1,061 research outputs found
<em>Rhodococcus indonesiensis</em> sp. nov. a new member of the <em>Rhodococcus ruber</em> lineage isolated from sediment of a neutral hot spring and reclassification of <em>Rhodococcus electrodiphilus</em> (Ramaprasad et al. 2018) as a later heterotypic synonym of <em>Rhodococcus ruber </em>(Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)
\ua9 2024 The Authors.A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03T, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus Rhodococcus. The isolate was found to have chemo-taxonomic, cultural and morphological properties typical of rhodococci. It has a rod–coccus lifecycle and grows from 10 to 39 \ub0C, from pH 6.5 to 8.0 and in the presence of 0–10% (w/v) sodium chloride. Whole-organism hydrolysates contain meso-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H2), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C16:0 is the major fatty acid. Whole-genome analyses show that the isolate and Rhodococcus electrodiphilus LMG 29881T (GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and Rhodococcus aetherivorans DSM 44752T and Rhodococcus ruber DSM 43338T form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of Rhodococcus rhodochrous and related Rhodococcus species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA–DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03T (=CCMM B1310T=ICEBB-06T=NCIMB 15214T) be classified in the genus Rhodococcus as Rhodococcus indonesiensis sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that Rhodococ-cus electrodiphilus LMG 29881T and Rhodococcus ruber DSM 43338T belong to a single species. It is, therefore, proposed that R. electrodiphilus be recognized as a heterotypic synonym of R. ruber
HeMIS: Hetero-Modal Image Segmentation
We introduce a deep learning image segmentation framework that is extremely
robust to missing imaging modalities. Instead of attempting to impute or
synthesize missing data, the proposed approach learns, for each modality, an
embedding of the input image into a single latent vector space for which
arithmetic operations (such as taking the mean) are well defined. Points in
that space, which are averaged over modalities available at inference time, can
then be further processed to yield the desired segmentation. As such, any
combinatorial subset of available modalities can be provided as input, without
having to learn a combinatorial number of imputation models. Evaluated on two
neurological MRI datasets (brain tumors and MS lesions), the approach yields
state-of-the-art segmentation results when provided with all modalities;
moreover, its performance degrades remarkably gracefully when modalities are
removed, significantly more so than alternative mean-filling or other synthesis
approaches.Comment: Accepted as an oral presentation at MICCAI 201
The Case for Learned Index Structures
Indexes are models: a B-Tree-Index can be seen as a model to map a key to the
position of a record within a sorted array, a Hash-Index as a model to map a
key to a position of a record within an unsorted array, and a BitMap-Index as a
model to indicate if a data record exists or not. In this exploratory research
paper, we start from this premise and posit that all existing index structures
can be replaced with other types of models, including deep-learning models,
which we term learned indexes. The key idea is that a model can learn the sort
order or structure of lookup keys and use this signal to effectively predict
the position or existence of records. We theoretically analyze under which
conditions learned indexes outperform traditional index structures and describe
the main challenges in designing learned index structures. Our initial results
show, that by using neural nets we are able to outperform cache-optimized
B-Trees by up to 70% in speed while saving an order-of-magnitude in memory over
several real-world data sets. More importantly though, we believe that the idea
of replacing core components of a data management system through learned models
has far reaching implications for future systems designs and that this work
just provides a glimpse of what might be possible
An Abstraction-Based Framework for Neural Network Verification
Deep neural networks are increasingly being used as controllers for safety-critical systems. Because neural networks are opaque, certifying their correctness is a significant challenge. To address this issue, several neural network verification approaches have recently been proposed. However, these approaches afford limited scalability, and applying them to large networks can be challenging. In this paper, we propose a framework that can enhance neural network verification techniques by using over-approximation to reduce the size of the network—thus making it more amenable to verification. We perform the approximation such that if the property holds for the smaller (abstract) network, it holds for the original as well. The over-approximation may be too coarse, in which case the underlying verification tool might return a spurious counterexample. Under such conditions, we perform counterexample-guided refinement to adjust the approximation, and then repeat the process. Our approach is orthogonal to, and can be integrated with, many existing verification techniques. For evaluation purposes, we integrate it with the recently proposed Marabou framework, and observe a significant improvement in Marabou’s performance. Our experiments demonstrate the great potential of our approach for verifying larger neural networks
Reluplex: An Efficient SMT Solver for Verifying Deep Neural Networks
Deep neural networks have emerged as a widely used and effective means for
tackling complex, real-world problems. However, a major obstacle in applying
them to safety-critical systems is the great difficulty in providing formal
guarantees about their behavior. We present a novel, scalable, and efficient
technique for verifying properties of deep neural networks (or providing
counter-examples). The technique is based on the simplex method, extended to
handle the non-convex Rectified Linear Unit (ReLU) activation function, which
is a crucial ingredient in many modern neural networks. The verification
procedure tackles neural networks as a whole, without making any simplifying
assumptions. We evaluated our technique on a prototype deep neural network
implementation of the next-generation airborne collision avoidance system for
unmanned aircraft (ACAS Xu). Results show that our technique can successfully
prove properties of networks that are an order of magnitude larger than the
largest networks verified using existing methods.Comment: This is the extended version of a paper with the same title that
appeared at CAV 201
Structural Material Property Tailoring Using Deep Neural Networks
Advances in robotics, artificial intelligence, and machine learning are
ushering in a new age of automation, as machines match or outperform human
performance. Machine intelligence can enable businesses to improve performance
by reducing errors, improving sensitivity, quality and speed, and in some cases
achieving outcomes that go beyond current resource capabilities. Relevant
applications include new product architecture design, rapid material
characterization, and life-cycle management tied with a digital strategy that
will enable efficient development of products from cradle to grave. In
addition, there are also challenges to overcome that must be addressed through
a major, sustained research effort that is based solidly on both inferential
and computational principles applied to design tailoring of functionally
optimized structures. Current applications of structural materials in the
aerospace industry demand the highest quality control of material
microstructure, especially for advanced rotational turbomachinery in aircraft
engines in order to have the best tailored material property. In this paper,
deep convolutional neural networks were developed to accurately predict
processing-structure-property relations from materials microstructures images,
surpassing current best practices and modeling efforts. The models
automatically learn critical features, without the need for manual
specification and/or subjective and expensive image analysis. Further, in
combination with generative deep learning models, a framework is proposed to
enable rapid material design space exploration and property identification and
optimization. The implementation must take account of real-time decision cycles
and the trade-offs between speed and accuracy
The Challenge of Machine Learning in Space Weather Nowcasting and Forecasting
The numerous recent breakthroughs in machine learning (ML) make imperative to
carefully ponder how the scientific community can benefit from a technology
that, although not necessarily new, is today living its golden age. This Grand
Challenge review paper is focused on the present and future role of machine
learning in space weather. The purpose is twofold. On one hand, we will discuss
previous works that use ML for space weather forecasting, focusing in
particular on the few areas that have seen most activity: the forecasting of
geomagnetic indices, of relativistic electrons at geosynchronous orbits, of
solar flares occurrence, of coronal mass ejection propagation time, and of
solar wind speed. On the other hand, this paper serves as a gentle introduction
to the field of machine learning tailored to the space weather community and as
a pointer to a number of open challenges that we believe the community should
undertake in the next decade. The recurring themes throughout the review are
the need to shift our forecasting paradigm to a probabilistic approach focused
on the reliable assessment of uncertainties, and the combination of
physics-based and machine learning approaches, known as gray-box.Comment: under revie
Applying machine learning to improve simulations of a chaotic dynamical system using empirical error correction
Dynamical weather and climate prediction models underpin many studies of the
Earth system and hold the promise of being able to make robust projections of
future climate change based on physical laws. However, simulations from these
models still show many differences compared with observations. Machine learning
has been applied to solve certain prediction problems with great success, and
recently it's been proposed that this could replace the role of
physically-derived dynamical weather and climate models to give better quality
simulations. Here, instead, a framework using machine learning together with
physically-derived models is tested, in which it is learnt how to correct the
errors of the latter from timestep to timestep. This maintains the physical
understanding built into the models, whilst allowing performance improvements,
and also requires much simpler algorithms and less training data. This is
tested in the context of simulating the chaotic Lorenz '96 system, and it is
shown that the approach yields models that are stable and that give both
improved skill in initialised predictions and better long-term climate
statistics. Improvements in long-term statistics are smaller than for single
time-step tendencies, however, indicating that it would be valuable to develop
methods that target improvements on longer time scales. Future strategies for
the development of this approach and possible applications to making progress
on important scientific problems are discussed.Comment: 26p, 7 figures To be published in Journal of Advances in Modeling
Earth System
Subitizing with Variational Autoencoders
Numerosity, the number of objects in a set, is a basic property of a given
visual scene. Many animals develop the perceptual ability to subitize: the
near-instantaneous identification of the numerosity in small sets of visual
items. In computer vision, it has been shown that numerosity emerges as a
statistical property in neural networks during unsupervised learning from
simple synthetic images. In this work, we focus on more complex natural images
using unsupervised hierarchical neural networks. Specifically, we show that
variational autoencoders are able to spontaneously perform subitizing after
training without supervision on a large amount images from the Salient Object
Subitizing dataset. While our method is unable to outperform supervised
convolutional networks for subitizing, we observe that the networks learn to
encode numerosity as basic visual property. Moreover, we find that the learned
representations are likely invariant to object area; an observation in
alignment with studies on biological neural networks in cognitive neuroscience
Reconstruction of three-dimensional porous media using generative adversarial neural networks
To evaluate the variability of multi-phase flow properties of porous media at
the pore scale, it is necessary to acquire a number of representative samples
of the void-solid structure. While modern x-ray computer tomography has made it
possible to extract three-dimensional images of the pore space, assessment of
the variability in the inherent material properties is often experimentally not
feasible. We present a novel method to reconstruct the solid-void structure of
porous media by applying a generative neural network that allows an implicit
description of the probability distribution represented by three-dimensional
image datasets. We show, by using an adversarial learning approach for neural
networks, that this method of unsupervised learning is able to generate
representative samples of porous media that honor their statistics. We
successfully compare measures of pore morphology, such as the Euler
characteristic, two-point statistics and directional single-phase permeability
of synthetic realizations with the calculated properties of a bead pack, Berea
sandstone, and Ketton limestone. Results show that GANs can be used to
reconstruct high-resolution three-dimensional images of porous media at
different scales that are representative of the morphology of the images used
to train the neural network. The fully convolutional nature of the trained
neural network allows the generation of large samples while maintaining
computational efficiency. Compared to classical stochastic methods of image
reconstruction, the implicit representation of the learned data distribution
can be stored and reused to generate multiple realizations of the pore
structure very rapidly.Comment: 21 pages, 20 figure
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