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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

ICAT: The Interactive Corpus Analysis Tool

The Interactive Corpus Analysis Tool (ICAT) is a Python library for creating dashboards to explore textual datasets and build simple binary classification models to help filter through them and focus on entries of interest. This tool uses a form of interactive machine learning (IML), a paradigm of “machine teaching” (Simard et al., 2017) that sits at the intersection of the fields of human computer interaction (HCI), visual analytics, and machine learning. The intent of ICAT is to allow subject matter experts (SME) with limited to no experience in machine learning to benefit from an iterative human-in-the-loop (HITL) approach to building their own model without needing to understand the details of the underlying algorithm. This interactivity is achieved by allowing the user to create features, label data points, and visually manipulate a representation of the features to manually cluster and investigate data, while a model is trained on the fly based on these actions. ICAT is built on top of the Panel (Holoviz, 2018) library, using a combination of Vega, a custom IPyWidget using D3, and ipyvuetify, and is intended to be used inside of a Jupyter environment.

Martindale, Nathan [Oak Ridge National Laboratory ↗
DOE OSTI2024

Recognizing Blazars Using Radio Morphology from the VLA Sky Survey

Abstract Blazars are radio-loud active galactic nuclei whose jets have a very small angle to our line of sight. Observationally, the radio emissions are mostly compact or compact-core with a one-sided jet. With 2.″5 resolution at 3 GHz, the Very Large Array Sky Survey (VLASS) enables us to resolve the structure of some blazar candidates in the sky north of decl. −40°. We introduce an algorithm to classify radio sources as either blazar-like or non-blazar-like based on their morphology in the VLASS images. We apply our algorithm to three existing catalogs, including one of the known blazars (Roma-BzCAT) and two blazar candidates identified by Wide-field Infrared Survey Explorer colors and radio emission (WIBRaLS, KDEBLLACS). We show that in all three catalogs, there are objects with morphologies inconsistent with being blazars. Considering all the catalogs, more than 12% of the candidates are unlikely to be blazars, based on this analysis. Notably, we show that 3% of the Roma-BzCATconfirmedblazars could be a misclassification based on their VLASS morphology. The resulting table with all sources and their radio morphological classification is available online.

Astronomy & Astrophysics↗
DOE OSTI2019

Identification of RR Lyrae stars in multiband, sparsely-sampled data from the Dark Energy Survey using template fitting and Random Forest classification

Many studies have shown that RR Lyrae variable stars (RRL) are powerful stellar tracers of Galactic halo structure and satellite galaxies. The Dark Energy Survey (DES), with its deep and wide coverage (g ~ 23.5 mag in a single exposure; over 5000 deg2) provides a rich opportunity to search for substructures out to the edge of the Milky Way halo. However, the sparse and unevenly sampled multiband light curves from the DES wide-field survey (a median of four observations in each of grizY over the first three years) pose a challenge for traditional techniques used to detect RRL. We present an empirically motivated and computationally efficient template-fitting method to identify these variable stars using three years of DES data. When tested on DES light curves of previously classified objects in SDSS stripe 82, our algorithm recovers 89% of RRL periods to within 1% of their true value with 85% purity and 76% completeness. Using this method, we identify 5783 RRL candidates, ~28% of which are previously undiscovered. This method will be useful for identifying RRL in other sparse multiband data sets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

The CHRS Data Portal, an easily accessible public repository for PERSIANN global satellite precipitation data

The Center for Hydrometeorology and Remote Sensing (CHRS) has created the CHRS Data Portal to facilitate easy access to the three open data licensed satellite-based precipitation datasets generated by our Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN) system: PERSIANN, PERSIANN-Cloud Classification System (CCS), and PERSIANN-Climate Data Record (CDR). These datasets have the potential for widespread use by various researchers, professionals including engineers, city planners, and so forth, as well as the community at large. Researchers at CHRS created the CHRS Data Portal with an emphasis on simplicity and the intention of fostering synergistic relationships with scientists and experts from around the world. The following paper presents an outline of the hosted datasets and features available on the CHRS Data Portal, an examination of the necessity of easily accessible public data, a comprehensive overview of the PERSIANN algorithms and datasets, and a walk-through of the procedure to access and obtain the data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Automated characterization of spatial and dynamical heterogeneity in supercooled liquids via implementation of machine learning

Abstract A computational approach by an implementation of the principle component analysis (PCA) with K -means and Gaussian mixture (GM) clustering methods from machine learning algorithms to identify structural and dynamical heterogeneities of supercooled liquids is developed. In this method, a collection of the average weighted coordination numbers ( W C N s ‾ ) of particles calculated from particles’ positions are used as an order parameter to build a low-dimensional representation of feature (structural) space for K -means clustering to sort the particles in the system into few meso-states using PCA. Nano-domains or aggregated clusters are also formed in configurational (real) space from a direct mapping using associated meso-states’ particle identities with some misclassified interfacial particles. These classification uncertainties can be improved by a co-learning strategy which utilizes the probabilistic GM clustering and the information transfer between the structural space and configurational space iteratively until convergence. A final classification of meso-states in structural space and domains in configurational space are stable over long times and measured to have dynamical heterogeneities. Armed with such a classification protocol, various studies over the thermodynamic and dynamical properties of these domains indicate that the observed heterogeneity is the result of liquid–liquid phase separation after quenching to a supercooled state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Graph learning for particle accelerator operations

Particle accelerators play a crucial role in scientific research, enabling the study of fundamental physics and materials science, as well as having important medical applications. This study proposes a novel graph learning approach to classify operational beamline configurations as good or bad. By considering the relationships among beamline elements, we transform data from components into a heterogeneous graph. We propose to learn from historical, unlabeled data via our self-supervised training strategy along with fine-tuning on a smaller, labeled dataset. Additionally, we extract a low-dimensional representation from each configuration that can be visualized in two dimensions. Leveraging our ability for classification, we map out regions of the low-dimensional latent space characterized by good and bad configurations, which in turn can provide valuable feedback to operators. This research demonstrates a paradigm shift in how complex, many-dimensional data from beamlines can be analyzed and leveraged for accelerator operations.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

PERSIANN-CNN: Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks–Convolutional Neural Networks

Abstract Accurate and timely precipitation estimates are critical for monitoring and forecasting natural disasters such as floods. Despite having high-resolution satellite information, precipitation estimation from remotely sensed data still suffers from methodological limitations. State-of-the-art deep learning algorithms, renowned for their skill in learning accurate patterns within large and complex datasets, appear well suited to the task of precipitation estimation, given the ample amount of high-resolution satellite data. In this study, the effectiveness of applying convolutional neural networks (CNNs) together with the infrared (IR) and water vapor (WV) channels from geostationary satellites for estimating precipitation rate is explored. The proposed model performances are evaluated during summer 2012 and 2013 over central CONUS at the spatial resolution of 0.08° and at an hourly time scale. Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks (PERSIANN)–Cloud Classification System (CCS), which is an operational satellite-based product, and PERSIANN–Stacked Denoising Autoencoder (PERSIANN-SDAE) are employed as baseline models. Results demonstrate that the proposed model (PERSIANN-CNN) provides more accurate rainfall estimates compared to the baseline models at various temporal and spatial scales. Specifically, PERSIANN-CNN outperforms PERSIANN-CCS (and PERSIANN-SDAE) by 54% (and 23%) in the critical success index (CSI), demonstrating the detection skills of the model. Furthermore, the root-mean-square error (RMSE) of the rainfall estimates with respect to the National Centers for Environmental Prediction (NCEP) Stage IV gauge–radar data, for PERSIANN-CNN was lower than that of PERSIANN-CCS (PERSIANN-SDAE) by 37% (14%), showing the estimation accuracy of the proposed model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

AGS-GNN: Attribute-guided Sampling for Graph Neural Networks

We propose AGS-GNN, a novel attribute-guided sampling algorithm for Graph Neural Networks (GNNs) that exploits node features and connectivity structure of a graph while simultaneously adapting for both homophily and heterophily in graphs. (In homophilic graphs vertices of the same class are more likely to be connected, and vertices of different classes tend to be linked in heterophilic graphs.) While GNNs have been successfully applied to homophilic graphs, their application to heterophilic graphs remains challenging. The best-performing GNNs for heterophilic graphs do not fit the sampling paradigm, suffer high computational costs, and are not inductive. We employ samplers based on feature-similarity and feature-diversity to select subsets of neighbors for a node, and adaptively capture information from homophilic and heterophilic neighborhoods using dual channels. Currently, AGS-GNN is the only algorithm that we know of that explicitly controls homophily in the sampled subgraph through similar and diverse neighborhood samples. For diverse neighborhood sampling, we employ submodularity, which was not used in this context prior to our work. The sampling distribution is pre-computed and highly parallel, achieving the desired scalability. Using an extensive dataset consisting of 35 small (<=100K nodes) and large (>100K nodes) homophilic and heterophilic graphs, we demonstrate the superiority of AGS-GNN compare to the current approaches in the literature. AGS-GNN achieves comparable test accuracy to the best-performing heterophilic GNNs, even outperforming methods using the entire graph for node classification. AGS-GNN also converges faster compared to methods that sample neighborhoods randomly, and can be incorporated into existing GNN models that employ node or graph sampling.

artificial intelligence↗
DOE OSTI2026

CHESS 2025: Spectrometer orthorectified at-sensor radiance from NEON AOP imaging spectroscopy surveys

This dataset provides Level 1 (L1) orthorectified at-sensor radiance derived from measurements collected by the Imaging Spectrometer-1 (NIS-1) onboard the NEON (National Ecological Observatory Network) Airborne Observation Platform (AOP) for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). NIS-1 captures light reflected from the Earth’s surface in 426 discrete wavelength bands as raw digital numbers (DNs; Level 0). These data are then calibrated to physical units (uW/cm²·sr·nm) following the processing steps described in the NEON Imaging Spectrometer Level 1B Calibrated Radiance Algorithm Theoretical Basis Document (ATBD; Gallery 2022). The data delivered here are the primary inputs for the surface reflectance product in “Custom surface reflectance, shade masks, and equivalent water thickness maps for the Colorado Headwaters Ecological Spectroscopy Study” (Carroll et al. 2026). For intertemporal comparison, the radiance data here are most directly relatable to the v2 radiance data in “NEON AOP Imaging Spectroscopy Survey of Upper East River Colorado Watersheds: Raw-Space Radiance and Observational Variable Dataset” (Goulden et al. 2018), to which the same processing methodology was applied. Together, the radiance and reflectance data enable users to exploit the unique reflection signatures of different surface objects for land cover classification, foliar trait mapping, plant vigor assessment, water content estimation, trace-element identification, and other scientific applications. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. Within each domain, data are delivered by flightline as orthorectified and calibrated hyperspectral rasters in Hierarchical Data Format version 5 (HDF5) format, with radiance values provided in uW/cm²·sr·nm on a fixed, uniform Universal Transverse Mercator (UTM) grid at 1 meter spatial resolution. The radiance rasters include all 426 NIS-1 spectral bands, along with associated quality-assurance (QA) and diagnostic and ancillary layers needed for atmospheric correction workflows. Orthorectified radiance is produced from pushbroom spectrometer observations by applying NEON’s radiometric calibration (including bad pixel masking, dark subtract, dark pedestal shift correction, electronic panel ghost correction, grating ghost correction, deblur correction and flat-fielding) and spectral calibration (using spectral response function band centers and full-width at half-maximum intensity), followed by geolocation and regridding to the fixed grid. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2025

Unrolled Video Super-Resolution Network with Autoregressive Prior for the Case of Known Motion

Real-time detection and classification of distant objects is necessary for many national security applications. However, when objects are far from the sensor, they occupy only a small number of pixels in the captured video, limiting the amount of visual detail available for recognition. State-of-the-art classification methods typically rely on high-resolution (HR) video streams to capture characteristic object features, but obtaining such detail is challenging for distant objects that occupy only a few pixels. This motivates the development of video super-resolution (VSR) methods that enhance object classification by recovering fine details from low-pixel representations. Current VSR methods rely either on model-based optimization, which is interpretable but computationally expensive, or on learning-based approaches, which are efficient and high-performing but often lack flexibility and interpretability. In this report, we propose an end-to-end trainable unrolled VSR network, UVSRNet, which super-resolves each frame in a video by exploiting sub-pixel motion between neighboring low-resolution (LR) frames as well as incorporating high-frequency detail from previously super-resolved frames. In particular, by unrolling a plug-and-play (PnP) half-quadratic splitting (HQS) algorithm, we leverage a model-based data-fitting module alongside a learning-based autoregressive prior module. This combination yields a method that maintains the flexibility and interpretability of model-based methods while achieving the performance advantages of learning-based methods.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2024

Evaluating cosmological biases using photometric redshifts for Type Ia Supernova cosmology with the Dark Energy Survey Supernova Program

Cosmological analyses with Type Ia Supernovae (SNe Ia) have traditionally been reliant on spectroscopy for both classifying the type of supernova and obtaining reliable redshifts to measure the distance–redshift relation. While obtaining a host-galaxy spectroscopic redshift for most SNe is feasible for small-area transient surveys, it will be too resource intensive for upcoming large-area surveys such as the Vera Rubin Observatory Legacy Survey of Space and Time, which will observe on the order of millions of SNe. Here, we use data from the Dark Energy Survey (DES) to address this problem with photometric redshifts (photo-z) inferred directly from the SN light curve in combination with Gaussian and full p(z) priors from host-galaxy photo-z estimates. Using the DES 5-yr photometrically classified SN sample, we consider several photo-z algorithms as host-galaxy photo-z priors, including the Self-Organizing Map redshifts (SOMPZ), Bayesian Photometric Redshifts (BPZ), and Directional-Neighbourhood Fitting (DNF) redshift estimates employed in the DES 3 × 2 point analyses. With detailed catalogue-level simulations of the DES 5-yr sample, we find that the simulated w can be recovered within ±0.02 when using SN+SOMPZ or DNF prior photo-z, smaller than the average statistical uncertainty for these samples of 0.03. With data, we obtain biases in w consistent with simulations within ~1σ for three of the five photo-z variants. We further evaluate how photo-z systematics interplay with photometric classification and find classification introduces a subdominant systematic component. This work lays the foundation for next-generation fully photometric SNe Ia cosmological analyses.

(cosmology:) dark energy↗
DOE OSTI2022

Combinatorial Evaluation of Physical Feature Engineering, Classical Machine Learning, and Deep Learning Models for Synchrophasor Data at Scale

A major objective of the project was to train and evaluate the effectiveness of multiple event and anomaly detection, identification and classification deep temporal learning models for processing of real-time phasor measurement unit (PMU) data streams. A vast dataset, consisting of two years of phasor measurements from all three U.S. Interconnections, was curated and released by the Department of Energy (DOE) through Pacific Northwest National Laboratory (PNNL). The dataset also included an event log that provided event times and types (e.g. generator trips, line trips, planned service events, transformer operations, etc.). Our analysis of this dataset addressed six (6) of the eleven (11) research priorities identified in Funding Opportunity Announcement (FOA) DE-FOA-0001861 “Big Data Analysis of Synchrophasor Data” (FOA 1861). Rather than being limited to pre-determined specific algorithms, this project relied on the uniquely structured, highly performant underlying time series database capabilities of the PredictiveGrid platform to assess the vast dataset utilizing a wide variety of algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

SQMS Quantum R&D in Machine Learning, Optimization and Sensing beyond Fundamental Physics Applications

This newly formed team at SQMS under the Ecosystem Thrust is looking to develop capabilities impacting societal advances outside the core domain of HEP and condensed matter physics. We explicitly leverage the experimental and algorithmic innovations developed across all groups as well as connect to broad-scope external projects of the diverse team of PIs. As the inaugural set of projects, we are studying numerically quantum machine learning models inspired by efficiently trainable echo-state and orthogonal neural networks and developing designs for related experiments to be performed on quantum processors based on SQMS SRF cQED technology and Rigetti s transmon arrays. Investigated models exploit ideas and lessons learned from multiple prior work by SQMS team members in a variety of internal and external activities [R1]. Target initial applications include noisy signal processing, potentially captured by quantum sensors or noisy QPUs, as well as simulation and classification of healthcare data. For instance, image reconstruction of the brain s electrical properties by solving the inverse Maxwell equation problem with uncertainty [R2] through a hybrid quantum-classical physics-informed architecture for time-dependent processes [R3]. The group is also investigating the application and development of novel quantum sensors based on magnetic levitation of a superconducting sphere coupled to a superconducting qubit. This coupling enables high-precision measurements of the position of the sphere, which can be used for sensitive detection of forces, enabling practical applications such as gravimetry for geophysics analysis, or accelerometry for GPS-denied navigation [R4] [R1] Rieffel, Eleanor G., Ata Akbari Asanjan, M. Sohaib Alam, Namit Anand, David E. Bernal Neira, Sophie Block, Lucas T. Brady et al. "Assessing and advancing the potential of quantum computing: A NASA case study." Future Generation Computer Systems (2024). [R2] Yu, X., Serrall s, J.E., Giannakopoulos, I.I., Liu, Z., Daniel, L., Lattanzi, R. and Zhang, Z., 2023. Pifon-ept: Mr-based electrical property tomography using physics-informed fourier networks. IEEE Journal on Multiscale and Multiphysics Computational Techniques. [R3] Wudarski, Filip, Daniel OConnor, Shaun Geaney, Ata Akbari Asanjan, Max Wilson, Elena Strbac, P. Aaron Lott, and Davide Venturelli. "Hybrid quantum-classical reservoir computing for simulating chaotic systems." arXiv preprint arXiv:2311.14105 (2023). [R4] Higgins, Gerard, Saarik Kalia, and Zhen Liu. "Maglev for dark matter: Dark-photon and axion dark matter sensing with levitated superconductors." Physical Review D 109.5 (2024): 055024.

Venturelli, Davide↗
DOE OSTI2023

CEGANN: CRYSTAL EDGE GRAPH ATTENTION NEURAL NETWORK

SF-22-156 Machine learning (ML) models and applications in materials design and discovery typically involve the use of feature representations or descriptors followed by a learning algorithm that maps them to user desired properties of interest. Most popular mathematical formulation-based descriptors are not unique across atomic environments and suffer from transferability issues across different application domains and/or material classes. The CEGANN code provides a unified interface to facilitate material characterization across materials across multiple scales (from atomic to mesoscale) and diverse classes of materials ranging from metals oxides, non-metals, and even hierarchical materials such as zeolites and semi ordered materials such as mesophases. CEGANN implements a Graph Attention Network (GAT) type convolution architecture. The details of network architecture can be found in the paper https://doi.org/10.48550/arXiv.2207.10168. The software comes with pretrained examples and dataset for the classification of the following representative systems: (1) Structure-level representation such as space group (2) Structural dimensionality (e.g., bulk, 2D, clusters etc.) (3) Grain boundary identification (4) Nucleation and growth of a zeolite polymorph (5) Characterization of binary mesophases and their phase transitions (6) Growth of ice. The code is written in python programming language.

CHAN, HENRYT↗
DOE OSTI2022

Data reduction through optimized scalar quantization for more compact neural networks

Raw data generation for several existing and planned large physics experiments now exceeds TB/s rates, generating untenable data sets in very little time. Those data often demonstrate high dimensionality while containing limited information. Meanwhile, Machine Learning algorithms are now becoming an essential part of data processing and data analysis. Those algorithms can be used offline for post processing and post data analysis, or they can be used online for real time processing providing ultra low latency experiment monitoring. Both use cases would benefit from data throughput reduction while preserving relevant information: one by reducing the offline storage requirements by several orders of magnitude and the other by allowing ultra fast online inferencing with low complexity Machine Learning models. Moreover, reducing the data source throughput also reduces material cost, power and data management requirements. In this work we demonstrate optimized nonuniform scalar quantization for data source reduction. This data reduction allows lower dimensional representations while preserving the relevant information of the data, thus enabling high accuracy Tiny Machine Learning classifier models for online fast inferences. We demonstrate this approach with an initial proof of concept targeting the CookieBox, an array of electron spectrometers used for angular streaking, that was developed for LCLS-II as an online beam diagnostic tool. We used the Lloyd-Max algorithm with the CookieBox dataset to design an optimized nonuniform scalar quantizer. Optimized quantization lets us reduce input data volume by 69% with no significant impact on inference accuracy. When we tolerate a 2% loss on inference accuracy, we achieved 81% of input data reduction. Finally, the change from a 7-bit to a 3-bit input data quantization reduces our neural network size by 38%.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

QoS-aware edge AI placement and scheduling with multiple implementations in FaaS-based edge computing

Resource constraints on the computing continuum require that we make smart decisions for serving AI-based services at the network edge. AI-based services typically have multiple implementations (e.g., image classification implementations include SqueezeNet, DenseNet, and others) with varying trade-offs (e.g., latency and accuracy). The question then is how should AI-based services be placed across Function-as-a-Service (FaaS) based edge computing systems in order to maximize total Quality-of-Service (QoS). To address this question, we propose a problem that jointly aims to solve (i) edge AI service placement and (ii) request scheduling. These are done across two time-scales (one for placement and one for scheduling). Here we first cast the problem as an integer linear program. We then decompose the problem into separate placement and scheduling subproblems and prove that both are NP-hard. We then propose a novel placement algorithm that places services while considering device-to-device communication across edge clouds to offload requests to one another. Our results show that the proposed placement algorithm is able to outperform a state-of-the-art placement algorithm for AI-based services, and other baseline heuristics, with regard to maximizing total QoS. Additionally, we present a federated learning-based framework, FLIES, to predict the future incoming service requests and their QoS requirements. Our results also show that our FLIES algorithm is able to outperform a standard decentralized learning baseline for predicting incoming requests and show comparable predictive performance when compared to centralized training.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

ABSTRACT In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variable-length protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw k-mer features. Availability Implementations of our method will be available under the Apache 2 licence at http://llp.berkeley.edu/dimotif and http://llp.berkeley.edu/protvecx .

Asgari, Ehsaneddin↗