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Cancer genomics predicts disease relapse and therapeutic response to neoadjuvant chemotherapy of hormone sensitive breast cancers

Several studies provide insight into the landscape of breast cancer genomics with the genomic characterization of tumors offering exceptional opportunities in defining therapies tailored to the patient’s specific need. However, translating genomic data into personalized treatment regimens has been hampered partly due to uncertainties in deviating from guideline based clinical protocols. Here we report a genomic approach to predict favorable outcome to treatment responses thus enabling personalized medicine in the selection of specific treatment regimens. The genomic data were divided into a training set of N = 835 cases and a validation set consisting of 1315 hormone sensitive, 634 triple negative breast cancer (TNBC) and 1365 breast cancer patients with information on neoadjuvant chemotherapy responses. Patients were selected by the following criteria: estrogen receptor (ER) status, lymph node invasion, recurrence free survival. The k-means classification algorithm delineated clusters with low- and high- expression of genes related to recurrence of disease; a multivariate Cox’s proportional hazard model defined recurrence risk for disease. Classifier genes were validated by Immunohistochemistry (IHC) using tissue microarray sections containing both normal and cancerous tissues and by evaluating findings deposited in the human protein atlas repository. Based on the leave-on-out cross validation procedure of 4 independent data sets we identified 51-genes associated with disease relapse and selected 10, i.e. TOP2A, AURKA, CKS2, CCNB2, CDK1 SLC19A1, E2F8, E2F1, PRC1, KIF11 for in depth validation. Expression of the mechanistically linked disease regulated genes significantly correlated with recurrence free survival among ER-positive and triple negative breast cancer patients and was independent of age, tumor size, histological grade and node status. Importantly, the classifier genes predicted pathological complete responses to neoadjuvant chemotherapy (P < 0.001) with high expression of these genes being associated with an improved therapeutic response toward two different anthracycline-taxane regimens; thus, highlighting the prospective for precision medicine. Our study demonstrates the potential of classifier genes to predict risk for disease relapse and treatment response to chemotherapies. The classifier genes enable rational selection of patients who benefit best from a given chemotherapy thus providing the best possible care. The findings encourage independent clinical validation.

59 BASIC BIOLOGICAL SCIENCES↗

The Zwicky Transient Facility Bright Transient Survey. III. BTSbot: Automated Identification and Follow-up of Bright Transients with Deep Learning

Abstract The Bright Transient Survey (BTS) aims to obtain a classification spectrum for all bright ( m peak ≤ 18.5 mag) extragalactic transients found in the Zwicky Transient Facility (ZTF) public survey. BTS critically relies on visual inspection (“scanning”) to select targets for spectroscopic follow-up, which, while effective, has required a significant time investment over the past ∼5 yr of ZTF operations. We present BTSbot , a multimodal convolutional neural network, which provides a bright transient score to individual ZTF detections using their image data and 25 extracted features. BTSbot is able to eliminate the need for daily human scanning by automatically identifying and requesting spectroscopic follow-up observations of new bright transient candidates. BTSbot recovers all bright transients in our test split and performs on par with scanners in terms of identification speed (on average, ∼1 hr quicker than scanners). We also find that BTSbot is not significantly impacted by any data shift by comparing performance across a concealed test split and a sample of very recent BTS candidates. BTSbot has been integrated into Fritz and Kowalski , ZTF’s first-party marshal and alert broker, and now sends automatic spectroscopic follow-up requests for the new transients it identifies. Between 2023 December and 2024 May, BTSbot selected 609 sources in real time, 96% of which were real extragalactic transients. With BTSbot and other automation tools, the BTS workflow has produced the first fully automatic end-to-end discovery and classification of a transient, representing a significant reduction in the human time needed to scan.

Rehemtulla, Nabeel (ORCID:0000000256832389)↗

Bayesian model selection for GRB 211211A through multiwavelength analyses

ABSTRACT Although GRB 211211A is one of the closest gamma-ray bursts (GRBs), its classification is challenging because of its partially inconclusive electromagnetic signatures. In this paper, we investigate four astrophysical scenarios as possible progenitors for GRB 211211A: a binary neutron star merger, a black hole–neutron star merger, a core-collapse supernova, and an r-process enriched core collapse of a rapidly rotating massive star (a collapsar). We perform a large set of Bayesian multiwavelength analyses based on different models describing these scenarios and priors to investigate which astrophysical scenarios and processes might be related to GRB 211211A. Our analysis supports previous studies in which the presence of an additional component, likely related to r-process nucleosynthesis, is required to explain the observed light curves of GRB 211211A, as it cannot be explained solely as a GRB afterglow. Fixing the distance to about $350~\rm Mpc$, namely the distance of the possible host galaxy SDSS J140910.47+275320.8, we find a statistical preference for a binary neutron star merger scenario.

(transients:) gamma-ray bursts↗

Micro-photoluminescence mapping and Chemometrics for the rapid classification of rare earth materials

This article introduces advancements in chemically mapping rare earth materials using photoluminescence (PL) and chemometrics. By leveraging the high sensitivity and selectivity of PL compared to alternative optical techniques, as well as its compatibility with microscopy, we present enhanced capabilities for noninvasive material screening and characterization. Exemplary PL spectra of samarium(III) and europium(III) in oxide, nitrate, and chloride forms demonstrated the ability to extract detailed chemical information of diverse rare earth particles. Additionally, we introduced efficient PL mapping sequences capable of covering a 9 mm diameter carbon tab within minutes, which highlighted the benefits of rapid, large-area imaging. Furthermore, an integrated approach combining PL mapping with principal component analysis and a random forest classifier enabled the resolution of overlapping spectral peaks from different chemistries and provided accurate material classification. In conclusion, these advancements underscored the versatility and robustness of PL for chemically mapping rare earth materials, with the potential to support applications in mining, energy, environmental monitoring, isotope production and beyond.

Chemometrics↗

Galaxy Zoo DECaLS: Detailed visual morphology measurements from volunteers and deep learning for 314,000 galaxies

We present Galaxy Zoo DECaLS: detailed visual morphological classifications for Dark Energy Camera Legacy Survey images of galaxies within the SDSS DR8 footprint. Deeper DECaLS images (r = 23.6 versus r = 22.2 from SDSS) reveal spiral arms, weak bars, and tidal features not previously visible in SDSS imaging. To best exploit the greater depth of DECaLS images, volunteers select from a new set of answers designed to improve our sensitivity to mergers and bars. Galaxy Zoo volunteers provide 7.5 million individual classifications over 314 000 galaxies. 140 000 galaxies receive at least 30 classifications, sufficient to accurately measure detailed morphology like bars, and the remainder receive approximately 5. All classifications are used to train an ensemble of Bayesian convolutional neural networks (a state-of-the-art deep learning method) to predict posteriors for the detailed morphology of all 314 000 galaxies. We use active learning to focus our volunteer effort on the galaxies which, if labelled, would be most informative for training our ensemble. When measured against confident volunteer classifications, the trained networks are approximately 99 per cent accurate on every question. Morphology is a fundamental feature of every galaxy; our human and machine classifications are an accurate and detailed resource for understanding how galaxies evolve.

79 ASTRONOMY AND ASTROPHYSICS↗

A Proxy Method to Bridge LCA Data Gaps Using Automated Material Classification and Probabilistic Under-Specification

Life cycle assessments (LCAs) are essential for understanding the environmental impacts of material production. However, gaps in life cycle inventory (LCI) data for material and chemical inputs present a key challenge for LCA practitioners, especially in the early design stages. Strategies for filling in these gaps require additional time and expertise, which can hinder the LCA’s completion. This study combined automatic material classification and probabilistic under-specification to create a time-efficient method to fill material LCI data gaps. To illustrate the proposed method, proxy environmental impact distributions were generated using publicly available material LCI data classified into the ChemOnt chemical taxonomy using the open-source chemical classification software ClassyFire. Input materials with data gaps were then classified into the same taxonomy, where proxy environmental impact values could be selected from the available distributions to quickly fill in any data gaps. Although these methods were applied to classify material production processes available in the Federal LCA Commons and Ecoinvent databases, they can be applied to any LCA database. This study shows that classifying materials by their chemical structure produces taxonomies with increased granularity relative to industrial classification, improving the ability of under-specified proxy data to be used for differentiating the environmental impacts of competing designs.

biological databases↗

Appropriate “marginal” farmlands for second‐generation biofuel crops in North Carolina

Abstract Current research on bioenergy crops shows that perennial grasses can yield substantial amounts of dry biomass with relatively low inputs of water and fertilizer. In order to minimize competition with food production, it has been suggested that bioenergy crops could be directed to land areas less suitable for commodity crops, commonly referred to as “marginal” lands. These are land units with inherent limitations to vegetative growth and production, which may be due to several factors (soil physical and chemical properties, climatic conditions, etc.). However the term “marginal” is an adjective with imprecise meaning, and objective criteria for determining “marginal” lands for siting bioenergy crops are necessary. Here we propose that such criteria may be based on soil survey classifications and realistic yield estimates, and we show an example of its use to justify site selection for bioenergy crops in different regions of North Carolina.

09 BIOMASS FUELS↗

Automation for Electric Vehicle Battery Pack Disassembly

Battery‐electric vehicles (EVs) are growing exponentially. The demand for these batteries is expected to increase sevenfold by 2035. The EV batteries reach their end of life when the capacity fades to 70%–80% of new, with some being removed from the primary applications with even lower levels of degradation. These batteries can be used in less demanding applications. The disassembly process is currently manual, slow, unsafe, and expensive. Automation is needed to increase the throughput. EV battery packs feature various continually changing designs and form factors, which limit the usefulness of deterministically programmed robotic solutions. The conceptual robotic disassembly of EV batteries has attracted the attention of researchers. However, while many approaches have been proposed, practical implementations are lacking. Here, we review proposed concepts for EV battery disassembly and describe the selected approach, with elements of partial solutions validated in a laboratory setting, including the selection of commercial solutions, the development of custom end effectors, and methodologies for detection, localization, and classification of fasteners. The computer vision tasks employed an overhead 2D camera to detect the type of battery pack and approximate localization of fasteners, and a 3D camera mounted on the robotic arm for precise localization (position and tilt) and classification.

Islam, Abu [Rochester Inst. of Technology, Rochest↗

Background-Aware 3-D Point Cloud Segmentation With Dynamic Point Feature Aggregation

With the proliferation of LiDAR sensors and 3-D vision cameras, 3-D point cloud analysis has attracted significant attention in recent years. In this article, we propose a novel 3-D point cloud learning network, referred to as dynamic point feature aggregation network (DPFA-Net), by selectively performing the neighborhood feature aggregation (FA) with dynamic pooling and an attention mechanism. DPFA-Net has two variants for semantic segmentation and classification of 3-D point clouds. As the core module of the DPFA-Net, we propose an FA layer, in which features of the dynamic neighborhood of each point are aggregated via a self-attention mechanism. In contrast to other segmentation models, which aggregate features from fixed neighborhoods, our approach can aggregate features from different neighbors in different layers providing a more selective and broader view to the query points and focusing more on the relevant features in a local neighborhood. In addition, to further improve the performance of semantic segmentation, we exploit the background–foreground (BF) information and present two novel approaches, namely, two-stage BF-Net and BF regularization. Experimental results show that the proposed DPFA-Net achieves the state-of-the-art overall accuracy score of 89.22% for semantic segmentation on the Stanford large-scale 3-D Indoor Spaces (S3DIS) dataset and provides consistently satisfactory performance across different tasks of semantic segmentation, part segmentation, and 3-D object classification. Furthermore, our model achieves 93.1% accuracy on the ModelNet40 dataset and provides a mean shape intersection-over-union (IoU) value of 85.5% for part segmentation on the ShapeNet-Part dataset. It is a also computationally more efficient compared to other methods.

3-D↗

Plasma image classification using cosine similarity constrained convolutional neural network

Plasma jets are widely investigated both in the laboratory and in nature. Astrophysical objects such as black holes, active galactic nuclei and young stellar objects commonly emit plasma jets in various forms. With the availability of data from plasma jet experiments resembling astrophysical plasma jets, classification of such data would potentially aid in not only investigating the underlying physics of the experiments but also the study of astrophysical jets. In this work we use deep learning to process all of the laboratory plasma images from the Caltech Spheromak Experiment spanning two decades. We found that cosine similarity can aid in feature selection, classify images through comparison of feature vector direction and be used as a loss function for the training of AlexNet for plasma image classification. We also develop a simple vector direction comparison algorithm for binary and multi-class classification. Using our algorithm we demonstrate 93 % accurate binary classification to distinguish unstable columns from stable columns and 92 % accurate five-way classification of a small, labelled data set which includes three classes corresponding to varying levels of kink instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Carbon- and Oxygen-rich stars in MaStar: identification and classification

ABSTRACT Carbon- and Oxygen-rich stars populating the Thermally Pulsing Asymptotic Giant Branch (TP-AGB) phase of stellar evolution are relevant contributors to the spectra of ∼1 Gyr old populations. Atmosphere models for these types are uncertain, due to complex molecules and mass-loss effects. Empirical spectra are then crucial, but samples are small due to the short (∼3 Myr) TP-AGB lifetime. Here we exploit the vastness of the MaNGA Stellar library MaStar (∼60 000 spectra) to identify C and O-rich type stars. We define an optical colour selection with cuts of (g − r) > 2 and (g − i) < 1.55(g − r) − 0.07, calibrated with known C- and O-rich spectra. This identifies C- and O-rich stars along clean, separated sequences. An analogue selection is found in V, R, I bands. Our equation identifies C-rich and O-rich spectra with predictive performance metric F1-scores of 0.72 and 0.74 (over 1), respectively. We finally identify 41 C- and 87 O-rich type AGB stars in MaStar, 5 and 49 of which do not have a SIMBAD counterpart. We also detect a sample of non-AGB, dwarf C-stars. We further design a fitting procedure to classify the spectra into broad spectral types, by using as fitting templates empirical C- and O-rich spectra. We find remarkably good fits for the majority of candidates and categorize them into C- and O-rich bins following existing classifications, which correlate to effective temperature. Our selection models can be applied to large photometric surveys (e.g. Euclid, Rubin). The classified spectra will facilitate future evolutionary population synthesis models.

Hill, Lewis (ORCID:0000000180528080)↗

A Cyber-Physical Anomaly Detection for Wide-Area Protection Using Machine Learning

Wide-area protection scheme (WAPS) provides system-wide protection by detecting and mitigating small and large-scale disturbances that are difficult to resolve using local protection schemes. As this protection scheme is evolving from a substation-based distributed remedial action scheme (DRAS) to the control center-based centralized RAS (CRAS), it presents severe challenges to their cybersecurity because of its heavy reliance on an insecure grid communication, and its compromise would lead to system failure. This article presents an architecture and methodology for developing a cyber-physical anomaly detection system (CPADS) that utilizes synchrophasor measurements and properties of network packets to detect data integrity and communication failure attacks on measurement and control signals in CRAS. The proposed machine leaning-based methodology applies a rules-based approach to select relevant input features, utilizes variational mode decomposition (VMD) and decision tree (DT) algorithms to develop multiple classification models, and performs final event identification using a rules-based decision logic. Here, we have evaluated the proposed methodology of CPADS using the IEEE 39 bus system for several performance measures (accuracy, recall, precision, and F-measure) in a cyber-physical testbed environment. Furthermore, our experimental results reveal that the proposed algorithm (VMD-DT) of CPADS outperforms the existing machine learning classifiers during noisy and noise-free measurements while incurring an acceptable processing overhead.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Improved Spectral Classification of Local K/M Dwarfs in SDSS Surveys. I. Chemodynamic Validation and Metallicity Calibration

An examination of 109,276 spectra of low-mass stars in the Sloan Digital Sky Survey (SDSS) data archive, collected pre-2010, provides a broad collection of K/M (sub)dwarfs tracing the local (d ≲ 250 pc) population of the thin-disk, thick-disk, and halo, based on 3D kinematics. These populations have distinct metallicities and kinematics, which should be reflected in lower-mass members. One complication is measuring metallicities of M dwarfs from low-resolution spectroscopy or photometry alone remains a challenge, even with the availability of Gaia data. To better characterize physical parameters of low-mass stars observed by SDSS, we define a set of 536 improved, empirical K/M dwarf classification templates to more accurately determine spectral subtypes (K5.5–M8.5) and morphology classes (MCs) (0.5–12.5). We select the best-fit template to every archival SDSS spectrum in the range 5000–8000 Å based on minimum χ 2 value. We then use secondary metallicity estimators to calibrate the most likely [Fe/H] values corresponding to the assigned MC. We confirm that the most metal-rich K/M dwarfs have thin-disk kinematics, and we observe the known effect of Galactic radial metallicity migration, which we confirm is strongly imprinted in the chemodynamics of the local disk M dwarfs. Confirmation of these chemodynamic trends validates the precision of our improved templates for estimating [Fe/H] for M (sub)dwarfs, notably at the low-metallicity end (–3 < [Fe/H] < –1). Substructure in the chemodynamics of the most metal-poor K/M subdwarfs begins to distinguish between local Gaia-Enceladus and local in situ halo objects. This methodology opens the door to use the ubiquitous, local K/M (sub)dwarfs to trace local Galactic chemodynamics with the highest possible resolution.

79 ASTRONOMY AND ASTROPHYSICS↗

The Earth Model Column Collaboratory (EMC 2 ) v1.1: an open-source ground-based lidar and radar instrument simulator and subcolumn generator for large-scale models

Abstract. Climate models are essential for our comprehensive understanding of Earth's atmosphere and can provide critical insights on future changes decades ahead. Because of these critical roles, today's climate models are continuously being developed and evaluated using constraining observations and measurements obtained by satellites, airborne, and ground-based instruments. Instrument simulators can provide a bridge between the measured or retrieved quantities and their sampling in models and field observations while considering instrument sensitivity limitations. Here we present the Earth Model Column Collaboratory (EMC2), an open-source ground-based lidar and radar instrument simulator and subcolumn generator, specifically designed for large-scale models, in particular climate models, but also applicable to high-resolution model output. EMC2 provides a flexible framework enabling direct comparison of model output with ground-based observations, including generation of subcolumns that may statistically represent finer model spatial resolutions. In addition, EMC2 emulates ground-based (and air- or space-borne) measurements while remaining faithful to large-scale models' physical assumptions implemented in their cloud or radiation schemes. The simulator uses either single particle or bulk particle size distribution lookup tables, depending on the selected scheme approach, to perform the forward calculations. To facilitate model evaluation, EMC2 also includes three hydrometeor classification methods, namely, radar- and sounding-based cloud and precipitation detection and classification, lidar-based phase classification, and a Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) lidar simulator emulator. The software is written in Python, is easy to use, and can be straightforwardly customized for different models, radars, and lidars. Following the description of the logic, functionality, features, and software structure of EMC2, we present a case study of highly supercooled mixed-phase cloud based on measurements from the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) West Antarctic Radiation Experiment (AWARE). We compare observations with the application of EMC2 to outputs from four configurations of the NASA Goddard Institute for Space Studies (GISS) climate model (ModelE3) in single-column model (SCM) mode and from a large-eddy simulation (LES) model. We show that two of the four ModelE3 configurations can form and maintain highly supercooled precipitating cloud for several hours, consistent with observations and LES. While our focus is on one of these ModelE3 configurations, which performed slightly better in this case study, both of these configurations and the LES results post-processed with EMC2 generally provide reasonable agreement with observed lidar and radar variables. As briefly demonstrated here, EMC2 can provide a lightweight and flexible framework for comparing the results of both large-scale and high-resolution models directly with observations, with relatively little overhead and multiple options for achieving consistency with model microphysical or radiation scheme physics.

58 GEOSCIENCES↗

Physics-Based Machine Learning Methods for U-235 Forensics Signatures

Signatures of low-intensity U-235 sources have been recently studied by utilizing a variety of machine learning (ML) classifiers using features derived from gamma spectral measurements collectedunder structured campaigns. Several ML classifiers, such as ensemble of tress and classification trees, revealed misleadingly-optimistic training error due to over-fitting, and furthermore,their performance is not directly relatable to the physical properties due to their data-driven, opaque designs. We present a regression-based ML method that first estimates the inverse distanceto the source and then utilizes a threshold to infer its presence, by representing the background as a source located at an infinite distance. For the inverse distance estimation, we study the ensembleof trees and Gaussian process regression methods, and a hyper parameter auto-tuning and selection method that employs five regression estimators. These methods avoid the over-fittingobserved in several ML classifiers, while providing the classification error nearly comparable to them based on independent test data. Their error is directly related to estimates of the inversephysical distance to source, and the precision of error determines the seperability property that determines the false alarm and missed detection rates. The property of monotonic decrease of thesource strength with increasing detector distance combined with Poisson distribution of measurements is utilized to analytically validate these methods by deriving the generalization equations ofunderlying regression methods.

Rao, Nageswara↗

‘Flux+Mutability’: a conditional generative approach to one-class classification and anomaly detection

Abstract Anomaly Detection is becoming increasingly popular within the experimental physics community. At experiments such as the Large Hadron Collider, anomaly detection is growing in interest for finding new physics beyond the Standard Model. This paper details the implementation of a novel Machine Learning architecture, called Flux+Mutability, which combines cutting-edge conditional generative models with clustering algorithms. In the ‘flux’ stage we learn the distribution of a reference class. The ‘mutability’ stage at inference addresses if data significantly deviates from the reference class. We demonstrate the validity of our approach and its connection to multiple problems spanning from one-class classification to anomaly detection. In particular, we apply our method to the isolation of neutral showers in an electromagnetic calorimeter and show its performance in detecting anomalous dijets events from standard QCD background. This approach limits assumptions on the reference sample and remains agnostic to the complementary class of objects of a given problem. We describe the possibility of dynamically generating a reference population and defining selection criteria via quantile cuts. Remarkably this flexible architecture can be deployed for a wide range of problems, and applications like multi-class classification or data quality control are left for further exploration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measuring Young Stars in Space and Time. II. The Pre-main-sequence Stellar Content of N44

The Hubble Space Telescope survey Measuring Young Stars in Space and Time (MYSST) entails some of the deepest photometric observations of extragalactic star formation, capturing even the lowest-mass stars of the active star-forming complex N44 in the Large Magellanic Cloud. We employ the new MYSST stellar catalog to identify and characterize the content of young pre-main-sequence (PMS) stars across N44 and analyze the PMS clustering structure. To distinguish PMS stars from more evolved line of sight contaminants, a non-trivial task due to several effects that alter photometry, we utilize a machine-learning classification approach. This consists of training a support vector machine (SVM) and a random forest (RF) on a carefully selected subset of the MYSST data and categorize all observed stars as PMS or non-PMS. Combining SVM and RF predictions to retrieve the most robust set of PMS sources, we find ∼26,700 candidates with a PMS probability above 95% across N44. Employing a clustering approach based on a nearest neighbor surface density estimate, we identify 16 prominent PMS structures at 1σ significance above the mean density with sub-clusters persisting up to and beyond 3σ significance. The most active star-forming center, located at the western edge of N44's bubble, is a subcluster with an effective radius of ∼5.6 pc entailing more than 1100 PMS candidates. Furthermore, we confirm that almost all identified clusters coincide with known H ii regions and are close to or harbor massive young O stars or YSOs previously discovered by MUSE and Spitzer observations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Physics-Based Machine Learning Methods for U-235 Forensics Signatures

Signatures of low-intensity U-235 sources have been recently studied by utilizing a variety of machine learning (ML) classifiers using features derived from gamma spectral measurements collected under structured campaigns. Several ML classifiers, such as ensemble of tress and classification trees, revealed misleadingly-optimistic training error due to over-fitting, and furthermore, their performance is not directly relatable to the physical properties due to their data-driven, opaque designs. We present a regression-based ML method that first estimates the inverse distance to the source and then utilizes a threshold to infer its presence, by representing the background as a source located at an infinite distance. For the inverse distance estimation, we study the ensemble of trees and Gaussian process regression methods, and a hyper parameter auto-tuning and selection method that employs five regression estimators. These methods avoid the over-fitting observed in several ML classifiers, while providing the classification error nearly comparable to them based on independent test data. Their error is directly related to estimates of the inverse physical distance to source, and the precision of error determines the seperability property that determines the false alarm and missed detection rates. The property of monotonic decrease of the source strength with increasing detector distance combined with Poisson distribution of measurements is utilized to analytically validate these methods by deriving the generalization equations of underlying regression methods.

Rao, Nageswara↗