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At least 1,045 records · Page 58

Large-scale deep learning for metastasis detection in pathology reports

Objectives No existing algorithm can reliably identify metastasis from pathology reports across multiple cancer types and the entire US population. In this study, we develop a deep learning model that automatically detects patients with metastatic cancer by using pathology reports from many laboratories and of multiple cancer types. Materials and Methods We use 60 471 unstructured pathology reports from 4 Surveillance, Epidemiology, and End Results (SEER) registries. The reports were coded into 1 of 3 labels: metastasis negative, metastases positive, or metastasis undetermined. We utilize a task-specific deep neural network trained from scratch and compare its performance with a widely used large language model (LLM). Results Our deep learning architecture trained on task-specific data outperforms a general-purpose LLM, with a recall of 0.894 compared to 0.824. We quantified model uncertainty and used it to defer reports for human review. We found that retaining 72.9% of reports increased recall from 0.894 to 0.969. Discussion A smaller deep learning architecture trained on task-specific data outperforms a general LLM. Equally critical to model performance is the incorporation of uncertainty quantification, achieved here through an abstention mechanism. Conclusions This study’s finding demonstrate the feasibility of developing algorithms to automatically identify metastatic cancer cases from unstructured pathology reports.

machine learning↗

In-Situ and Remote-Sensing Data Fusion Using Machine Learning Techniques to Infer Urban and Fire Related Pollution Plumes

Airmass type characterization is key in understanding the relative contribution of various emission sources to atmospheric composition and air quality and can be useful in bottom-up model validation and emission inventories. However, classification of pollution plumes from space is often not trivial. Sub-orbital campaigns, such as SEAC4RS (Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys) give us a unique opportunity to study atmospheric composition in detail, by using a vast suite of in-situ instruments for the detection of trace gases and aerosols. These measurements allow identification of spatial and temporal atmospheric composition changes due to various pollution plumes resulting from urban, biogenic and smoke emissions. Nevertheless, to transfer the knowledge gathered from such campaigns into a global spatial and temporal context, there is a need to develop workflow that can be applicable to measurements from space. In this work we rely on sub-orbital in-situ and total column remote sensing measurements of various pollution plumes taken aboard the NASA DC-8 during 2013 SEAC4RS campaign, linking them through a neural-network (NN) algorithm to allow inference of pollution plume types by input of columnar aerosol and trace-gas measurements. In particular, we use the 4STAR (Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research) airborne measurements of wavelength dependent aerosol optical depth (AOD), particle size proxies, O3, NO2 and water vapor to classify different pollution plumes. Our method relies on assigning a-priori ground-truth labeling to the various plumes, which include urban pollution, different fire types (i.e. forest and agriculture) and fire stage (i.e. fresh and aged) using cluster analysis of aerosol and trace-gases in-situ and auxiliary (e.g. trajectory) data and the training of a NN scheme to fit the best prediction parameters using 4STAR measurements as input. We explore our misclassification rates as related to our ground-truth labels, and with multi-layered pollution plume cases. The next step in our analysis is to optimize parameter selection for a scheme that can be applied to space-borne aerosol and trace-gas observation platforms such as OMI, and future geostationary satellites such as TEMPO and GEO-CAPE.

Neural-network↗

Polyconvex neural network models of thermoelasticity

Machine-learning function representations such as neural networks have proven to be excellent constructs for constitutive modeling due to their flexibility to represent highly nonlinear data and their ability to incorporate constitutive constraints, which also allows them to generalize well to unseen data. Here, in this work, we extend a polyconvex hyperelastic neural network framework to (isotropic) thermo-hyperelasticity by specifying the thermodynamic and material theoretic requirements for an expansion of the Helmholtz free energy expressed in terms of deformation invariants and temperature. Different formulations which a priori ensure polyconvexity with respect to deformation and concavity with respect to temperature are proposed and discussed. The physics-augmented neural networks are furthermore calibrated with a recently proposed sparsification algorithm that not only aims to fit the training data but also penalizes the number of active parameters, which prevents overfitting in the low data regime and promotes generalization. The performance of the proposed framework is demonstrated on synthetic data, which illustrate the expected thermomechanical phenomena, and existing temperature-dependent uniaxial tension and tension-torsion experimental datasets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improved GEO Derived LW Broadband Fluxes for the Edition5 CERES SYN1Deg Data Product

The NASA Clouds and the Earth's Radiant Energy System (CERES) project provides over 24 years of accurately observed top-of-the-atmosphere (TOA) and surface flux data record for climate monitoring and diagnostic studies. The major level-3 data products include SSF1deg, SYN1deg, FluxByCldTyp, and EBAF data. The CERES SYN1deg product provides 1° gridded observed TOA fluxes and computed surface fluxes based on hourly GEO clouds and derived broadband TOA fluxes. The hourly GEO derived fluxes fill in the temporal gaps between the Terra and Aqua CERES observations. In order to maintain a climate quality dataset the GEO cloud and flux retrievals are consistent over the record. The CERES project is preparing for Edition 5 product providing an opportunity to improve the GEO flux retrieval algorithms. To achieve this, the GEO satellite channel radiances are calibrated against the Aqua-MODIS calibration reference. For SW the GEO channel radiances are then converted to broadband radiances using empirical and theoretical models. The SW broadband radiances are then converted to fluxes using the same CERES angular directional models. For LW the GEO channel radiances are directly converted to LW fluxes utilizing empirical models. The resulting GEO derived broadband fluxes are then normalized to the CERES fluxes regionally by regressing the instantaneous coincident flux pairs. The normalized GEO fluxes are then tied to the CERES instrument calibration, which is very stable over time. This study will attempt to improve the GEO derived LW fluxes based on machine learning technique for the future Edition5 SYN1deg data product.

Moguo Sun↗

Classifying Forest Type in the National Forest Inventory Context with Airborne Hyperspectral and Lidar Data

Forest structure and composition regulate a range of ecosystem services, including biodiversity, water and nutrient cycling, and wood volume for resource extraction. Forest type is an important metric measured in the US Forest Service Forest Inventory and Analysis (FIA) program, the national forest inventory of the USA. Forest type information can be used to quantify carbon and other forest resources within specific domains to support ecological analysis and forest management decisions, such as managing for disease and pests. In this study, we developed a methodology that uses a combination of airborne hyperspectral and lidar data to map FIA-defined forest type between sparsely sampled FIA plot data collected in interior Alaska. To determine the best classification algorithm and remote sensing data for this task, five classification algorithms were tested with six different combinations of raw hyperspectral data, hyperspectral vegetation indices, and lidar-derived canopy and topography metrics. Models were trained using forest type information from 632 FIA subplots collected in interior Alaska. Of the thirty model and input combinations tested, the random forest classification algorithm with hyperspectral vegetation indices and lidar-derived topography and canopy height metrics had the highest accuracy (78% overall accuracy). This study supports random forest as a powerful classifier for natural resource data. It also demonstrates the benefits from combining both structural (lidar) and spectral (imagery) data for forest type classification.

random forest↗

Shadow molecular dynamics for flexible multipole models

Shadow molecular dynamics provide an efficient and stable atomistic simulation framework for flexible charge models with long-range electrostatic interactions. Shadow molecular dynamics simulations are driven by approximate “shadow” Born–Oppenheimer potentials for which the exact charges and forces are directly accessible without relying on costly (and approximate) iterative solvers. While previous implementations have been limited to atomic monopole charge distributions, we extend this approach to flexible multipole models. We derive detailed expressions for the shadow energy functions, potentials, and force terms, explicitly incorporating monopole–monopole, dipole–monopole, and dipole–dipole interactions. In our formulation, both atomic monopoles and atomic dipoles are treated as extended dynamical variables alongside the propagation of the nuclear degrees of freedom. We demonstrate that introducing the additional dipole degrees of freedom preserves the stability and accuracy previously seen in monopole-only shadow molecular dynamics simulations. In addition, we present a shadow molecular dynamics scheme where the monopole charges are held fixed while the dipoles remain flexible. Our extended shadow dynamics provide a framework for stable, computationally efficient, and versatile molecular dynamics simulations involving long-range interactions between flexible multipoles. This is of particular current interest in combination with machine-learned interatomic potentials, including long-range electrostatic interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GSplit: Scaling Graph Neural Network Training on Large Graphs via Split-Parallelism

Graph neural networks (GNNs), an emerging class of machine learning models for graphs, have gained popularity for their superior performance in various graph analytical tasks. Mini-batch training is commonly used to train GNNs on large graphs, and data parallelism is the standard approach to scale mini-batch training across multiple GPUs. Data parallel approaches contain redundant work as subgraphs sampled by different GPUs contain significant overlap. To address this issue, we introduce a hybrid parallel mini-batch training paradigm called Split parallelism. Split parallelism avoids redundant work by splitting the sampling, loading, and training of each mini-batch across multiple GPUs. Split parallelism, however, introduces communication overheads that can be more than the savings from removing redundant work. We further present a lightweight partitioning algorithm that probabilistically minimizes these overheads. We implement spllit parllelism in GSplit and show that it outperforms state-of-the-art mini-batch training systems like DGL, Quiver, and P3.

Lim, Seung-Hwan [ORNL] (ORCID:0000000194616866)↗

Machine Learning (ML) Classifier to Assist Metadata Creation

The Atmospheric Radiation Measurement (ARM) Data Center is responsible for the timely collection, archival, and curation of science data products. These products are freely available through an online data repository. Metadata creation is paramount for scientific users to find and access over seven petabytes of atmospheric science data. The hierarchical metadata structure allows users to search for information at both broad and narrow levels. This project aims to leverage 30 years’ worth of manually created metadata to enable machine predictions of broad-term classifications from narrow-term descriptions. These classification predictions would assist metadata coordinators with their term selections. This paper discusses the cleaning and preprocessing of the training data, the pipeline developed to determine the best model for this task, and the creation of an API metadata classifier for ARM measurement metadata. Our results show that the Linear Support Vector Classification (LinearSVC) algorithm, along with the Term Frequency – Inverse Document Frequency (TF-IDF) vectorizer, is well-suited for our multi-class classification task. Lengthier input training data led to better results, and artificial balancing was unnecessary for this particular use case. This predictive classifier enhances efficiency in metadata creation, as well as supports greater consistency and accuracy in metadata tagging.

Collier, Hannah [ORNL] (ORCID:0000000341284292)↗

gRASPA

GPU Monte Carlo Simulation Code with a taste of RASPA We present enhancements in Monte Carlo simulation speed and functionality within an open-source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant performance improvements compared to serial, CPU implementations of Monte Carlo. The code supports a wide range of Monte Carlo simulations, including canonical ensemble (NVT), grand canonical, NVT Gibbs, Widom test particle insertions, and continuous-fractional component Monte Carlo. Implementation of grand canonical transition matrix Monte Carlo (GC-TMMC) and a novel feature to allow different moves for the different components of metal-organic framework (MOF) structures exemplify the capabilities of gRASPA for precise free energy calculations and enhanced adsorption studies, respectively. The introduction of a High-Throughput Computing (HTC) mode permits many Monte Carlo simulations on a single GPU device for accelerated materials discovery. The code can incorporate machine learning (ML) potentials. The open-source nature of gRASPA promotes reproducibility and openness in science, and users may add features to the code and optimize it for their own purposes. The code is written in CUDA/C++ and SYCL/C++ to support different GPU vendors. The gRASPA code is publicly available at https://github.com/snurr-group/gRASPA.

Li, Zhao [Purdue/Northwestern/Notre Dame Universit↗

SRBench++: Principled Benchmarking of Symbolic Regression With Domain-Expert Interpretation

Symbolic regression searches for analytic expressions that accurately describe studied phenomena. The main promise of this approach is that it may return an interpretable model that can be insightful to users, while maintaining high accuracy. The current standard for benchmarking these algorithms is SRBench, which evaluates methods on hundreds of datasets that are a mix of real-world and simulated processes spanning multiple domains. At present, the ability of SRBench to evaluate interpretability is limited to measuring the size of expressions on real-world data, and the exactness of model forms on synthetic data. In practice, model size is only one of many factors used by subject experts to determine how interpretable a model truly is. Furthermore, SRBench does not characterize algorithm performance on specific, challenging sub-tasks of regression such as feature selection and evasion of local minima. In this work, we propose and evaluate an approach to benchmarking SR algorithms that addresses these limitations of SRBench by 1) incorporating expert evaluations of interpretability on a domain-specific task, and 2) evaluating algorithms over distinct properties of data science tasks. We evaluate 12 modern symbolic regression algorithms on these benchmarks and present an in-depth analysis of the results, discuss current challenges of symbolic regression algorithms and highlight possible improvements for the benchmark itself.

97 MATHEMATICS AND COMPUTING↗

Transient Optimization for the Betterment of Turbine Electrified Energy Management

Gas turbine engine transients are associated with degraded compressor operability, which must be addressed by the engine control system and accounted for in the engine design. Failure to do so may result in events such as compressor stall/surge and combustor blow out. Transient operability concerns constrain the engine design and can result in sacrifices of efficiency and/or thrust responsiveness. The traditional approach to transient operability management is control logic that limits the fuel flow command. A companion paper presents a strategy for optimizing the transient fuel flow control logic taking into consideration transient operability and thrust responsiveness. The study covered here extends this idea to an electrified gas turbine engine that employs a power/energy management concept known as Turbine Electrified Energy Management (TEEM). TEEM uses an electric power system interfaced with the engine (hence the term ‘electrified gas turbine engine’) to further improve transient operability and alleviate associated design constraints. There can be costs associated with implementing TEEM in terms of power and energy requirements that impact the size of the electrical power system. However, the results of this study show that through optimization of the transient limit logic, power and energy requirements needed to implement TEEM can be significantly reduced. Among the conclusions that can be drawn from the results of the illustrative application covered herein are: (1) there is a reduction in the electric machine power requirement to manage operability during accelerations by 200 to 400 hp, and (2) power transfer from the low pressure spool (LPS) to the high pressure spool (HPS) is the most effective option for improving operability during decelerations, followed by the options of only injecting power on the HPS or only extracting power from the LPS.

transient↗

Transient Optimization for the Betterment of Turbine Electrified Energy Management

Gas turbine engine transients are associated with degraded compressor operability, which must be addressed by the engine control system and accounted for in the engine design. Failure to do so may result in events such as compressor stall/surge and combustor blow out. Transient operability concerns constrain the engine design and can result in sacrifices of efficiency and/or thrust responsiveness. The traditional approach to transient operability management is control logic that limits the fuel flow command. A companion paper presents a strategy for optimizing the transient fuel flow control logic taking into consideration transient operability and thrust responsiveness. The study covered here extends this idea to an electrified gas turbine engine that employs a power/energy management concept known as Turbine Electrified Energy Management (TEEM). TEEM uses an electric power system interfaced with the engine (hence the term ‘electrified gas turbine engine’) to further improve transient operability and alleviate associated design constraints. There can be costs associated with implementing TEEM in terms of power and energy requirements that impact the size of the electrical power system. However, the results of this study show that through optimization of the transient limit logic, power and energy requirements needed to implement TEEM can be significantly reduced. Among the conclusions that can be drawn from the results of the illustrative application covered herein are: (1) there is a reduction in the electric machine power requirement to manage operability during accelerations by 200 to 400 hp, and (2) power transfer from the low pressure spool (LPS) to the high pressure spool (HPS) is the most effective option for improving operability during decelerations, followed by the options of only injecting power on the HPS or only extracting power from the LPS.

transient↗

Recommendations on Evidence and Process for Certification of Learning-enabled Components in Aerospace Systems

This report primarily identifies a collection of relevant and necessary evidence for assurance of machine learnt components (MLCs)—also known as learning-enabled components—integrated into aircraft systems, and gives preliminary suggestions on the elements of a certification process that invoke the identified evidence. The main focus is on feedforward neural networks that are static and trained offline through supervised learning. A brief background on the generic elements of the lifecycle of an MLC is given to contextualize the assurance considerations and, consequently, the evidence that is relevant and necessary to support certification. At the level of an MLC, those considerations relate to: (i) the consistency and correctness of MLC contributions to system functions in the context of a validated functional intent; and (ii) the absence of MLC contributions to aircraft-level failure conditions. At an ML model level, confidence in model and data properties contribute to assurance of the containing MLC, in particular: (a) generalizability and robustness of models, in the presence of inputs not previously seen during training, disturbances to inputs, and unexpected inputs; and (b) valid data, i.e., data that are at least representative, relevant, complete, and accurate. Evidence for the above span the elements of the ML lifecycle, and includes, at a minimum, lifecycle artifacts that pertain to: (1) properties of requirements capturing functional intent, safety constraints, and aspects of the intended use and operating environment; (2) model performance, model complexity and design, and algorithm choice; (3) achievement of required performance at the levels of a trained model during model development, a trained model after model development is complete, and a trained model that is transformed into an executable equivalent; (4) model implementation aspects necessary for transforming a trained model into the executable equivalent; (5) integration of the executable trained model into the containing MLC, and eventually the larger system; and, (6) lastly, the verification and validation (V&V) of each of the above. Such V&V lifecycle artifacts themselves include: aspects of coverage, e.g., of various levels of requirements by the input space of the model and the data; traceability (where applicable); application of formal methods for property specification, analysis, and checking. Examples of evidence generation methods and tools further ground the discussion on what constitutes evidence, and the contribution to assurance during certification. The identified assurance considerations and supporting evidence is not a comprehensive set. Additionally, neither what should be considered as sufficient evidence relative to the assigned criticality of an MLC, nor how criticality ought to be determined and adjusted, have been considered in this report. However, suggestions are made for potential activities of the ML lifecycle that are aimed at providing confidence that an MLC can be relied upon when integrated into its containing (aircraft) system. Those activities are proposed as candidate elements of a certification process for MLCs. The main purpose of this report to inform regulatory guidance and consensus standards that may be used to meet the safety intent of the applicable regulations.

Aviation safety↗

1D-Convolutional Neural Network Architecture for Generalized Time-Segmentation Tasks

Time segmentation of experimental data is a common and often difficult task. Consequently, it is of interest to automate this type of segmentation to reduce manual inputs, which are labor intensive and less consistent. However, simple thresholding algorithms are often insufficiently robust due either to noise or inconsistent data. This paper proposes a simple 1D CNN architecture as a generalized solution for typical time segmentation tasks. The layer architecture, training methods, and methods for simple customization are described as well as the results of application to three separate arc jet data streams: facility condition segmentation, video highlight segmentation, and calorimeter time-series segmentation.

Machine learning↗

1d-Convolutional Neural Network Architecture for Generalized Time-Segmentation Tasks

Time segmentation of experimental data is a common and often difficult task. Consequently, it is of interest to automate this type of segmentation to reduce manual inputs, which are labor intensive and less consistent. However, simple thresholding algorithms are often insufficiently robust due either to noise or inconsistent data. This paper proposes a simple 1D CNN architecture as a generalized solution for typical time segmentation tasks. The layer architecture, training methods, and methods for simple customization are described as well as the results of application to three separate arc jet data streams: facility condition segmentation, video highlight segmentation, and calorimeter time-series segmentation.

Machine learning↗

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗

Arbitrary Polynomial Separations in Trainable Quantum Machine Learning

Recent theoretical results in quantum machine learning have demonstrated a general trade-off between the expressive power of quantum neural networks (QNNs) and their trainability; as a corollary of these results, practical exponential separations in expressive power over classical machine learning models are believed to be infeasible as such QNNs take a time to train that is exponential in the model size. We here circumvent these negative results by constructing a hierarchy of efficiently trainable QNNs that exhibit unconditionally provable, polynomial memory separations of arbitrary constant degree over classical neural networks—including state-of-the-art models, such as Transformers—in performing a classical sequence modeling task. This construction is also computationally efficient, as each unit cell of the introduced class of QNNs only has constant gate complexity. We show that contextuality—informally, a quantitative notion of semantic ambiguity—is the source of the expressivity separation, suggesting that other learning tasks with this property may be a natural setting for the use of quantum learning algorithms.

Anschuetz, Eric R. [California Institute of Techno↗

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine↗