6,501 research outputs found
Vaccinia virus B5 protein affects the glycosylation, localization and stability of the A34 protein
Vaccinia virus has two infectious forms, the intracellular mature virus, which has a single envelope, and the extracellular enveloped virus (EEV), which is surrounded by two lipid bilayers. The outer membrane of the EEV contains at least six viral proteins. Among them A34, a type II membrane glycoprotein, and B5, a type I membrane glycoprotein, form a complex and are involved in processes such as morphogenesis and EEV entry. A34 is required for normal incorporation of B5 into the EEV membrane. Here, we used a virus lacking B5 and viruses with mutations in the B5 membrane-proximal stalk region and looked at the effect of those modifications on A34. Data presented show that B5 is required for the correct glycosylation, trafficking and stability of A34, emphasizing the complex interactions and mutual dependence of these vaccinia EEV proteins.This work was supported by the Medical Research Council. G. L. S. is a Wellcome Trust Principal Research Fellow
Ensemble learning of linear perceptron; Online learning theory
Within the framework of on-line learning, we study the generalization error
of an ensemble learning machine learning from a linear teacher perceptron. The
generalization error achieved by an ensemble of linear perceptrons having
homogeneous or inhomogeneous initial weight vectors is precisely calculated at
the thermodynamic limit of a large number of input elements and shows rich
behavior. Our main findings are as follows. For learning with homogeneous
initial weight vectors, the generalization error using an infinite number of
linear student perceptrons is equal to only half that of a single linear
perceptron, and converges with that of the infinite case with O(1/K) for a
finite number of K linear perceptrons. For learning with inhomogeneous initial
weight vectors, it is advantageous to use an approach of weighted averaging
over the output of the linear perceptrons, and we show the conditions under
which the optimal weights are constant during the learning process. The optimal
weights depend on only correlation of the initial weight vectors.Comment: 14 pages, 3 figures, submitted to Physical Review
Optimization of the Asymptotic Property of Mutual Learning Involving an Integration Mechanism of Ensemble Learning
We propose an optimization method of mutual learning which converges into the
identical state of optimum ensemble learning within the framework of on-line
learning, and have analyzed its asymptotic property through the statistical
mechanics method.The proposed model consists of two learning steps: two
students independently learn from a teacher, and then the students learn from
each other through the mutual learning. In mutual learning, students learn from
each other and the generalization error is improved even if the teacher has not
taken part in the mutual learning. However, in the case of different initial
overlaps(direction cosine) between teacher and students, a student with a
larger initial overlap tends to have a larger generalization error than that of
before the mutual learning. To overcome this problem, our proposed optimization
method of mutual learning optimizes the step sizes of two students to minimize
the asymptotic property of the generalization error. Consequently, the
optimized mutual learning converges to a generalization error identical to that
of the optimal ensemble learning. In addition, we show the relationship between
the optimum step size of the mutual learning and the integration mechanism of
the ensemble learning.Comment: 13 pages, 3 figures, submitted to Journal of Physical Society of
Japa
Analysis of ensemble learning using simple perceptrons based on online learning theory
Ensemble learning of nonlinear perceptrons, which determine their outputs
by sign functions, is discussed within the framework of online learning and
statistical mechanics. One purpose of statistical learning theory is to
theoretically obtain the generalization error. This paper shows that ensemble
generalization error can be calculated by using two order parameters, that is,
the similarity between a teacher and a student, and the similarity among
students. The differential equations that describe the dynamical behaviors of
these order parameters are derived in the case of general learning rules. The
concrete forms of these differential equations are derived analytically in the
cases of three well-known rules: Hebbian learning, perceptron learning and
AdaTron learning. Ensemble generalization errors of these three rules are
calculated by using the results determined by solving their differential
equations. As a result, these three rules show different characteristics in
their affinity for ensemble learning, that is ``maintaining variety among
students." Results show that AdaTron learning is superior to the other two
rules with respect to that affinity.Comment: 30 pages, 17 figure
Mixing hetero- and homogeneous models in weighted ensembles
The effectiveness of ensembling for improving classification performance is well documented. Broadly speaking, ensemble design can be expressed as a spectrum where at one end a set of heterogeneous classifiers model the same data, and at the other homogeneous models derived from the same classification algorithm are diversified through data manipulation. The cross-validation accuracy weighted probabilistic ensemble is a heterogeneous weighted ensemble scheme that needs reliable estimates of error from its base classifiers. It estimates error through a cross-validation process, and raises the estimates to a power to accentuate differences. We study the effects of maintaining all models trained during cross-validation on the final ensemble's predictive performance, and the base model's and resulting ensembles' variance and robustness across datasets and resamples. We find that augmenting the ensemble through the retention of all models trained provides a consistent and significant improvement, despite reductions in the reliability of the base models' performance estimates
Searching for Ground Truth: a stepping stone in automating genre classification
This paper examines genre classification of documents and
its role in enabling the effective automated management of digital documents by digital libraries and other repositories. We have previously presented genre classification as a valuable step toward achieving automated extraction of descriptive metadata for digital material. Here, we present results from experiments using human labellers, conducted to assist in genre characterisation and the prediction of obstacles which need to be overcome by an automated system, and to contribute to the process of creating a solid testbed corpus for extending automated genre classification and testing metadata extraction tools across genres. We also describe the performance of two classifiers based on image and stylistic modeling features in labelling the data resulting from the agreement of three human labellers across fifteen genre classes.
A Non-Sequential Representation of Sequential Data for Churn Prediction
We investigate the length of event sequence giving best predictions
when using a continuous HMM approach to churn prediction from sequential
data. Motivated by observations that predictions based on only the few most recent
events seem to be the most accurate, a non-sequential dataset is constructed
from customer event histories by averaging features of the last few events. A simple
K-nearest neighbor algorithm on this dataset is found to give significantly
improved performance. It is quite intuitive to think that most people will react
only to events in the fairly recent past. Events related to telecommunications occurring
months or years ago are unlikely to have a large impact on a customer’s
future behaviour, and these results bear this out. Methods that deal with sequential
data also tend to be much more complex than those dealing with simple nontemporal
data, giving an added benefit to expressing the recent information in a
non-sequential manner
Sampling, Intervention, Prediction, Aggregation: A Generalized Framework for Model-Agnostic Interpretations
Model-agnostic interpretation techniques allow us to explain the behavior of
any predictive model. Due to different notations and terminology, it is
difficult to see how they are related. A unified view on these methods has been
missing. We present the generalized SIPA (sampling, intervention, prediction,
aggregation) framework of work stages for model-agnostic interpretations and
demonstrate how several prominent methods for feature effects can be embedded
into the proposed framework. Furthermore, we extend the framework to feature
importance computations by pointing out how variance-based and
performance-based importance measures are based on the same work stages. The
SIPA framework reduces the diverse set of model-agnostic techniques to a single
methodology and establishes a common terminology to discuss them in future
work
A Jackknife and Voting Classifier Approach to Feature Selection and Classification
With technological advances now allowing measurement of thousands of genes, proteins and metabolites, researchers are using this information to develop diagnostic and prognostic tests and discern the biological pathways underlying diseases. Often, an investigator’s objective is to develop a classification rule to predict group membership of unknown samples based on a small set of features and that could ultimately be used in a clinical setting. While common classification methods such as random forest and support vector machines are effective at separating groups, they do not directly translate into a clinically-applicable classification rule based on a small number of features.We present a simple feature selection and classification method for biomarker detection that is intuitively understandable and can be directly extended for application to a clinical setting. We first use a jackknife procedure to identify important features and then, for classification, we use voting classifiers which are simple and easy to implement. We compared our method to random forest and support vector machines using three benchmark cancer ‘omics datasets with different characteristics. We found our jackknife procedure and voting classifier to perform comparably to these two methods in terms of accuracy. Further, the jackknife procedure yielded stable feature sets. Voting classifiers in combination with a robust feature selection method such as our jackknife procedure offer an effective, simple and intuitive approach to feature selection and classification with a clear extension to clinical applications
Simultaneous Matrix Diagonalization for Structural Brain Networks Classification
This paper considers the problem of brain disease classification based on
connectome data. A connectome is a network representation of a human brain. The
typical connectome classification problem is very challenging because of the
small sample size and high dimensionality of the data. We propose to use
simultaneous approximate diagonalization of adjacency matrices in order to
compute their eigenstructures in more stable way. The obtained approximate
eigenvalues are further used as features for classification. The proposed
approach is demonstrated to be efficient for detection of Alzheimer's disease,
outperforming simple baselines and competing with state-of-the-art approaches
to brain disease classification
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