KiDS-1000 cosmology: machine learning – accelerated constraints on interacting dark energy with CosmoPower
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A Spurio Mancini↗
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Results for “Interactive machine learning”
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Multiscale Optimization of Integrated Energy Systems Using Machine Learning Models for Market Interactions
The presentation was delivered at the 2022 American Institute of Chemical Engineers (AIChE) annual meeting.
Ghouse, Jaffer↗
A machine learning inversion scheme for determining interaction from scattering
Small angle scattering techniques have now been routinely used to quantitatively determine the potential of mean force in colloidal suspensions. However the numerical accuracy of data interpretation is often compounded by the approximations adopted by liquid state analytical theories. To circumvent this long standing issue, here we outline a machine learning strategy for determining the effective interaction in the condensed phases of matter using scattering. Via a case study of colloidal suspensions, we show that the effective potential can be probabilistically inferred from the scattering spectra without any restriction imposed by model assumptions. Comparisons to existing parametric approaches demonstrate the superior performance of this method in accuracy, efficiency, and applicability. This method can effectively enable quantification of interaction in highly correlated systems using scattering and diffraction experiments.
74 ATOMIC AND MOLECULAR PHYSICS↗
Characterization of Fuel Cladding Chemical Interaction on a High Burnup U-10Zr Metallic Fuel via Electron Energy Loss Spectroscopy Enhanced by Machine Learning
Fuel cladding chemical interaction (FCCI) is one of the main performance limiting factors for metallic nuclear fuels. The interaction destabilizes the martensitic microstructure and deteriorates mechanical properties of HT-9 cladding. The detection of low atomic number elements (Z<10) and overlapping of elemental peaks can be problematic in interpreting energy dispersive X-ray spectroscopy (EDS) data. Electron energy loss spectroscopy (EELS) provides precise elemental edge energy values and can detect elements with a low atomic number. This work utilizes EELS to study the distribution of lanthanides and light elements at the interaction region. The sample was prepared from the FCCI region of a U-10Zr (wt.%) solid fuel with HT-9 cladding, irradiated to a burnup of 13.2 at.%. Processing the EELS data included three major steps: 1) enhance the signal to noise ratio by denoising the spectrum with principal component analysis (PCA) method, removing background and performing deconvolution; 2) identify chemical elements with core energy loss edges; 3) confirm different phases using a popular machine learning method, K-means. This work presents qualitative assessment of lanthanides and light elements like carbon (C) and oxygen (O) enhanced by the application of machine learning algorithms. By comparing with EDS elemental maps, EELS provides higher resolution chemical maps, reveals the distribution of carbon at the interaction region supporting the formation of zirconium carbide, a rind-like microstructure feature that was proposed to mitigate the chemical interaction. Furthermore, the plasmon peak map was also found to indicate an energy shift associated with the formation of phases/compounds. K-means clustering method was used on the processed electron energy loss (EEL) spectrum to automatically reveal different phases. The resulting clustered maps from K-means clustering align well with elemental maps confirming certain phases, especially Fe-Ce and Zr-C, in the FCCI region.
EELS↗
Upscaling cross-scale flow and respiration interactions at river sediment interface leveraging observation, numerical models, and machine learning
Challenges include: The multiscale interactions among water, microbial respiration, and sediment under realistic riverbed conditions; The transferability of the scientific understanding of interactions at multiple sites; and the upscaling of these interactions from pore to reach scales.
54 ENVIRONMENTAL SCIENCES↗
Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption
A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.
97 MATHEMATICS AND COMPUTING↗
Beyond optimization—supervised learning applications in relativistic laser-plasma experiments
We explore the applications of machine learning techniques in relativistic laser-plasma experiments beyond optimization purposes. We predict the beam charge of electrons produced in a laser wakefield accelerator given the laser wavefront change caused by a deformable mirror. Machine learning enables feature analysis beyond merely searching for an optimal beam charge, showing that specific aberrations in the laser wavefront are favored in generating higher beam charges. Supervised learning models allow characterizing the measured data quality as well as recognizing irreproducible data and potential outliers. Furthermore, we also include virtual measurement errors in the experimental data to examine the model robustness under these conditions. This work demonstrates how machine learning methods can benefit data analysis and physics interpretation in a highly nonlinear problem of relativistic laser-plasma interaction.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
When do short-range atomistic machine-learning models fall short?
In this work, we explore the role of long-range interactions in atomistic machine-learning models by analyzing the effects on fitting accuracy, isolated cluster properties, and bulk thermodynamic properties. Such models have become increasingly popular in molecular simulations given their ability to learn highly complex and multi-dimensional interactions within a local environment; however, many of them fundamentally lack a description of explicit long-range interactions. In order to provide a well-defined benchmark system with precisely known pairwise interactions, we chose as the reference model a flexible version of the Extended Simple Point Charge (SPC/E) water model. Our analysis shows that while local representations are sufficient for predictions of the condensed liquid phase, the short-range nature of machine-learning models falls short in representing cluster and vapor phase properties. These findings provide an improved understanding of the role of long-range interactions in machine learning models and the regimes where they are necessary.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SDSS-IV MaNGA: Unveiling Galaxy Interaction by Merger Stages with Machine Learning
We use machine-learning techniques to classify galaxy merger stages, which can unveil physical processes that drive the star formation and active galactic nucleus (AGN) activities during galaxy interaction. The sample contains 4690 galaxies from the integral field spectroscopy survey SDSS-IV MaNGA and can be separated into 1060 merging galaxies and 3630 nonmerging or unclassified galaxies. For the merger sample, there are 468, 125, 293, and 174 galaxies (1) in the incoming pair phase, (2) in the first pericentric passage phase, (3) approaching or just passing the apocenter, and (4) in the final coalescence phase or post-mergers. With the information of projected separation, line-of-sight velocity difference, Sloan Digital Sky Survey (SDSS) gri images, and MaNGA Hα velocity map, we are able to classify the mergers and their stages with good precision, which is the most important score to identify interacting galaxies. For the two-phase classification (binary; nonmerger and merger), the performance can be high (precision > 0.90) with LGBMClassifier . We find that sample size can be increased by rotation, so the five-phase classification (nonmerger, and merger stages 1, 2, 3, and 4) can also be good (precision > 0.85). The most important features come from SDSS gri images. The contribution from the MaNGA Hα velocity map, projected separation, and line-of-sight velocity difference can further improve the performance by 0%–20%. In other words, the image and the velocity information are sufficient to capture important features of galaxy interactions, and our results can apply to all the MaNGA data, as well as future all-sky surveys.
79 ASTRONOMY AND ASTROPHYSICS↗
Higher-order factorization machine for accurate surrogate modeling in material design
Efficient and robust optimization is important in material science for identifying optimal structural parameters and enhancing material performance. Surrogate-based active learning algorithms have recently gained great attention for their ability to efficiently navigate large, high-dimensional design spaces. Among surrogate models, 2 nd -order factorization machine (FM) models are widely employed as the surrogate model in active learning algorithms due to their balance between simplicity and effectiveness. However, their quadratic nature limits their capacity to capture complex, higher-order interactions among variables, often leading to suboptimal solutions. To overcome this limitation, we propose an active learning scheme integrating a 3 rd -order FM model, capable of modeling three-variable interactions and more intricate relationships in material systems. We comprehensively evaluate the surrogate modeling performance of the 3 rd -order FM case using various objective functions. Furthermore, we examine the optimization reliability and efficiency of the 3 rd -order FM-based active learning in a real-world material design task (e.g., nanophotonic structures for transparent radiative cooling). Our study shows that the 3 rd -order FM outperforms the 2 nd -order model in both surrogate accuracy and optimization performance, highlighting higher-order models’ promises for material design and optimization problems.
Factorization machine↗
MLPF: efficient machine-learned particle-flow reconstruction using graph neural networks
In general-purpose particle detectors, the particle-flow algorithm may be used to reconstruct a comprehensive particle-level view of the event by combining information from the calorimeters and the trackers, significantly improving the detector resolution for jets and the missing transverse momentum. In view of the planned high-luminosity upgrade of the CERN Large Hadron Collider (LHC), it is necessary to revisit existing reconstruction algorithms and ensure that both the physics and computational performance are sufficient in an environment with many simultaneous proton–proton interactions (pileup). Machine learning may offer a prospect for computationally efficient event reconstruction that is well-suited to heterogeneous computing platforms, while significantly improving the reconstruction quality over rule-based algorithms for granular detectors. We introduce MLPF, a novel, end-to-end trainable, machine-learned particle-flow algorithm based on parallelizable, computationally efficient, and scalable graph neural network optimized using a multi-task objective on simulated events. We report the physics and computational performance of the MLPF algorithm on a Monte Carlo dataset of top quark–antiquark pairs produced in proton–proton collisions in conditions similar to those expected for the high-luminosity LHC. The MLPF algorithm improves the physics response with respect to a rule-based benchmark algorithm and demonstrates computationally scalable particle-flow reconstruction in a high-pileup environment.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states
We report molecular-orbital-based machine learning (MOB-ML) provides a general framework for the prediction of accurate correlation energies at the cost of obtaining molecular orbitals. The application of Nesbet’s theorem makes it possible to recast a typical extrapolation task, training on correlation energies for small molecules and predicting correlation energies for large molecules, into an interpolation task based on the properties of orbital pairs. We demonstrate the importance of preserving physical constraints, including invariance conditions and size consistency, when generating the input for the machine learning model. Numerical improvements are demonstrated for different datasets covering total and relative energies for thermally accessible organic and transition-metal containing molecules, non-covalent interactions, and transition-state energies. MOB-ML requires training data from only 1% of the QM7b-T dataset (i.e., only 70 organic molecules with seven and fewer heavy atoms) to predict the total energy of the remaining 99% of this dataset with sub-kcal/mol accuracy. This MOB-ML model is significantly more accurate than other methods when transferred to a dataset comprising of 13 heavy atom molecules, exhibiting no loss of accuracy on a size intensive (i.e., per-electron) basis. It is shown that MOB-ML also works well for extrapolating to transition-state structures, predicting the barrier region for malonaldehyde intramolecular proton-transfer to within 0.35 kcal/mol when only trained on reactant/product-like structures. Finally, the use of the Gaussian process variance enables an active learning strategy for extending the MOB-ML model to new regions of chemical space with minimal effort. We demonstrate this active learning strategy by extending a QM7b-T model to describe non-covalent interactions in the protein backbone–backbone interaction dataset to an accuracy of 0.28 kcal/mol.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing
Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units–accelerated quantum chemistry in the cloud, artificial intelligence–driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Laser Wakefield Accelerator modelling with Variational Neural Networks
A machine learning model was created to predict the electron spectrum generated by a GeV-class laser wakefield accelerator. The model was constructed from variational convolutional neural networks, which mapped the results of secondary laser and plasma diagnostics to the generated electron spectrum. An ensemble of trained networks was used to predict the electron spectrum and to provide an estimation of the uncertainty of that prediction. It is anticipated that this approach will be useful for inferring the electron spectrum prior to undergoing any process that can alter or destroy the beam. In addition, the model provides insight into the scaling of electron beam properties due to stochastic fluctuations in the laser energy and plasma electron density.
43 PARTICLE ACCELERATORS↗
The Impact of Streaming Data on Sensemaking with Mixed-Initative Visual Analytics
Visual data analysis helps people gain insights into data via interactive visualizations. People generate and test hypotheses and questions about data in context of the domain. This process can generally be referred to as sensemaking. Much of the work on studying sensemaking (and creating visual analytic techniques in support of it) has been focused on static datasets. However, how do the cognitive processes of sensemaking change when data are changing? Further, what implication for design does this create for mixed-initiative visual analytics systems? This paper presents the results of a user study analyzing the impact of streaming data on sensemaking. To perform this study, we developed a mixed-initiative visual analytic prototype, the Streaming Canvas, that affords the analysis of streaming text data. We compare the sensemaking process of people using this tool for a static and streaming dataset. We present the results of this study and discuss the implications on future visual analytic systems that combine machine learning and interactive visualization to help people make sense of streaming data.
visualization↗
Knowledge graph-aided Bayesian active learning for top- K genetic interaction discovery
In silico methods for predicting the effects of multi-gene perturbations hold great promise for advancing functional genomics, computational drug discovery, and disease modeling. However, the development of these predictive algorithms for mammalian systems has been hampered by limited datasets and high experimental costs. In this study, we present a Bayesian active learning framework designed to discover pairwise host gene knockdowns that effectively inhibit viral proliferation in an in vitro HIV-1 infection model. Our method leverages a biological knowledge graph as side information and employs a computationally efficient batch diversification approach. We evaluated this framework using a dataset of viral load measurements obtained from multi-day dual-gene depletion experiments, encompassing all possible pairwise knockdowns of over 350 host genes associated with HIV infection. We demonstrate that our framework rapidly identifies the most effective gene knockdown pairs for reducing viral load. Furthermore, we show that incorporating side information enhances performance during the early stages of active learning (low data regime), while our batch diversification strategy significantly boosts performance in later stages (high data regime). This framework is general and can be adapted to explore gene interactions in other contexts, such as synthetic lethality prediction and mapping epistatic effects across quantitative trait loci.
Computational biology and bioinformatics↗
Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials
There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.
97 MATHEMATICS AND COMPUTING↗
Inelastic Neutron Scattering Study of Magnetic Exchange Pathways in MnS
We report an investigation of the magnetic structure and magnetic exchange pathways in MnS via neutron scattering methods, aided by density functional theory (DFT) modeling. The material has been confirmed to undergo antiferromagnetic (AFM) ordering at 152 K, with the magnetic structure representing AFM stacking of ferromagnetic (FM) (111) planes of Mn magnetic moments. Correspondingly, the magnetic structure is described by a propagation vector k = (1/2, 1/2, 1/2), with the volume of the magnetic unit cell being 8 times larger than the volume of the nuclear unit cell. Analysis of inelastic neutron scattering (INS) data collected on a powder sample of MnS revealed that the next-nearest-neighbor magnetic exchange constant (J 2 ) exceeds the nearest-neighbor exchange constant (J 1 ) by more than 3 times, while in the case of MnO, which exhibits the same nuclear and magnetic structures as MnS, the J 2 /J 1 ratio was reported to be below 1.5. Although for MnO the signs of both J 1 and J 2 indicated AFM exchange interactions, machine-learning INS data analysis in combination with DFT calculations suggests that the INS data collected on MnS are best described with J 1 < 0 and J 2 > 0, corresponding to FM and AFM exchange couplings, respectively. To achieve a satisfactory fit to the experimentally observed data, the Hamiltonian used to model the INS spectra also included the next-next-nearest-neighbor magnetic exchange constant (J 3 ). The best-fit model has been obtained with the values of the exchange constants J 1 = -0.27 meV, J 2 = 1.05 meV, and J 3 = -0.19 meV.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗