A 2.1 GS/s 2-Channel Pipeline-SAR ADC With Speed-Enhanced Bootstrap Switch and Low-Latency SAR Logic
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Fu, Tao [Department of Electrical and Computer Eng↗
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Results for “Computational pipelines”
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Outlook for artificial intelligence and machine learning at the NSLS-II
Abstract We describe the current and future plans for using artificial intelligence and machine learning (AI/ML) methods at the National Synchrotron Light Source II (NSLS-II), a scientific user facility at the Brookhaven National Laboratory. We discuss the opportunity for using the AI/ML tools and techniques developed in the data and computational science areas to greatly improve the scientific output of large scale experimental user facilities. We describe our current and future plans in areas including from detecting and recovering from faults, optimizing the source and instrument configurations, streamlining the pipeline from measurement to insight, through data acquisition, processing, analysis. The overall strategy and direction of the NSLS-II facility in relation to AI/ML is presented.
97 MATHEMATICS AND COMPUTING↗
A Length Adaptive Algorithm-Hardware Co-design of Transformer on FPGA Through Sparse Attention and Dynamic Pipelining
Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm–hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 × and 2.6 × speedup compared to CPU and GPU implementation, and 4 × higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.
Peng, Hongwu↗
Cosmic shear in harmonic space from the Dark Energy Survey Year 1 Data: compatibility with configuration space results
ABSTRACT We perform a cosmic shear analysis in harmonic space using the first year of data collected by the Dark Energy Survey (DES-Y1). We measure the cosmic weak lensing shear power spectra using the metacalibration catalogue and perform a likelihood analysis within the framework of CosmoSIS. We set scale cuts based on baryonic effects contamination and model redshift and shear calibration uncertainties as well as intrinsic alignments. We adopt as fiducial covariance matrix an analytical computation accounting for the mask geometry in the Gaussian term, including non-Gaussian contributions. A suite of 1200 lognormal simulations is used to validate the harmonic space pipeline and the covariance matrix. We perform a series of stress tests to gauge the robustness of the harmonic space analysis. Finally, we use the DES-Y1 pipeline in configuration space to perform a similar likelihood analysis and compare both results, demonstrating their compatibility in estimating the cosmological parameters S8, σ8, and Ωm. We use the DES-Y1 metacalibration shape catalogue, with photometric redshifts estimates in the range of 0.2−1.3, divided in four tomographic bins finding σ8(Ωm/0.3)0.5 = 0.766 ± 0.033 at 68 per cent CL. The methods implemented and validated in this paper will allow us to perform a consistent harmonic space analysis in the upcoming DES data.
79 ASTRONOMY AND ASTROPHYSICS↗
Why is the winner the best?
International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi- center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), im- age preprocessing (97%), data curation (79%), and post- processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.
Eisenmann, Matthias↗
Enhanced polymorph metastability drives glycine nucleation in aqueous salt solutions
Crystal nucleation from aqueous solutions influences countless geological, biochemical, astrophysical, environmental, and materials science–related phenomena, including ice formation, the manufacturing of active pharmaceutical ingredients, development of diseases such as Alzheimer’s and the origin of life itself. Understanding and controlling nucleation is essential for designing materials with specific properties, developing strategies to inhibit or promote crystallization in various contexts and preventing pathological aggregation in neurodegenerative diseases. Similar to the protein structure prediction problem—where a single amino acid sequence can in theory adopt one most stable conformation but in practice may sample multiple competing conformations—crystal nucleation faces a parallel challenge: the same chemical species can form diverse polymorphs under different environmental conditions (e.g., temperature, pressure, solvent). Each polymorph presents its own set of physical and chemical properties, highlighting the importance of understanding and controlling polymorph selection in fields ranging from pharmaceuticals to materials design. Despite advances in experimental and computational methods for studying phase transitions and polymorph stability, nucleation remains challenging due to its nanoscale nature. Furthermore, in practical settings, salts and impurities can further influence crystal nucleation in diverse contexts, from scaling in pipelines and desalination plants to the durability of concrete and the efficiency of battery materials. This can lead to the formation of polymorphs that may differ from the most stable phase in pure solutions. Or, even though the final structure might appear same irrespective of whether the environment contained impurities or not, the mechanism through which it was formed might be completely different and not intuitive.
Wang, Ruiyu [University of Maryland, College Park,↗
TomoPyUI : a user-friendly tool for rapid tomography alignment and reconstruction
The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data ( i.e. organizing data/metadata, applying image filters etc. ) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI , a user interface for the well known tomography data processing package TomoPy . This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI , along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI , and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Understanding the Design Space of Sparse/Dense Multiphase Dataflows for Mapping Graph Neural Networks on Spatial Accelerators
Graph Neural Networks (GNNs) have garnered a lot of recent interest because of their success in learning representations from graph-structured data across several critical applications in cloud and HPC. Owing to their unique compute and memory characteristics that come from an interplay between dense and sparse phases of computations, the emergence of reconfigurable dataflow (aka spatial) accelerators offers promise for acceleration by mapping optimized dataflows (i.e., computation order and parallelism) for both phases. The goal of this work is to characterize and understand the design-space of dataflow choices for running GNNs on spatial accelerators in order for the compilers to optimize the dataflow based on the workload. Specifically, we propose a taxonomy to describe all possible choices for mapping the dense and sparse phases of GNNs spatially and temporally over a spatial accelerator, capturing both the intra-phase dataflow and the inter-phase (pipelined) dataflow. Using this taxonomy, we do deep-dives into the cost and benefits of several dataflows and perform case studies on implications of hardware parameters for dataflows and value of flexibility to support pipelined execution.
97 MATHEMATICS AND COMPUTING↗
Full forward model of galaxy clustering statistics with AbacusSummit light cones
ABSTRACT Novel summary statistics beyond the standard 2-point correlation function (2PCF) are necessary to capture the full astrophysical and cosmological information from the small-scale (r < 30h−1Mpc) galaxy clustering. However, the analysis of beyond-2PCF statistics on small scales is challenging because we lack the appropriate treatment of observational systematics for arbitrary summary statistics of the galaxy field. In this paper, we develop a full forward modelling pipeline for a wide range of summary statistics using the large high-fidelity AbacusSummit light cones that account for many systematic effects as well as remain flexible and computationally efficient to enable posterior sampling. We apply our forward model approach to a fully realistic mock galaxy catalog and demonstrate that we can recover unbiased constraints on the underlying galaxy–halo connection model using two separate summary statistics: the standard 2PCF and the novel k-th nearest neighbour (kNN) statistics, which are sensitive to correlation functions of all orders. We will demonstrate its strong constraining power on extended galaxy–halo connection models and cosmology in follow up papers. We expect this to become a powerful approach when applying to upcoming surveys such as DESI where we can leverage a multitude of summary statistics across a wide redshift range to maximally extract information from the non-linear scales.
79 ASTRONOMY AND ASTROPHYSICS↗
A knowledge-informed large language model framework for U.S. nuclear power plant shutdown initiating event classification for probabilistic risk assessment
Identifying and classifying shutdown initiating events (SDIEs) is critical for developing shutdown probabilistic risk assessment for nuclear power plants. Existing computational approaches cannot achieve satisfactory performance due to the challenges of unavailable large, labeled datasets, imbalanced event types, and label noise. To address these challenges, we propose a hybrid pipeline that integrates a knowledge-informed machine learning model to prescreen non-SDIEs and a large language model (LLM) to classify SDIEs into four types. In the prescreening stage, we proposed a set of 44 SDIE text patterns that consist of the most salient keywords and phrases from six SDIE types. Text vectorization based on the SDIE patterns generates feature vectors that are highly separable by using a simple binary classifier. The second stage builds Bidirectional Encoder Representations from Transformers (BERT)-based LLM, which learns generic English language representations from self-supervised pretraining on a large dataset and adapts to SDIE classification by fine-tuning it on an SDIE dataset. The proposed approaches are evaluated on a dataset with 10,928 events using precision, recall ratio, F 1 score, and average accuracy. In conclusion, the results demonstrate that the prescreening stage can exclude more than 97% non-SDIEs, and the LLM achieves an average accuracy of 95.1% for SDIE classification.
99 - GENERAL AND MISCELLANEOUS↗
Effectiveness of Deep Learning Trained on SynthCity Data for Urban Point-Cloud Classification
3D object recognition is one of the most popular areas of study in computer vision. Many of the more recent algorithms focus on indoor point clouds, classifying 3D geometric objects, and segmenting outdoor 3D scenes. One of the challenges of the classification pipeline is finding adequate and accurate training data. Hence, this article seeks to evaluate the accuracy of a synthetically generated data set called SynthCity, tested on two mobile laser-scan data sets. Varying levels of noise were applied to the training data to reflect varying levels of noise in different scanners. The chosen deep-learning algorithm was Kernel Point Convolution, a convolutional neural network that uses kernel points in Euclidean space for convolution weights.
Geology↗
EJFAT Scientific Perspective
Presented new computing model to the test by deploying the EJFAT system alongside a data-stream processing framework running the production-level CLAS12 event reconstruction application. In this experiment, a continuous stream of CLAS12 Level-1 identified events was processed in real-time using the EJFAT load balancer, distributing the workload across 90 computing nodes located across the U.S. This marks the first-ever large-scale, real-time distributed data stream processing experiment, demonstrating that scientific data-streaming pipelines can efficiently scale across four dimensions, thanks to EJFAT’s advanced hardware and software capabilities.
Gyurjyan, Vardan [Thomas Jefferson National Accele↗
DEEP CELLULAR RECURRENT NEURAL ARCHITECTURE FOR EFFICIENT MULTIDIMENSIONAL TIME-SERIES DATA PROCESSING
Efficient processing of time series data is a fundamental yet challenging problem in pattern recognition. Though recent developments in machine learning and deep learning have enabled remarkable improvements in processing large scale datasets in many application domains, most are designed and regulated to handle inputs that are static in time. Many real-world data, such as in biomedical, surveillance and security, financial, manufacturing and engineering applications, are rarely static in time, and demand models able to recognize patterns in both space and time. Current machine learning (ML) and deep learning (DL) models adapted for time series processing tend to grow in complexity and size to accommodate the additional dimensionality of time. Specifically, the biologically inspired learning based models known as artificial neural networks that have shown extraordinary success in pattern recognition, tend to grow prohibitively large and cumbersome in the presence of large scale multi-dimensional time series biomedical data such as EEG. Consequently, this work aims to develop representative ML and DL models for robust and efficient large scale time series processing. First, we design a novel ML pipeline with efficient feature engineering to process a large scale multi-channel scalp EEG dataset for automated detection of epileptic seizures. With the use of a sophisticated yet computationally efficient time-frequency analysis technique known as harmonic wavelet packet transform and an efficient self-similarity computation based on fractal dimension, we achieve state-of-the-art performance for automated seizure detection in EEG data. Subsequently, we investigate the development of a novel efficient deep recurrent learning model for large scale time series processing. For this, we first study the functionality and training of a biologically inspired neural network architecture known as cellular simultaneous recurrent neural network (CSRN). We obtain a generalization of this network for multiple topological image processing tasks and investigate the learning efficacy of the complex cellular architecture using several state-of-the?art training methods. Finally, we develop a novel deep cellular recurrent neural network (CDRNN) architecture based on the biologically inspired distributed processing used in CSRN for processing time series data. The proposed DCRNN leverages the cellular recurrent architecture to promote extensive weight sharing and efficient, individualized, synchronous processing of multi-source time series data. Experiments on a large scale multi-channel scalp EEG, and a machine fault detection dataset show that the proposed DCRNN offers state-of-the-art recognition performance while using substantially fewer trainable recurrent units.
Vidyaratne, Lasitha S.↗
Data readiness pipeline patterns for scientific AI at scale: Insights from climate, fusion, life sciences, and materials
This article examines how data readiness for AI principles apply to large scientific datasets used to train foundation models. We analyze archetypal workflows across four representative domains—climate, nuclear fusion, life sciences, and materials—to identify common preprocessing patterns and domain‐specific constraints. We introduce a two‐dimensional readiness model that combines canonical preprocessing patterns with a five‐level operational readiness scale, both tailored to high‐performance computing (HPC) environments. This construct helps outline key challenges in transforming large‐scale scientific data into formats suitable for scalable AI training. Together, these dimensions form a conceptual maturity matrix that characterizes scientific data readiness and guides infrastructure development toward standardized, cross‐domain support for scalable and reproducible AI for science. Finally, we evaluate this maturity matrix in the context of case studies including ClimaX (climate), AFLOW (materials), OpenFold (proteomics), and DIII‐D fusion disruption‐prediction workflows, from which we distill lessons learned and provide recommendations to guide practitioners in developing robust AI‐readiness pipelines. Finally, we discuss remaining cross‐cutting challenges that persist across scientific domains.
97 MATHEMATICS AND COMPUTING↗
Machine learning pipeline for denoising low signal-to-noise ratio and out-of-distribution transmission electron microscopy datasets
High-resolution transmission electron microscopy (HRTEM) is crucial for observing material’s structural and morphological evolution at Angstrom scales, but the electron beam can alter these processes. Devices such as CMOS-based direct-electron detectors operating in electron-counting mode can be utilized to substantially reduce the electron dosage. However, the resulting images often lead to a low signal-to-noise ratio, which requires frame integration that sacrifices temporal resolution. Several machine learning (ML) models have been recently developed to successfully denoise HRTEM images. Yet, these models are often computationally expensive, and their inference speeds on GPUs are outpaced by the imaging speed of advanced detectors, precluding in situ analysis. Furthermore, the performance of these denoising models on datasets with imaging conditions that deviate from the training datasets has not been evaluated. To mitigate these gaps, we propose a new self-supervised ML denoising pipeline specifically designed for time-series HRTEM images. This pipeline integrates a blind-spot convolution neural network with pre-processing and post-processing steps, including drift correction and low-pass filtering. Results demonstrate that our model outperforms various other ML and non-ML denoising methods in noise reduction and contrast enhancement, leading to improved visual clarity of atomic features. Additionally, the model is drastically faster than U-Net-based ML models and demonstrates excellent out-of-distribution generalization. The model’s computational inference speed is in the order of milliseconds per image, rendering it suitable for application in in-situ HRTEM experiments.
36 MATERIALS SCIENCE↗
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Constraining galaxy–halo connection with high-order statistics
ABSTRACT We investigate using three-point statistics in constraining the galaxy–halo connection. We show that for some galaxy samples, the constraints on the halo occupation distribution parameters are dominated by the three-point function signal (over its two-point counterpart). We demonstrate this on mock catalogues corresponding to the Luminous red galaxies (LRGs), Emission-line galaxies (ELGs), and quasars (QSOs) targeted by the Dark Energy Spectroscopic Instrument (DESI) Survey. The projected three-point function for triangle sides less up to 20 h−1 Mpc measured from a cubic Gpc of data can constrain the characteristic minimum mass of the LRGs with a preci sion of 0.46 per cent. For comparison, similar constraints from the projected two-point function are 1.55 per cent. The improvements for the ELGs and QSOs targets are more modest. In the case of the QSOs, it is caused by the high shot-noise of the sample, and in the case of the ELGs, it is caused by the range of halo masses of the host haloes. The most time-consuming part of our pipeline is the measurement of the three-point functions. We adopt a tabulation method, proposed in earlier works for the two-point function, to significantly reduce the required compute time for the three-point analysis.
79 ASTRONOMY AND ASTROPHYSICS↗
Utilization of Existing Pipelines in Hydrogen Transport: Literature Review Report
This report critically reviews the flow behavior of hydrogen-natural gas (H 2 -NG) mixtures in pipelines and examines the critical factors of hydrogen integration into existing natural gas infrastructure. It addresses the choking behavior characterized by velocity increase and pressure drop, as well as the effects of flow restrictions and pressure losses during hydrogen transport. Computational and analytical models are used to investigate these effects, and their effects on thermodynamic properties and system performance are evaluated. The study also reviews the energy efficiency and flow dynamics of hydrogen and methane-hydrogen mixtures and optimizes the hydrogen flow rate. In addition, the effects of these mixtures on the flow characteristics are discussed in detail, with special emphasis on the compressibility factor (z factor) and fluid properties based on equations of state for hydrogen-natural gas mixtures. The study also analyzes the mixture ratios and highlights the thermophysical properties, flow dynamics, and hydrogen-blended natural gas application potential. These investigations assess flow stability, material interactions, and operational feasibility of transporting hydrogen mixtures through natural gas pipelines, which contribute to developing sustainable and efficient energy systems.
08 HYDROGEN↗