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At least 1,801 records · Page 100

A phase transition for finding needles in nonlinear haystacks with LASSO artificial neural networks

To fit sparse linear associations, a LASSO sparsity inducing penalty with a single hyperparameter provably allows to recover the important features (needles) with high probability in certain regimes even if the sample size is smaller than the dimension of the input vector (haystack). More recently learners known as artificial neural networks (ANN) have shown great successes in many machine learning tasks, in particular fitting nonlinear associations. Small learning rate, stochastic gradient descent algorithm and large training set help to cope with the explosion in the number of parameters present in deep neural networks. Yet few ANN learners have been developed and studied to find needles in nonlinear haystacks. Driven by a single hyperparameter, our ANN learner, like for sparse linear associations, exhibits a phase transition in the probability of retrieving the needles, which we do not observe with other ANN learners. To select our penalty parameter, we generalize the universal threshold of Donoho and Johnstone (Biometrika 81(3):425–455, 1994) which is a better rule than the conservative (too many false detections) and expensive cross-validation. In the spirit of simulated annealing, we propose a warm-start sparsity inducing algorithm to solve the high-dimensional, non-convex and non-differentiable optimization problem. We perform simulated and real data Monte Carlo experiments to quantify the effectiveness of our approach.

97 MATHEMATICS AND COMPUTING↗

Reduced electron exposure for energy-dispersive spectroscopy using dynamic sampling

Analytical electron microscopy and spectroscopy of biological specimens, polymers, and other beam sensitive materials has been a challenging area due to irradiation damage. There is a pressing need to develop novel imaging and spectroscopic imaging methods that will minimize such sample damage as well as reduce the data acquisition time. The latter is useful for high-throughput analysis of materials structure and chemistry. Here, in this work, we present a novel machine learning based method for dynamic sparse sampling of EDS data using a scanning electron microscope. Our method, based on the supervised learning approach for dynamic sampling algorithm and neural networks based classification of EDS data, allows a dramatic reduction in the total sampling of up to 90%, while maintaining the fidelity of the reconstructed elemental maps and spectroscopic data. In conclusion, we believe this approach will enable imaging and elemental mapping of materials that would otherwise be inaccessible to these analysis techniques.

36 MATERIALS SCIENCE↗

Deep neural network improves the estimation of polygenic risk scores for breast cancer

Polygenic risk scores (PRS) estimate the genetic risk of an individual for a complex disease based on many genetic variants across the whole genome. Here, we compared a series of computational models for estimation of breast cancer PRS. A deep neural network (DNN) was found to outperform alternative machine learning techniques and established statistical algorithms, including BLUP, BayesA, and LDpred. In the test cohort with 50% prevalence, the Area Under the receiver operating characteristic Curve (AUC) were 67.4% for DNN, 64.2% for BLUP, 64.5% for BayesA, and 62.4% for LDpred. BLUP, BayesA, and LPpred all generated PRS that followed a normal distribution in the case population. However, the PRS generated by DNN in the case population followed a bimodal distribution composed of two normal distributions with distinctly different means. This suggests that DNN was able to separate the case population into a high-genetic-risk case subpopulation with an average PRS significantly higher than the control population and a normal-genetic-risk case subpopulation with an average PRS similar to the control population. This allowed DNN to achieve 18.8% recall at 90% precision in the test cohort with 50% prevalence, which can be extrapolated to 65.4% recall at 20% precision in a general population with 12% prevalence. Interpretation of the DNN model identified salient variants that were assigned insignificant p values by association studies, but were important for DNN prediction. These variants may be associated with the phenotype through nonlinear relationships.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting wind-driven spatial deposition through simulated color images using deep autoencoders

Abstract For centuries, scientists have observed nature to understand the laws that govern the physical world. The traditional process of turning observations into physical understanding is slow. Imperfect models are constructed and tested to explain relationships in data. Powerful new algorithms can enable computers to learn physics by observing images and videos. Inspired by this idea, instead of training machine learning models using physical quantities, we used images, that is, pixel information. For this work, and as a proof of concept, the physics of interest are wind-driven spatial patterns. These phenomena include features in Aeolian dunes and volcanic ash deposition, wildfire smoke, and air pollution plumes. We use computer model simulations of spatial deposition patterns to approximate images from a hypothetical imaging device whose outputs are red, green, and blue (RGB) color images with channel values ranging from 0 to 255. In this paper, we explore deep convolutional neural network-based autoencoders to exploit relationships in wind-driven spatial patterns, which commonly occur in geosciences, and reduce their dimensionality. Reducing the data dimension size with an encoder enables training deep, fully connected neural network models linking geographic and meteorological scalar input quantities to the encoded space. Once this is achieved, full spatial patterns are reconstructed using the decoder. We demonstrate this approach on images of spatial deposition from a pollution source, where the encoder compresses the dimensionality to 0.02% of the original size, and the full predictive model performance on test data achieves a normalized root mean squared error of 8%, a figure of merit in space of 94% and a precision-recall area under the curve of 0.93.

54 ENVIRONMENTAL SCIENCES↗

The PAU Survey: narrow-band photometric redshifts using Gaussian processes

Here, we study the performance of the hybrid template machine learning photometric redshift (photo- z ) algorithm delight , which uses Gaussian processes, on a subset of the early data release of the Physics of the Accelerating Universe Survey (PAUS). We calibrate the fluxes of the 40 PAUS narrow bands with six broad-band fluxes ( uBVriz ) in the Cosmic Evolution Survey (COSMOS) field using three different methods, including a new method that utilizes the correlation between the apparent size and overall flux of the galaxy. We use a rich set of empirically derived galaxy spectral templates as guides to train the Gaussian process, and we show that our results are competitive with other standard photometric redshift algorithms. delight achieves a photo- z 68th percentile error of σ 68 = 0.0081(1 + z ) without any quality cut for galaxies with i auto < 22.5 as compared to 0.0089(1 + z ) and 0.0202(1 + z ) for the bpz and annz 2 codes, respectively. delight is also shown to produce more accurate probability distribution functions for individual redshift estimates than bpz and annz 2. Common photo- z outliers of delight and bcnz 2 (previously applied to PAUS) are found to be primarily caused by outliers in the narrow-band fluxes, with a small number of cases potentially indicating spectroscopic redshift failures in the reference sample. In the process, we introduce performance metrics derived from the results of bcnz 2 and delight , allowing us to achieve a photo- z quality of σ 68 < 0.0035(1 + z ) at a magnitude of i auto < 22.5 while keeping 50 per cent objects of the galaxy sample.

79 ASTRONOMY AND ASTROPHYSICS↗

Evidence for $CP$ violation and measurement of $CP$-violating parameters in B$^0_\mathrm{s}$ $\to$ J/$\psi\,\phi$(1020) decays in pp collisions at $\sqrt{s} =$ 13 TeV

A pioneering machine-learning-based flavor-tagging algorithm combining same-side and opposite-side tagging is used to obtain the equivalent of 27$\,$000 tagged B$^0_\mathrm{s}$$\to$ J/$\psi\, \phi$(1020) decays from pp collisions at $\sqrt{s} =$ 13 TeV, collected by the CMS experiment and corresponding to an integrated luminosity of 96.5 fb$^{-1}$. A time- and flavor-dependent angular analysis of the $\mu^+\mu^-$K$^+$K$^-$ final state is used to measure parameters of the $\mathrm{B}^0_\mathrm{s}$-$\overline{\mathrm{B}}^0_\mathrm{s}$ system. The weak phase is measured to be $\phi_\mathrm{s}$ = $-$73 $\pm$ 23 (stat) $\pm$ 7 (syst) mrad, which, combined with a $\sqrt{s}$ = 8 TeV CMS result, gives $\phi_\mathrm{s}$ = $-$74 $\pm$ 23 mrad. This value differs from zero by 3.2 standard deviations, providing evidence for $CP$ violation in B$^0_\mathrm{s}$$\to$ J/$\psi\,\phi$(1020) decays. All measured physics parameters are found to agree with standard model predictions where available.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Reconstruction of beam parameters and betatron radiation spectra measured with a Compton spectrometer

The photon flux resulting from high-energy electron beam interactions with high-field systems, such as those found in the upcoming FACET-II experiments at the SLAC National Accelerator Laboratory, yields deep insight into the electron beam’s underlying dynamics during the interaction. However, extracting this information is an intricate process. To demonstrate how to approach this challenge using modern methods, this paper utilizes simulated data that models plasma wakefield acceleration-derived betatron radiation in experiments to determine reliable methods of reconstructing key beam and beam-plasma interaction properties. For betatron radiation measurements, translating the observed 200⁢ keV to 30⁢ MeV photon double-differential energy-angle spectra obtained from an advanced Compton spectrometer requires testing multiple methods to optimize the pipeline from its response to incident electron beam information. The paper compares maximum likelihood estimation and machine learning to refine the translation of photon spectra into precise electron beam metrics, such as spot size, energy, and emittance, enhancing the understanding of beam behavior within these dense, high-field environments. We also introduce machine learning and the expected maximization algorithm to reconstruct the primary photon spectrum, employing a multilayer neural network for regression analysis of the energy and angle spectra. With appropriate modifications, the advanced methods reproduce relevant incident beam parameters with high accuracy, even for beam sizes in the <10 μ⁢m range. This capacity is critical to understanding intense beam propagation and its optimization in plasma.

Beam code development & simulation techniques↗

Fast and Accurate Support Vector Machines on Large Scale Systems

Support Vector Machines (SVM) is a supervised Machine Learning and Data Mining (MLDM) algorithm, which has become ubiquitous largely due to its high accuracy and obliviousness to dimensionality. The objective of SVM is to find an optimal boundary --- also known as hyperplane --- which separates the samples (examples in a dataset) of different classes by a maximum margin. Usually, very few samples contribute to the definition of the boundary. However, existing parallel algorithms use the entire dataset for finding the boundary, which is sub-optimal for performance reasons. In this paper, we propose a novel distributed memory algorithm to eliminate the samples which do not contribute to the boundary definition in SVM. We propose several heuristics, which range from early (aggressive) to late (conservative) elimination of the samples, such that the overall time for generating the boundary is reduced considerably. In a few cases, a sample may be eliminated (shrunk) pre-emptively --- potentially resulting in an incorrect boundary. We propose a scalable approach to synchronize the necessary data structures such that the proposed algorithm maintains its accuracy. We consider the necessary trade-offs of single/multiple synchronization using in-depth time-space complexity analysis. We implement the proposed algorithm using MPI and compare it with libsvm--- de facto sequential SVM software --- which we enhance with OpenMP for multi-core/many-core parallelism. Our proposed approach shows excellent efficiency using up to 4096 processes on several large datasets such as UCI HIGGS Boson dataset and Offending URL dataset.

Vishnu, Abhinav↗

MICCO: An Enhanced Multi-GPU Scheduling Framework for Many-Body Correlation Functions

Calculation of many-body correlation functions is one of the critical kernels utilized in many scientific computing areas, especially in Lattice Quantum Chromodynamics (Lattice QCD). It is formalized as a sum of a large number of contraction terms each of which can be represented by a graph consisting of vertices describing quarks inside a hadron node and edges designating quark propagations at specific time intervals. Due to its computation- and memory-intensive nature, real-world physics systems (e.g., multi-meson or multi-baryon systems) explored by Lattice QCD prefer to leverage multi-GPUs. Different from general graph processing, many-body correlation function calculations show two specific features: a large number of computation-/data-intensive kernels and frequently repeated appearances of original and intermediate data. The former results in expensive memory operations such as tensor movements and evictions. The latter offers data reuse opportunities to mitigate the data-intensive nature of many-body correlation function calculations. However, existing graph-based multi-GPU schedulers cannot capture these data-centric features, thus resulting in a sub-optimal performance for many-body correlation function calculations. To address this issue, this paper presents a multi-GPU scheduling framework, MICCO, to accelerate contractions for correlation functions particularly by taking the data dimension (e.g., data reuse and data eviction) into account. This work first performs a comprehensive study on the interplay of data reuse and load balance, and designs two new concepts: local reuse pattern and reuse bound to study the opportunity of achieving the optimal trade-off between them. Based on this study, MICCO proposes a heuristic scheduling algorithm and a machine-learning-based regression model to generate the optimal setting of reuse bounds. Specifically, MICCO is integrated into a real-world Lattice QCD system, Redstar, for the first time running on multiple GPUs. The evaluation demonstrates MICCO outperforms other state-of-art works, achieving up to 2.25× speedup in synthesized datasets, and 1.49× speedup in real-world correlation functions.

Wang, Qihan↗

ShiftNMFk 1.2

The ShiftNMFk1.2 code, or as we call it, GreenNMFk, represents a hybrid algorithm combining unsupervised adaptive machine learning and Green's function inverse method. GreenNMFk allows an efficient and high performance de-mixing and feature extraction of a multitude of nonnegative signals that change their shape propagating through the medium. The signals are mixed and recorded by a network of uncorrelated sensors. The code couples Non-negative Matrix Factorization (NMF) and inverse-analysis Green's functions method. GreenNMF synergistically performs decomposition of the recorded mixtures, finds the number of the unknown sources and uses the Green's function of the governing partial differential equation to identify the unknown sources and their charecteristics. GreenNMF can be applied directly to any problem controlled by a known partial-differential parabolic equation where mixtures of an unknown number of sources are measured at multiple locations. Full GreenNMFk method is a subject LANL U.S. Patent application S133364.000 August, 2017. The ShiftNMFk 1.2 version here is a toy version of this method that can work with a limited number of unknown sources (4 or less).

Alexandrov, BoianS.↗

Hpc Natural Language Understanding (nlu) Dataset

This code provides natural language annotation and labels for multiple activities in high performance. The purpose is to enable machine learning for natural language processing algorithms with high performance computing systems.

Biggs, BrandonS↗

Benders Cut Classification via Support Vector Machines for Solving Two-Stage Stochastic Programs

In this work, we consider Benders decomposition for solving two-stage stochastic programs with complete recourse based on finite samples of the uncertain parameters. We define the Benders cuts binding at the final optimal solution or the ones significantly improving bounds over iterations as valuable cuts. We propose a learning-enhanced Benders decomposition (LearnBD) algorithm, which adds a cut classification step in each iteration to selectively generate cuts that are more likely to be valuable cuts. The LearnBD algorithm includes two phases: (i) sampling cuts and collecting information from training problems and (ii) solving testing problems with a support vector machine (SVM) cut classifier. We run the LearnBD algorithm on instances of capacitated facility location and multicommodity network design under uncertain demand. Our results show that SVM cut classifier works effectively for identifying valuable cuts, and the LearnBD algorithm reduces the total solving time of all instances for different problems with various sizes and complexities.

97 MATHEMATICS AND COMPUTING↗

Smart Pixels: In-pixel AI for on-sensor data filtering

We present a smart pixel prototype readout integrated circuit (ROIC) designed in CMOS 28 nm bulk process, with in-pixel implementation of an artificial intelligence (AI) / machine learning (ML) based data filtering algorithm designed as proof-of-principle for a Phase III upgrade at the Large Hadron Collider (LHC) pixel detector. The first version of the ROIC consists of two matrices of 256 smart pixels, each 25$\times$25 µm\textsuperscript{2} in size. Each pixel consists of a charge-sensitive preamplifier with leakage current compensation and three auto-zero comparators for a 2-bit flash-type ADC. The frontend is capable of synchronously digitizing the sensor charge within 25 ns. Measurement results show an equivalent noise charge (ENC) of $\sim$30e\textsuperscript{-} and a total dispersion of $\sim$100e\textsuperscript{-} The second version of the ROIC uses a fully connected two-layer neural network (NN) to process information from a cluster of 256 pixels to determine if the pattern corresponds to highly desirable high-momentum particle tracks for selection and readout. The digital NN is embedded in-between analog signal processing regions of the 256 pixels without increasing the pixel size and is implemented as fully combinatorial digital logic to minimize power consumption and eliminate clock distribution, and is active only in the presence of an input signal. The total power consumption of the neural network is $\sim$ 300 $\mu$W. The NN performs momentum classification based on the generated cluster patterns and even with a modest momentum threshold, it is capable of 54.4\% – 75.4\% total data rejection, opening the possibility of using the pixel information at 40MHz for the trigger. The total power consumption of analog and digital functions per pixel is $\sim$ 6 $\mu$W per pixel, which corresponds to $\sim$ 1 W/cm\textsuperscript{2} staying within the experimental constraints.

Parpillon, Benjamin↗

Variance Preserving Spectral Subsampling

Generating statistically faithful short-duration gamma-ray spectra from a single long measurement is essential in nuclear safeguards, supporting tasks such as algorithm development and machine-learning applications, especially when list-mode data are unavailable. Existing subsampling methods often distort the statistical characteristics of genuine short-duration measurements, leading to biased or unreliable analytical outcomes and thereby undermining downstream tasks. In this work, we compare five subsampling approaches using a benchmark set of 156 genuine replicate spectra collected with a high-purity germanium detector. We evaluate each method with respect to run-to-run variance, channel-to-channel variance, and preservation of total counts (losslessness). Across a wide range of subsampling ratios, only binomial subsampling without replacement consistently reproduces the statistical properties of genuine short-duration spectra, maintaining proper dispersion even in sparse spectral regions and perfectly preserving total counts. These results provide a mathematically principled and practically validated framework for generating synthetically shortened spectra when true short-duration measurements are unavailable.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

PRMI: A Dataset of Minirhizotron Images for Diverse Plant Root Study

Understanding a plant's root system architecture (RSA) is crucial for a variety of plant science problem domains including sustainability and climate adaptation. Minirhizotron (MR) technology is a widely-used approach for phenotyping RSA non-destructively by capturing root imagery over time. Precisely segmenting roots from the soil in MR imagery is a critical step in studying RSA features. In this paper, we introduce a large-scale dataset of plant root images captured by MR technology. In total, there are over 72K RGB root images across six different species including cotton, papaya, peanut, sesame, sunflower, and switchgrass in the dataset. The images span a variety of conditions including varied root age, root structures, soil types, and depths under the soil surface. All of the images have been annotated with weak image-level labels indicating whether each image contains roots or not. The image-level labels can be used to support weakly supervised learning in plant root segmentation tasks. In addition, 63K images have been manually annotated to generate pixel-level binary masks indicating whether each pixel corresponds to root or not. These pixel-level binary masks can be used as ground truth for supervised learning in semantic segmentation tasks. By introducing this dataset, we aim to facilitate the automatic segmentation of roots and the research of RSA with deep learning and other image analysis algorithms.

Xu, Weihuang↗

Climate data for bioclimate research of Amazon Basin central region near the city of Manaus

The current research/data set deals with environmental data related to the region around the city of Manaus, Brazil, located in the Amazon Basin central region. The research problem encompasses the answers to the questions: 'What correlations can arise from the data of climate and fauna in the Amazon Basin?" "How useful is the data from instrumented stations related to that area, related to the fauna and climatic conditions?" To answer these questions, an initial data set was generated, taking into account the main pollutants with sources from NASA satellites, the Amazon Tall Tower Observatory (ATTO) experiment, and the GOAmazon project, from 2014 to 2015, along with other local data, such as the position of thermal electric power stations. It has been worth noting the data available was not coherent among the sources, due to different measuring time intervals, heights, and geographical locations. Equally important, for future bioclimatic research, a grid space of 5-km interval and a 30-minute time period was considered within the data set, covering a surface area within the boundaries of Latitude 2.00 S to 4.25 S and Longitude 59.00 to 61.25 W. The data from NASA satellites, ATTO, and GOAmazon do not have this kind of detailed grid and time mesh. To carry on, the machine learning (ML) Random Forest (RF) algorithm was selected and used, among other ML algorithms, to fill in the data into this new grid. The features considered were: data from NASA satellites and from the two projects above, covering the pollutants: ozone, NOx, particulates with diameter down to 10 nanometers, isoprene, CO, and acetonitrile. Moreover, distances and bearings to Manaus and 11 thermal power stations nearby, night and day time periods, dry and wet seasons, were also considered to compose the features. The interpolation produced by the Random Forest algorithm aimed at the pollutants: acetonitrile, ozone, NOx, Particulate N, isoprene, and CO, which are related to bioclimatic research commonly. In total, a data set was created with 51,148,800 rows, with 44 columns, 38 for the features and 6 for the targets.

54 ENVIRONMENTAL SCIENCES↗

Unobtrusive Multi-Static Serial LiDAR Imager (UMSLI) First Generation Shape-Matching Based Classifier for 2D Contours

A multi-static serial LiDAR system prototype was developed under DE-EE0006787 to detect, classify, and record interactions of marine life with marine hydrokinetic generation equipment. This software implements a shape-matching based classifier algorithm for the underwater automated detection of marine life for that system. In addition to applying shape descriptors, the algorithm also adopts information theoretical learning based affine shape registration, improving point correspondences found by shape descriptors as well as the final similarity measure.

Cao, Zheng↗

Efficient Parallelization of Irregular Applications on GPU Architectures

With the enlarging computation capacity of general Graphics Processing Units (GPUs), leveraging GPUs to accelerate parallel applications has become a critical topic in academia and industry. However, a wide range of irregular applications with the computation-/memory-intensive nature cannot easily achieve high GPU utilization. The challenges mainly involve the following aspects: first, data dependence leads to coarse-grained kernel and inefficient parallelism; second, heavy GPU memory usage may cause frequent memory evictions and extra overhead of I/O; third, specific computation patterns produce memory redundancies; last, workload balance and data reusability conjunctly benefit the overall performance, but there may exist a dynamic trade-off between them. Targeting these challenges, this dissertation proposes multiple optimizations to accelerate two real-world applications: many-body correlation functions to simulate nuclear physics in a large-scale scientific system; the other is the eALS-based matrix factorization recommendation system. To accelerate the calculations of many-body correlation functions, this dissertation presents three frameworks in GPU memory management and multi-GPU scheduling. Firstly, an optimized systematic GPU memory management framework, MemHC, utilizes a series of new memory reduction designs in GPU memory allocation, CPU/GPU communications, and GPU memory oversubscription. Secondly, an enhanced multi-GPU scheduling framework, MICCO, particularly by taking both data dimension (e.g., data reuse and data eviction) and computation dimension into account. MICCO designs a heuristic scheduling algorithm and a machine learning-based regression model to generate the optimal settings of a proposed new concept to manage the trade-off. Thirdly, a locality-aware multi-GPU scheduling framework. This scheduler leverages pipeline batch generation with a looking-ahead strategy by building local dependency graphs for memory transfer reduction and better data reuse, achieving up to 79.92% memory cost reduction and 1.67x speedup. To parallelize the eALS-based recommendation system, this dissertation proposes an efficient CPU/GPU heterogeneous recommendation system, HEALS. HEALS employs newly designed architecture-adaptive data formats to achieve load balance and good data locality on CPU and GPU. To mitigate the data dependence, HEALS presents a CPU/GPU collaboration model for both task parallelism and data parallelism with multiple kernel computation optimizations. In summary, this dissertation efficiently accelerates two typical irregular applications on GPUs by building four frameworks, including CPU/GPU collaboration, GPU memory management, and multi-GPU scheduling.

Wang, Qihan↗

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