CONVOLUTIONAL NEURAL NETWORKS AS AN AID TO BIOSTRATIGRAPHY AND MICROPALEONTOLOGY: A TEST ON LATE PALEOZOIC MICROFOSSILS

Palaios ◽  
2020 ◽  
Vol 35 (9) ◽  
pp. 391-402 ◽  
Author(s):  
RAFAEL PIRES DE LIMA ◽  
KATIE F. WELCH ◽  
JAMES E. BARRICK ◽  
KURT J. MARFURT ◽  
ROGER BURKHALTER ◽  
...  

ABSTRACT Accurate taxonomic classification of microfossils in thin-sections is an important biostratigraphic procedure. As paleontological expertise is typically restricted to specific taxonomic groups and experts are not present in all institutions, geoscience researchers often suffer from lack of quick access to critical taxonomic knowledge for biostratigraphic analyses. Moreover, diminishing emphasis on education and training in systematics poses a major challenge for the future of biostratigraphy, and on associated endeavors reliant on systematics. Here we present a machine learning approach to classify and organize fusulinids—microscopic index fossils for the late Paleozoic. The technique we employ has the potential to use such important taxonomic knowledge in models that can be applied to recognize and categorize fossil specimens. Our results demonstrate that, given adequate images and training, convolutional neural network models can correctly identify fusulinids with high levels of accuracy. Continued efforts in digitization of biological and paleontological collections at numerous museums and adoption of machine learning by paleontologists can enable the development of highly accurate and easy-to-use classification tools and, thus, facilitate biostratigraphic analyses by non-experts as well as allow for cross-validation of disparate collections around the world. Automation of classification work would also enable expert paleontologists and others to focus efforts on exploration of more complex interpretations and concepts.

2022 ◽  
Author(s):  
Leon Faure ◽  
Bastien Mollet ◽  
Wolfram Liebermeister ◽  
Jean-Loup Faulon

Metabolic networks have largely been exploited as mechanistic tools to predict the behavior of microorganisms with a defined genotype in different environments. However, flux predictions by constraint-based modeling approaches are limited in quality unless labor-intensive experiments including the measurement of media intake fluxes, are performed. Using machine learning instead of an optimization of biomass flux - on which most existing constraint-based methods are based - provides ways to improve flux and growth rate predictions. In this paper, we show how Recurrent Neural Networks can surrogate constraint-based modeling and make metabolic networks suitable for backpropagation and consequently be used as an architecture for machine learning. We refer to our hybrid - mechanistic and neural network - models as Artificial Metabolic Networks (AMN). We showcase AMN and illustrate its performance with an experimental dataset of Escherichia coli growth rates in 73 different media compositions. We reach a regression coefficient of R2=0.78 on cross-validation sets. We expect AMNs to provide easier discovery of metabolic insights and prompt new biotechnological applications.


2021 ◽  
Author(s):  
V.Y. Ilichev ◽  
I.V. Chukhraev

The article is devoted to the consideration of one of the areas of application of modern and promising computer technology – machine learning. This direction is based on the creation of models consisting of neural networks and their deep learning. At present, there is a need to generate new, not yet existing, images of objects of different types. Most often, text files or images act as such objects. To achieve a high quality of results, a generation method based on the adversarial work of two neural networks (generator and discriminator) was once worked out. This class of neural network models is distinguished by the complexity of topography, since it is necessary to correctly organize the structure of neural layers in order to achieve maximum accuracy and minimal error. The described program is created using the Python language and special libraries that extend the set of commands for performing additional functions: working with neural networks Keras (main library), integrating with the operating system Os, outputting graphs Matplotlib, working with data arrays Numpy and others. A description is given of the type and features of each neural layer, as well as the use of library connection functions, input of initial data, compilation and training of the obtained model. Next, the implementation of the procedure for outputting the results of evaluating the errors of the generator and discriminator and the accuracy achieved by the model depending on the number of cycles (eras) of its training is considered. Based on the results of the work, conclusions were drawn and recommendations were made for the use and development of the considered methodology for creating and training generative and adversarial neural networks. Studies have demonstrated the procedure for operating with comparatively simple and accessible, but effective means of a universal Python language with the Keras library to create and teach a complex neural network model. In fact, it has been proved that the use of this method allows to achieve high-quality results of machine learning, previously achievable only when using special software systems for working with neural networks.


Author(s):  
Padmavathi .S ◽  
M. Chidambaram

Text classification has grown into more significant in managing and organizing the text data due to tremendous growth of online information. It does classification of documents in to fixed number of predefined categories. Rule based approach and Machine learning approach are the two ways of text classification. In rule based approach, classification of documents is done based on manually defined rules. In Machine learning based approach, classification rules or classifier are defined automatically using example documents. It has higher recall and quick process. This paper shows an investigation on text classification utilizing different machine learning techniques.


2021 ◽  
Vol 9 (5) ◽  
pp. 1034
Author(s):  
Carlos Sabater ◽  
Lorena Ruiz ◽  
Abelardo Margolles

This study aimed to recover metagenome-assembled genomes (MAGs) from human fecal samples to characterize the glycosidase profiles of Bifidobacterium species exposed to different prebiotic oligosaccharides (galacto-oligosaccharides, fructo-oligosaccharides and human milk oligosaccharides, HMOs) as well as high-fiber diets. A total of 1806 MAGs were recovered from 487 infant and adult metagenomes. Unsupervised and supervised classification of glycosidases codified in MAGs using machine-learning algorithms allowed establishing characteristic hydrolytic profiles for B. adolescentis, B. bifidum, B. breve, B. longum and B. pseudocatenulatum, yielding classification rates above 90%. Glycosidase families GH5 44, GH32, and GH110 were characteristic of B. bifidum. The presence or absence of GH1, GH2, GH5 and GH20 was characteristic of B. adolescentis, B. breve and B. pseudocatenulatum, while families GH1 and GH30 were relevant in MAGs from B. longum. These characteristic profiles allowed discriminating bifidobacteria regardless of prebiotic exposure. Correlation analysis of glycosidase activities suggests strong associations between glycosidase families comprising HMOs-degrading enzymes, which are often found in MAGs from the same species. Mathematical models here proposed may contribute to a better understanding of the carbohydrate metabolism of some common bifidobacteria species and could be extrapolated to other microorganisms of interest in future studies.


IEEE Access ◽  
2021 ◽  
Vol 9 ◽  
pp. 45993-45999
Author(s):  
Ung Yang ◽  
Seungwon Oh ◽  
Seung Gon Wi ◽  
Bok-Rye Lee ◽  
Sang-Hyun Lee ◽  
...  

2021 ◽  
Vol 11 (15) ◽  
pp. 6918
Author(s):  
Chidubem Iddianozie ◽  
Gavin McArdle

The effectiveness of a machine learning model is impacted by the data representation used. Consequently, it is crucial to investigate robust representations for efficient machine learning methods. In this paper, we explore the link between data representations and model performance for inference tasks on spatial networks. We argue that representations which explicitly encode the relations between spatial entities would improve model performance. Specifically, we consider homogeneous and heterogeneous representations of spatial networks. We recognise that the expressive nature of the heterogeneous representation may benefit spatial networks and could improve model performance on certain tasks. Thus, we carry out an empirical study using Graph Neural Network models for two inference tasks on spatial networks. Our results demonstrate that heterogeneous representations improves model performance for down-stream inference tasks on spatial networks.


Author(s):  
Alexis Falcin ◽  
Jean-Philippe Métaxian ◽  
Jérôme Mars ◽  
Éléonore Stutzmann ◽  
Jean-Christophe Komorowski ◽  
...  

Mekatronika ◽  
2020 ◽  
Vol 2 (2) ◽  
pp. 1-12
Author(s):  
Muhammad Nur Aiman Shapiee ◽  
Muhammad Ar Rahim Ibrahim ◽  
Muhammad Amirul Abdullah ◽  
Rabiu Muazu Musa ◽  
Noor Azuan Abu Osman ◽  
...  

The skateboarding scene has arrived at new statures, particularly with its first appearance at the now delayed Tokyo Summer Olympic Games. Hence, attributable to the size of the game in such competitive games, progressed creative appraisal approaches have progressively increased due consideration by pertinent partners, particularly with the enthusiasm of a more goal-based assessment. This study purposes for classifying skateboarding tricks, specifically Frontside 180, Kickflip, Ollie, Nollie Front Shove-it, and Pop Shove-it over the integration of image processing, Trasnfer Learning (TL) to feature extraction enhanced with tradisional Machine Learning (ML) classifier. A male skateboarder performed five tricks every sort of trick consistently and the YI Action camera captured the movement by a range of 1.26 m. Then, the image dataset were features built and extricated by means of  three TL models, and afterward in this manner arranged to utilize by k-Nearest Neighbor (k-NN) classifier. The perception via the initial experiments showed, the MobileNet, NASNetMobile, and NASNetLarge coupled with optimized k-NN classifiers attain a classification accuracy (CA) of 95%, 92% and 90%, respectively on the test dataset. Besides, the result evident from the robustness evaluation showed the MobileNet+k-NN pipeline is more robust as it could provide a decent average CA than other pipelines. It would be demonstrated that the suggested study could characterize the skateboard tricks sufficiently and could, over the long haul, uphold judges decided for giving progressively objective-based decision.


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