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At least 271 records · Page 15

Iterative methods in GPU-resident linear solvers for nonlinear constrained optimization

Linear solvers are major computational bottlenecks in a wide range of decision support and optimization computations. The challenges become even more pronounced on heterogeneous hardware, where traditional sparse numerical linear algebra methods are often inefficient. For example, methods for solving ill-conditioned linear systems have relied on conditional branching, which degrades performance on hardware accelerators such as graphical processing units (GPUs). To improve the efficiency of solving ill-conditioned systems, our computational strategy separates computations that are efficient on GPUs from those that need to run on traditional central processing units (CPUs). Our strategy maximizes the reuse of expensive CPU computations. Iterative methods, which thus far have not been broadly used for ill-conditioned linear systems, play an important role in our approach. In particular, we extend ideas from Arioli et al., (2007) to implement iterative refinement using inexact LU factors and flexible generalized minimal residual (FGMRES), with the aim of efficient performance on GPUs. In conclusion, we focus on solutions that are effective within broader application contexts, and discuss how early performance tests could be improved to be more predictive of the performance in a realistic environment.

97 MATHEMATICS AND COMPUTING↗

Detecting False Data Injection Attacks Against Power System State Estimation With Fast Go-Decomposition Approach

State estimation is a fundamental function in modern energy management system, but its results may be vulnerable to false data injection attacks (FDIAs). FDIA is able to change the estimation results without being detected by the traditional bad data detection algorithms. In this paper, we propose an accurate and computational attractive approach for FDIA detection. In this work, we first rely on the low rank characteristic of the measurement matrix and the sparsity of the attack matrix to reformulate the FDIA detection as a matrix separation problem. Then, four algorithms that solve this problem are presented and compared, including the traditional augmented Lagrange multipliers (ALMs), double-noise-dual-problem (DNDP) ALM, the low rank matrix factorization, and the proposed new “Go Decomposition (GoDec).” Numerical simulation results show that our GoDec algorithm outperforms the other three alternatives and demonstrates a much higher computational efficiency. Furthermore, GoDec is shown to be able to handle measurement noise and applicable for large-scale attacks.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Quantitative Analysis of {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography Identifies Novel Prognostic Imaging Biomarkers in Locally Advanced Pancreatic Cancer Patients Treated With Stereotactic Body Radiation Therapy

Purpose: To identify prognostic biomarkers in pancreatic cancer using high-throughput quantitative image analysis. Methods and Materials: In this institutional review board–approved study, we retrospectively analyzed images and outcomes for 139 locally advanced pancreatic cancer patients treated with stereotactic body radiation therapy (SBRT). The overall population was split into a training cohort (n=90) and a validation cohort (n=49) according to the time of treatment. We extracted quantitative imaging characteristics from pre-SBRT {sup 18}F-fluorodeoxyglucose positron emission tomography, including statistical, morphologic, and texture features. A Cox proportional hazard regression model was built to predict overall survival (OS) in the training cohort using 162 robust image features. To avoid over-fitting, we applied the elastic net to obtain a sparse set of image features, whose linear combination constitutes a prognostic imaging signature. Univariate and multivariate Cox regression analyses were used to evaluate the association with OS, and concordance index (CI) was used to evaluate the survival prediction accuracy. Results: The prognostic imaging signature included 7 features characterizing different tumor phenotypes, including shape, intensity, and texture. On the validation cohort, univariate analysis showed that this prognostic signature was significantly associated with OS (P=.002, hazard ratio 2.74), which improved upon conventional imaging predictors including tumor volume, maximum standardized uptake value, and total legion glycolysis (P=.018-.028, hazard ratio 1.51-1.57). On multivariate analysis, the proposed signature was the only significant prognostic index (P=.037, hazard ratio 3.72) when adjusted for conventional imaging and clinical factors (P=.123-.870, hazard ratio 0.53-1.30). In terms of CI, the proposed signature scored 0.66 and was significantly better than competing prognostic indices (CI 0.48-0.64, Wilcoxon rank sum test P<1e-6). Conclusion: Quantitative analysis identified novel {sup 18}F-fluorodeoxyglucose positron emission tomography image features that showed improved prognostic value over conventional imaging metrics. If validated in large, prospective cohorts, the new prognostic signature might be used to identify patients for individualized risk-adaptive therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Fast-decaying plant litter enhances soil carbon in temperate forests but not through microbial physiological traits

Abstract Conceptual and empirical advances in soil biogeochemistry have challenged long-held assumptions about the role of soil micro-organisms in soil organic carbon (SOC) dynamics; yet, rigorous tests of emerging concepts remain sparse. Recent hypotheses suggest that microbial necromass production links plant inputs to SOC accumulation, with high-quality (i.e., rapidly decomposing) plant litter promoting microbial carbon use efficiency, growth, and turnover leading to more mineral stabilization of necromass. We test this hypothesis experimentally and with observations across six eastern US forests, using stable isotopes to measure microbial traits and SOC dynamics. Here we show, in both studies, that microbial growth, efficiency, and turnover are negatively (not positively) related to mineral-associated SOC. In the experiment, stimulation of microbial growth by high-quality litter enhances SOC decomposition, offsetting the positive effect of litter quality on SOC stabilization. We suggest that microbial necromass production is not the primary driver of SOC persistence in temperate forests. Factors such as microbial necromass origin, alternative SOC formation pathways, priming effects, and soil abiotic properties can strongly decouple microbial growth, efficiency, and turnover from mineral-associated SOC.

54 ENVIRONMENTAL SCIENCES↗

Spatial Mapping of Riverbed Grain-Size Distribution Using Machine Learning

Recent alluvial sediments in riverbeds play a significant role in controlling hydrologic exchange flows (HEFs) in river systems. The alluvial layer is usually associated with strong heterogeneity in physical properties (e.g., permeability and hydraulic conductivity), which affects local HEFs and therefore biogeochemical processes. The spatial distribution of these physical properties needs to be determined to inform the numerical models used to reveal the realistic hydro-biogeochemical behaviors. Such information can be obtained based on the intrinsic link between sediment grain-size distribution and hydraulic properties where sediment texture information is available. However, grain-size measurements are usually spatially sparse and do not have adequate coverage and resolution, particularly for a relatively large domain such as the Hanford Reach of the Columbia River. In this paper, we adopted machine learning (ML) approaches for categorizing and mapping the spatial distributions of riverbed substrate grain size and filling in missing areas of substrate data using the ML models along the reach. Such ML models for substrate size mapping were trained at 13,372 locations using measured substrate sizes along with observed and simulated attributes, including bathymetric attributes (e.g., elevation, slope, and aspect ratio) from LIDAR and bathymetric surveys, and hydrodynamic properties (e.g., water depth, velocity, shear stress, and their statistical moments). An ensemble bagging-based ML technique, Random Forest, was adopted to identify the most influential factors as predictors to develop the predictive models with over-fitting issues addressed. The models were evaluated with respect to each individual substrate size class and the lumped group, and then used to generate the final substrate size maps covering all the grid cells in the numerical modeling domain.

54 ENVIRONMENTAL SCIENCES↗

Characterizing Walk Trips in communities by Using Data from 2009 National Household Travel Survey, American Community Survey, and Other Sources

Non-motorized travel (i.e. walking and bicycling) are of increasing interest to the transportation profession, especially in context with energy consumption, reducing vehicular congestion, urban development patterns, and promotion of healthier life styles. This research project aimed to identify factors impacting the amount of travel for both walk and bike trips at the Census block group or tract level, using several public and private data sources. The key survey of travel behavior is the 2009 National Household Travel Survey (NHTS) which had over 87,000 walk trips for persons 16 and over, and over 6000 bike trips for persons 16 and over. The NHTS, in conjunction with the Census Bureau s American Community Survey, street density measures using Census Bureau TIGER, WalkScore , Nielsen Claritas employment estimates, and several other sources were used for this study. Stepwise Logistic Regression modeling techniques as well as Discriminant Analysis were applied using the integrated data set. While the models performed reasonably well for walk trips, travel by bike was abandoned due to sparseness of data. This paper discusses data sources utilized and modeling processes conducted under this study. It also presents a summary of findings and addresses data challenges and lesson-learned from this research effort.

NHTS↗

Predicting Seafloor Seismic Noise from Sea Surface Wave Heights and Vice Versa

Seismic hazard monitoring and global seismic tomography efforts are improved by recording seismic signals close to sources and at a variety of azimuths surrounding the source. While seismic networks have been deployed at many locations on land, seafloor stations are still sparse. Inclusion of ocean-based data would greatly improve the global coverage of seismic networks. However, the use of seafloor seismic data to complement land-based detection and characterization of events is complicated by the fact that ambient noise on the seafloor is in general much higher than noise levels on land. This noise is driven primarily by sea surface waves and tides. In this project, I define an empirical relationship between wave height and seafloor seismic displacement, and tie this relationship to the microseism noise theory of Longuet-Higgins and Ursell (1948). I find that while there appears to be a linear relationship between wave height and seismic displacement, wave height values can only be used with low confidence to predict seismic displacement and vice versa, and furthermore, factors other than wave height are significant in determining the level of seismic noise at a particular site.

58 GEOSCIENCES↗

Russian anthropogenic black carbon: Emission reconstruction and Arctic black carbon simulation

Development of reliable source emission inventories is needed to advance the understanding of the origin of Arctic haze using chemical transport modeling. This paper develops a regional anthropogenic black carbon (BC) emission inventory for the Russian Federation, the largest country by land area in the Arctic Council. Activity data from combination of local Russia information and international resources, emission factors based on either Russian documents or adjusted values for local conditions, and other emission source data are used to approximate the BC emissions. Emissions are gridded at a resolution of 0.1° × 0.1° and developed into a monthly temporal profile. Total anthropogenic BC emission of Russia in 2010 is estimated to be around 224 Gg. Gas flaring, a commonly ignored black carbon source, contributes a significant fraction of 36.2% to Russia's total anthropogenic BC emissions. Other sectors, i.e., residential, transportation, industry, and power plants, contribute 25.0%, 20.3%, 13.1%, and 5.4%, respectively. Three major BC hot spot regions are identified: the European part of Russia, the southern central part of Russia where human population densities are relatively high, and the Urals Federal District where Russia's major oil and gas fields are located but with sparse human population. BC simulations are conducted using the hemispheric version of Community Multi-scale Air Quality Model with emission inputs from a global emission database EDGAR (Emissions Database for Global Atmospheric Research)-HTAPv2 (Hemispheric Transport of Air Pollution) and EDGAR-HTAPv2 with its Russian part replaced by the newly developed Russian BC emissions, respectively. The simulation using the new Russian BC emission inventory could improve 30–65% of absorption aerosol optical depth measured at the AERONET sites in Russia throughout the whole year as compared to that using the default HTAPv2 emissions. At the four ground monitoring sites (Zeppelin, Barrow, Alert, and Tiksi) in the Arctic Circle, surface BC simulations are improved the most during the Arctic haze periods (October–March). The poor performance of Arctic BC simulations in previous studies may be partly ascribed to the Russian BC emissions built on out-of-date and/or missing information, which could result in biases to both emission rates and the spatial distribution of emissions. Finally, this study highlights that the impact of Russian emissions on the Arctic haze has likely been underestimated, and its role in the Arctic climate system needs to be reassessed. The Russian black carbon emission source data generated in this study can be obtained via http://abci.ornl.gov/download.shtml or http://acs.engr.utk.edu/Data.php.

54 ENVIRONMENTAL SCIENCES↗

Conservative Estimation of Tail Probabilities from Limited Sample Data

Several sparse-sample uncertainty quantification (UQ) methods are compared for conservative but not overly conservative estimation of small tail probabilities involving responses that lay beyond specified thresholds in the tails of probability distributions. Sixteen very differently shaped distributions (or probability density functions, PDFs) and tail probability magnitudes ranging from 10 -5 to 10 -1 are considered in order for the study to be relevant to a wide range of risk analysis and quantification of margins and uncertainty (QMU) problems. The emphasis of the study is on limited data regimes ranging from N = 2 to 20 samples, reflective of most experimental and some expensive computational situations. Relatively simple sparse-sample UQ methods tested for this regime involve statistical tolerance interval "Equivalent Normal and related "Ensemble of Normals" and "Superdistribution (SD) approaches. (The independently derived SD is effectively equivalent to the Bayesian posterior predictive distribution given the assumptions of the derivation.) The performance of the methods was generally improved for N ≥ 5 samples with a generalized Jackknife resampling technique, which determines a tail probability estimate by averaging estimates from smaller sub-samples. Several quantitative metrics for method conservatism and accuracy of tail probability estimation are used to assess and rank the methods' performance over many random trials for each test PDF and probability magnitude. A variant of Bootstrap resampling was also tried, but did not significantly improve tail probability estimates in most cases. Detailed results are presented from over 100-million tests over the above factors that provide useful granular information on which methods or combination of methods perform best in various areas of the factor space.

97 MATHEMATICS AND COMPUTING↗

Structural Heterogeneity and Hydrodynamics of an Intrinsically Disordered Protein Condensate

Biology demonstrates precise control over the free-energy landscape through the selective partitioning of biomacromolecules into membraneless organelles, enabling essential functions such as biochemical transformations, signaling cascades, and mechanical reinforcement. Although the function of these condensates depends on their underlying structure and hydrodynamics, molecular-scale information on these systems remains sparse. Here, in this study, neutron scattering is used to probe the organization and dynamics of the intrinsically disordered N-terminal domain of Galectin-3, an extracellular lectin responsible for facilitating liquid–liquid phase separation on the cellular surface, in both dilute and condensed phases. Dilute solutions contain isolated protein chains in equilibrium with mesoscopic clusters, whereas the condensed phase adopts a bicontinuous, microemulsion-like morphology. The dilute phase behavior is quantitatively described by coarse-grained polymer models from soft-matter physics, demonstrating their predictive power for complex biological proteins. At elevated concentrations, the proteins self-assemble akin to block copolymers, microphase separating through the aggregation of hydrophobic domains along the protein contour. The resulting condensate remains fluid-like despite a 25-fold increase in concentration; its internal hydrodynamics slow by only a factor of 3 relative to dilute protein chains. These results provide a molecular-level framework for how disordered proteins achieve both the structural complexity and dynamic fluidity of biomolecular condensates.

Carrick, Brian R. [Massachusetts Inst. of Technolo↗

Cloud condensation nuclei concentrations derived from the CAMS reanalysis

Determining number concentrations of cloud condensation nuclei (CCN) is one of the first steps in the chain in analysis of cloud droplet formation, the direct microphysical link between aerosols and cloud droplets, and a process key for aerosol–cloud interactions (ACI). However, due to sparse coverage of in situ measurements and difficulties associated with retrievals from satellites, a global exploration of their magnitude, source as well as temporal and spatial distribution cannot be easily obtained. Thus, a better representation of CCN numbers is one of the goals for quantifying ACI processes and achieving uncertainty-reduced estimates of their associated radiative forcing. Here, we introduce a new CCN dataset which is derived based on aerosol mass mixing ratios from the latest Copernicus Atmosphere Monitoring Service reanalysis (CAMSRA) in a diagnostic model that uses CAMSRA aerosol properties and a simplified kappa-Köhler framework suitable for global models. The emitted aerosols in CAMSRA are not only based on input from emission inventories using aerosol observations, they also have a strong tie to satellite-retrieved aerosol optical depth (AOD) as this is assimilated as a constraining factor in the reanalysis. Furthermore, the reanalysis interpolates for cases of poor or missing retrievals and thus allows for a full spatiotemporal quantification of CCN numbers. The derived CCN dataset captures the general trend and spatial and temporal distribution of total CCN number concentrations and CCN from different aerosol species. A brief evaluation with ground-based in situ measurements demonstrates the improvement of the modelled CCN over the sole use of AOD as a proxy for CCN as the overall correlation coefficient improved from 0.37 to 0.71. However, we find the modelled CCN from CAMSRA to be generally high biased and find a particular erroneous overestimation at one heavily polluted site which emphasises the need for further validation. The CCN dataset (https://doi.org/10.26050/WDCC/QUAERERE_CCNCAMS_v1, Block, 2023), which is now freely available to users, features 3-D CCN number concentrations of global coverage for various supersaturations and aerosol species covering the years 2003–2021 with daily frequency. This dataset is one of its kind as it offers lots of opportunities to be used for evaluation in models and in ACI studies.

54 ENVIRONMENTAL SCIENCES↗

WE-G-BRD-02: Characterizing Information Loss in a Sparse-Sampling-Based Dynamic MRI Sequence (k-T BLAST) for Lung Motion Monitoring

Purpose: Rapid MRI is an attractive, non-ionizing tool for soft-tissue-based monitoring of respiratory motion in thoracic and abdominal radiotherapy. One big challenge is to achieve high temporal resolution while maintaining adequate spatial resolution. K-t BLAST, sparse-sampling and reconstruction sequence based on a-priori information represents a potential solution. In this work, we investigated how much “true” motion information is lost as a-priori information is progressively added for faster imaging. Methods: Lung tumor motions in superior-inferior direction obtained from ten individuals were replayed into an in-house, MRI-compatible, programmable motion platform (50Hz refresh and 100microns precision). Six water-filled 1.5ml tubes were placed on it as fiducial markers. Dynamic marker motion within a coronal slice (FOV: 32×32cm{sup 2}, resolution: 0.67×0.67mm{sup 2}, slice-thickness: 5mm) was collected on 3.0T body scanner (Ingenia, Philips). Balanced-FFE (TE/TR: 1.3ms/2.5ms, flip-angle: 40degrees) was used in conjunction with k-t BLAST. Each motion was repeated four times as four k-t acceleration factors 1, 2, 5, and 16 (corresponding frame rates were 2.5, 4.7, 9.8, and 19.1Hz, respectively) were compared. For each image set, one average motion trajectory was computed from six marker displacements. Root mean square error (RMS) was used as a metric of spatial accuracy where measured trajectories were compared to original data. Results: Tumor motion was approximately 10mm. The mean(standard deviation) of respiratory rates over ten patients was 0.28(0.06)Hz. Cumulative distributions of tumor motion frequency spectra (0–25Hz) obtained from the patients showed that 90% of motion fell on 3.88Hz or less. Therefore, the frame rate must be a double or higher for accurate monitoring. The RMS errors over patients for k-t factors of 1, 2, 5, and 16 were.10(.04),.17(.04), .21(.06) and.26(.06)mm, respectively. Conclusions: K-t factor of 5 or higher can cover the high frequency component of tumor respiratory motion, while the estimated error of spatial accuracy was approximately.2mm.

60 APPLIED LIFE SCIENCES↗

The Formation of Uranus and Neptune: Fine-tuning in Core Accretion

Uranus and Neptune are ice giants with ∼15% atmospheres by mass, which places them in a category intermediate between rocky planets and gas giants. These atmospheres are too massive to have been primarily outgassed, but they never underwent runaway gas accretion. The ice giants never reached critical core mass (M{sub crit}) in a full gas disk, but their cores are ≳M{sub crit}, suggesting that their envelopes were mainly accreted at the end of the disk lifetime. Pebble accretion calls into question traditional slow atmospheric growth during this phase. We show that the full-sized ice giants predominantly accreted gas from a disk depleted by at least a factor of ∼100. Such a disk dissipates in ≲10{sup 5} years. Why would both cores stay subcritical for the entire ∼Myr disk lifetime, only to reach M{sub crit} in the final 10{sup 5} years? This is fine tuned. Ice giants in the outer disk have atmospheric mass fractions comparable to the disk gas-to-solid ratio during the bulk of their gas accretion. This point in disk evolution coincides with a dynamical upheaval: the gas loses its ability to efficiently damp the core random velocities, allowing them to be gravitationally excited by Jupiter and Saturn. We suggest that the ice giants’ cores began growing on closer-in orbits (staying subcritical), and migrated out during this dynamical instability. There, their orbits circularized after accreting much of their mass in solids. Finally, they accreted their envelopes from a depleted nebula, where the sparseness of feeding-zone gas prevented runaway.

79 ASTRONOMY AND ASTROPHYSICS↗

Growth and Stability of Stratiform Carrollite (CuCo2S4) in the Tenke-Fungurume Ore District, Central African Copperbelt

Abstract Carrollite (CuCo2S4) is the main ore mineral of the critical battery metal cobalt, yet, surprisingly, detailed characterization of its thermodynamic properties and of its trace element contents remain sparse in the scientific literature. To fill these knowledge gaps, we generated the first thermodynamic data set for carrollite using well-characterized samples obtained from the stratiform sulfide mineralization style at Fungurume 88 deposit in the Democratic Republic of Congo. Detailed mineralogical investigation of these same samples suggests that carrollite has limited ability to incorporate other ‘sweetener’ elements (except Cu and Ni) by substitution mechanisms. Modeling using CHNOSZ 2.0.0. software and an integrated Cu-Co-S-O thermodynamic data set provides insights into the stability of carrollite relative to other Co-bearing minerals under physicochemical conditions relevant to the Central African Copperbelt. Further exploration of these models indicates that dropping redox potential in the mineralizing system is insufficient to explain the mineral-scale and deposit-scale zonation patterns commonly observed in Cu-Co deposits of the Central African Copperbelt. Instead, factors such as increasing pH, decreasing T, decreasing sulfur activity, or some combination of changing physicochemical parameters may need to be invoked to explain these zonation trends. At the Fungurume 88 deposit, the absence of linnaeite (Co3S4) suggests that ore precipitation occurred at temperatures cooler than 211 °C. From our pH-logfO2 diagrams, and relative to higher temperatures, such a lower T regime is marked by a greater degree of offset between the modeled Cu and Co solubility contours, thus facilitating a more differentiated and zoned distribution of these two metals at the deposit scale. Our models are offered to the geoscience community as exceptionally useful tools for modeling and visualizing the Cu-Co-S-O systematics and may be applied to a variety of geological and geometallurgical questions in the Central African Copperbelt and other deposits elsewhere.

Mineralogy↗

Improving signal strength in serial crystallography with DIALS geometry refinement

The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.

36 MATERIALS SCIENCE↗

Practical Considerations in the Re-Irradiation of Recurrent and Second Primary Head-and-Neck Cancer: Who, Why, How, and How Much?

Despite progress in surgical and reconstructive techniques, as well as advances in radiotherapy delivery methods, a significant proportion of patients irradiated for head-and-neck cancer develop locoregional recurrence. These patients are also at high risk of developing new second primary cancers of the head and neck. Because of the heterogeneity of this population with respect to disease-related and patient-related factors, such as previous treatment, tumor recurrence site, disease extent, and performance status, the optimal treatment of locoregionally recurrent or second primary cancers of the head and neck remains to be defined. Although surgical resection typically constitutes the mainstay of treatment, effective salvage therapy is often precluded by anatomic inaccessibility and the risk of perioperative complications. Although chemotherapy alone has traditionally been considered an alternative to surgery, the response rates have been poor, with nearly all patients dying of disease progression within months. Similarly, salvage therapy using re-irradiation has historically been avoided because of concerns regarding toxicity. Although the results of more recent studies using contemporary treatment techniques and conformal delivery methods have been somewhat more promising, the role of re-irradiation after previous full-course radiotherapy is still considered investigational by many. Numerous questions remain unanswered, and practical guidelines for clinical decision-making are sparse.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set of Drosophila early embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation of Drosophila expression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. In conclusion, the performance of PP with the Drosophila data suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

59 BASIC BIOLOGICAL SCIENCES↗

Physics informed deep neural network embedded in a chemical transport model for the Amazon rainforest

Secondary organic aerosols (SOA) are fine particles in the atmosphere, which interact with clouds, radiation and affect the Earth’s energy budget. SOA formation involves chemistry in gas phase, aqueous aerosols, and clouds. Simulating these chemical processes involve solving a stiff set of differential equations, which are computationally expensive steps for three-dimensional chemical transport models. Deep neural networks (DNNs) are universal function approximators that could be used to represent the complex nonlinear changes in aerosol physical and chemical processes; however, key challenges such as generalizability to extended time periods, preservation of mass balance, simulating sparse model outputs, and maintaining physical constraints have limited their use in atmospheric chemistry. Here, we develop an approach of using a physics-informed DNN that overcomes previous such challenges and demonstrates its applicability for the chemical formation processes of isoprene epoxydiol SOA (IEPOX-SOA) over the Amazon rainforest. The DNN is trained with data generated by simulating IEPOX-SOA over the entire atmospheric column, using the Weather Research and Forecasting Model coupled with Chemistry (WRF-Chem). The trained DNN is then embedded within WRF-Chem to replace the computationally expensive default solver of IEPOX-SOA formation. The trained DNN predictions generalizes well with the default model simulation of the IEPOX-SOA mass concentrations and its size distribution (20 size bins) over several days of simulations in both dry and wet seasons. The embedded DNN reduces the computational expense of WRF-Chem by a factor of 2. Our approach shows promise in terms of application to other computationally expensive chemistry solvers in climate models.

54 ENVIRONMENTAL SCIENCES↗