12,642 research outputs found
Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks
The gene regulatory network (GRN) is the central decision‐making module of the cell. We have developed a theory called Buffered Qualitative Stability (BQS) based on the hypothesis that GRNs are organised so that they remain robust in the face of unpredictable environmental and evolutionary changes. BQS makes strong and diverse predictions about the network features that allow stable responses under arbitrary perturbations, including the random addition of new connections. We show that the GRNs of E. coli, M. tuberculosis, P. aeruginosa, yeast, mouse, and human all verify the predictions of BQS. BQS explains many of the small- and large‐scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response. BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation. DOI: http://dx.doi.org/10.7554/eLife.02863.00
A Posterior Probability Approach for Gene Regulatory Network Inference in Genetic Perturbation Data
Inferring gene regulatory networks is an important problem in systems
biology. However, these networks can be hard to infer from experimental data
because of the inherent variability in biological data as well as the large
number of genes involved. We propose a fast, simple method for inferring
regulatory relationships between genes from knockdown experiments in the NIH
LINCS dataset by calculating posterior probabilities, incorporating prior
information. We show that the method is able to find previously identified
edges from TRANSFAC and JASPAR and discuss the merits and limitations of this
approach
Cycloidal CT with CNN-based sinogram completion and in-scan generation of training data
In x-ray computed tomography (CT), the achievable image resolution is typically limited by several pre-fixed characteristics of the x-ray source and detector. Structuring the x-ray beam using a mask with alternating opaque and transmitting septa can overcome this limit. However, the use of a mask imposes an undersampling problem: to obtain complete datasets, significant lateral sample stepping is needed in addition to the sample rotation, resulting in high x-ray doses and long acquisition times. Cycloidal CT, an alternative scanning scheme by which the sample is rotated and translated simultaneously, can provide high aperture-driven resolution without sample stepping, resulting in a lower radiation dose and faster scans. However, cycloidal sinograms are incomplete and must be restored before tomographic images can be computed. In this work, we demonstrate that high-quality images can be reconstructed by applying the recently proposed Mixed Scale Dense (MS-D) convolutional neural network (CNN) to this task. We also propose a novel training approach by which training data are acquired as part of each scan, thus removing the need for large sets of pre-existing reference data, the acquisition of which is often not practicable or possible. We present results for both simulated datasets and real-world data, showing that the combination of cycloidal CT and machine learning-based data recovery can lead to accurate high-resolution images at a limited dose
3D Shape Segmentation with Projective Convolutional Networks
This paper introduces a deep architecture for segmenting 3D objects into
their labeled semantic parts. Our architecture combines image-based Fully
Convolutional Networks (FCNs) and surface-based Conditional Random Fields
(CRFs) to yield coherent segmentations of 3D shapes. The image-based FCNs are
used for efficient view-based reasoning about 3D object parts. Through a
special projection layer, FCN outputs are effectively aggregated across
multiple views and scales, then are projected onto the 3D object surfaces.
Finally, a surface-based CRF combines the projected outputs with geometric
consistency cues to yield coherent segmentations. The whole architecture
(multi-view FCNs and CRF) is trained end-to-end. Our approach significantly
outperforms the existing state-of-the-art methods in the currently largest
segmentation benchmark (ShapeNet). Finally, we demonstrate promising
segmentation results on noisy 3D shapes acquired from consumer-grade depth
cameras.Comment: This is an updated version of our CVPR 2017 paper. We incorporated
new experiments that demonstrate ShapePFCN performance under the case of
consistent *upright* orientation and an additional input channel in our
rendered images for encoding height from the ground plane (upright axis
coordinate values). Performance is improved in this settin
The tetrapod Caerorhachis bairdi Holmes and Carroll from the Lower Carboniferous of Scotland
The tetrapod Caerorhachis bairdi, probably from the Pendleian Limestone Coal
Group in the Scottish Midland Valley, is redi agnosed and redescribed, and its affinities are
discussed. Caerorachis was originally interpreted as a temnospondyl amphibian, based on
characters that are now regarded as primitive for tetrapods, or of uncertain polarity. Several
features of Caerorhachis (e.g. gastrocentrous vertebrae, curved trunk ribs, reduced dorsal iliac
blade, L-shaped tarsal intermedium) are observed in certain primitive amniotes. In particular,
Caerorhachis resembles ‘anthracosaurs’, generally considered to be among the most primitive of
stem-group amniotes.
The phylogenetic position of Caerorhachis is considered in the light of recently published cladistic
analyses of Palaeozoic tetrapods. Most analyses place Caerorhachis at the base of, or within, ‘anthra-
cosaurs’. When multiple, equally parsimonious solutions are found, its ‘anthracosaur’ affinities are
shown in at least some trees, and are supported by several informative and, generally, highly
consistent characters. Alternative phylogenetic placements (e.g. sister taxon to temnospondyls) are
usually less well corroborated.
If the fundamental evolutionary split of most early tetrapods into stem-group lissamphibians (e.g.
temnospondyl s) and stem-group amniotes (e.g. ‘anthracosaurs’) is accepted, then the revised
interpretation of Caerorhachi s sheds light on near-ancestral conditions for Amniota
A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community
In recent years, deep learning (DL), a re-branding of neural networks (NNs),
has risen to the top in numerous areas, namely computer vision (CV), speech
recognition, natural language processing, etc. Whereas remote sensing (RS)
possesses a number of unique challenges, primarily related to sensors and
applications, inevitably RS draws from many of the same theories as CV; e.g.,
statistics, fusion, and machine learning, to name a few. This means that the RS
community should be aware of, if not at the leading edge of, of advancements
like DL. Herein, we provide the most comprehensive survey of state-of-the-art
RS DL research. We also review recent new developments in the DL field that can
be used in DL for RS. Namely, we focus on theories, tools and challenges for
the RS community. Specifically, we focus on unsolved challenges and
opportunities as it relates to (i) inadequate data sets, (ii)
human-understandable solutions for modelling physical phenomena, (iii) Big
Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and
learning algorithms for spectral, spatial and temporal data, (vi) transfer
learning, (vii) an improved theoretical understanding of DL systems, (viii)
high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote
Sensin
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