1,901 research outputs found
Evolving stochastic learning algorithm based on Tsallis entropic index
In this paper, inspired from our previous algorithm, which was based on the theory of Tsallis statistical mechanics, we develop a new evolving stochastic learning algorithm for neural networks. The new algorithm combines deterministic and stochastic search steps by employing a different adaptive stepsize for each network weight, and applies a form of noise that is characterized by the nonextensive entropic index q, regulated by a weight decay term. The behavior of the learning algorithm can be made more stochastic or deterministic depending on the trade off between the temperature T and the q values. This is achieved by introducing a formula that defines a time-dependent relationship between these two important learning parameters. Our experimental study verifies that there are indeed improvements in the convergence speed of this new evolving stochastic learning algorithm, which makes learning faster than using the original Hybrid Learning Scheme (HLS). In addition, experiments are conducted to explore the influence of the entropic index q and temperature T on the convergence speed and stability of the proposed method
Improved sign-based learning algorithm derived by the composite nonlinear Jacobi process
In this paper a globally convergent first-order training algorithm is proposed that uses sign-based information of the batch error measure in the framework of the nonlinear Jacobi process. This approach allows us to equip the recently proposed Jacobi–Rprop method with the global convergence property, i.e. convergence to a local minimizer from any initial starting point. We also propose a strategy that ensures the search direction of the globally convergent Jacobi–Rprop is a descent one. The behaviour of the algorithm is empirically investigated in eight benchmark problems. Simulation results verify that there are indeed improvements on the convergence success of the algorithm
An incremental approach to automated protein localisation
Tscherepanow M, Jensen N, Kummert F. An incremental approach to automated protein localisation. BMC Bioinformatics. 2008;9(1): 445.Background:
The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted based on amino acid sequences. Besides increasing our knowledge about intracellular processes, this information facilitates the development of innovative therapies and new diagnostic methods. In order to perform such a localisation, the proteins under analysis are usually fused with a fluorescent protein. So, they can be observed by means of a fluorescence microscope and analysed. In recent years, several automated methods have been proposed for performing such analyses. Here, two different types of approaches can be distinguished: techniques which enable the recognition of a fixed set of protein locations and methods that identify new ones. To our knowledge, a combination of both approaches – i.e. a technique, which enables supervised learning using a known set of protein locations and is able to identify and incorporate new protein locations afterwards – has not been presented yet. Furthermore, associated problems, e.g. the recognition of cells to be analysed, have usually been neglected.
Results:
We introduce a novel approach to automated protein localisation in living cells. In contrast to well-known techniques, the protein localisation technique presented in this article aims at combining the two types of approaches described above: After an automatic identification of unknown protein locations, a potential user is enabled to incorporate them into the pre-trained system. An incremental neural network allows the classification of a fixed set of protein location as well as the detection, clustering and incorporation of additional patterns that occur during an experiment. Here, the proposed technique achieves promising results with respect to both tasks. In addition, the protein localisation procedure has been adapted to an existing cell recognition approach. Therefore, it is especially well-suited for high-throughput investigations where user interactions have to be avoided.
Conclusion:
We have shown that several aspects required for developing an automatic protein localisation technique – namely the recognition of cells, the classification of protein distribution patterns into a set of learnt protein locations, and the detection and learning of new locations – can be combined successfully. So, the proposed method constitutes a crucial step to render image-based protein localisation techniques amenable to large-scale experiments
AI Solutions for MDS: Artificial Intelligence Techniques for Misuse Detection and Localisation in Telecommunication Environments
This report considers the application of Articial Intelligence (AI) techniques to
the problem of misuse detection and misuse localisation within telecommunications
environments. A broad survey of techniques is provided, that covers inter alia
rule based systems, model-based systems, case based reasoning, pattern matching,
clustering and feature extraction, articial neural networks, genetic algorithms, arti
cial immune systems, agent based systems, data mining and a variety of hybrid
approaches. The report then considers the central issue of event correlation, that
is at the heart of many misuse detection and localisation systems. The notion of
being able to infer misuse by the correlation of individual temporally distributed
events within a multiple data stream environment is explored, and a range of techniques,
covering model based approaches, `programmed' AI and machine learning
paradigms. It is found that, in general, correlation is best achieved via rule based approaches,
but that these suffer from a number of drawbacks, such as the difculty of
developing and maintaining an appropriate knowledge base, and the lack of ability
to generalise from known misuses to new unseen misuses. Two distinct approaches
are evident. One attempts to encode knowledge of known misuses, typically within
rules, and use this to screen events. This approach cannot generally detect misuses
for which it has not been programmed, i.e. it is prone to issuing false negatives.
The other attempts to `learn' the features of event patterns that constitute normal
behaviour, and, by observing patterns that do not match expected behaviour, detect
when a misuse has occurred. This approach is prone to issuing false positives,
i.e. inferring misuse from innocent patterns of behaviour that the system was not
trained to recognise. Contemporary approaches are seen to favour hybridisation,
often combining detection or localisation mechanisms for both abnormal and normal
behaviour, the former to capture known cases of misuse, the latter to capture
unknown cases. In some systems, these mechanisms even work together to update
each other to increase detection rates and lower false positive rates. It is concluded
that hybridisation offers the most promising future direction, but that a rule or state
based component is likely to remain, being the most natural approach to the correlation
of complex events. The challenge, then, is to mitigate the weaknesses of
canonical programmed systems such that learning, generalisation and adaptation
are more readily facilitated
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When the machine does not know measuring uncertainty in deep learning models of medical images
This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonRecently, Deep learning (DL), which involves powerful black box predictors, has outperformed
human experts in several medical diagnostic problems. However, these methods focus
exclusively on improving the accuracy of point predictions without assessing their outputs’
quality and ignore the asymmetric cost involved in different types of misclassification errors.
Neural networks also do not deliver confidence in predictions and suffer from over and
under confidence, i.e. are not well calibrated. Knowing how much confidence there is in a
prediction is essential for gaining clinicians’ trust in the technology.
Calibrated uncertainty quantification is a challenging problem as no ground truth is
available. To address this, we make two observations: (i) cost-sensitive deep neural networks
with Dropweights models better quantify calibrated predictive uncertainty, and (ii) estimated
uncertainty with point predictions in Deep Ensembles Bayesian Neural Networks with
DropWeights can lead to a more informed decision and improve prediction quality.
This dissertation focuses on quantifying uncertainty using concepts from cost-sensitive
neural networks, calibration of confidence, and Dropweights ensemble method. First, we
show how to improve predictive uncertainty by deep ensembles of neural networks with Dropweights
learning an approximate distribution over its weights in medical image segmentation
and its application in active learning. Second, we use the Jackknife resampling technique
to correct bias in quantified uncertainty in image classification and propose metrics to measure
uncertainty performance. The third part of the thesis is motivated by the discrepancy
between the model predictive error and the objective in quantified uncertainty when costs for
misclassification errors or unbalanced datasets are asymmetric. We develop cost-sensitive
modifications of the neural networks in disease detection and propose metrics to measure the
quality of quantified uncertainty. Finally, we leverage an adaptive binning strategy to measure
uncertainty calibration error that directly corresponds to estimated uncertainty performance
and address problematic evaluation methods.
We evaluate the effectiveness of the tools on nuclei images segmentation, multi-class
Brain MRI image classification, multi-level cell type-specific protein expression prediction in
ImmunoHistoChemistry (IHC) images and cost-sensitive classification for Covid-19 detection
from X-Rays and CT image dataset. Our approach is thoroughly validated by measuring the
quality of uncertainty. It produces an equally good or better result and paves the way for the
future that addresses the practical problems at the intersection of deep learning and Bayesian
decision theory.
In conclusion, our study highlights the opportunities and challenges of the application of
estimated uncertainty in deep learning models of medical images, representing the confidence of the model’s prediction, and the uncertainty quality metrics show a significant improvement
when using Deep Ensembles Bayesian Neural Networks with DropWeights
The effect of organelle discovery upon sub-cellular protein localisation.
Prediction of protein sub-cellular localisation by employing quantitative mass spectrometry experiments is an expanding field. Several methods have led to the assignment of proteins to specific subcellular localisations by partial separation of organelles across a fractionation scheme coupled with computational analysis. Methods developed to analyse organelle data have largely employed supervised machine learning algorithms to map unannotated abundance profiles to known protein–organelle associations. Such approaches are likely to make association errors if organelle-related groupings present in experimental output are not included in data used to create a protein–organelle classifier. Currently, there is no automated way to detect organelle-specific clusters within such datasets. In order to address the above issues we adapted a phenotype discovery algorithm, originally created to filter image-based output for RNAi screens, to identify putative subcellular groupings in organelle proteomics experiments. We were able to mine datasets to a deeper level and extract interesting phenotype clusters for more comprehensive evaluation in an unbiased fashion upon application of this approach. Organelle-related protein clusters were identified beyond those sufficiently annotated for use as training data. Furthermore, we propose avenues for the incorporation of observations made into general practice for the classification of protein–organelle membership from quantitative MS experiments. Biological significance Protein sub-cellular localisation plays an important role in molecular interactions, signalling and transport mechanisms. The prediction of protein localisation by quantitative mass-spectrometry (MS) proteomics is a growing field and an important endeavour in improving protein annotation. Several such approaches use gradient-based separation of cellular organelle content to measure relative protein abundance across distinct gradient fractions. The distribution profiles are commonly mapped in silico to known protein–organelle associations via supervised machine learning algorithms, to create classifiers that associate unannotated proteins to specific organelles. These strategies are prone to error, however, if organelle-related groupings present in experimental output are not represented, for example owing to the lack of existing annotation, when creating the protein–organelle mapping. Here, the application of a phenotype discovery approach to LOPIT gradient-based MS data identifies candidate organelle phenotypes for further evaluation in an unbiased fashion. Software implementation and usage guidelines are provided for application to wider protein–organelle association experiments. In the wider context, semi-supervised organelle discovery is discussed as a paradigm with which to generate new protein annotations from MS-based organelle proteomics experiments. This article is part of a Special Issue entitled: New Horizons and Applications for Proteomics [EuPA 2012]
Single-cell Subcellular Protein Localisation Using Novel Ensembles of Diverse Deep Architectures
Unravelling protein distributions within individual cells is key to
understanding their function and state and indispensable to developing new
treatments. Here we present the Hybrid subCellular Protein Localiser (HCPL),
which learns from weakly labelled data to robustly localise single-cell
subcellular protein patterns. It comprises innovative DNN architectures
exploiting wavelet filters and learnt parametric activations that successfully
tackle drastic cell variability. HCPL features correlation-based ensembling of
novel architectures that boosts performance and aids generalisation.
Large-scale data annotation is made feasible by our "AI-trains-AI" approach,
which determines the visual integrity of cells and emphasises reliable labels
for efficient training. In the Human Protein Atlas context, we demonstrate that
HCPL defines state-of-the-art in the single-cell classification of protein
localisation patterns. To better understand the inner workings of HCPL and
assess its biological relevance, we analyse the contributions of each system
component and dissect the emergent features from which the localisation
predictions are derived
Accurate and highly interpretable prediction of gene expression from histone modifications
Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with several diseases, including cancer. HMs are, however, reversible modifications: understanding their role in disease would allow the design of 'epigenetic drugs' for specific, non-invasive treatments. Standard statistical techniques were not entirely successful in extracting representative features from raw HM signals over gene locations. On the other hand, deep learning approaches allow for effective automatic feature extraction, but at the expense of model interpretation
Empirical analysis of neural networks training optimisation
A Dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science in
Mathematical Statistics,School of Statistics and Actuarial Science.
October 2016.Neural networks (NNs) may be characterised by complex error functions with attributes such as saddle-points, local minima, even-spots and plateaus. This complicates the associated training process in terms of efficiency, convergence and accuracy given that it is done by minimising such complex error functions. This study empirically investigates the performance of two NNs training algorithms which are based on unconstrained and global optimisation theories, i.e. the Resilient propagation (Rprop) and the Conjugate Gradient with Polak-Ribière updates (CGP). It also shows how the network structure plays a role in the training optimisation of NNs. In this regard, various training scenarios are used to classify two protein data, i.e. the Escherichia coli and Yeast data. These training scenarios use varying numbers of hidden nodes and training iterations. The results show that Rprop outperforms CGP. Moreover, it appears that the performance of classifiers varies under various training scenarios.LG201
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