Supervised and Unsupervised learning framework for latent feature and knowledge extraction
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Machine learning, AI, unsupervised learning, calib↗
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Novel CHI3L1 ‐Associated Angiogenic Phenotypes Define Glioma Microenvironments: Insights From Multi‐Omics Integration
ABSTRACT The CHI3L1 signaling pathway significantly influences glioma angiogenesis, but its role in the tumor microenvironment (TME) remains elusive. We propose a novelCHI3L1‐associated vascular phenotype classification for glioma through integrative analyses of multiple datasets with bulk and single‐cell transcriptome, genomics, digital pathology, and clinical data. We investigated the biological characteristics, genomic alterations, therapeutic vulnerabilities, and immune profiles within these phenotypes through a comprehensive multi‐omics approach. We constructed the vascular‐related risk (VR) score based onCHI3L1‐associated vascular signatures (CAVS) identified by machine learning algorithms. Utilizing unsupervised consensus clustering, gliomas were stratified into three distinct vascular phenotypes: Cluster A, marked by high vascularization and stromal activation with a relatively low levels of tumor‐infiltrating lymphocytes (TILs); Cluster B, characterized by moderate vascularization and stromal activity, coupled with a high density of TILs; and Cluster C, defined by low vascularization and sparse immune cell infiltration. We observed that the CAVS effectively indicated glioma‐associated angiogenesis and immune suppression by single‐cell RNA‐seq analysis. Moreover, the high‐VR‐score group exhibited enhanced angiogenic activity, reduced immune response, resistance to immunotherapy, and poorer clinical outcomes. The VR score independently predicted glioma prognosis and, combined with a nomogram, provided a robust clinical decision‐making tool. Potential drug prediction based on transcription factors for high‐risk patients was also performed. Our study reveals thatCHI3L1‐associated vascular phenotypes shape distinct immune landscapes in gliomas, offering insights for optimizing therapeutic strategies to improve patient outcomes.
Oncology↗
Training Restricted Boltzmann Machines With a D-Wave Quantum Annealer
Restricted Boltzmann Machine (RBM) is an energy-based, undirected graphical model. It is commonly used for unsupervised and supervised machine learning. Typically, RBM is trained using contrastive divergence (CD). However, training with CD is slow and does not estimate the exact gradient of the log-likelihood cost function. In this work, the model expectation of gradient learning for RBM has been calculated using a quantum annealer (D-Wave 2000Q), where obtaining samples is faster than Markov chain Monte Carlo (MCMC) used in CD. Training and classification results of RBM trained using quantum annealing are compared with the CD-based method. The performance of the two approaches is compared with respect to the classification accuracies, image reconstruction, and log-likelihood results. The classification accuracy results indicate comparable performances of the two methods. Image reconstruction and log-likelihood results show improved performance of the CD-based method. It is shown that the samples obtained from quantum annealer can be used to train an RBM on a 64-bit “bars and stripes” dataset with classification performance similar to an RBM trained with CD. Though training based on CD showed improved learning performance, training using a quantum annealer could be useful as it eliminates computationally expensive MCMC steps of CD.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Efficient solutions of fermionic systems using artificial neural networks
In this study, we explore the similarities and differences between variational Monte Carlo techniques that employ conventional and artificial neural network representations of the ground-state wave function for fermionic systems. Our primary focus is on shallow neural network architectures, specifically the restricted Boltzmann machine, and we examine unsupervised learning algorithms that are appropriate for modeling complex many-body correlations. We assess the advantages and drawbacks of conventional and neural network wave functions by applying them to a range of circular quantum dot systems. Our findings, which include results for systems containing up to 90 electrons, emphasize the efficient implementation of these methods on both homogeneous and heterogeneous high-performance computing facilities.
97 MATHEMATICS AND COMPUTING↗
Unsupervised quantum circuit learning in high energy physics
Unsupervised training of generative models is a machine learning task that has many applications in scientific computing. Here, in this work, we evaluate the efficacy of using quantum circuit-based generative models to generate synthetic data of high energy physics processes. We use nonadversarial, gradient-based training of quantum circuit Born machines to generate joint distributions over two and three variables.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Unified architecture for data-driven metadata tagging of building automation systems
This article presents a Unified Architecture (UA) for automated point tagging of Building Automation System (BAS) data, based on a combination of data-driven approaches. Advanced energy analytics applications—including fault detection and diagnostics and supervisory control—have emerged as a significant opportunity for improving the performance of our built environment. Effective application of these analytics depends on harnessing structured data from the various building control and monitoring systems, but typical BAS implementations do not employ any standardized metadata schema. While standards such as Project Haystack and Brick Schema have been developed to address this issue, the process of structuring the data, i.e., tagging the points to apply a standard metadata schema, has, to date, been a manual process. This process is typically costly, labor-intensive, and error-prone. In this work we address this gap by proposing a UA that automates the process of point tagging by leveraging the data accessible through connection to the BAS, including time-series data and the raw point names. The UA intertwines supervised classification and unsupervised clustering techniques from machine learning and leverages both their deterministic and probabilistic outputs to inform the point tagging process. Furthermore, we extend the UA to embed additional input and output data-processing modules that are designed to address the challenges associated with the real-time deployment of this automation solution. We test the UA on two datasets for real-life buildings: (i) commercial retail buildings and (ii) office buildings from the National Renewable Energy Laboratory (NREL) campus. We report the proposed methodology correctly applied 85–90% and 70–75% of the tags in each of these test scenarios, respectively for two significantly different building types used for testing UA's fully-functional prototype. The proposed UA, therefore, offers promising approach for automatically tagging BAS data as it reaches close to 90% accuracy. Further building upon this framework to algorithmically identify the equipment type and their relationships is an apt future research direction to pursue.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Machine learning for analyzing atomic force microscopy (AFM) images generated from polymer blends
In this paper, we present a new machine learning (ML) workflow with unsupervised learning techniques to identify domains within atomic force microscopy (AFM) images obtained from polymer films.
Paruchuri, Aanish [Master of Science in Data Scien↗
Unsupervised discovery of extreme weather events using universal representations of emergent organization
Spontaneous self-organization is ubiquitous in systems far from thermodynamic equilibrium. While organized structures that emerge dominate transport properties, universal representations that identify and describe these key objects remain elusive. Here, we introduce a theoretically grounded framework for describing emergent organization that, via data-driven algorithms, is constructive in practice. Its building blocks are spacetime lightcones that embody how information propagates across a system through local interactions. We show that predictive equivalence classes of lightcones—local causal states—capture organized behaviors in complex spatiotemporal systems. Employing an unsupervised physics-informed machine learning algorithm and a high-performance computing implementation, we demonstrate automatically discovering organized structures in two real-world domain science problems. We show that local causal states identify vortices and track their power-law decay behavior in two-dimensional fluid turbulence. We then show how to detect and track familiar extreme weather events—hurricanes and atmospheric rivers—and discover other novel structures associated with precipitation extremes in high-resolution climate data at the grid-cell level.
Rupe, Adam [Pacific Northwest National Laboratory ↗
Optimal Electrification Using Renewable Energies: Microgrid Installation Model with Combined Mixture k-Means Clustering Algorithm, Mixed Integer Linear Programming, and Onsset Method
Optimal planning and design of microgrids are priorities in the electrification of off-grid areas. Indeed, in one of the Sustainable Development Goals (SDG 7), the UN recommends universal access to electricity for all at the lowest cost. Several optimization methods with different strategies have been proposed in the literature as ways to achieve this goal. This paper proposes a microgrid installation and planning model based on a combination of several techniques. The programming language Python 3.10 was used in conjunction with machine learning techniques such as unsupervised learning based on K-means clustering and deterministic optimization methods based on mixed linear programming. These methods were complemented by the open-source spatial method for optimal electrification planning: onsset. Four levels of study were carried out. The first level consisted of simulating the model obtained with a cluster, which is considered based on the elbow and k-means clustering method as a case study. The second level involved sizing the microgrid with a capacity of 40 kW and optimizing all the resources available on site. The example of the different resources in the Togo case was considered. At the third level, the work consisted of proposing an optimal connection model for the microgrid based on voltage stability constraints and considering, above all, the capacity limit of the source substation. Finally, the fourth level involved a planning study of electrification strategies based mainly on microgrids according to the study scenario. The results of the first level of study enabled us to obtain an optimal location for the centroid of the cluster under consideration, according to the different load positions of this cluster. Then, the results of the second level of study were used to highlight the optimal resources obtained and proposed by the optimization model formulated based on the various technology costs, such as investment, maintenance, and operating costs, which were based on the technical limits of the various technologies. In these results, solar systems account for 80% of the maximum load considered, compared to 7.5% for wind systems and 12.5% for battery systems. Next, an optimal microgrid connection model was proposed based on the constraints of a voltage stability limit estimated to be 10% of the maximum voltage drop. The results obtained for the third level of study enabled us to present selective results for load nodes in relation to the source station node. Finally, the last results made it possible to plan electrification using different network technologies and systems in the short and long term. The case study of Togo was taken into account. The various results obtained from the different techniques provide the necessary leads for a feasibility study for optimal electrification of off-grid areas using microgrid systems.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Unsupervised atomic data mining via multi-kernel graph autoencoders for machine learning force fields
Constructing a chemically diverse dataset while avoiding sampling bias is critical to training efficient and generalizable force fields. However, in computational chemistry and materials science, many common dataset generation techniques are prone to oversampling regions of the potential energy surface. Furthermore, these regions can be difficult to identify and isolate from each other or may not align well with human intuition, making it challenging to systematically remove bias in the dataset. While traditional clustering and pruning (down-sampling) approaches can be useful for this, they can often lead to information loss or a failure to properly identify distinct regions of the potential energy surface due to difficulties associated with the high dimensionality of atomic descriptors. In this work, we introduce the Multi-kernel Edge Attention-based Graph Autoencoder (MEAGraph) model, an unsupervised approach for analyzing atomic datasets. MEAGraph combines multiple linear kernel transformations with attention-based message passing to capture geometric sensitivity and enable effective dataset pruning without relying on labels or extensive training. Demonstrated applications on niobium, tantalum, and iron datasets show that MEAGraph efficiently groups similar atomic environments, allowing for the use of basic pruning techniques for removing sampling bias. This approach provides an effective method for representation learning and clustering that can be used for data analysis, outlier detection, and dataset optimization.
Materials science↗
Multi-kernel Edge Attention Graph Autoencoder
MEAGraph (Multi-kernel Edge Attention Graph Autoencoder) is a graph-based autoencoder model designed for unsupervised data mining for datasets used in machine learning potentials. It provides accurate clustering for atomic environment identification, unsupervised and unlabeled data pruning for dataset construction.
Sun, Hong↗
GeoThermalCloud framework for fusion of big data and multi-physics models in Nevada and Southwest New Mexico
Our GeoThermalCloud framework is designed to process geothermal datasets using a novel toolbox for unsupervised and physics-informed machine learning called SmartTensors. More information about GeoThermalCloud can be found at the GeoThermalCloud GitHub Repository. More information about SmartTensors can be found at the SmartTensors Github Repository and the SmartTensors page at LANL.gov. Links to these pages are included in this submission. GeoThermalCloud.jl is a repository containing all the data and codes required to demonstrate applications of machine learning methods for geothermal exploration. GeoThermalCloud.jl includes: - site data - simulation scripts - jupyter notebooks - intermediate results - code outputs - summary figures - readme markdown files GeoThermalCloud.jl showcases the machine learning analyses performed for the following geothermal sites: - Brady: geothermal exploration of the Brady geothermal site, Nevada - SWNM: geothermal exploration of the Southwest New Mexico (SWNM) region - GreatBasin: geothermal exploration of the Great Basin region, Nevada Reports, research papers, and presentations summarizing these machine learning analyses are also available and will be posted soon.
15 GEOTHERMAL ENERGY↗
AI to Automate ModEx for Optimal Predictive Improvement and Scientific Discovery
Focal Areas: Data acquisition and assimilation enabled by machine learning, AI, advanced experimental optimization, unsupervised learning, and hardware-related AI efforts; Predictive modeling through AI techniques and AI-derived model components; Using AI to design a hierarchical model prediction system consisting and model selection; and, Interrogating complex data (observed and simulated) using AI, big data analytics, and other advanced methods such as explainable AI and physics- or knowledge-guided AI.
54 ENVIRONMENTAL SCIENCES↗
The value of human data annotation for machine learning based anomaly detection in environmental systems
Anomaly detection is the process of identifying unexpected data samples in datasets. Automated anomaly detection is either performed using supervised machine learning models, which require a labelled dataset for their calibration, or unsupervised models, which do not require labels. While academic research has produced a vast array of tools and machine learning models for automated anomaly detection, the research community focused on environmental systems still lacks a comparative analysis that is simultaneously comprehensive, objective, and systematic. This knowledge gap is addressed for the first time in this study, where 15 different supervised and unsupervised anomaly detection models are evaluated on 5 different environmental datasets from engineered and natural aquatic systems. To this end, anomaly detection performance, labelling efforts, as well as the impact of model and algorithm tuning are taken into account. As a result, our analysis reveals the relative strengths and weaknesses of the different approaches in an objective manner without bias for any particular paradigm in machine learning. Most importantly, our results show that expert-based data annotation is extremely valuable for anomaly detection based on machine learning.
54 ENVIRONMENTAL SCIENCES↗
Unsupervised Learning for Improved Gamma-Ray Spectrometry in Pixelated Cadmium Zinc Telluride (CZT) Detectors
Machine learning has been found to be ubiquitously useful across many industries, presenting an opportunity to improve radiation detection performance using data-driven algorithms. Improved detector resolution can aid in the detection, identification, and quantification of radionuclides. Here, in this work, a novel, data-driven, unsupervised learning approach is developed to improve detector spectral characteristics by learning, and subsequently rejecting, poorly performing regions of the pixelated detector. Feature engineering is used to fit individual characteristic photo peaks to a Doniach lineshape with a linear background model. Then, principal component analysis is used to learn a lower-dimension latent space representation of each photo peak where the pixels are clustered, and subsequently ranked, based on the cluster mean distance to an optimal point. Pixels within the worst cluster(s) are rejected to improve the full-width at half-maximum (FWHM) by 10% to 15% (relative to the bulk detector) at 50% net efficiency when applied to training data obtained from measurements of a 100 μCi 154 Eu source using a H3D M400i pixelated cadmium zinc telluride detector. These results compare well with, but do not outperform, a greedy algorithm that accumulates pixels in order of FWHM from lowest to highest used as a benchmark. In the future, this approach can be extended to include the detector energy and angular response. Finally, the model is applied to newly seen natural and enriched uranium spectra relevant for nuclear safeguards applications.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Integrating Models with Real-time Field Data for Extreme Events: From Field Sensors to Models and Back with AI in the Loop
Focal Area(s): This whitepaper is responsive to focal area (1) Data acquisition and assimilation enabled by machine learning, AI, and advanced methods including experimental/network design/optimization, unsupervised learning (including deep learning), and hardware-related efforts involving AI (e.g., edge computing). We discuss Artificial Intelligence and Machine Learning (AI/ML) enabled integration of real-time data into the extreme event modeling workflow to improve the predictive capabilities of these models, and deliver real-time feedback to remote sensors, including software and data engineering challenges.
54 ENVIRONMENTAL SCIENCES↗
New Understanding of Cloud Processes via Unsupervised Cloud Classification in Satellite Images
This white paper addresses DOE AI4ESP focus areas #1 and #3. We propose to leverage advances in machine learning and artificial intelligence to create a new unsupervised cloud classification framework that will produce new datasets and cloud process understanding to reduce biases in Earth system models.
58 GEOSCIENCES↗
Continuous-time probabilistic models for longitudinal electronic health records
Analysis of longitudinal Electronic Health Record (EHR) data is an important goal for precision medicine. Difficulty in applying Machine Learning (ML) methods, either predictive or unsupervised, stems in part from the heterogeneity and irregular sampling of EHR data. Here, we present an unsupervised probabilistic model that captures nonlinear relationships between variables over continuous-time. This method works with arbitrary sampling patterns and captures the joint probability distribution between variable measurements and the time intervals between them. Inference algorithms are derived that can be used to evaluate the likelihood of future using under a trained model. As an example, we consider data from the United States Veterans Health Administration (VHA) in the areas of diabetes and depression. Likelihood ratio maps are produced showing the likelihood of risk for moderate-severe vs minimal depression as measured by the Patient Health Questionnaire-9 (PHQ-9).
59 BASIC BIOLOGICAL SCIENCES↗