Annotated Translated Disassembled Code
Procedure for generating function/library embedding based on disassembled binary data from a graph database and processing those embedding through supervised machine learning techniques.
Beckman, BryanR.↗
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smol_model_benchmark
Machine learning models for protein–small molecule binding prediction using graph (GAT), image-based (ResNet), and transformer-based SMILES approaches (ChemBERTa and MIST). The code includes training pipelines and experiments on the dataset from the BELKA Kaggle competition.
Gibson, Kaetlyn [Los Alamos National Lab]↗
HydraGNN_Predictive_GFM_2024 - Ensemble of predictive graph foundation models for ground state atomistic materials modeling
We provide the ensemble of fifteen pre-trained graph foundation models (GFMs) for atomistic materials modeling applications. Each one of the fifteen GFMs has been trained on five open-source datasets that (once aggregated) amount to over 154 million atomistic structures, which cover over two-thirds of the natural elements of the periodic table and that comprises a broad set of organic and inorganic compounds. This vast set of atomistic structures comprises ground state configurations that are dynamically stable (i.e., equilibrated structures with atomic forces approximately close to zero values) as well as dynamically unstable structures (i.e., non-equilibrium structures with non-negligible non-zero values of atomic forces). The ensemble of datasets aggregated does NOT include excited states. The datasets have been curated to remove atomistic structures with spectral norm of the force tensor above 100 eV/angstrom. Moreover, a linear term of the energy was computed for each dataset using a linear regression model that uses the chemical concentration of each natural element as regressor. The linear term predicted by the linear regression model has been subtracted from each original energy value to perform a re-alignment of the energy values across different electronic structures approximation theories performed to generate the diverse multi-source, multi-fidelity datasets. The folder "ADIOS_files" contains the set of pre-processed datasets in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used for the development and training of GFMs in this work. The "ADIOS_files" directory contains 6 sub-directories named as follows: - ANI1x-v3.bp - MPTrj-v3.bp - OC2020-20M-v3.bp - OC2020-v3.bp - OC2022-v3.bp - qm7x-v3.bp Each sub-directory contains the pre-processed datasets converted in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used to the development, training, and performance testing of the ensemble go predictive graph foundation models. Each GFM was developed using HydraGNN (https://github.com/ORNL/HydraGNN) as underlying graph neural network (GNN) architecture. The multi-task learning (MTL) capability of HydraGNN was used to simultaneously train the GFMs on labeled values for direct predictions of energy (a total system property of an atomistic structure that measures the chemical stability) and atomic forces (an atomic level property of an atomistic structure that measures the dynamical stability). The hyper parameters of the GFM have been tuned using scalable hyperparameter optimization (HPO) algorithms implemented in the software DeepHyper (https://github.com/deephyper/deephyper). The pre-training of each HPO trial was performed using distributed data parallelism (DDP) to scale the training across 128 compute nodes of the exascale OLCF supercomputer Frontier. Each HPO trial was trained only for 10 epochs and an early stopping was performed to avoid wasting significant computational resources on GNN architectures that were clearly underperforming. For each HPO trial, the 'omnistat' tool developed by (AMD Research - Advanced Micro Device) was used to measure the total energy consumption in kWh. The ensemble of GFMs was obtained by selecting the fifteen best performing HPO trials. Four models have been selected for their clear advantage in accuracy, and these are the GFMs with IDs 229, 156, 147, 260. Additional eleven models have been selected based on judicious balance between accuracy and energy consumption needed for training, and these are the GFMs with IDs 165, 78, 137, 1, 175, 171, 181, 67, 179, 167, 351. Each selected GFM of the ensemble was continued to cumulate a total of at most 30 epochs. In some cases, the total number of epochs actually performed was les than 30 due to two combined factors: (1) the size of the GFM (i.e., the number of model parameters to train) and (2) the total wall-clock time for which the computational resources could be allocated on OLCF-Frontier. The "Ensemble_of_models" directory contains 15 sub-directories named as follows: - gfm_0.229 - gfm_0.156 - gfm_0.147 - gfm_0.260 - gfm_0.165 - gfm_0.78 - gfm_0.137 - gfm_0.1 - gfm_0.175 - gfm_0.171 - gfm_0.181 - gfm_0.67 - gfm_0.179 - gfm_0.167 - gfm_0.351 Each one of these sub-directories refers to one of the fifteen HPO trials that have been selected to continue the pre-training with at most 30 epochs. With each sub-directory associated with a specific HPO trial, the following files can be found: - config.json: file for argument parsing to develop and train an HydraGNN architecture - gfm_0.ID_epoch_N.pk: file with model parameters for HPO ID trial after N epochs of training The ensemble of fifteen GFM architectures was used for (1) ensemble averaging to stabilize the predictions of energy and atomic forces after pre-training for post-processing analysis and (2) ensemble uncertainty quantification (UQ). The code used to develop, pre-train, and load the pre-trained models for post-processing analysis is available on the ORNL-GitHub at the following link: https://github.com/ORNL/HydraGNN/tree/Predictive_GFM_2024
36 MATERIALS SCIENCE↗
GEDet: Detecting Erroneous Nodes with A Few Examples
Detecting nodes with erroneous values in real-world graphs re- mains challenging due to the lack of examples and various error scenarios. We demonstrate GEDet, an error detection engine that can detect erroneous nodes in graphs with a few examples. The GEDet framework tackles error detection as a few-shot node classification problem. We invite the attendees to experience the following unique features. (1) Few-shot detection. Users only need to provide a few examples of erroneous nodes to perform error detection with GEDet. GEDet achieves desirable accuracy with (a) a graph augmentation module, which automatically generates synthetic examples to learn the classifier, and (b) an adversarial detection module, which improves classifiers to better distinguish erroneous nodes from both cleaned nodes and synthetic examples. We show that GEDet significantly improves the state-of-the-art error detection methods. (2) Diverse error scenarios. GEDet profiles data errors with a built-in library of transformation functions from correct values to errors. Users can also easily “plug in” new error types or examples. (3) User-centric detection. GEDet supports (a) an active learning mode to engage users to verify detected results, and adapts the error detection process accordingly; and (b) visual interfaces to interpret and track detected errors.
Guan, Sheng↗
Intelligent experiments through real-time AI: Fast Data Processing and Autonomous Detector Control for sPHENIX and future EIC detectors
This R&D project, initiated by the DOE Nuclear Physics AI-Machine Learning initiative in 2022, leverages AI to address data processing challenges in high-energy nuclear experiments (RHIC, LHC, and future EIC). Our focus is on developing a demonstrator for real-time processing of high-rate data streams from sPHENIX experiment tracking detectors. The limitations of a 15 kHz maximum trigger rate imposed by the calorimeters can be negated by intelligent use of streaming technology in the tracking system. The approach efficiently identifies low momentum rare heavy flavor events in high-rate p+p collisions (3MHz), using Graph Neural Network (GNN) and High Level Synthesis for Machine Learning (hls4ml). Success at sPHENIX promises immediate benefits, minimizing resources and accelerating the heavy-flavor measurements. The approach is transferable to other fields. For the EIC, we develop a DIS-electron tagger using Artificial Intelligence - Machine Learning (AI-ML) algorithms for real-time identification, showcasing the transformative potential of AI and FPGA technologies in high-energy nuclear and particle experiments real-time data processing pipelines.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
A Privacy First Path Analysis using Clickstream Data
In the modern digital economy, data-driven decision making is crucial for effectively meeting the ever-evolving demands of consumer engagement and satisfaction. Clickstream data has become invaluable for understanding customer behavior, yet concerns over privacy and security persist, especially with some internet service providers profiting from its sale. This article introduces an innovative methodology that blends experiential learning with advanced cryptographic techniques, including differential privacy and graph analytics. The core objective of this methodology is to estimate Customer Lifetime Value (CLV) by analyzing clickstream data, achieving an average prediction accuracy of 92.4% in user engagement levels while ensuring user anonymity through Recency, Frequency, and Monetary (RFM) analysis. Our study introduces the concept of a “data depositor” and a privacy manager, employing the composition theorem to merge non-adaptive queries effectively. Privacy budgets (? = 1.0, d = 10-5), sensitivity-specific techniques, and data partitioning were applied. Randomization and noise addition protect data integrity, with special handling for categorical values. This approach, differing from prior studies, offers a 12.6% improvement in privacy-preserving targeting accuracy while maintaining strict confidentiality, presenting a novel path forward in data-driven decision-making.
Frequency and Monetary (RFM) analysis↗
Power System Event Identification Based on Deep Neural Network With Information Loading
Online power system event identification and classification are crucial to enhancing the reliability of transmission systems. In this study, we develop a deep neural network (DNN) based approach to identify and classify power system events by leveraging real-world measurements from hundreds of phasor measurement units (PMUs) and labels from thousands of events. Two innovative designs are embedded into the baseline model built on convolutional neural networks (CNNs) to improve the event classification accuracy. First, we propose a graph signal processing based PMU sorting algorithm to improve the learning efficiency of CNNs. Second, we deploy information loading based regularization to strike the right balance between memorization and generalization for the DNN. Numerical results based on real-world dataset from the Eastern Interconnection of the U.S power transmission grid show that the combination of PMU based sorting and the information loading based regularization techniques help the proposed DNN approach achieve highly accurate event identification and classification results.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Scaling kinetic Monte-Carlo simulations of grain growth with combined convolutional and graph neural networks
Graph neural networks (GNN) have emerged as a promising machine learning method for microstructure simulations such as grain growth. However, accurate modeling of realistic grain boundary networks requires large simulation cells, which GNN has difficulty scaling up to. To alleviate the computational costs and memory footprint of GNN, we suggest a hybrid architecture combining a convolutional neural network (CNN) based bijective autoencoder to compress the spatial dimensions, and a GNN that evolves the microstructure in the latent space of reduced spatial sizes. Our results demonstrate that the new design significantly reduces computational costs with using fewer message passing layer (from 12 down to 3) compared with GNN alone. The reduction in computational cost becomes more pronounced as the spatial size increases, indicating strong computational scalability. For the largest mesh evaluated (160 3 ), our method reduces memory usage and runtime in inference by 117× and 115×, respectively, compared with GNN-only baseline. More importantly, it shows higher accuracy and stronger spatiotemporal capability than the GNN-only baseline, especially in long-term testing. Such combination of scalability and accuracy is essential for simulating realistic material microstructures over extended time scales. The improvements can be attributed to the bijective autoencoder’s ability to compress information losslessly from spatial domain into a high dimensional feature space, thereby producing more expressive latent features for the GNN to learn from, while also contributing its own spatiotemporal modeling capability. Training data are generated from stochastic grain growth simulations, providing realistic variability for learning robust microstructure evolution. Comprehensive system validation confirms that the model is accurate, robust, and scalable.
36 MATERIALS SCIENCE↗
Conflation of Geospatial POI Data and Ground-level Imagery via Link Prediction on Joint Semantic Graph
With the proliferation of smartphone cameras and social networks, we have rich, multi-modal data about points of interest (POIs) - like cultural landmarks, institutions, businesses, etc. - within a given areas of interest (AOI) (e.g., a county, city or a neighborhood) available to us. Data conflation across multiple modalities of data sources is one of the key challenges in maintaining a geographical information system (GIS) which accumulate data about POIs. Given POI data from nine different sources, and ground-level geo-tagged and scene-captioned images from two different image hosting platforms, in this work we explore the application of graph neural networks (GNNs) to perform data conflation, while leveraging a natural graph structure evident in geospatial data. The preliminary results demonstrate the capacity of a GNN operation to learn distributions of entity (POIs and images) features, coupled with topological structure of entity's local neighborhood in a semantic nearest neighbor graph, in order to predict links between a pair of entities.
Gurav, Rutuja↗
Risk-Aware Measurement Synchronization and Recovery for DSSE With Heterogeneous Data Sources
Power distribution systems are increasingly integrating heterogeneous sensors with varying data reporting rates and types, which pose challenges to achieving observability at the desired temporal resolution of distribution system state estimation (DSSE). Multisensor failures caused by extreme events exacerbate these issues, introducing substantial uncertainties into DSSE. This article proposes a novel solution to these challenges by ensuring high-resolution system observability despite heterogeneous data sources and multisensor failures. First, a deep learning architecture combining long short-term memory (LSTM) and graph convolutional network (GCN) is employed to synchronize meters with different reporting rates, aiming to achieve system observability. A random-walk-model-based approach is introduced to generate pseudo-measurements while properly characterizing their uncertainties under multisensor failures. Finally, a disaster-risk-informed observability metric (RiOM) is defined to quantify the uncertainty associated with state estimation results. The proposed framework offers deeper insights into the system observability on the fly compared with conventional analysis. The effectiveness of the framework is demonstrated on an IEEE standard test case and a large-scale real-world distribution feeder in mid-Minnesota in the U.S.
97 MATHEMATICS AND COMPUTING↗
Unsupervised learning-enabled pulsed infrared thermographic microscopy of subsurface defects in stainless steel
Metallic structures produced with laser powder bed fusion (LPBF) additive manufacturing method (AM) frequently contain microscopic porosity defects, with typical approximate size distribution from one to 100 microns. Presence of such defects could lead to premature failure of the structure. In principle, structural integrity assessment of LPBF metals can be accomplished with nondestructive evaluation (NDE). Pulsed infrared thermography (PIT) is a non-contact, one-sided NDE method that allows for imaging of internal defects in arbitrary size and shape metallic structures using heat transfer. PIT imaging is performed using compact instrumentation consisting of a flash lamp for deposition of a heat pulse, and a fast frame infrared (IR) camera for measuring surface temperature transients. However, limitations of imaging resolution with PIT include blurring due to heat diffusion, sensitivity limit of the IR camera. We demonstrate enhancement of PIT imaging capability with unsupervised learning (UL), which enables PIT microscopy of subsurface defects in high strength corrosion resistant stainless steel 316 alloy. PIT images were processed with UL spatial–temporal separation-based clustering segmentation (STSCS) algorithm, refined by morphology image processing methods to enhance visibility of defects. The STSCS algorithm starts with wavelet decomposition to spatially de-noise thermograms, followed by UL principal component analysis (PCA), fine-tuning optimization, and neural learning-based independent component analysis (ICA) algorithms to temporally compress de-noised thermograms. The compressed thermograms were further processed with UL-based graph thresholding K-means clustering algorithm for defects segmentation. The STSCS algorithm also includes online learning feature for efficient re-training of the model with new data. For this study, metallic specimens with calibrated microscopic flat bottom hole defects, with diameters in the range from 203 to 76 µm, were produced using electro discharge machining (EDM) drilling. While the raw thermograms do not show any material defects, using STSCS algorithm to process PIT images reveals defects as small as 101 µm in diameter. To the best of our knowledge, this is the smallest reported size of a sub-surface defect in a metal imaged with PIT, which demonstrates the PIT capability of detecting defects in the size range relevant to quality control requirements of LPBF-printed high-strength metals.
36 MATERIALS SCIENCE↗
Spatiotemporal Graph Convolutional Networks for Earthquake Source Characterization
Abstract Accurate earthquake location and magnitude estimation play critical roles in seismology. Recent deep learning frameworks have produced encouraging results on various seismological tasks (e.g., earthquake detection, phase picking, seismic classification, and earthquake early warning). Many existing machine learning earthquake location methods utilize waveform information from a single station. However, multiple stations contain more complete information for earthquake source characterization. Inspired by recent successes in applying graph neural networks (GNNs) in graph‐structured data, we develop a Spatiotemporal Graph Neural Network (STGNN) for estimating earthquake locations and magnitudes. Our graph neural network leverages geographical and waveform information from multiple stations to construct graphs automatically and dynamically by adaptive message passing based on graphs' edges. Using a recent graph neural network and a fully convolutional neural network as baselines, we apply STGNN to earthquakes recorded by the Southern California Seismic Network from 2000 to 2019 and earthquakes collected in Oklahoma from 2014 to 2015. STGNN yields more accurate earthquake locations than those obtained by the baseline models and performs comparably in terms of depth and magnitude prediction, though the ability to predict depth and magnitude remains weak for all tested models. Our work demonstrates the potential of using GNNs and multiple stations for better automatic estimation of earthquake epicenters.
58 GEOSCIENCES↗
Accelerate microstructure evolution simulation using graph neural networks with adaptive spatiotemporal resolution
Abstract Surrogate models driven by sizeable datasets and scientific machine-learning methods have emerged as an attractive microstructure simulation tool with the potential to deliver predictive microstructure evolution dynamics with huge savings in computational costs. Taking 2D and 3D grain growth simulations as an example, we present a completely overhauled computational framework based on graph neural networks with not only excellent agreement to both the ground truth phase-field methods and theoretical predictions, but enhanced accuracy and efficiency compared to previous works based on convolutional neural networks. These improvements can be attributed to the graph representation, both improved predictive power and a more flexible data structure amenable to adaptive mesh refinement. As the simulated microstructures coarsen, our method can adaptively adopt remeshed grids and larger timesteps to achieve further speedup. The data-to-model pipeline with training procedures together with the source codes are provided.
36 MATERIALS SCIENCE↗
Unsupervised Resource Allocation with Graph Neural Networks
We present an approach for maximizing a global utility function by learning how to allocate resources in an unsupervised way. We expect interactions between allocation targets to be important and therefore propose to learn the reward structure for near-optimal allocation policies with a GNN. By relaxing the resource constraint, we can employ gradient-based optimization in contrast to more standard evolutionary algorithms. Our algorithm is motivated by a problem in modern astronomy, where one needs to select-based on limited initial information-among $10^9$ galaxies those whose detailed measurement will lead to optimal inference of the composition of the universe. Our technique presents a way of flexibly learning an allocation strategy by only requiring forward simulators for the physics of interest and the measurement process. We anticipate that our technique will also find applications in a range of resource allocation problems.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Data efficiency and extrapolation trends in neural network interatomic potentials
Abstract Recently, key architectural advances have been proposed for neural network interatomic potentials (NNIPs), such as incorporating message-passing networks, equivariance, or many-body expansion terms. Although modern NNIP models exhibit small differences in test accuracy, this metric is still considered the main target when developing new NNIP architectures. In this work, we show how architectural and optimization choices influence the generalization of NNIPs, revealing trends in molecular dynamics (MD) stability, data efficiency, and loss landscapes. Using the 3BPA dataset, we uncover trends in NNIP errors and robustness to noise, showing these metrics are insufficient to predict MD stability in the high-accuracy regime. With a large-scale study on NequIP, MACE, and their optimizers, we show that our metric of loss entropy predicts out-of-distribution error and data efficiency despite being computed only on the training set. This work provides a deep learning justification for probing extrapolation and can inform the development of next-generation NNIPs.
36 MATERIALS SCIENCE↗
Open-source generation of sigma profiles: impact of quantum chemistry and solvation treatment on machine learning performance
The combination of machine learning (ML) models with chemistry-related tasks requires the description of molecular structures in a machine-readable way. The nature of these so-called molecular descriptors has a direct and major impact on the performance of ML models and remains an open problem in the field. Structural descriptors like SMILES strings or molecular graphs lack size-independence and can be memory intensive. Machine-learned descriptors can be of low dimensionality and constant size but lack physical significance and human interpretability. Sigma profiles, which are unnormalized histograms of the surface charge distributions of solvated molecules, combine physical significance with low dimensionality and size-independence, making them a suitable candidate for a universal molecular descriptor. However, their widespread adoption in ML applications requires open access to sigma profile generation, which is currently not available. This work details the development of OpenSPGen – an open-source tool for generating sigma profiles. Also presented are studies on the effect of different settings on the efficacy of the generated sigma profiles at predicting thermophysical material properties when used as inputs to a Gaussian process as a simple surrogate ML model. We find that a higher level of theory does not translate to more accurate results. We also provide further recommendations for sigma profile calculation and use in ML models.
Salih, Fathya Y. M. [University of Notre Dame, IN ↗
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function
Abstract Motivation Millions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently. Results We developed TransFun—a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating that the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy. Availability and implementation The source code of TransFun is available at https://github.com/jianlin-cheng/TransFun.
59 BASIC BIOLOGICAL SCIENCES↗
Domain Adaptive Graph Neural Networks for Constraining Cosmological Parameters Across Multiple Data Sets
State of the art astronomical simulations have provided datasets which enabled the training of novel deep learning techniques for constraining cosmological parameters. However, differences in subgrid physics implementation and numerical approximations among simulation suites lead to differences in simulated datasets, which pose a hard challenge when trying to generalize across diverse data domains and ultimately when applying models to observational data. Recent work reveals deep learning algorithms are able to extract more information from complex cosmological simulations than summary statistics like power spectra. We introduce Domain Adaptive Graph Neural Networks (DA-GNNs), trained on CAMELS data, inspired by CosmoGraphNet (Villanueva-Domingo et al 2023). By utilizing GNNs, we can capitalize on their capacity to capture both astrophysical and topological features of galaxy distributions. Mixing these capabilities with domain adaptation techniques such as Maximum Mean Discrepancy (MMD), which enable extraction of domain-invariant features, our framework demonstrates enhanced accuracy and robustness. We present experimental results, including the alignment of distributions across domains through data visualization. These findings suggest that DA-GNNs are an efficient way of extracting domain independent cosmological information, a vital step toward robust deep learning for real cosmic survey data.
79 ASTRONOMY AND ASTROPHYSICS↗