2,917 research outputs found
Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks
© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript
Learning to detect chest radiographs containing lung nodules using visual attention networks
Machine learning approaches hold great potential for the automated detection
of lung nodules in chest radiographs, but training the algorithms requires vary
large amounts of manually annotated images, which are difficult to obtain. Weak
labels indicating whether a radiograph is likely to contain pulmonary nodules
are typically easier to obtain at scale by parsing historical free-text
radiological reports associated to the radiographs. Using a repositotory of
over 700,000 chest radiographs, in this study we demonstrate that promising
nodule detection performance can be achieved using weak labels through
convolutional neural networks for radiograph classification. We propose two
network architectures for the classification of images likely to contain
pulmonary nodules using both weak labels and manually-delineated bounding
boxes, when these are available. Annotated nodules are used at training time to
deliver a visual attention mechanism informing the model about its localisation
performance. The first architecture extracts saliency maps from high-level
convolutional layers and compares the estimated position of a nodule against
the ground truth, when this is available. A corresponding localisation error is
then back-propagated along with the softmax classification error. The second
approach consists of a recurrent attention model that learns to observe a short
sequence of smaller image portions through reinforcement learning. When a
nodule annotation is available at training time, the reward function is
modified accordingly so that exploring portions of the radiographs away from a
nodule incurs a larger penalty. Our empirical results demonstrate the potential
advantages of these architectures in comparison to competing methodologies
What's the Situation with Intelligent Mesh Generation: A Survey and Perspectives
Intelligent Mesh Generation (IMG) represents a novel and promising field of
research, utilizing machine learning techniques to generate meshes. Despite its
relative infancy, IMG has significantly broadened the adaptability and
practicality of mesh generation techniques, delivering numerous breakthroughs
and unveiling potential future pathways. However, a noticeable void exists in
the contemporary literature concerning comprehensive surveys of IMG methods.
This paper endeavors to fill this gap by providing a systematic and thorough
survey of the current IMG landscape. With a focus on 113 preliminary IMG
methods, we undertake a meticulous analysis from various angles, encompassing
core algorithm techniques and their application scope, agent learning
objectives, data types, targeted challenges, as well as advantages and
limitations. We have curated and categorized the literature, proposing three
unique taxonomies based on key techniques, output mesh unit elements, and
relevant input data types. This paper also underscores several promising future
research directions and challenges in IMG. To augment reader accessibility, a
dedicated IMG project page is available at
\url{https://github.com/xzb030/IMG_Survey}
A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation
Cellular electron cryo-tomography enables the 3D visualization of cellular
organization in the near-native state and at submolecular resolution. However,
the contents of cellular tomograms are often complex, making it difficult to
automatically isolate different in situ cellular components. In this paper, we
propose a convolutional autoencoder-based unsupervised approach to provide a
coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate
that the autoencoder can be used for efficient and coarse characterization of
features of macromolecular complexes and surfaces, such as membranes. In
addition, the autoencoder can be used to detect non-cellular features related
to sample preparation and data collection, such as carbon edges from the grid
and tomogram boundaries. The autoencoder is also able to detect patterns that
may indicate spatial interactions between cellular components. Furthermore, we
demonstrate that our autoencoder can be used for weakly supervised semantic
segmentation of cellular components, requiring a very small amount of manual
annotation.Comment: Accepted by Journal of Structural Biolog
Inversion using a new low-dimensional representation of complex binary geological media based on a deep neural network
Efficient and high-fidelity prior sampling and inversion for complex
geological media is still a largely unsolved challenge. Here, we use a deep
neural network of the variational autoencoder type to construct a parametric
low-dimensional base model parameterization of complex binary geological media.
For inversion purposes, it has the attractive feature that random draws from an
uncorrelated standard normal distribution yield model realizations with spatial
characteristics that are in agreement with the training set. In comparison with
the most commonly used parametric representations in probabilistic inversion,
we find that our dimensionality reduction (DR) approach outperforms principle
component analysis (PCA), optimization-PCA (OPCA) and discrete cosine transform
(DCT) DR techniques for unconditional geostatistical simulation of a
channelized prior model. For the considered examples, important compression
ratios (200 - 500) are achieved. Given that the construction of our
parameterization requires a training set of several tens of thousands of prior
model realizations, our DR approach is more suited for probabilistic (or
deterministic) inversion than for unconditional (or point-conditioned)
geostatistical simulation. Probabilistic inversions of 2D steady-state and 3D
transient hydraulic tomography data are used to demonstrate the DR-based
inversion. For the 2D case study, the performance is superior compared to
current state-of-the-art multiple-point statistics inversion by sequential
geostatistical resampling (SGR). Inversion results for the 3D application are
also encouraging
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