Timed and Probabilistic Automata for Automatic Animal Call Recognition

Automatic Call Recognition is vital for environmental monitoring. Patten recognition has been applied in automatic species recognition for years. However, few studies have applied formal syntactic methods to species call structure analysis. This paper introduces a novel method to adopt timed and probabilistic automata in automatic species recognition based upon acoustic components as the primitives. We demonstrate this through one kind of birds in Australia: Eastern Yellow Robin.

Automatic Audio Segmentation Using the Generalized Likelihood Ratio

This paper presents a novel technique for segmenting an audio stream into homogeneous regions according to speaker identities, background noise, music, environmental and channel conditions. Audio segmentation is useful in audio diarization systems, which aim to annotate an input audio stream with information that attributes temporal regions of the audio into their specific sources. The segmentation method introduced in this paper is performed using the Generalized Likelihood Ratio (GLR), computed between two adjacent sliding windows over preprocessed speech. This approach is inspired by the popular segmentation method proposed by the pioneering work of Chen and Gopalakrishnan, using the Bayesian Information Criterion (BIC) with an expanding search window. This paper will aim to identify and address the shortcomings associated with such an approach. The result obtained by the proposed segmentation strategy is evaluated on the 2002 Rich Transcription (RT-02) Evaluation dataset, and a miss rate of 19.47% and a false alarm rate of 16.94% is achieved at the optimal threshold.

Classification of the Johnson Space Center stratospheric dust collection

A review of 291 catalogued particles on the bases of particle size, shape, bulk chemistry, and texture is used to establish a reliable taxonomy. Extraterrestrial materials occur in three defined categories: spheres, aggregates and fragments. Approximately 76% of aggregates are of probable extraterrestrial origin, whereas spheres contain the smallest amount of extraterrestrial material (approx 43%). -B.M.

Supplementary Information : Hogan, Holland, Holloway, Petit and Read : Read Classification for Next Generation Sequencing, ESANN 2013, April 2013

This item provides supplementary materials for the paper mentioned in the title, specifically a range of organisms used in the study. The full abstract for the main paper is as follows: Next Generation Sequencing (NGS) technologies have revolutionised molecular biology, allowing clinical sequencing to become a matter of routine. NGS data sets consist of short sequence reads obtained from the machine, given context and meaning through downstream assembly and annotation. For these techniques to operate successfully, the collected reads must be consistent with the assumed species or species group, and not corrupted in some way. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans,with some strains exhibiting antibiotic resistance. In this paper, we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from alternative pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Using static analysis for automatic assessment and mitigation of unwanted and malicious activities within Android applications

In the last decade, smartphones have gained widespread usage. Since the advent of online application stores, hundreds of thousands of applications have become instantly available to millions of smart-phone users. Within the Android ecosystem, application security is governed by digital signatures and a list of coarse-grained permissions. However, this mechanism is not fine-grained enough to provide the user with a sufficient means of control of the applications' activities. Abuse of highly sensible private information such as phone numbers without users' notice is the result. We show that there is a high frequency of privacy leaks even among widely popular applications. Together with the fact that the majority of the users are not proficient in computer security, this presents a challenge to the engineers developing security solutions for the platform. Our contribution is twofold: first, we propose a service which is able to assess Android Market applications via static analysis and provide detailed, but readable reports to the user. Second, we describe a means to mitigate security and privacy threats by automated reverse-engineering and refactoring binary application packages according to the users' security preferences.

An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Classification of railway bridges based on criticality and vulnerability factors

Bridges are currently rated individually for maintenance and repair action according to the structural conditions of their elements. Dealing with thousands of bridges and the many factors that cause deterioration, makes this rating process extremely complicated. The current simplified but practical methods are not accurate enough. On the other hand, the sophisticated, more accurate methods are only used for a single or particular bridge type. It is therefore necessary to develop a practical and accurate rating system for a network of bridges. The first most important step in achieving this aim is to classify bridges based on the differences in nature and the unique characteristics of the critical factors and the relationship between them, for a network of bridges. Critical factors and vulnerable elements will be identified and placed in different categories. This classification method will be used to develop a new practical rating method for a network of railway bridges based on criticality and vulnerability analysis. This rating system will be more accurate and economical as well as improve the safety and serviceability of railway bridges.

Refinements and developments on the stratospheric dust database and classification scheme

Greater than 750 individual particles have now been selected from collection flags housed in the JSC Cosmic Dust Curatorial Facility and most have been documented in the Cosmic Dust Catalogs [1]. As increasing numbers of particles are placed in Cosmic Dust Collections, and a greater diversity of particles are introduced to the stratosphere through natural and man-made processes (e.g. decaying orbits of space debris [2]), there is an even greater need for a classification scheme to encompass all stratospheric particles rather than only extraterrestrial particles. The fundamental requirements for a suitable classification scheme have been outlined in earlier communications [3,4]. A quantitative survey of particles on collection flag W7017 indicates that there is some bias in the number of samples selected within a given category for the Cosmic Dust Catalog [5]. However, the sample diversity within this selection is still appropriate for the development of a reliable classification scheme. In this paper, we extend the earlier works on stratospheric particle classification to include particles collected during the period May 1981 to November 1983.

Effects of eco-driving instructions using a vehicle with automatic transmission on urban roads

Eco-driving instructions could reduce fuel consumption to up to 20% (EcoMove, 2010). Participants (N=13) drove an instrumented vehicle (i.e. Toyota Camry 2007) with an automatic transmission. Fuel consumption of the participants were compared before and after they received eco-driving instructions. Participants drove the same vehicle on the same urban route under similar traffic conditions. Results show that, on free flow sections of the track, all participants drove slightly faster (on average, 0.7 Km/h faster), during the lap for which they were instructed to drive in an eco-friendly manner as compared to when they were not given the eco-driving instruction. Suprisingly, eco-driving instructions increased the RPM significantly in most cases. Fuel consumption slightly decreased (6%) after the eco-driving instructions. We have found strong evidence showing that the fuel saving observed in our experiment (urban environment, automatic transmission) fall short of the 20% reduction claimed in other international trials.

Robust automatic speaker linking and attribution

This research makes a major contribution which enables efficient searching and indexing of large archives of spoken audio based on speaker identity. It introduces a novel technique dubbed as “speaker attribution” which is the task of automatically determining ‘who spoke when?’ in recordings and then automatically linking the unique speaker identities within each recording across multiple recordings. The outcome of the research will also have significant impact in improving the performance of automatic speech recognition systems through the extracted speaker identities.

Automatic query expansion : a structural linguistic perspective

A user’s query is considered to be an imprecise description of their information need. Automatic query expansion is the process of reformulating the original query with the goal of improving retrieval effectiveness. Many successful query expansion techniques ignore information about the dependencies that exist between words in natural language. However, more recent approaches have demonstrated that by explicitly modeling associations between terms significant improvements in retrieval effectiveness can be achieved over those that ignore these dependencies. State-of-the-art dependency-based approaches have been shown to primarily model syntagmatic associations. Syntagmatic associations infer a likelihood that two terms co-occur more often than by chance. However, structural linguistics relies on both syntagmatic and paradigmatic associations to deduce the meaning of a word. Given the success of dependency-based approaches and the reliance on word meanings in the query formulation process, we argue that modeling both syntagmatic and paradigmatic information in the query expansion process will improve retrieval effectiveness. This article develops and evaluates a new query expansion technique that is based on a formal, corpus-based model of word meaning that models syntagmatic and paradigmatic associations. We demonstrate that when sufficient statistical information exists, as in the case of longer queries, including paradigmatic information alone provides significant improvements in retrieval effectiveness across a wide variety of data sets. More generally, when our new query expansion approach is applied to large-scale web retrieval it demonstrates significant improvements in retrieval effectiveness over a strong baseline system, based on a commercial search engine.

Automatic object segmentation of unstructured scenes using colour and depth maps

This study presents a segmentation pipeline that fuses colour and depth information to automatically separate objects of interest in video sequences captured from a quadcopter. Many approaches assume that cameras are static with known position, a condition which cannot be preserved in most outdoor robotic applications. In this study, the authors compute depth information and camera positions from a monocular video sequence using structure from motion and use this information as an additional cue to colour for accurate segmentation. The authors model the problem similarly to standard segmentation routines as a Markov random field and perform the segmentation using graph cuts optimisation. Manual intervention is minimised and is only required to determine pixel seeds in the first frame which are then automatically reprojected into the remaining frames of the sequence. The authors also describe an automated method to adjust the relative weights for colour and depth according to their discriminative properties in each frame. Experimental results are presented for two video sequences captured using a quadcopter. The quality of the segmentation is compared to a ground truth and other state-of-the-art methods with consistently accurate results.

Read classification for next generation sequencing

Next Generation Sequencing (NGS) has revolutionised molec- ular biology, allowing routine clinical sequencing. NGS data consists of short sequence reads, given context through downstream assembly and annotation, a process requiring reads consistent with the assumed species or species group. The common bacterium Staphylococcus aureus may cause severe and life-threatening infections in humans, with some strains exhibiting antibiotic resistance. Here we apply an SVM classifier to the important problem of distinguishing S. aureus sequencing projects from other pathogens, including closely related Staphylococci. Using a sequence k-mer representation, we achieve precision and recall above 95%, implicating features with important functional associations.

Cardiomyopathy classification : ongoing debate in the genomics era

Cardiomyopathies represent a group of diseases of the myocardium of the heart and include diseases both primarily of the cardiac muscle and systemic diseases leading to adverse effects on the heart muscle size, shape, and function. Traditionally cardiomyopathies were defined according to phenotypical appearance. Now, as our understanding of the pathophysiology of the different entities classified under each of the different phenotypes improves and our knowledge of the molecular and genetic basis for these entities progresses, the traditional classifications seem oversimplistic and do not reflect current understanding of this myriad of diseases and disease processes. Although our knowledge of the exact basis of many of the disease processes of cardiomyopathies is still in its infancy, it is important to have a classification system that has the ability to incorporate the coming tide of molecular and genetic information. This paper discusses how the traditional classification of cardiomyopathies based on morphology has evolved due to rapid advances in our understanding of the genetic and molecular basis for many of these clinical entities.

Non-linear position control for hover and automatic landing of unmanned aerial vehicles

This study presents a disturbance attenuation controller for horizontal position stabilisation for hover and automatic landings of a rotary-wing unmanned aerial vehicle (RUAV) operating close to the landing deck in rough seas. Based on a helicopter model representing aerodynamics during the landing phase, a non-linear state feedback H∞ controller is designed to achieve rapid horizontal position tracking in a gusty environment. Practical constraints including flapping dynamics, servo dynamics and time lag effect are considered. A high-fidelity closed-loop simulation using parameters of the Vario XLC gas-turbine helicopter verifies performance of the proposed horizontal position controller. The proposed controller not only increases the disturbance attenuation capability of the RUAV, but also enables rapid position response when gusts occur. Comparative studies show that the H∞ controller exhibits performance improvement and can be applied to ship/RUAV landing systems.