arXiv subjects

Ulisses Braga-Neto

Publications and source records attributed to Ulisses Braga-Neto.

31 records · Page 2Linked to original sources

arXiv2022

Using Physics Informed Neural Networks for Supernova Radiative Transfer Simulation

We use physics informed neural networks (PINNs) to solve the radiative transfer equation and calculate a synthetic spectrum for a Type Ia supernova (SN~Ia) SN 2011fe. The calculation is based on local thermodynamic equilibrium (LTE) and 9 elements are included. Physical processes included are approximate radiative equilibrium, bound-bound transitions, and the Doppler effect. A PINN based gamma-ray scattering approximation is used for radioactive decay energy deposition. The PINN synthetic spectrum is compared to an observed spectrum, a synthetic spectrum calculated by the Monte-Carlo radiative transfer program TARDIS, and the formal solution of the radiative transfer equation. We discuss the challenges and potential of this deep-learning based radiative transfer equation solver. In fact, PINNs offer the prospect of simultaneous solution of the atmosphere problem for both radiation field and thermal state throughout spacetime. We have made modest steps to realizing that prospect with our calculations which required many approximations in order to be feasible at this point in the development of PINN atmosphere solutions.

astro-ph.HE↗

arXiv2022

PSO-PINN: Physics-Informed Neural Networks Trained with Particle Swarm Optimization

Physics-informed neural networks (PINN) have recently emerged as a promising application of deep learning in a wide range of engineering and scientific problems based on partial differential equation (PDE) models. However, evidence shows that PINN training by gradient descent displays pathologies that often prevent convergence when solving PDEs with irregular solutions. In this paper, we propose the use of a particle swarm optimization (PSO) approach to train PINNs. The resulting PSO-PINN algorithm not only mitigates the undesired behaviors of PINNs trained with standard gradient descent but also presents an ensemble approach to PINN that affords the possibility of robust predictions with quantified uncertainty. We also propose PSO-BP-CD (PSO with Back-Propagation and Coefficient Decay), a hybrid PSO variant that combines swarm optimization with gradient descent, putting more weight on the latter as training progresses and the swarm zeros in on a good local optimum. Comprehensive experimental results show that PSO-PINN with the proposed PSO-BP-CD algorithm outperforms PINN ensembles trained with other PSO variants or with pure gradient descent.

cs.LG↗

arXiv2022

Assessing The Performance of YOLOv5 Algorithm for Detecting Volunteer Cotton Plants in Corn Fields at Three Different Growth Stages

The boll weevil (Anthonomus grandis L.) is a serious pest that primarily feeds on cotton plants. In places like Lower Rio Grande Valley of Texas, due to sub-tropical climatic conditions, cotton plants can grow year-round and therefore the left-over seeds from the previous season during harvest can continue to grow in the middle of rotation crops like corn (Zea mays L.) and sorghum (Sorghum bicolor L.). These feral or volunteer cotton (VC) plants when reach the pinhead squaring phase (5-6 leaf stage) can act as hosts for the boll weevil pest. The Texas Boll Weevil Eradication Program (TBWEP) employs people to locate and eliminate VC plants growing by the side of roads or fields with rotation crops but the ones growing in the middle of fields remain undetected. In this paper, we demonstrate the application of computer vision (CV) algorithm based on You Only Look Once version 5 (YOLOv5) for detecting VC plants growing in the middle of corn fields at three different growth stages (V3, V6, and VT) using unmanned aircraft systems (UAS) remote sensing imagery. All the four variants of YOLOv5 (s, m, l, and x) were used and their performances were compared based on classification accuracy, mean average precision (mAP), and F1-score. It was found that YOLOv5s could detect VC plants with a maximum classification accuracy of 98% and mAP of 96.3 % at the V6 stage of corn while YOLOv5s and YOLOv5m resulted in the lowest classification accuracy of 85% and YOLOv5m and YOLOv5l had the least mAP of 86.5% at the VT stage on images of size 416 x 416 pixels. The developed CV algorithm has the potential to effectively detect and locate VC plants growing in the middle of corn fields as well as expedite the management aspects of TBWEP.

cs.CV↗

arXiv2022

Computer Vision for Volunteer Cotton Detection in a Corn Field with UAS Remote Sensing Imagery and Spot Spray Applications

To control boll weevil (Anthonomus grandis L.) pest re-infestation in cotton fields, the current practices of volunteer cotton (VC) (Gossypium hirsutum L.) plant detection in fields of rotation crops like corn (Zea mays L.) and sorghum (Sorghum bicolor L.) involve manual field scouting at the edges of fields. This leads to many VC plants growing in the middle of fields remain undetected that continue to grow side by side along with corn and sorghum. When they reach pinhead squaring stage (5-6 leaves), they can serve as hosts for the boll weevil pests. Therefore, it is required to detect, locate and then precisely spot-spray them with chemicals. In this paper, we present the application of YOLOv5m on radiometrically and gamma-corrected low resolution (1.2 Megapixel) multispectral imagery for detecting and locating VC plants growing in the middle of tasseling (VT) growth stage of cornfield. Our results show that VC plants can be detected with a mean average precision (mAP) of 79% and classification accuracy of 78% on images of size 1207 x 923 pixels at an average inference speed of nearly 47 frames per second (FPS) on NVIDIA Tesla P100 GPU-16GB and 0.4 FPS on NVIDIA Jetson TX2 GPU. We also demonstrate the application of a customized unmanned aircraft systems (UAS) for spot-spray applications based on the developed computer vision (CV) algorithm and how it can be used for near real-time detection and mitigation of VC plants growing in corn fields for efficient management of the boll weevil pests.

eess.IV↗

arXiv2022

Detecting Volunteer Cotton Plants in a Corn Field with Deep Learning on UAV Remote-Sensing Imagery

The cotton boll weevil, Anthonomus grandis Boheman is a serious pest to the U.S. cotton industry that has cost more than 16 billion USD in damages since it entered the United States from Mexico in the late 1800s. This pest has been nearly eradicated; however, southern part of Texas still faces this issue and is always prone to the pest reinfestation each year due to its sub-tropical climate where cotton plants can grow year-round. Volunteer cotton (VC) plants growing in the fields of inter-seasonal crops, like corn, can serve as hosts to these pests once they reach pin-head square stage (5-6 leaf stage) and therefore need to be detected, located, and destroyed or sprayed . In this paper, we present a study to detect VC plants in a corn field using YOLOv3 on three band aerial images collected by unmanned aircraft system (UAS). The two-fold objectives of this paper were : (i) to determine whether YOLOv3 can be used for VC detection in a corn field using RGB (red, green, and blue) aerial images collected by UAS and (ii) to investigate the behavior of YOLOv3 on images at three different scales (320 x 320, S1; 416 x 416, S2; and 512 x 512, S3 pixels) based on average precision (AP), mean average precision (mAP) and F1-score at 95% confidence level. No significant differences existed for mAP among the three scales, while a significant difference was found for AP between S1 and S3 (p = 0.04) and S2 and S3 (p = 0.02). A significant difference was also found for F1-score between S2 and S3 (p = 0.02). The lack of significant differences of mAP at all the three scales indicated that the trained YOLOv3 model can be used on a computer vision-based remotely piloted aerial application system (RPAAS) for VC detection and spray application in near real-time.

cs.CV↗

arXiv2021

Generalized Resubstitution for Classification Error Estimation

We propose the family of generalized resubstitution classifier error estimators based on empirical measures. These error estimators are computationally efficient and do not require re-training of classifiers. The plain resubstitution error estimator corresponds to choosing the standard empirical measure. Other choices of empirical measure lead to bolstered, posterior-probability, Gaussian-process, and Bayesian error estimators; in addition, we propose bolstered posterior-probability error estimators as a new family of generalized resubstitution estimators. In the two-class case, we show that a generalized resubstitution estimator is consistent and asymptotically unbiased, regardless of the distribution of the features and label, if the corresponding generalized empirical measure converges uniformly to the standard empirical measure and the classification rule has a finite VC dimension. A generalized resubstitution estimator typically has hyperparameters that can be tuned to control its bias and variance, which adds flexibility. Numerical experiments with various classification rules trained on synthetic data assess the thefinite-sample performance of several representative generalized resubstitution error estimators. In addition, results of an image classification experiment using the LeNet-5 convolutional neural network and the MNIST data set demonstrate the potential of this class of error estimators in deep learning for computer vision.

stat.ML↗

arXiv2021

A stochastic metapopulation state-space approach to modeling and estimating Covid-19 spread

Mathematical models are widely recognized as an important tool for analyzing and understanding the dynamics of infectious disease outbreaks, predict their future trends, and evaluate public health intervention measures for disease control and elimination. We propose a novel stochastic metapopulation state-space model for COVID-19 transmission, based on a discrete-time spatio-temporal susceptible/exposed/infected/recovered/deceased (SEIRD) model. The proposed framework allows the hidden SEIRD states and unknown transmission parameters to be estimated from noisy, incomplete time series of reported epidemiological data, by application of unscented Kalman filtering (UKF), maximum-likelihood adaptive filtering, and metaheuristic optimization. Experiments using both synthetic data and real data from the Fall 2020 Covid-19 wave in the state of Texas demonstrate the effectiveness of the proposed model.

eess.SP↗

arXiv2021

Comparison of Classification Algorithms Towards Subject-Specific and Subject-Independent BCI

Motor imagery brain computer interface designs are considered difficult due to limitations in subject-specific data collection and calibration, as well as demanding system adaptation requirements. Recently, subject-independent (SI) designs received attention because of their possible applicability to multiple users without prior calibration and rigorous system adaptation. SI designs are challenging and have shown low accuracy in the literature. Two major factors in system performance are the classification algorithm and the quality of available data. This paper presents a comparative study of classification performance for both SS and SI paradigms. Our results show that classification algorithms for SS models display large variance in performance. Therefore, distinct classification algorithms per subject may be required. SI models display lower variance in performance but should only be used if a relatively large sample size is available. For SI models, LDA and CART had the highest accuracy for small and moderate sample size, respectively, whereas we hypothesize that SVM would be superior to the other classifiers if large training sample-size was available. Additionally, one should choose the design approach considering the users. While the SS design sound more promising for a specific subject, an SI approach can be more convenient for mentally or physically challenged users.

cs.LG↗

arXiv2020

A Semi-Supervised Generative Adversarial Network for Prediction of Genetic Disease Outcomes

For most diseases, building large databases of labeled genetic data is an expensive and time-demanding task. To address this, we introduce genetic Generative Adversarial Networks (gGAN), a semi-supervised approach based on an innovative GAN architecture to create large synthetic genetic data sets starting with a small amount of labeled data and a large amount of unlabeled data. Our goal is to determine the propensity of a new individual to develop the severe form of the illness from their genetic profile alone. The proposed model achieved satisfactory results using real genetic data from different datasets and populations, in which the test populations may not have the same genetic profiles. The proposed model is self-aware and capable of determining whether a new genetic profile has enough compatibility with the data on which the network was trained and is thus suitable for prediction. The code and datasets used can be found at https://github.com/caio-davi/gGAN.

cs.LG↗

arXiv2020

Deep Multimodal Transfer-Learned Regression in Data-Poor Domains

In many real-world applications of deep learning, estimation of a target may rely on various types of input data modes, such as audio-video, image-text, etc. This task can be further complicated by a lack of sufficient data. Here we propose a Deep Multimodal Transfer-Learned Regressor (DMTL-R) for multimodal learning of image and feature data in a deep regression architecture effective at predicting target parameters in data-poor domains. Our model is capable of fine-tuning a given set of pre-trained CNN weights on a small amount of training image data, while simultaneously conditioning on feature information from a complimentary data mode during network training, yielding more accurate single-target or multi-target regression than can be achieved using the images or the features alone. We present results using phase-field simulation microstructure images with an accompanying set of physical features, using pre-trained weights from various well-known CNN architectures, which demonstrate the efficacy of the proposed multimodal approach.

cs.CV↗

arXiv2019

Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty

Single-cell gene expression measurements offer opportunities in deriving mechanistic understanding of complex diseases, including cancer. However, due to the complex regulatory machinery of the cell, gene regulatory network (GRN) model inference based on such data still manifests significant uncertainty. The goal of this paper is to develop optimal classification of single-cell trajectories accounting for potential model uncertainty. Partially-observed Boolean dynamical systems (POBDS) are used for modeling gene regulatory networks observed through noisy gene-expression data. We derive the exact optimal Bayesian classifier (OBC) for binary classification of single-cell trajectories. The application of the OBC becomes impractical for large GRNs, due to computational and memory requirements. To address this, we introduce a particle-based single-cell classification method that is highly scalable for large GRNs with much lower complexity than the optimal solution. The performance of the proposed particle-based method is demonstrated through numerical experiments using a POBDS model of the well-known T-cell large granular lymphocyte (T-LGL) leukemia network with noisy time-series gene-expression data.

q-bio.GN↗

arXiv2017

Control of Gene Regulatory Networks with Noisy Measurements and Uncertain Inputs

This paper is concerned with the problem of stochastic control of gene regulatory networks (GRNs) observed indirectly through noisy measurements and with uncertainty in the intervention inputs. The partial observability of the gene states and uncertainty in the intervention process are accounted for by modeling GRNs using the partially-observed Boolean dynamical system (POBDS) signal model with noisy gene expression measurements. Obtaining the optimal infinite-horizon control strategy for this problem is not attainable in general, and we apply reinforcement learning and Gaussian process techniques to find a near-optimal solution. The POBDS is first transformed to a directly-observed Markov Decision Process in a continuous belief space, and the Gaussian process is used for modeling the cost function over the belief and intervention spaces. Reinforcement learning then is used to learn the cost function from the available gene expression data. In addition, we employ sparsification, which enables the control of large partially-observed GRNs. The performance of the resulting algorithm is studied through a comprehensive set of numerical experiments using synthetic gene expression data generated from a melanoma gene regulatory network.

q-bio.MN↗

arXiv2017

Particle Filters for Partially-Observed Boolean Dynamical Systems

Partially-observed Boolean dynamical systems (POBDS) are a general class of nonlinear models with application in estimation and control of Boolean processes based on noisy and incomplete measurements. The optimal minimum mean square error (MMSE) algorithms for POBDS state estimation, namely, the Boolean Kalman filter (BKF) and Boolean Kalman smoother (BKS), are intractable in the case of large systems, due to computational and memory requirements. To address this, we propose approximate MMSE filtering and smoothing algorithms based on the auxiliary particle filter (APF) method from sequential Monte-Carlo theory. These algorithms are used jointly with maximum-likelihood (ML) methods for simultaneous state and parameter estimation in POBDS models. In the presence of continuous parameters, ML estimation is performed using the expectation-maximization (EM) algorithm; we develop for this purpose a special smoother which reduces the computational complexity of the EM algorithm. The resulting particle-based adaptive filter is applied to a POBDS model of Boolean gene regulatory networks observed through noisy RNA-Seq time series data, and performance is assessed through a series of numerical experiments using the well-known cell cycle gene regulatory model.

stat.ME↗