2,136 research outputs found
Maximum Entropy Linear Manifold for Learning Discriminative Low-dimensional Representation
Representation learning is currently a very hot topic in modern machine
learning, mostly due to the great success of the deep learning methods. In
particular low-dimensional representation which discriminates classes can not
only enhance the classification procedure, but also make it faster, while
contrary to the high-dimensional embeddings can be efficiently used for visual
based exploratory data analysis.
In this paper we propose Maximum Entropy Linear Manifold (MELM), a
multidimensional generalization of Multithreshold Entropy Linear Classifier
model which is able to find a low-dimensional linear data projection maximizing
discriminativeness of projected classes. As a result we obtain a linear
embedding which can be used for classification, class aware dimensionality
reduction and data visualization. MELM provides highly discriminative 2D
projections of the data which can be used as a method for constructing robust
classifiers.
We provide both empirical evaluation as well as some interesting theoretical
properties of our objective function such us scale and affine transformation
invariance, connections with PCA and bounding of the expected balanced accuracy
error.Comment: submitted to ECMLPKDD 201
Interferon responses to norovirus infections: current and future perspectives.
Human noroviruses (HuNoVs) are increasingly becoming the main cause of transmissible gastroenteritis worldwide, with hundreds of thousands of deaths recorded annually. Yet, decades after their discovery, there is still no effective treatment or vaccine. Efforts aimed at developing vaccines or treatment will benefit from a greater understanding of norovirus-host interactions, including the host response to infection. In this review, we provide a concise overview of the evidence establishing the significance of type I and type III interferon (IFN) responses in the restriction of noroviruses. We also critically examine our current understanding of the molecular mechanisms of IFN induction in norovirus-infected cells, and outline the diverse strategies deployed by noroviruses to supress and/or avoid host IFN responses. It is our hope that this review will facilitate further discussion and increase interest in this area
Vesivirus 2117 capsids more closely resemble sapovirus and lagovirus particles than other known vesivirus structures
Vesivirus 2117 is an adventitious agent that in 2009, was identified as a contaminant of CHO cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher disease respectively), caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae; a family of small icosahedral viruses encoding a positive sense RNA genome. We have used cryo-electron microscopy and three dimensional image reconstruction to calculate a structure of vesivirus 2117 virus like particles as well as feline calicivirus and a chimeric sapovirus. We present a structural comparison of several members of the Caliciviridae, showing that the distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures. Furthermore, at intermediate resolutions we found a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera, such as sapovirus and rabbit haemorrhagic disease virus. Phylogenetic analysis confirms vesivirus 2117 as a vesivirus closely related to canine vesiviruses. We postulate that morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage
Dynamic mechanisms of neocortical focal seizure onset.
Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tRecent experimental and clinical studies have provided diverse insight into the mechanisms of human focal seizure initiation and propagation. Often these findings exist at different scales of observation, and are not reconciled into a common understanding. Here we develop a new, multiscale mathematical model of cortical electric activity with realistic mesoscopic connectivity. Relating the model dynamics to experimental and clinical findings leads us to propose three classes of dynamical mechanisms for the onset of focal seizures in a unified framework. These three classes are: (i) globally induced focal seizures; (ii) globally supported focal seizures; (iii) locally induced focal seizures. Using model simulations we illustrate these onset mechanisms and show how the three classes can be distinguished. Specifically, we find that although all focal seizures typically appear to arise from localised tissue, the mechanisms of onset could be due to either localised processes or processes on a larger spatial scale. We conclude that although focal seizures might have different patient-specific aetiologies and electrographic signatures, our model suggests that dynamically they can still be classified in a clinically useful way. Additionally, this novel classification according to the dynamical mechanisms is able to resolve some of the previously conflicting experimental and clinical findings.This work was supported by the Doctoral Training Centre in Systems Biology (University of Manchester), the Biotechnology and Biological Sciences Research Council, and the Engineering and Physical Sciences Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Recovery of genetically defined murine norovirus in tissue culture by using a fowlpox virus expressing T7 RNA polymerase.
Despite the significant disease burden caused by human norovirus infection, an efficient tissue-culture system for these viruses remains elusive. Murine norovirus (MNV) is an ideal surrogate for the study of norovirus biology, as the virus replicates efficiently in tissue culture and a low-cost animal model is readily available. In this report, a reverse-genetics system for MNV is described, using a fowlpox virus (FWPV) recombinant expressing T7 RNA polymerase to recover genetically defined MNV in tissue culture for the first time. These studies demonstrated that approaches that have proved successful for other members of the family Caliciviridae failed to lead to recovery of MNV. This was due to our observation that vaccinia virus infection had a negative effect on MNV replication. In contrast, FWPV infection had no deleterious effect and allowed the recovery of infectious MNV from cells previously transfected with MNV cDNA constructs. These studies also indicated that the nature of the 3'-terminal nucleotide is critical for efficient virus recovery and that inclusion of a hepatitis delta virus ribozyme at the 3' end can increase the efficiency with which virus is recovered. This system now allows the recovery of genetically defined noroviruses and will facilitate the analysis of the effects of genetic variation on norovirus pathogenesis
Dynamic mechanisms of neocortical focal seizure onset.
Recent experimental and clinical studies have provided diverse insight into the mechanisms of human focal seizure initiation and propagation. Often these findings exist at different scales of observation, and are not reconciled into a common understanding. Here we develop a new, multiscale mathematical model of cortical electric activity with realistic mesoscopic connectivity. Relating the model dynamics to experimental and clinical findings leads us to propose three classes of dynamical mechanisms for the onset of focal seizures in a unified framework. These three classes are: (i) globally induced focal seizures; (ii) globally supported focal seizures; (iii) locally induced focal seizures. Using model simulations we illustrate these onset mechanisms and show how the three classes can be distinguished. Specifically, we find that although all focal seizures typically appear to arise from localised tissue, the mechanisms of onset could be due to either localised processes or processes on a larger spatial scale. We conclude that although focal seizures might have different patient-specific aetiologies and electrographic signatures, our model suggests that dynamically they can still be classified in a clinically useful way. Additionally, this novel classification according to the dynamical mechanisms is able to resolve some of the previously conflicting experimental and clinical findings
HoloDetect: Few-Shot Learning for Error Detection
We introduce a few-shot learning framework for error detection. We show that
data augmentation (a form of weak supervision) is key to training high-quality,
ML-based error detection models that require minimal human involvement. Our
framework consists of two parts: (1) an expressive model to learn rich
representations that capture the inherent syntactic and semantic heterogeneity
of errors; and (2) a data augmentation model that, given a small seed of clean
records, uses dataset-specific transformations to automatically generate
additional training data. Our key insight is to learn data augmentation
policies from the noisy input dataset in a weakly supervised manner. We show
that our framework detects errors with an average precision of ~94% and an
average recall of ~93% across a diverse array of datasets that exhibit
different types and amounts of errors. We compare our approach to a
comprehensive collection of error detection methods, ranging from traditional
rule-based methods to ensemble-based and active learning approaches. We show
that data augmentation yields an average improvement of 20 F1 points while it
requires access to 3x fewer labeled examples compared to other ML approaches.Comment: 18 pages
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
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