PySSM : a Python module for Bayesian inference of linear Gaussian state space models

PySSM is a Python package that has been developed for the analysis of time series using linear Gaussian state space models (SSM). PySSM is easy to use; models can be set up quickly and efficiently and a variety of different settings are available to the user. It also takes advantage of scientific libraries Numpy and Scipy and other high level features of the Python language. PySSM is also used as a platform for interfacing between optimised and parallelised Fortran routines. These Fortran routines heavily utilise Basic Linear Algebra (BLAS) and Linear Algebra Package (LAPACK) functions for maximum performance. PySSM contains classes for filtering, classical smoothing as well as simulation smoothing.

A high sensitive fiber Bragg grating strain sensor with automatic temperature compensation

A high sensitive fiber Bragg grating (FBG) strain sensor with automatic temperature compensation is demonstrated. FBG is axially linked with a stick and their free ends are fixed to the measured object. When the measured strain changes, the stick does not change in length, but the FBG does. When the temperature changes, the stick changes in length to pull the FBG to realize temperature compensation. In experiments, 1.45 times strain sensitivity of bare FBG with temperature compensation of less than 0.1 nm Bragg wavelength drift over 100 ◦C shift is achieved.

Towards semantic search and inference in electronic medical records : an approach using concept-based information retrieval

Background This paper presents a novel approach to searching electronic medical records that is based on concept matching rather than keyword matching. Aim The concept-based approach is intended to overcome specific challenges we identified in searching medical records. Method Queries and documents were transformed from their term-based originals into medical concepts as defined by the SNOMED-CT ontology. Results Evaluation on a real-world collection of medical records showed our concept-based approach outperformed a keyword baseline by 25% in Mean Average Precision. Conclusion The concept-based approach provides a framework for further development of inference based search systems for dealing with medical data.

Abatement of energy loss by insulating system and designing automatic water heater

The most suitable temperature range for domestic purposes is about 200C to 260C .Besides, both cold and hot water appear to be essential frequently for industrial purposes. In summer bringing down the water temperature at a comfortable range causes significant energy consumption. This project aims at saving energy to control water temperature by making water tank insulated .Therefore applying better insulation system which would reduce the disparity between the desired temperature and the actual temperature and hence saving energy significantly. Following the investigation, this project used cotton jacket to insulate the tank and the tank was placed under a paddy straw shade with a view to attaining the maximum energy saving. Finally, it has been found that reduction in energy consumption is to be about 50-60% which is quite satisfactory. Since comfortable temperature range varies from person to person this project thus combines insulating effect with automatic water heater.

Automatic region-of-interest detection and prioritisation for visually optimised coding of low bit rate videos

The increasing popularity of video consumption from mobile devices requires an effective video coding strategy. To overcome diverse communication networks, video services often need to maintain sustainable quality when the available bandwidth is limited. One of the strategy for a visually-optimised video adaptation is by implementing a region-of-interest (ROI) based scalability, whereby important regions can be encoded at a higher quality while maintaining sufficient quality for the rest of the frame. The result is an improved perceived quality at the same bit rate as normal encoding, which is particularly obvious at the range of lower bit rate. However, because of the difficulties of predicting region-of-interest (ROI) accurately, there is a limited research and development of ROI-based video coding for general videos. In this paper, the phase spectrum quaternion of Fourier Transform (PQFT) method is adopted to determine the ROI. To improve the results of ROI detection, the saliency map from the PQFT is augmented with maps created from high level knowledge of factors that are known to attract human attention. Hence, maps that locate faces and emphasise the centre of the screen are used in combination with the saliency map to determine the ROI. The contribution of this paper lies on the automatic ROI detection technique for coding a low bit rate videos which include the ROI prioritisation technique to give different level of encoding qualities for multiple ROIs, and the evaluation of the proposed automatic ROI detection that is shown to have a close performance to human ROI, based on the eye fixation data.

Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

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.

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.

Likelihood‐free inference for transmission rates of nosocomial pathogens

This chapter contains sections titled: Introduction Case study: Estimating transmission rates of nosocomial pathogens Models and methods Data analysis and results Discussion References

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.

Exact and approximate Bayesian inference for low count time series models with intractable likelihoods

In this paper we present a new simulation methodology in order to obtain exact or approximate Bayesian inference for models for low-valued count time series data that have computationally demanding likelihood functions. The algorithm fits within the framework of particle Markov chain Monte Carlo (PMCMC) methods. The particle filter requires only model simulations and, in this regard, our approach has connections with approximate Bayesian computation (ABC). However, an advantage of using the PMCMC approach in this setting is that simulated data can be matched with data observed one-at-a-time, rather than attempting to match on the full dataset simultaneously or on a low-dimensional non-sufficient summary statistic, which is common practice in ABC. For low-valued count time series data we find that it is often computationally feasible to match simulated data with observed data exactly. Our particle filter maintains $N$ particles by repeating the simulation until $N+1$ exact matches are obtained. Our algorithm creates an unbiased estimate of the likelihood, resulting in exact posterior inferences when included in an MCMC algorithm. In cases where exact matching is computationally prohibitive, a tolerance is introduced as per ABC. A novel aspect of our approach is that we introduce auxiliary variables into our particle filter so that partially observed and/or non-Markovian models can be accommodated. We demonstrate that Bayesian model choice problems can be easily handled in this framework.

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.