The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem

<p>Abstract</p> <p>Background</p> <p>This paper discusses the problem of automated annotation. It is a continuation of the previous work on the A⁴-algorithm (Adaptive algorithm of automated annotation) developed by Leontovich and others.</p> <p>Results</p> <p>A number of new statistics for the automated annotation of biological sequences is introduced. All these statistics are based on the likelihood ratio criterion.</p> <p>Conclusion</p> <p>Some of the statistics yield a prediction quality that is significantly higher (up to 1.5 times higher) in comparison with the results obtained with the A⁴-procedure.</p

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach

Motivation: The use of liquid chromatography coupled to mass spectrometry (LC–MS) has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This paper looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.&lt;p&gt;&lt;/p&gt; Results: The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.&lt;p&gt;&lt;/p&gt; Availability: The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/

Joint segmentation and classification of retinal arteries/veins from fundus images

Objective Automatic artery/vein (A/V) segmentation from fundus images is required to track blood vessel changes occurring with many pathologies including retinopathy and cardiovascular pathologies. One of the clinical measures that quantifies vessel changes is the arterio-venous ratio (AVR) which represents the ratio between artery and vein diameters. This measure significantly depends on the accuracy of vessel segmentation and classification into arteries and veins. This paper proposes a fast, novel method for semantic A/V segmentation combining deep learning and graph propagation. Methods A convolutional neural network (CNN) is proposed to jointly segment and classify vessels into arteries and veins. The initial CNN labeling is propagated through a graph representation of the retinal vasculature, whose nodes are defined as the vessel branches and edges are weighted by the cost of linking pairs of branches. To efficiently propagate the labels, the graph is simplified into its minimum spanning tree. Results The method achieves an accuracy of 94.8% for vessels segmentation. The A/V classification achieves a specificity of 92.9% with a sensitivity of 93.7% on the CT-DRIVE database compared to the state-of-the-art-specificity and sensitivity, both of 91.7%. Conclusion The results show that our method outperforms the leading previous works on a public dataset for A/V classification and is by far the fastest. Significance The proposed global AVR calculated on the whole fundus image using our automatic A/V segmentation method can better track vessel changes associated to diabetic retinopathy than the standard local AVR calculated only around the optic disc.Comment: Preprint accepted in Artificial Intelligence in Medicin

Anomaly Detection, Rule Adaptation and Rule Induction Methodologies in the Context of Automated Sports Video Annotation.

Automated video annotation is a topic of considerable interest in computer vision due to its applications in video search, object based video encoding and enhanced broadcast content. The domain of sport broadcasting is, in particular, the subject of current research attention due to its fixed, rule governed, content. This research work aims to develop, analyze and demonstrate novel methodologies that can be useful in the context of adaptive and automated video annotation systems. In this thesis, we present methodologies for addressing the problems of anomaly detection, rule adaptation and rule induction for court based sports such as tennis and badminton. We first introduce an HMM induction strategy for a court-model based method that uses the court structure in the form of a lattice for two related modalities of singles and doubles tennis to tackle the problems of anomaly detection and rectification. We also introduce another anomaly detection methodology that is based on the disparity between the low-level vision based classifiers and the high-level contextual classifier. Another approach to address the problem of rule adaptation is also proposed that employs Convex hulling of the anomalous states. We also investigate a number of novel hierarchical HMM generating methods for stochastic induction of game rules. These methodologies include, Cartesian product Label-based Hierarchical Bottom-up Clustering (CLHBC) that employs prior information within the label structures. A new constrained variant of the classical Chinese Restaurant Process (CRP) is also introduced that is relevant to sports games. We also propose two hybrid methodologies in this context and a comparative analysis is made against the flat Markov model. We also show that these methods are also generalizable to other rule based environments

Committee-Based Sample Selection for Probabilistic Classifiers

In many real-world learning tasks, it is expensive to acquire a sufficient number of labeled examples for training. This paper investigates methods for reducing annotation cost by `sample selection'. In this approach, during training the learning program examines many unlabeled examples and selects for labeling only those that are most informative at each stage. This avoids redundantly labeling examples that contribute little new information. Our work follows on previous research on Query By Committee, extending the committee-based paradigm to the context of probabilistic classification. We describe a family of empirical methods for committee-based sample selection in probabilistic classification models, which evaluate the informativeness of an example by measuring the degree of disagreement between several model variants. These variants (the committee) are drawn randomly from a probability distribution conditioned by the training set labeled so far. The method was applied to the real-world natural language processing task of stochastic part-of-speech tagging. We find that all variants of the method achieve a significant reduction in annotation cost, although their computational efficiency differs. In particular, the simplest variant, a two member committee with no parameters to tune, gives excellent results. We also show that sample selection yields a significant reduction in the size of the model used by the tagger

All mixed up? Finding the optimal feature set for general readability prediction and its application to English and Dutch

Readability research has a long and rich tradition, but there has been too little focus on general readability prediction without targeting a specific audience or text genre. Moreover, though NLP-inspired research has focused on adding more complex readability features there is still no consensus on which features contribute most to the prediction. In this article, we investigate in close detail the feasibility of constructing a readability prediction system for English and Dutch generic text using supervised machine learning. Based on readability assessments by both experts and a crowd, we implement different types of text characteristics ranging from easy-to-compute superficial text characteristics to features requiring a deep linguistic processing, resulting in ten different feature groups. Both a regression and classification setup are investigated reflecting the two possible readability prediction tasks: scoring individual texts or comparing two texts. We show that going beyond correlation calculations for readability optimization using a wrapper-based genetic algorithm optimization approach is a promising task which provides considerable insights in which feature combinations contribute to the overall readability prediction. Since we also have gold standard information available for those features requiring deep processing we are able to investigate the true upper bound of our Dutch system. Interestingly, we will observe that the performance of our fully-automatic readability prediction pipeline is on par with the pipeline using golden deep syntactic and semantic information