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At least 145 records · Page 8

Material Identification From Radiographs Without Energy Resolution

We propose a method for performing material identification from radiographs without energy-resolved measurements. Material identification has a wide variety of applications, including in biomedical imaging, nondestructive testing, and security. While existing techniques for radiographic material identification make use of dual energy sources, energy-resolving detectors, or additional (e.g., neutron) measurements, such setups are not always practical— requiring additional hardware and complicating imaging. We tackle material identification without energy resolution, allowing standard X-ray systems to provide material identification information without requiring additional hardware. Assuming a setting where the geometry of each object in the scene is known and the materials come from a known set of possible materials, we pose the problem as a combinatorial optimization with a loss function that accounts for the presence of scatter and an unknown gain and propose a branch and bound algorithm to efficiently solve it. We present experiments on both synthetic data and real, experimental data with relevance to security applications— thick, dense objects imaged with MeV X-rays. We show that material identification can be efficient and accurate, for example, in a scene with three shells (two copper, one aluminum), our algorithm ran in six minutes on a consumer-level laptop and identified the correct materials as being among the top 10 best matches out of 8,000 possibilities.

36 MATERIALS SCIENCE↗

Impact of graph structures for QAOA on MaxCut

The quantum approximate optimization algorithm (QAOA) is a promising method of solving combinatorial optimization problems using quantum computing. QAOA on the MaxCut problem has been studied extensively on graphs with specific structure; however, little is known about the general performance of the algorithm on arbitrary graphs. Here, we investigate how different graph characteristics correlate with QAOA performance at depths at most three on the MaxCut problem for all connected non-isomorphic graphs with at most eight vertices. Some good predictors of QAOA success relate to graph symmetries, odd cycles, and density. For example, on eight vertex graphs, the average probability for selecting an optimal solution for graphs that contain no odd cycles after three iterations of QAOA is 60.6% compared to 48.2% for those that do. The data generated from these studies are shared in a publicly accessible database to serve as a benchmark for QAOA calculations and experiments. Knowing the relationship between structure and performance can be used to identify classes of combinatorial problems that are likely to exhibit a quantum advantage.

97 MATHEMATICS AND COMPUTING↗

Towards Generalizable and Efficient Circuit Topology Design: A Graph-Transformer-based Surrogate Model with Curriculum Learning

Unlike circuit parameter and sizing optimizations, the automated design of analog circuit topologies poses significant challenges for learning-based approaches. One challenge arises from the combinatorial growth of the topology space with circuit size, which limits the topology optimization efficiency. Moreover, traditional circuit evaluation methods are time-consuming, while the presence of data discontinuity in the topology space makes the accurate prediction of circuit performance exceptionally difficult for unseen topologies. To tackle these challenges, we design a novel Graph-Transformer-based Network (GTN) as the surrogate model for circuit evaluation, offering a substantial acceleration in the speed of circuit topology optimization without sacrificing performance. Our GTN model architecture is designed to embed voltage changes in circuit loops and current flows in connected devices, enabling accurate performance predictions for circuits with unseen topologies. To address the cold start problem when scaling GTN to large-scale circuits, we further introduce a curriculum learning strategy that progressively trains GTN from small-scale to large-scale circuits. This approach enables the model to first learn fundamental physical principles from simpler topologies and gradually adapt to complex configurations, effectively bridging the circuit complexity gap and improving prediction accuracy. Taking the power converter circuit design as an experimental task, our GTN model significantly outperforms an analytical approach and baseline methods directly utilizing graph neural networks. Furthermore, GTN achieves less than 5% relative error and 196× speed-up compared with high-fidelity simulation. Notably, our GTN surrogate model empowers an automatic circuit design framework to discover circuits of comparable quality to those identified through high-fidelity simulation while reducing the time required by up to 98.2%. With curriculum learning, the enhanced GTN achieves a 51% improvement for performance prediction of large-scale circuits compared to the GTN model without this strategy. These advancements establish GTN as a scalable framework for automated analog circuit design across varying circuit complexity levels.

Lu, Haoshu [New Jersey Institute of Technology (NJ↗

Runway Configuration Management with Offline Reinforcement Learning

Runway configuration management (RCM) is a challenging task, and it affects the efficiency of the National Airspace System (NAS) and airport surface operations significantly. Each airport, depending on the geometry, capacity, local climate patterns, etc. has multiple configurations for the runway usage for arriving and departing flights. Many factors such as the incoming/outgoing traffic load, wind direction and speed, convective weather, cloud ceiling and other environmental factors might affect the choice of a runway configuration at any point in time. However, other factors such as safety measures and regulations, noise abatement, capacity of each configuration, and preference of the air traffic controllers (ATCs) can also play a significant role in selecting the configuration. A sub-optimal selection of the runway configuration, or delay in making configuration changes might result in significant increase in taxi times for aircraft on the surface of the airport, fuel and energy use of the aircraft, and maintenance costs. It can also lead to safety concerns, such as an aircraft performing one or more go-arounds before being able to land. All these factors make RCM an extremely important and challenging decision-making process for the ATCs. The current state of practice sets the runway configuration by the ATCs based on relevant information available at the time including weather, traffic, noise abatement, safety bounds, etc. This makes the decision-making process subjective based on the accuracy of the available information and the bias in human decision making. Unfortunately, this approach yields poor results (e.g., significant delays) if the predicted outcomes are uncertain and their relative impact is not well understood. This is especially evident when the uncertainty increases the size of possible predicted outcomes (combinatorial explosion in possible scenarios) that cannot be handled by human reasoning. On the other hand, an automated approach based on machine intelligence can make use of historical data and search through all (or significant amount of) possible scenarios under uncertainty and make well-informed decisions.

Milad Memarzadeh↗

Machine Learning-Enabled Image Classification for Automated Electron Microscopy

Abstract Traditionally, materials discovery has been driven more by evidence and intuition than by systematic design. However, the advent of “big data” and an exponential increase in computational power have reshaped the landscape. Today, we use simulations, artificial intelligence (AI), and machine learning (ML) to predict materials characteristics, which dramatically accelerates the discovery of novel materials. For instance, combinatorial megalibraries, where millions of distinct nanoparticles are created on a single chip, have spurred the need for automated characterization tools. This paper presents an ML model specifically developed to perform real-time binary classification of grayscale high-angle annular dark-field images of nanoparticles sourced from these megalibraries. Given the high costs associated with downstream processing errors, a primary requirement for our model was to minimize false positives while maintaining efficacy on unseen images. We elaborate on the computational challenges and our solutions, including managing memory constraints, optimizing training time, and utilizing Neural Architecture Search tools. The final model outperformed our expectations, achieving over 95% precision and a weighted F-score of more than 90% on our test data set. This paper discusses the development, challenges, and successful outcomes of this significant advancement in the application of AI and ML to materials discovery.

Materials Science↗

Multiplexed binary assembly and quantitative tracking of bacterial populations

Compositions and methods for tracking combinations of mutations in populations by coupling DNA assembly and paired-end sequencing technology with high-throughput sequencing. This allows for an unlimited number of mutation sites in a population of microorganisms to be identified, and allows sites to be sequenced across several replicates. Unique identifiers (DNA barcodes) can be used to measure fitness data by sequencing of the barcodes multiplexed with the mutation sites with high-throughput short sequencing read technology, allowing selections to be rapidly performed on populations of known combinatorial genotypes.

59 BASIC BIOLOGICAL SCIENCES↗

Invariant discovery of features across multiple length scales: Applications in microscopy and autonomous materials characterization

Physical imaging is a foundational characterization method in areas from condensed matter physics and chemistry to astronomy and spans length scales from atomic to universe. Images encapsulate crucial data regarding atomic bonding, materials microstructures, and dynamic phenomena such as microstructural evolution and turbulence, among other phenomena. The challenge lies in effectively extracting and interpreting this information. Variational Autoencoders (VAEs) have emerged as powerful tools for identifying the underlying factors of variation in image data, providing a systematic approach to distilling meaningful patterns from complex data sets. However, a significant hurdle in their application is the definition and selection of appropriate descriptors reflecting local structures. Here, we introduce the scale-invariant VAE approach (SI-VAE) based on the progressive training of the VAE with the descriptors sampled at different length scales. The SI-VAE allows the discovery of the length scale-dependent factors of variation in the system. Here, we illustrate this approach using the ferroelectric domain images and generalize it to the movies of the electron-beam induced phenomena in graphene and topography evolution across combinatorial libraries. This approach can further be used to initialize the decision making in automated experiments including structure–property discovery and can be applied across a broad range of imaging methods. This approach is universal and can be applied to any spatially resolved data including both experimental imaging studies and simulations, and can be particularly useful for exploration of phenomena such as turbulence and scale-invariant transformation fronts.

36 MATERIALS SCIENCE↗

Discovery of unknown posttranslational modifications by top-down mass spectrometry

Post-translational modifications can be important biomarkers of function within biological systems. Top-down mass spectrometry is a valuable tool for the characterization of combinatorial modifications on proteins such as histones that have a range of complex modifications. In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel modifications on proteins. The data analysis workflow presented here is reliant on the combination of proteoform searching using TopPIC and data visualization and fragment ion spectral confirmation using LcMsSpectator, part of the Informed-Proteomics package of software.

Wilson, Jesse W.↗

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei

Recently, advantages concerning targeting specificity of PCR constructed oligonucleotide FISH probes in contrast to established FISH probes, e.g. BAC clones, have been demonstrated. These techniques, however, are still using labelling protocols with DNA denaturing steps applying harsh heat treatment with or without further denaturing chemical agents. COMBO-FISH (COMBinatorial Oligonucleotide FISH) allows the design of specific oligonucleotide probe combinations in silico. Thus, being independent from primer libraries or PCR laboratory conditions, the probe sequences extracted by computer sequence data base search can also be synthesized as single stranded PNA-probes (Peptide Nucleic Acid probes). Gene targets can be specifically labelled with at least about 20 PNA-probes obtaining visibly background free specimens. By using appropriately designed triplex forming oligonucleotides, the denaturing procedures can completely be omitted. These results reveal a significant step towards oligonucleotide-FISH maintaining the 3D-nanostructure and even the viability of the cell target. The method is demonstrated with the detection of Her2/neu and GRB7 genes, which are indicators in breast cancer diagnosis and therapy. - Highlights: • Denaturation free protocols preserve 3D architecture of chromosomes and nuclei. • Labelling sets are determined in silico for duplex and triplex binding. • Probes are produced chemically with freely chosen backbones and base variants. • Peptide nucleic acid backbones reduce hindering charge interactions. • Intercalating side chains stabilize binding of short oligonucleotides.

60 APPLIED LIFE SCIENCES↗

Revealing EDL-driven reduction mechanisms in binary, ternary, and quaternary fluorinated electrolytes via an integrated MD–DFT–ML framework

Accurately predicting solid electrolyte interphase (SEI) formation requires explicitly resolving the electric double layer (EDL) structure, which deviates significantly from that of the bulk electrolyte. Although an established molecular dynamics (MD) and Density Functional Theory (DFT) framework can model SEI formation by evaluating reduction reactions of local clusters in the EDL, it suffers from a combinatorial computational bottleneck. To overcome this limitation, we introduce a machine-learning-accelerated simulation workflow (MD–DFT–ML), integrating a gradient-boosted regression model trained on EDL composition data to efficiently predict reduction potentials. We apply this framework to seven fluorinated electrolytes comprising fluorinated anions, a fluorinated ester solvent, two types of diluent (ion-solvating ester vs. non-solvating ether), and an FEC additive. The analysis shows that the EDL selectively accumulates cation-binding species; consequently, the non–cation-binding ether diluent rarely enters the EDL and makes minimal contributions to SEI formation. DFT calculations on statistically representative EDL clusters provide reduction potentials and fluorine-release pathways, while the ML model, which substantially reduces the DFT workload, predicts cluster reduction energies with a mean absolute error of 0.1 eV. The combined MD–DFT–ML approach also quantifies contributions from different sources to LiF formation in the SEI. This methodology establishes a generalizable route for multiscale modeling electrolyte and interphase design for next-generation electrochemical energy-storage systems.

DFT-MD-ML workflow↗

High-throughput investigation of crystal-to-glass transformation of Ti–Ni–Cu ternary alloy

A high-throughput investigation of metallic glass formation via solid-state reaction was reported in this paper. Combinatorial multilayered thin-film chips covering the entire Ti-Ni-Cu ternary system were prepared using ion beam sputtering technique. Microbeam synchrotron X-ray diffraction (XRD) and X-ray fluorescence (XRF) measurements were conducted, with 1,325 data points collected from each chip, to map out the composition and the phase constitution before and after annealing at 373 K for 110 hours. The composition dependence of the crystal-to-glass transition by solid-state reaction was surveyed using this approach. The resulting composition-phase map is consistent with previously reported results. Time-of-flight secondary ion mass spectroscopy (ToF-SIMS) was performed on the representative compositions to determine the inter-diffusion between layers, the result shows that the diffusion of Ti is the key factor for the crystal-to-glass transition. In addition, both layer thickness and layer sequence play important roles as well. This work demonstrates that combinatorial chip technique is an efficient way for systematic and rapid study of crystal-to-glass transition for multi-component alloy systems.

36 MATERIALS SCIENCE↗

A combined machine learning and density functional theory study of binary Ti-Nb and Ti-Zr alloys: Stability and Young’s modulus

The multicomponent Ti alloys, specifically the -phase, have experienced a strong growth over the last decades, due to their outstanding properties of ultra-high strength and low Young’s modulus. These properties play a significant role in many aerospace and biomedical applications. Selection and optimization of multicomponent alloys is challenging due to the vast chemical and compositional space. Here we investigate the use of machine learning techniques informed by density functional calculations to guide the selection of Nb- and Zr-based Ti binary alloys. From the cubic structures obtained from high throughput calculations and literature, we identify several structures with Young’s moduli below 40 GPa. The multivariant decision tree methods provide efficient surrogate models to identify structure variables have high influences on the energetic stability and Young’s modulus. Furthermore, we implement a workflow of incorporating DFT provided results and machine learning method to explore the chemical and composition space of other binary and multicomponent alloys, to eventually accelerate the material design via taking advantages of identified key variables.

36 MATERIALS SCIENCE↗

Measurement of charged hadron multiplicity in Au + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV with the sPHENIX detector

The pseudorapidity distribution of charged hadrons produced in Au + Au collisions at a center-of-mass energy of $\sqrt{s_{NN}}$ = 200 GeV is measured using data collected by the sPHENIX detector. Charged hadron yields are extracted by counting cluster pairs in the inner and outer layers of the Intermediate Silicon Tracker, with corrections applied for detector acceptance, reconstruction efficiency, combinatorial pairs, and contributions from secondary decays. The measured distributions cover |η| < 1.1 across various centralities, and the average pseudorapidity density of charged hadrons at mid-rapidity is compared to predictions from Monte Carlo heavy-ion event generators. This result, featuring full azimuthal coverage at mid-rapidity, is consistent with previous experimental measurements at the Relativistic Heavy Ion Collider, thereby supporting the broader sPHENIX physics program.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Toward Accelerating Discovery via Physics-Driven and Interactive Multifidelity Bayesian Optimization

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often nondifferentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest toward active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge of the system in the form of partially known physics laws and exploration policies often vary during the experiment. Here, we propose an interactive workflow building on multifidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) structured MFBO (sMFBO), and finally extend it to allow human-in-the-loop interactive interactive MFBO (iMFBO) workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly nonsmooth multifidelity simulation data generated from an Ising model, considering spin–spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real-time human decisions for improved exploration with increased alignment to ground truth. Here, the associated notebooks allow to reproduce the reported analyses and apply them to other systems.

97 MATHEMATICS AND COMPUTING↗

High-throughput fabrication and semi-automated characterization of oxide thin film transistors

High throughput experimental methods are known to accelerate the rate of research, development, and deployment of electronic materials. For example, thin films with lateral gradients in composition, thickness, or other parameters have been used alongside spatiallyresolved characterization to assess how various physical factors affect material properties under varying measurement conditions. Similarly, multi-layer electronic devices that contain such graded thin films as one or more of their layers can also be characterized spatially in order to optimize the performance. In this work, we apply these high throughput experimental methods to thin film transistors (TFTs), demonstrating combinatorial device fabrication and semiautomated characterization using sputtered oxide TFTs as a case study. Here, we show that both extrinsic and intrinsic types of device gradients can be generated in a TFT library, such as channel thickness and length, channel cation compositions, and oxygen atmosphere during deposition. We also present a semi-automated method to measure the 44 devices fabricated on a 50x50mm substrate that can help to identify properly functioning TFTs in the library and finish the measurement in a short time. Finally, we propose a fully automated characterization system for similar TFT libraries, which can be coupled with high throughput data analysis. These results demonstrate that high throughput methods can accelerate the investigation of TFTs and other electronic devices.

36 MATERIALS SCIENCE↗

In vitro cardiotoxicity assessment of environmental chemicals using an organotypic human induced pluripotent stem cell-derived model

An important target area for addressing data gaps through in vitro screening is the detection of potential cardiotoxicants. Despite the fact that current conservative estimates relate at least 23% of all cardiovascular disease cases to environmental exposures, the identities of the causative agents remain largely uncharacterized. Here, we evaluate the feasibility of a combinatorial in vitro/in silico screening approach for functional and mechanistic cardiotoxicity profiling of environmental hazards using a library of 69 representative environmental chemicals and drugs. Human induced pluripotent stem cell-derived cardiomyocytes were exposed in concentration-response for 30 min or 24 h and effects on cardiomyocyte beating and cellular and mitochondrial toxicity were assessed by kinetic measurements of intracellular Ca{sup 2+} flux and high-content imaging using the nuclear dye Hoechst 33342, the cell viability marker Calcein AM, and the mitochondrial depolarization probe JC-10. More than half of the tested chemicals exhibited effects on cardiomyocyte beating after 30 min of exposure. In contrast, after 24 h, effects on cell beating without concomitant cytotoxicity were observed in about one third of the compounds. Concentration-response data for in vitro bioactivity phenotypes visualized using the Toxicological Prioritization Index (ToxPi) showed chemical class-specific clustering of environmental chemicals, including pesticides, flame retardants, and polycyclic aromatic hydrocarbons. For environmental chemicals with human exposure predictions, the activity-to-exposure ratios between modeled blood concentrations and in vitro bioactivity were between one and five orders of magnitude. These findings not only demonstrate that some ubiquitous environmental pollutants might have the potential at high exposure levels to alter cardiomyocyte function, but also indicate similarities in the mechanism of these effects both within and among chemicals and classes. - Highlights: • The cardiotoxic potential of a broad range of environmental chemicals was evaluated. • Human iPSC cardiomyocytes were used for multiparametric in vitro profiling. • Dose-response relationships were established for functional and cytotoxicity assays. • Computational data integration provided chemical-specific bioactivity profiles. • An assessment of the profiles revealed chemical class-specific similarities.

60 APPLIED LIFE SCIENCES↗