metadata Updated construction of balance expressions in Control Volumes to remove unneeded terms In the past, unneeded terms were added as a constant 0 term, however they will now be dropped entirely from the expression This was necessary due to more strict unit checking in the new Pyomo solver writer which no longer ignores 0 terms Updates to metadata for thermophysical properties to better define known properties and units of measurement This results in more strict enforcement of standard naming for thermophysical and reaction properties Users can still define custom properties, but these must be done explicitly using the define_custom_properties() method instead of being implicitly created by add_property() Updated convergence tester utility tool to support definition of benchmark files (JSON format) and comparison of performance to benchmarks Set default iteration limit for IPOPT in IDAES config to 200 iterations Update scaling of example models to work with new Pyomo NL solver writer Improve testing of extensions and examples infrastructure to avoid need for downloading files Updated distillation column to centralize common functionality and remove a number of Pyomo warnings

IDAES↗