scholarly journals Bridging knowledge gaps with hybrid machine-learning forest ecosystem models (ML-FEMs): inferential simulation of past understory light regimes

2021 ◽  
Author(s):  
Adam Erickson ◽  
Craig Nistchke
Keyword(s):  
Machine Learning ◽  
Forest Ecosystem ◽  
Canopy Cover ◽  
Ground Truth ◽  
Ecosystem Model ◽  
Solar Irradiation ◽  
Limiting Factor ◽  
Model Parameters ◽  
Evaporative Demand ◽  
Primary Driver

Soil moisture is a key limiting factor of plant productivity in boreal and montane regions, producing additional climate feedbacks through evaporation, regeneration, mortality, and respiration. Understory solar irradiation – the primary driver of surface temperature and evaporative demand – remains poorly represented in vegetation models due to a lack of 3-D canopy geometry. Existing models are further unable to represent processes lacking sufficient parameterization and/or knowledge, with no land model to date utilizing machine learning (ML) to represent vegetation processes. Here, we developed the first hybrid forest ecosystem model using ML (ML-FEM), a specific case of hybrid AI land model (a concept also invented here). In this approach, ML models are trained and validated with a ground-truth dataset, whether observations or high-fidelity simulations, before being applied to vegetation model parameters for inference, internally or externally to the model. Using this approach, we simulated annual understory global solar irradiation (Iu) across 25.2 Mha in southwestern Canada at 1-ha resolution under historical climate and fire scenarios. In cross-validation, we found that linear and ML regression models performed comparably well in the prediction of angular canopy cover (ACC), due to the linearity of its relationship to predictors (linear R2 = 0.938, RMSE = 0.079; ML R2 = 0.939, RMSE = 0.074). Reduced area burned, increased ignitions, and reduced regeneration potential for recent periods resulted in stable or reduced Iu. This suggests that diminished disturbance may reduce Iu through forest aging, masking latent regeneration decline. Only in the most extreme and unconstrained scenarios did Iu increase. In these experiments, conducted in late 2015, we demonstrated an entirely new class of hybrid models that we anticipated to be of vital importance to understanding and representing pattern-based processes in Earth system models.

scholarly journals A Machine Learning and Cross-Validation Approach for the Discrimination of Vegetation Physiognomic Types Using Satellite Based Multispectral and Multitemporal Data

Scientifica ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Ram C. Sharma ◽  
Keitarou Hara ◽  
Hidetake Hirayama
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Cross Validation ◽  
Coniferous Forest ◽  
Ground Truth ◽  
Model Parameters ◽  
Broadleaf Forest ◽  
Ground Truth Data ◽  
Supervised Classifiers ◽  
Performance And Evaluation

This paper presents the performance and evaluation of a number of machine learning classifiers for the discrimination between the vegetation physiognomic classes using the satellite based time-series of the surface reflectance data. Discrimination of six vegetation physiognomic classes, Evergreen Coniferous Forest, Evergreen Broadleaf Forest, Deciduous Coniferous Forest, Deciduous Broadleaf Forest, Shrubs, and Herbs, was dealt with in the research. Rich-feature data were prepared from time-series of the satellite data for the discrimination and cross-validation of the vegetation physiognomic types using machine learning approach. A set of machine learning experiments comprised of a number of supervised classifiers with different model parameters was conducted to assess how the discrimination of vegetation physiognomic classes varies with classifiers, input features, and ground truth data size. The performance of each experiment was evaluated by using the 10-fold cross-validation method. Experiment using the Random Forests classifier provided highest overall accuracy (0.81) and kappa coefficient (0.78). However, accuracy metrics did not vary much with experiments. Accuracy metrics were found to be very sensitive to input features and size of ground truth data. The results obtained in the research are expected to be useful for improving the vegetation physiognomic mapping in Japan.

Nanosecond Photodynamics Simulations of a Cis-Trans Isomerization Are Enabled by Machine Learning

2020 ◽  
Author(s):  
Jingbai Li ◽  
Patrick Reiser ◽  
André Eberhard ◽  
Pascal Friederich ◽  
Steven Lopez
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Excited State ◽  
Adaptive Sampling ◽  
Computational Cost ◽  
Ground Truth ◽  
Absolute Error ◽  
Photochemical Reactions ◽  
Computational Techniques ◽  
Full Potential

<p>Photochemical reactions are being increasingly used to construct complex molecular architectures with mild and straightforward reaction conditions. Computational techniques are increasingly important to understand the reactivities and chemoselectivities of photochemical isomerization reactions because they offer molecular bonding information along the excited-state(s) of photodynamics. These photodynamics simulations are resource-intensive and are typically limited to 1–10 picoseconds and 1,000 trajectories due to high computational cost. Most organic photochemical reactions have excited-state lifetimes exceeding 1 picosecond, which places them outside possible computational studies. Westermeyr <i>et al.</i> demonstrated that a machine learning approach could significantly lengthen photodynamics simulation times for a model system, methylenimmonium cation (CH<sub>2</sub>NH<sub>2</sub><sup>+</sup>).</p><p>We have developed a Python-based code, Python Rapid Artificial Intelligence <i>Ab Initio</i> Molecular Dynamics (PyRAI<sup>2</sup>MD), to accomplish the unprecedented 10 ns <i>cis-trans</i> photodynamics of <i>trans</i>-hexafluoro-2-butene (CF<sub>3</sub>–CH=CH–CF<sub>3</sub>) in 3.5 days. The same simulation would take approximately 58 years with ground-truth multiconfigurational dynamics. We proposed an innovative scheme combining Wigner sampling, geometrical interpolations, and short-time quantum chemical trajectories to effectively sample the initial data, facilitating the adaptive sampling to generate an informative and data-efficient training set with 6,232 data points. Our neural networks achieved chemical accuracy (mean absolute error of 0.032 eV). Our 4,814 trajectories reproduced the S<sub>1</sub> half-life (60.5 fs), the photochemical product ratio (<i>trans</i>: <i>cis</i> = 2.3: 1), and autonomously discovered a pathway towards a carbene. The neural networks have also shown the capability of generalizing the full potential energy surface with chemically incomplete data (<i>trans</i> → <i>cis</i> but not <i>cis</i> → <i>trans</i> pathways) that may offer future automated photochemical reaction discoveries.</p>

scholarly journals Field-Scale Soil Moisture Retrieval Using PALSAR-2 Polarimetric Decomposition and Machine Learning

Agronomy ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 35
Author(s):  
Xiaodong Huang ◽  
Beth Ziniti ◽  
Michael H. Cosh ◽  
Michele Reba ◽  
Jinfei Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Soil Moisture ◽  
Canopy Cover ◽  
The United States ◽  
Optical Data ◽  
Study Region ◽  
Model Based ◽  
Key Indicator ◽  
Ground Measurement ◽  
L Band

Soil moisture is a key indicator to assess cropland drought and irrigation status as well as forecast production. Compared with the optical data which are obscured by the crop canopy cover, the Synthetic Aperture Radar (SAR) is an efficient tool to detect the surface soil moisture under the vegetation cover due to its strong penetration capability. This paper studies the soil moisture retrieval using the L-band polarimetric Phased Array-type L-band SAR 2 (PALSAR-2) data acquired over the study region in Arkansas in the United States. Both two-component model-based decomposition (SAR data alone) and machine learning (SAR + optical indices) methods are tested and compared in this paper. Validation using independent ground measurement shows that the both methods achieved a Root Mean Square Error (RMSE) of less than 10 (vol.%), while the machine learning methods outperform the model-based decomposition, achieving an RMSE of 7.70 (vol.%) and R2 of 0.60.

scholarly journals Trigonometric Inference Providing Learning in Deep Neural Networks

2021 ◽  
Vol 11 (15) ◽  
pp. 6704
Author(s):  
Jingyong Cai ◽  
Masashi Takemoto ◽  
Yuming Qiu ◽  
Hironori Nakajo
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
Activation Function ◽  
Trigonometric Approximation ◽  
Model Parameters ◽  
Training Algorithms ◽  
Activation Functions ◽  
Classical Training ◽  
Sum Formula

Despite being heavily used in the training of deep neural networks (DNNs), multipliers are resource-intensive and insufficient in many different scenarios. Previous discoveries have revealed the superiority when activation functions, such as the sigmoid, are calculated by shift-and-add operations, although they fail to remove multiplications in training altogether. In this paper, we propose an innovative approach that can convert all multiplications in the forward and backward inferences of DNNs into shift-and-add operations. Because the model parameters and backpropagated errors of a large DNN model are typically clustered around zero, these values can be approximated by their sine values. Multiplications between the weights and error signals are transferred to multiplications of their sine values, which are replaceable with simpler operations with the help of the product to sum formula. In addition, a rectified sine activation function is utilized for further converting layer inputs into sine values. In this way, the original multiplication-intensive operations can be computed through simple add-and-shift operations. This trigonometric approximation method provides an efficient training and inference alternative for devices with insufficient hardware multipliers. Experimental results demonstrate that this method is able to obtain a performance close to that of classical training algorithms. The approach we propose sheds new light on future hardware customization research for machine learning.

A NOVEL EXTENSIVE EX-VIVO OCT DATABASE FROM MURINE MODELS OF COLORECTAL CANCER

2021 ◽  
Vol 108 (Supplement_3) ◽  
Author(s):  
J Bote ◽  
J F Ortega-Morán ◽  
C L Saratxaga ◽  
B Pagador ◽  
A Picón ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Machine Learning ◽  
Structural Information ◽  
Ex Vivo ◽  
Ground Truth ◽  
Colon Polyps ◽  
Learning Methods ◽  
Non Invasive ◽  
Machine Learning Methods ◽  
In Situ Methods

Abstract INTRODUCTION New non-invasive technologies for improving early diagnosis of colorectal cancer (CRC) are demanded by clinicians. Optical Coherence Tomography (OCT) provides sub-surface structural information and offers diagnosis capabilities of colon polyps, further improved by machine learning methods. Databases of OCT images are necessary to facilitate algorithms development and testing. MATERIALS AND METHODS A database has been acquired from rat colonic samples with a Thorlabs OCT system with 930nm centre wavelength that provides 1.2KHz A-scan rate, 7μm axial resolution in air, 4μm lateral resolution, 1.7mm imaging depth in air, 6mm x 6mm FOV, and 107dB sensitivity. The colon from anaesthetised animals has been excised and samples have been extracted and preserved for ex-vivo analysis with the OCT equipment. RESULTS This database consists of OCT 3D volumes (C-scans) and 2D images (B-scans) of murine samples from: 1) healthy tissue, for ground-truth comparison (18 samples; 66 C-scans; 17,478 B-scans); 2) hyperplastic polyps, obtained from an induced colorectal hyperplastic murine model (47 samples; 153 C-scans; 42,450 B-scans); 3) neoplastic polyps (adenomatous and adenocarcinomatous), obtained from clinically validated Pirc F344/NTac-Apcam1137 rat model (232 samples; 564 C-scans; 158,557 B-scans); and 4) unknown tissue (polyp adjacent, presumably healthy) (98 samples; 157 C-scans; 42,070 B-scans). CONCLUSIONS A novel extensive ex-vivo OCT database of murine CRC model has been obtained and will be openly published for the research community. It can be used for classification/segmentation machine learning methods, for correlation between OCT features and histopathological structures, and for developing new non-invasive in-situ methods of diagnosis of colorectal cancer.

scholarly journals Experimental Evaluation of Computer Vision and Machine Learning-Based UAV Detection and Ranging

Drones ◽  
2021 ◽  
Vol 5 (2) ◽  
pp. 37
Author(s):  
Bingsheng Wei ◽  
Martin Barczyk
Keyword(s):  
Machine Learning ◽  
Mean Squared Error ◽  
Tracking System ◽  
Ground Truth ◽  
White Background ◽  
Cascade Classifier ◽  
Detection Algorithms ◽  
Squared Error ◽  
Test Conditions ◽  
Video Feed

We consider the problem of vision-based detection and ranging of a target UAV using the video feed from a monocular camera onboard a pursuer UAV. Our previously published work in this area employed a cascade classifier algorithm to locate the target UAV, which was found to perform poorly in complex background scenes. We thus study the replacement of the cascade classifier algorithm with newer machine learning-based object detection algorithms. Five candidate algorithms are implemented and quantitatively tested in terms of their efficiency (measured as frames per second processing rate), accuracy (measured as the root mean squared error between ground truth and detected location), and consistency (measured as mean average precision) in a variety of flight patterns, backgrounds, and test conditions. Assigning relative weights of 20%, 40% and 40% to these three criteria, we find that when flying over a white background, the top three performers are YOLO v2 (76.73 out of 100), Faster RCNN v2 (63.65 out of 100), and Tiny YOLO (59.50 out of 100), while over a realistic background, the top three performers are Faster RCNN v2 (54.35 out of 100, SSD MobileNet v1 (51.68 out of 100) and SSD Inception v2 (50.72 out of 100), leading us to recommend Faster RCNN v2 as the recommended solution. We then provide a roadmap for further work in integrating the object detector into our vision-based UAV tracking system.

scholarly journals Unraveling the deep learning gearbox in optical coherence tomography image segmentation towards explainable artificial intelligence

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Peter M. Maloca ◽  
Philipp L. Müller ◽  
Aaron Y. Lee ◽  
Adnan Tufail ◽  
Konstantinos Balaskas ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Optical Coherence Tomography ◽  
Image Segmentation ◽  
Convolutional Neural Network ◽  
Learning Algorithm ◽  
Ground Truth ◽  
Optical Coherence Tomography Image ◽  
Optical Coherence ◽  
Tomography Image

AbstractMachine learning has greatly facilitated the analysis of medical data, while the internal operations usually remain intransparent. To better comprehend these opaque procedures, a convolutional neural network for optical coherence tomography image segmentation was enhanced with a Traceable Relevance Explainability (T-REX) technique. The proposed application was based on three components: ground truth generation by multiple graders, calculation of Hamming distances among graders and the machine learning algorithm, as well as a smart data visualization (‘neural recording’). An overall average variability of 1.75% between the human graders and the algorithm was found, slightly minor to 2.02% among human graders. The ambiguity in ground truth had noteworthy impact on machine learning results, which could be visualized. The convolutional neural network balanced between graders and allowed for modifiable predictions dependent on the compartment. Using the proposed T-REX setup, machine learning processes could be rendered more transparent and understandable, possibly leading to optimized applications.

Robust dynamics of Amazon dieback to climate change with perturbed ecosystem model parameters

2010 ◽  
Author(s):  
BENJAMIN POULTER ◽  
FRED HATTERMANN ◽  
ED HAWKINS ◽  
SÖNKE ZAEHLE ◽  
STEPHEN SITCH ◽  
...  
Keyword(s):  
Climate Change ◽  
Ecosystem Model ◽  
Model Parameters

scholarly journals Analysis and Prediction of COVID-19 Using SIR, SEIQR, and Machine Learning Models: Australia, Italy, and UK Cases

Information ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 109 ◽  
Author(s):  
Iman Rahimi ◽  
Amir H. Gandomi ◽  
Panagiotis G. Asteris ◽  
Fang Chen
Keyword(s):  
Machine Learning ◽  
Logistic Function ◽  
Prediction Performance ◽  
Machine Learning Algorithms ◽  
Model Parameters ◽  
The Novel ◽  
Chinese City ◽  
Limited Memory ◽  
Increasing Trend ◽  
Novel Coronavirus

The novel coronavirus disease, also known as COVID-19, is a disease outbreak that was first identified in Wuhan, a Central Chinese city. In this report, a short analysis focusing on Australia, Italy, and UK is conducted. The analysis includes confirmed and recovered cases and deaths, the growth rate in Australia compared with that in Italy and UK, and the trend of the disease in different Australian regions. Mathematical approaches based on susceptible, infected, and recovered (SIR) cases and susceptible, exposed, infected, quarantined, and recovered (SEIQR) cases models are proposed to predict epidemiology in the above-mentioned countries. Since the performance of the classic forms of SIR and SEIQR depends on parameter settings, some optimization algorithms, namely Broyden–Fletcher–Goldfarb–Shanno (BFGS), conjugate gradients (CG), limited memory bound constrained BFGS (L-BFGS-B), and Nelder–Mead, are proposed to optimize the parameters and the predictive capabilities of the SIR and SEIQR models. The results of the optimized SIR and SEIQR models were compared with those of two well-known machine learning algorithms, i.e., the Prophet algorithm and logistic function. The results demonstrate the different behaviors of these algorithms in different countries as well as the better performance of the improved SIR and SEIQR models. Moreover, the Prophet algorithm was found to provide better prediction performance than the logistic function, as well as better prediction performance for Italy and UK cases than for Australian cases. Therefore, it seems that the Prophet algorithm is suitable for data with an increasing trend in the context of a pandemic. Optimization of SIR and SEIQR model parameters yielded a significant improvement in the prediction accuracy of the models. Despite the availability of several algorithms for trend predictions in this pandemic, there is no single algorithm that would be optimal for all cases.

scholarly journals Assessing biases, relaxing moralism: On ground-truthing practices in machine learning design and application

2021 ◽  
Vol 8 (1) ◽  
pp. 205395172110135
Author(s):  
Florian Jaton
Keyword(s):  
Machine Learning ◽  
William James ◽  
A Priori ◽  
Learning Algorithms ◽  
Three Dimensional ◽  
Ground Truth ◽  
Machine Learning Algorithms ◽  
Ground Truthing ◽  
Set Up ◽  
The Moment

This theoretical paper considers the morality of machine learning algorithms and systems in the light of the biases that ground their correctness. It begins by presenting biases not as a priori negative entities but as contingent external referents—often gathered in benchmarked repositories called ground-truth datasets—that define what needs to be learned and allow for performance measures. I then argue that ground-truth datasets and their concomitant practices—that fundamentally involve establishing biases to enable learning procedures—can be described by their respective morality, here defined as the more or less accounted experience of hesitation when faced with what pragmatist philosopher William James called “genuine options”—that is, choices to be made in the heat of the moment that engage different possible futures. I then stress three constitutive dimensions of this pragmatist morality, as far as ground-truthing practices are concerned: (I) the definition of the problem to be solved (problematization), (II) the identification of the data to be collected and set up (databasing), and (III) the qualification of the targets to be learned (labeling). I finally suggest that this three-dimensional conceptual space can be used to map machine learning algorithmic projects in terms of the morality of their respective and constitutive ground-truthing practices. Such techno-moral graphs may, in turn, serve as equipment for greater governance of machine learning algorithms and systems.

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