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At least 163 records · Page 9

Multimodal representation learning for predicting molecule–disease relations

Motivation: Predicting molecule–disease indications and side effects is important for drug development and pharmacovigilance. Comprehensively mining molecule–molecule, molecule–disease and disease–disease semantic dependencies can potentially improve prediction performance. Methods: We introduce a Multi-Modal REpresentation Mapping Approach to Predicting molecular-disease relations (M2REMAP) by incorporating clinical semantics learned from electronic health records (EHR) of 12.6 million patients. Specifically, M2REMAP first learns a multimodal molecule representation that synthesizes chemical property and clinical semantic information by mapping molecule chemicals via a deep neural network onto the clinical semantic embedding space shared by drugs, diseases and other common clinical concepts. To infer molecule–disease relations, M2REMAP combines multimodal molecule representation and disease semantic embedding to jointly infer indications and side effects. Results: We extensively evaluate M2REMAP on molecule indications, side effects and interactions. Results show that incorporating EHR embeddings improves performance significantly, for example, attaining an improvement over the baseline models by 23.6% in PRC-AUC on indications and 23.9% on side effects. Further, M2REMAP overcomes the limitation of existing methods and effectively predicts drugs for novel diseases and emerging pathogens. Availability and implementation: The code is available at https://github.com/celehs/M2REMAP, and prediction results are provided at https://shiny.parse-health.org/drugs-diseases-dev/.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-state Catalysts Modulated by Mechanical Force (Final Report)

The development of more efficient catalytic processes and new approaches to control catalytic activity and selectivity are central to the realization of more selective, atom economic, and energy efficient routes to value added chemicals and polymers. The reactivity and selectivity of a transition metal catalyst is intimately related to the ligand-sphere geometry and, in many cases, the ideal ligand geometry for one step of a catalytic cycle is poorly matched to the ideal ligand geometry for another, resulting in sub-optimal efficiency. Macroscopic mechanical forces are both large, potentially much larger than interatomic forces, and are directional and localized to an extent that differentiates them from other forms of energy input such as heat or light. As such, mechanical force represents a heretofore untapped approach to modulate catalyst geometry, with the potential to reversibly modulate catalyst geometry on the timescale of catalytic turnover or monomer enchainment. This project has addressed the fundamental challenges in material-to-molecule strain coupling associated with the development of a new class of mechanically responsive catalysts (mechanocatalysts) in which active organotransition metal catalysts are strategically embedded in a flexible polymer network such that application of external mechanical force (stretching or deformation) leads to modulation of catalyst geometry, and hence reactivity and selectivity. Our efforts during the tenure of this grant were directed toward the elucidation of force-reactivity relationships of elementary transformations that occur within the first coordination sphere of a transition metal complex employing stiff stilbene photoswitches tethered to a flexible bidentate phosphine ligand derived from MeOBiphep as molecular force probes which provide a range of compressive and extension forces to the coupled transition metal complex depending on the geometry of the stiff stilbene and length of the tethering chains. During the tenure of this grant, we have quantified the rate of C(sp 2 )-C(sp 2 ) reductive elimination from platinum(II) diaryl complexes containing bis(phosphine) force probe ligands as a function of mechanical force; compressive forces decreased the rate of reductive elimination whereas extension forces increased the rate relative to the strain-free MeOBiphep complex with a 3.4-fold change in rate over a ~290 pN range of restoring forces. In a similar manner, we have quantified the rate of oxidative addition of bromobenzene to low-ligated palladium(0) complexes containing force probe ligands as a function of mechanical force; compressive forces increase the rate of oxidative addition, whereas tensile forces decrease the rate with a ~6 fold change in rate across ~340 pN of force applied to the complexes. In both cases, experimental and computational analyses argue strongly against any significant force-induced perturbation of ground state geometry within the first coordination sphere of the reactant complexes. Rather, the force/rate behavior observed for these transformations across these ranges of forces is attributed to the coupling of force to the nuclear motion comprising the reaction coordinates for reductive elimination and oxidative addition. These results together inform the development of catalysts whose activity can be tuned by an external force that is adjusted within a catalytic cycle and suggest opportunities to experimentally map geometry changes associated with reactions in transition metal complexes and potential strategies for force-modulated catalysis.

99 GENERAL AND MISCELLANEOUS↗

Error control techniques for satellite and space communications

The unequal error protection capabilities of convolutional and trellis codes are studied. In certain environments, a discrepancy in the amount of error protection placed on different information bits is desirable. Examples of environments which have data of varying importance are a number of speech coding algorithms, packet switched networks, multi-user systems, embedded coding systems, and high definition television. Encoders which provide more than one level of error protection to information bits are called unequal error protection (UEP) codes. In this work, the effective free distance vector, d, is defined as an alternative to the free distance as a primary performance parameter for UEP convolutional and trellis encoders. For a given (n, k), convolutional encoder, G, the effective free distance vector is defined as the k-dimensional vector d = (d(sub 0), d(sub 1), ..., d(sub k-1)), where d(sub j), the j(exp th) effective free distance, is the lowest Hamming weight among all code sequences that are generated by input sequences with at least one '1' in the j(exp th) position. It is shown that, although the free distance for a code is unique to the code and independent of the encoder realization, the effective distance vector is dependent on the encoder realization.

Costello, Daniel J., Jr.↗

Simulator of Space Communication Networks

Multimission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE) is a suite of software tools that simulates the behaviors of communication networks to be used in space exploration, and predict the performance of established and emerging space communication protocols and services. MACHETE consists of four general software systems: (1) a system for kinematic modeling of planetary and spacecraft motions; (2) a system for characterizing the engineering impact on the bandwidth and reliability of deep-space and in-situ communication links; (3) a system for generating traffic loads and modeling of protocol behaviors and state machines; and (4) a system of user-interface for performance metric visualizations. The kinematic-modeling system makes it possible to characterize space link connectivity effects, including occultations and signal losses arising from dynamic slant-range changes and antenna radiation patterns. The link-engineering system also accounts for antenna radiation patterns and other phenomena, including modulations, data rates, coding, noise, and multipath fading. The protocol system utilizes information from the kinematic-modeling and link-engineering systems to simulate operational scenarios of space missions and evaluate overall network performance. In addition, a Communications Effect Server (CES) interface for MACHETE has been developed to facilitate hybrid simulation of space communication networks with actual flight/ground software/hardware embedded in the overall system.

Clare, Loren↗

Model-Agnostic Algorithm for Real-Time Attack Identification in Power Grid using Koopman Modes

Malicious activities on measurements from sensors like Phasor Measurement Units (PMUs) can mislead the control center operator into taking wrong control actions resulting in disruption of operation, financial losses, and equipment damage. In particular, false data attacks initiated during power systems transients caused due to abrupt changes in load and generation can fool the conventional model-based detection methods relying on thresholds comparison to trigger an anomaly. In this paper, we propose a Koopman mode decomposition (KMD) based algorithm to detect and identify false data attacks in real-time. The Koopman modes (KMs) are capable of capturing the nonlinear modes of oscillation in the transient dynamics of the power networks and reveal the spatial embedding of both natural and anomalous modes of oscillations in the sensor measurements. The Koopman-based spatio-temporal nonlinear modal analysis is used to filter out the false data injected by an attacker. The performance of the algorithm is illustrated on the IEEE 68-bus test system using synthetic attack scenarios generated on GridSTAGE, a recently developed multivariate spatio-temporal data generation framework for simulation of adversarial scenarios in cyber-physical power systems.

Nandanoori, Sai Pushpak↗

Automating Discovery of Physics-Informed Neural State Space Models via Learning and Evolution

Recent works exploring deep learning application to dynamical systems modeling have demonstrated that embedding physical priors into neural networks can yield more effective, physically-realistic, and data-efficient models. However, in the absence of complete prior knowledge of a dynamical system's physical characteristics, determining the optimal structure and optimization strategy for these models can be difficult. In this work, we explore methods for discovering neural state space dynamics models for system identification. Starting with a design space of block-oriented state space models and structured linear maps with strong physical priors, we encode these components into a model genome alongside network structure, penalty constraints, and optimization hyperparameters. Demonstrating the overall utility of the design space, we employ an asynchronous genetic search algorithm that alternates between model selection and optimization and obtains accurate physically consistent models of three physical systems: an aerodynamics body, a continuous stirred tank reactor, and a two tank interacting system.

genetic algorithms, neural architecture search, ne↗

Systems and methods for customizing kernel machines with deep neural networks

A method including receiving an input data set. The input data set can include one of a feature domain set or a kernel matrix. The method also can include constructing dense embeddings using: (i) Nyström approximations on the input data set when the input data set comprises the kernel matrix, and (ii) clustered Nyström approximations on the input data set when the input data set comprises the feature domain set. The method additionally can include performing representation learning on each of the dense embeddings using a multi-layer fully-connected network for each of the dense embeddings to generate latent representations corresponding to each of the dense embeddings. The method further can include applying a fusion layer to the latent representations corresponding to the dense embeddings to generate a combined representation. The method additionally can include performing classification on the combined representation. Other embodiments of related systems and methods are also disclosed.

Song, Huan↗

Coronal Heating, Spicules, and Solar-B

Falconer et al. investigated the heating of the quiet corona by measuring the increase of coronal luminosity with the amount of the magnetic flux in the underlying network at solar minimum when there were no active regions on the face of the Sun. The coronal luminosity was measured from Fe IX/X - Fe XII pairs of coronal images from SOHO/EIT, under the assumption that practically all of the coronal luminosity in these very quiet regions came from plasma in the temperature range 0.9 x 10(exp 6) K is less than or equal to T is less than or equal to 1.3 x 10(exp 6) K. The network magnetic flux content was measured from SOHO/MDI magnetograms. It was found that luminosity of the corona in these quiet regions increased roughly in proportion to the square root of the magnetic flux content of the network and roughly in proportion to the length of the perimeter of the network flux clumps. From 1) this result; 2) the observed occurrence of many fine-scale explosive events (e.g., spicules) at the edges of network flux clumps; and 3) a demonstration that it is energetically feasible for the heating of the corona in quiet regions to be driven by explosions of granule-sized sheared-core magnetic bipoles embedded in the edges of the network flux clumps, Falconer et al. infer that in quiet regions that are not influenced by active regions the corona is mainly heated by such magnetic activity in the edges of the network flux clumps. From their observational results together with their feasibility analysis, Falconer et al. predict that 1) At the edges of the network flux clumps there are many transient sheared core bipoles of the size and lifetime of granules and having transverse field strengths greater than approx. 100 G; 2) Approx. 30 of these bipoles are present per supergranule; and 3) Most spicules are produced by explosions of these bipoles. The photospheric vector magnetograms, chromospheric filtergrams, and EUV spectra from Solar-B are expected to have sufficient sensitivity, spatial resolution, and cadence to test these predictions. The Falconer et al. (2003) inferred mixed-polarity magnetic flux at the base of spicules is compatible with the observed magnetic structure of Ha macrospicules recently found by Yamuchi et al. (2003).

Moore, Ron↗

Equipping Neural Network Surrogates with Uncertainty for Propagation in Physical Systems

Coarse-grained or filtered models typically rely on closure models to account for unresolved scales. For instance, large eddy simulation for modeling turbulent fluid flows explicitly resolves the largest scales, but requires modeling closure terms to account for the sub-filter scales. With the vast amount of data available from high-fidelity simulations, there are unique opportunities to leverage data-driven modeling techniques to formulate expressive and flexible closure models. Despite their flexibility, data-driven models struggle in domain shift settings, i.e. when deployed in configurations not captured in the training dataset. In particular, the efficacy of neural network surrogates is difficult to assess a priori due to the deterministic, point-estimate nature of predictions. In high-consequence applications, such models require reliable uncertainty estimates in the data-informed and out-of-distribution regimes. To quantify uncertainties in both regimes, we employ Bayesian neural networks which are able to capture both epistemic and aleatoric uncertainties. We will discuss challenges associated with the training and evaluation of these networks. Furthermore, we will discuss uncertainty embedding strategies to enable efficient sampling and propagation of uncertainty through high-fidelity simulations.

Bayesian neural networks↗

A graph embedding‐based approach for automatic cyber‐physical power system risk assessment to prevent and mitigate threats at scale

Abstract Power systems are facing an increasing number of cyber incidents, potentially leading to damaging consequences to both physical and cyber aspects. However, the development of analytical methods for the study of large‐scale power infrastructures as cyber‐physical systems is still in its early stages. Drawing inspiration from machine‐learning techniques, the authors introduce a method inspired by the principles of graph embedding that is tailored for quantitative risk assessment and the exploration of possible mitigation strategies of large‐scale cyber‐physical power systems. The primary advantage of the graph embedding approach lies in its ability to generate numerous random walks on a graph, simulating potential access paths. Meanwhile, it enables capturing high‐dimensional structures in low‐dimensional spaces, facilitating advanced machine‐learning applications, and ensuring scalability and adaptability for comprehensive network analysis. By employing this graph embedding‐based approach, the authors present a structured and methodical framework for risk assessment in cyber‐physical systems. The proposed graph embedding‐based risk analysis framework aims to provide a more insightful perspective on cyber‐physical risk assessment and situation awareness for power systems. To validate and demonstrate its applicability, the method has been tested on two cyber‐physical power system models: the Western System Coordinating Council (WSCC) 9‐Bus System and the Illinois 200‐Bus System , thereby showing its advantages in enhancing the accuracy of risk analysis and comprehensiveness of situational awareness.

Sun, Shining↗

Mitigating Algorithmic Bias in Cancer Site Classification Models

Purpose Integrating artificial intelligence in cancer diagnostics has improved tumor classification beyond rule-based systems. Despite these advancements, these models may still encode demographic biases. We conducted a large-scale, applied bias-probing study of a deep learning–based cancer site classifier to quantify race information encoded in document embeddings. We then evaluated how performance changes when race-correlated embedding dimensions are removed in a post-training sensitivity analysis. Methods The cancer site classifier was trained using 3.5 million electronic cancer pathology reports from six of the National Cancer Institute's SEER registries. We trained a hierarchical self-attention network to generate 400-dimensional document embeddings. These embeddings were used to train two downstream, gradient-boosted decision tree classifiers: one to classify the cancer sites and another to predict racial categories. We identified overlapping features by intersecting the top 50 feature-importance rankings from the site and race models and computed their cumulative feature importance in each model. As a post hoc sensitivity analysis, we progressively pruned these overlapping dimensions, retrained the site model, and compared overall macro-F1 and accuracy, race-stratified macro-F1, and group fairness metrics on the basis of demographic parity and equalized odds before and after pruning. Results The analysis revealed minimal feature overlap between the cancer site and race prediction models, and the cumulative importance scores indicated a negligible influence of racial information on clinical predictions. Post-training pruning of overlapping features did not compromise the models' diagnostic accuracy, with a 0.07% loss in accuracy. Conclusion Our findings demonstrate that HiSAN-generated embeddings from SEER data can be used effectively in cancer site classification without significant demographic bias influencing the outcomes. Post-training pruning therefore functions as a practical audit and sensitivity check.

Shivanna, Abhishek [ORNL] (ORCID:0009000665228593)↗

Classification of Notices to Airmen using Natural Language Processing

This paper establishes the feasibility of using Natural Language Processing (NLP) to classify NOTAMs or Notices to Airmen – a pilot messaging framework to gather real-time situational awareness. Present day air mobility operations heavily rely on NOTAMs. However, pilots often have difficulty interpreting NOTAMs due to the sheer volume of inapplicable messages and unclear abbreviations. Using NLP, the presented study analyzes the accuracy of classifying NOTAMs and, thereby, the efficiency of generating actionable interpretations in real time. To this effect, efficacies of four NLP neural network architectures were analyzed, including three Recurrent Neural Networks (RNNs) with GloVe, Word2Vec, and FastText word embeddings, and one trained Bi-Directional Encoder Representations from Transformers (BERT) model. The four neural networks were trained and evaluated on three open-source datasets of varying text lengths, vocabularies, and grammars, taken from e-commerce product descriptions, social media tweets, and unstructured descriptions for data and analytics services on open data marketplaces such as NASA’s Data and Reasoning Fabric (DRF) platform. This provided cross-analysis of each neural network architecture’s performance per text type. The best performing architecture, BERT, was then fine-tuned on a collection of open-source NOTAM data. Post-training, a real-time NOTAM classification service was implemented to draw inference on new NOTAMs using the trained model, which demonstrated close to 99% accuracy in classification. This modular classification service is envisioned to be integrated with a data and analytics delivery platform, such as the DRF, thus availing real-time contextualization of NOTAMs to air mobility clients, humans, and machines for enhanced decision making.

Aiden C. Szeto↗

Classification of Notices to Airmen using Natural Language Processing

This paper establishes the feasibility of using Natural Language Processing (NLP) to classify NOTAMs or Notices to Airmen – a pilot messaging framework to gather real-time situational awareness. Present day air mobility operations heavily rely on NOTAMs. However, pilots often have difficulty interpreting NOTAMs due to the sheer volume of inapplicable messages and unclear abbreviations. Using NLP, the presented study analyzes the accuracy of classifying NOTAMs and, thereby, the efficiency of generating actionable interpretations in real time. To this effect, efficacies of four NLP neural network architectures were analyzed, including three Recurrent Neural Networks (RNNs) with GloVe, Word2Vec, and FastText word embeddings, and one trained Bi-Directional Encoder Representations from Transformers (BERT) model. The four neural networks were trained and evaluated on three open-source datasets of varying text lengths, vocabularies, and grammars, taken from e-commerce product descriptions, social media tweets, and unstructured descriptions for data and analytics services on open data marketplaces such as NASA’s Data and Reasoning Fabric (DRF) platform. This provided cross-analysis of each neural network architecture’s performance per text type. The best performing architecture, BERT, was then fine-tuned on a collection of open-source NOTAM data. Post-training, a real-time NOTAM classification service was implemented to draw inference on new NOTAMs using the trained model, which demonstrated close to 99% accuracy in classification. This modular classification service is envisioned to be integrated with a data and analytics delivery platform, such as the DRF, thus availing real-time contextualization of NOTAMs to air mobility clients, humans, and machines for enhanced decision making.

Aiden Szeto↗

Integrating the Design of Desalination Technologies into Produced Water Network Optimization

The oil and gas energy sector uses billions of gallons of water for hydraulic fracturing each year to extract oil and gas. The water injected into the ground for fracturing along with naturally occurring formation water from oil wells surfaces back in the form of produced water. Produced water can contain high concentrations of total dissolved solids and is unfit for reuse outside the oil and gas industry without desalination. In semi-arid shale plays, produced water desalination for beneficial reuse could play a crucial role in alleviating water shortages and addressing extreme drought conditions. In this poster we co-optimize the design and operation of desalination technologies along with operational decisions across produced water networks. A multi-period produced water network model with simplified split-fraction-based desalination nodes is developed. Rigorous steady-state desalination mathematical models based on mechanical vapor recompression are developed and embedded at the desalination sites in the network model. An optimal common design across all periods is ensured using global capacity constraints. The solution approach is demonstrated for multi-period planning problems on networks from the PARETO open-source library. Model formulation and challenges associated with scalability are discussed.

Naik, Sakshi↗

Integrating the Design of Desalination Technologies into Produced Water Network Optimization

The oil and gas energy sector uses billions of gallons of water for hydraulic fracturing each year to extract oil and gas. The water injected into the ground for fracturing along with naturally occur-ring formation water from the oil wells surfaces back in the form of produced water. Produced water can contain high concentrations of total dissolved solids and is unfit for reuse outside the oil and gas industry without desalination. In semi-arid shale plays, produced water desalination for beneficial reuse could play a crucial role in alleviating water shortages and addressing extreme drought conditions. In this paper we co-optimize the design and operation of desalination technologies along with operational decisions across produced water networks. A multi-period produced water network model with simplified split-fraction-based desalination nodes is developed. Rigorous steady-state desalination mathematical models based on mechanical vapor recompression are developed and embedded at the desalination sites in the network model. An optimal common design is ensured across all periods using global capacity constraints. The solution approach is demonstrated for multi-period planning problems on networks from the PARETO open-source library. Model formulation and challenges associated with scalability are discussed.

Naik, Sakshi↗

Hybrid Additive Manufacturing and Electric Field-Assisted Sintering of High-temperature Heat Exchangers via Sacrificial Channel Molds

A hybrid manufacturing approach, integrating additive manufacturing (AM) with powder methodology via electric field-assisted sintering (EFAS), was developed for the fabrication of high-temperature compact heat exchangers (CHX) from refractory metals. The methodology employed additively manufactured sacrificial channel molds (SCMs) as shapeholders for CHX channels, which were embedded in metal powders using EFAS. Following embedding, the SCMs were chemically dissolved to form the internal channel network. SCMs were fabricated using both digital light processing (DLP) and direct ink writing (DIW) from chemically reactive, calcium-based ceramic feedstocks with varying ratios of Al2O3 reinforcement. The microstructure, phase composition, and dissolution behavior of both as-printed and embedded SCMs were investigated. The shrinkage behavior of the SCMs embedded in refractory metals, as well as the interfacial characteristics between the SCMs and metal matrix, were studied. The results showed that the SCMs containing sufficient chemical reactive ceramics dissolved effectively before and after embedding. The as-printed SCMs retained the phase composition of their feedstocks, but the embedded SCMs containing calcium-based ceramics and Al2O3 exhibited the formation of calcium aluminates due to high temperature exposure during embedding. Most SCMs exhibited a cellular Al2O3 network filled with Ca-rich ceramics. Shrinkage after embedding was strongly dependent on SCM density, with lower density SCMs exhibiting greater shrinkage. A thin SCM-affected zone was observed at the metal matrix surface, characterized by increased porosity compared to the bulk matrix. This effect was attributed to infiltration of the SCM materials into powder particle boundaries under pressure, followed by their removal during dissolution. This study demonstrates the feasibility of manufacturing CHXs from hard-to-process refractory metals for use in harsh environments.

36 - MATERIALS SCIENCE↗

Topological and Dynamical Representations for Radio Frequency Signal Classification

Radio Frequency (RF) signals are found throughout our world, carrying over-the-air information for both digital and analog uses with applications ranging from WiFi to the radio. One area of focus in RF signal analysis is determining the modulation schemes employed in these signals which is crucial in many RF signal processing domains from secure communication to spectrum monitoring. This work investigates the accuracy and noise robustness of novel Topological Data Analysis (TDA) and dynamic representation based approaches paired with a small convolution neural network for RF signal modulation classification with a comparison to state-of-the-art deep neural network approaches. We show that using TDA tools, like Vietoris-Rips and lower star filtrations, and the Takens' embedding in conjunction with a standard shallow neural network we can capture the intrinsic dynamical, geometric, and topological features of the underlying signal's manifold, offering informative representations of the RF signals. Our approach is effective in handling the modulation classification task and is notably noise robust, outperforming the commonly used deep neural network approaches in mode classification. Moreover, our fusion of dynamical and topological information is able to attain similar performance to deep neural network architectures with significantly smaller training datasets.

Myers, Audun D.↗

Novel artificial neural network model for instantaneous power losses and operational efficiency mapping of MW-scale vanadium redox flow battery for improved technoeconomic analysis

A novel data-driven, machine-learning-based method for modeling the instantaneous power losses of a distribution-sited 2 MW/8MWh vanadium redox flow battery (VRFB), a grid-scale electrochemical storage technology, is introduced and compared against benchmark empirical modeling approaches, including symmetric and asymmetric models, as well as a recent convex hull modeling approach. The novel loss modeling method introduces several advantages over the benchmark models and over simplistic efficiency estimates, the most significant of which is that the model can accurately reflect the stepwise and non-linear parasitic losses associated with the duty cycles of mechanical auxiliary systems like pump motor drives and blower fans. Residuals of the models are compared; the proposed data driven model features significantly improved accuracy over the benchmark models. The model's coefficient of determination is also improved relative to that of the benchmark models. Furthermore, a novel method for visualization of operational efficiency of the grid-scale storage technology is introduced. To demonstrate the benefits of the novel data-driven method for modeling the VRFB, the benchmark models and the proposed models are embedded into an Open DSS distribution network model to study two applications of the grid-scale electrical storage system: load leveling for grid support and energy arbitrage. This article demonstrates that the accuracy of the instantaneous power loss model significantly impacts the understanding of the state of charge of the VRFB. In turn, the accuracy of the efficiency modeling of the VRFB impacts the understanding of the potential economic value and technical benefits to the distribution network operators. In conclusion, the presented power loss modeling approach is, therefore, highly relevant for utility-stakeholders, battery asset owners, system engineers, system designers, and financial planners interested in evaluating or optimizing the operation of grid-scale VRFBs.

24 POWER TRANSMISSION AND DISTRIBUTION↗