Experiences with implementing common mathematical operations using field programmable gate arrays

Many computationally intensive scientific applications involve repetitive floating point operations other than addition and multiplication which may present a significant performance bottleneck due to the relatively large latency or low throughput involved in executing such arithmetic primitives on commod- ity processors. A promising alternative is to execute such primitives on Field Programmable Gate Array (FPGA) hardware acting as an application-specific custom co-processor in a high performance reconfig- urable computing platform. The use of FPGAs can provide advantages such as fine-grain parallelism but issues relating to code development in a hardware description language and efficient data transfer to and from the FPGA chip can present significant application development challenges. In this paper, we discuss our practical experiences in developing a selection of floating point hardware designs to be implemented using FPGAs. Our designs include some basic mathemati cal library functions which can be implemented for user defined precisions suitable for novel applications requiring non-standard floating point represen- tation. We discuss the details of our designs along with results from performance and accuracy analysis tests.

An examination of keystroke dynamics for continuous user authentication

Most current computer systems authorise the user at the start of a session and do not detect whether the current user is still the initial authorised user, a substitute user, or an intruder pretending to be a valid user. Therefore, a system that continuously checks the identity of the user throughout the session is necessary without being intrusive to end-user and/or effectively doing this. Such a system is called a continuous authentication system (CAS). Researchers have applied several approaches for CAS and most of these techniques are based on biometrics. These continuous biometric authentication systems (CBAS) are supplied by user traits and characteristics. One of the main types of biometric is keystroke dynamics which has been widely tried and accepted for providing continuous user authentication. Keystroke dynamics is appealing for many reasons. First, it is less obtrusive, since users will be typing on the computer keyboard anyway. Second, it does not require extra hardware. Finally, keystroke dynamics will be available after the authentication step at the start of the computer session. Currently, there is insufficient research in the CBAS with keystroke dynamics field. To date, most of the existing schemes ignore the continuous authentication scenarios which might affect their practicality in different real world applications. Also, the contemporary CBAS with keystroke dynamics approaches use characters sequences as features that are representative of user typing behavior but their selected features criteria do not guarantee features with strong statistical significance which may cause less accurate statistical user-representation. Furthermore, their selected features do not inherently incorporate user typing behavior. Finally, the existing CBAS that are based on keystroke dynamics are typically dependent on pre-defined user-typing models for continuous authentication. This dependency restricts the systems to authenticate only known users whose typing samples are modelled. This research addresses the previous limitations associated with the existing CBAS schemes by developing a generic model to better identify and understand the characteristics and requirements of each type of CBAS and continuous authentication scenario. Also, the research proposes four statistical-based feature selection techniques that have highest statistical significance and encompasses different user typing behaviors which represent user typing patterns effectively. Finally, the research proposes the user-independent threshold approach that is able to authenticate a user accurately without needing any predefined user typing model a-priori. Also, we enhance the technique to detect the impostor or intruder who may take over during the entire computer session.

Radiotherapy Monte Carlo simulation using cloud computing technology

Cloud computing allows for vast computational resources to be leveraged quickly and easily in bursts as and when required. Here we describe a technique that allows for Monte Carlo radiotherapy dose calculations to be performed using GEANT4 and executed in the cloud, with relative simulation cost and completion time evaluated as a function of machine count. As expected, simulation completion time decreases as 1=n for n parallel machines, and relative simulation cost is found to be optimal where n is a factor of the total simulation time in hours. Using the technique, we demonstrate the potential usefulness of cloud computing as a solution for rapid Monte Carlo simulation for radiotherapy dose calculation without the need for dedicated local computer hardware as a proof of principal. Funding source Cancer Australia (Department of Health and Ageing) Research Grant 614217

Solving tri-diagonal linear systems using field programmable gate arrays

In this paper, we present the outcomes of a project on the exploration of the use of Field Programmable Gate Arrays(FPGAs) as co-processors for scientific computation. We designed a custom circuit for the pipelined solving of multiple tri-diagonal linear systems. The design is well suited for applications that require many independent tri diagonal system solves, such as finite difference methods for solving PDEs or applications utilising cubic spline interpolation. The selected solver algorithm was the Tri Diagonal Matrix Algorithm (TDMA or Thomas Algorithm). Our solver supports user specified precision thought the use of a custom floating point VHDL library supporting addition, subtraction, multiplication and division. The variable precision TDMA solver was tested for correctness in simulation mode. The TDMA pipeline was tested successfully in hardware using a simplified solver model. The details of implementation, the limitations, and future work are also discussed.

BabelFuse data fusion unit with precision wireless clock synchronisation

A significant issue encountered when fusing data received from multiple sensors is the accuracy of the timestamp associated with each piece of data. This is particularly important in applications such as Simultaneous Localisation and Mapping (SLAM) where vehicle velocity forms an important part of the mapping algorithms; on fastmoving vehicles, even millisecond inconsistencies in data timestamping can produce errors which need to be compensated for. The timestamping problem is compounded in a robot swarm environment due to the use of non-deterministic readily-available hardware (such as 802.11-based wireless) and inaccurate clock synchronisation protocols (such as Network Time Protocol (NTP)). As a result, the synchronisation of the clocks between robots can be out by tens-to-hundreds of milliseconds making correlation of data difficult and preventing the possibility of the units performing synchronised actions such as triggering cameras or intricate swarm manoeuvres. In this thesis, a complete data fusion unit is designed, implemented and tested. The unit, named BabelFuse, is able to accept sensor data from a number of low-speed communication buses (such as RS232, RS485 and CAN Bus) and also timestamp events that occur on General Purpose Input/Output (GPIO) pins referencing a submillisecondaccurate wirelessly-distributed "global" clock signal. In addition to its timestamping capabilities, it can also be used to trigger an attached camera at a predefined start time and frame rate. This functionality enables the creation of a wirelessly-synchronised distributed image acquisition system over a large geographic area; a real world application for this functionality is the creation of a platform to facilitate wirelessly-distributed 3D stereoscopic vision. A ‘best-practice’ design methodology is adopted within the project to ensure the final system operates according to its requirements. Initially, requirements are generated from which a high-level architecture is distilled. This architecture is then converted into a hardware specification and low-level design, which is then manufactured. The manufactured hardware is then verified to ensure it operates as designed and firmware and Linux Operating System (OS) drivers are written to provide the features and connectivity required of the system. Finally, integration testing is performed to ensure the unit functions as per its requirements. The BabelFuse System comprises of a single Grand Master unit which is responsible for maintaining the absolute value of the "global" clock. Slave nodes then determine their local clock o.set from that of the Grand Master via synchronisation events which occur multiple times per-second. The mechanism used for synchronising the clocks between the boards wirelessly makes use of specific hardware and a firmware protocol based on elements of the IEEE-1588 Precision Time Protocol (PTP). With the key requirement of the system being submillisecond-accurate clock synchronisation (as a basis for timestamping and camera triggering), automated testing is carried out to monitor the o.sets between each Slave and the Grand Master over time. A common strobe pulse is also sent to each unit for timestamping; the correlation between the timestamps of the di.erent units is used to validate the clock o.set results. Analysis of the automated test results show that the BabelFuse units are almost threemagnitudes more accurate than their requirement; clocks of the Slave and Grand Master units do not di.er by more than three microseconds over a running time of six hours and the mean clock o.set of Slaves to the Grand Master is less-than one microsecond. The common strobe pulse used to verify the clock o.set data yields a positive result with a maximum variation between units of less-than two microseconds and a mean value of less-than one microsecond. The camera triggering functionality is verified by connecting the trigger pulse output of each board to a four-channel digital oscilloscope and setting each unit to output a 100Hz periodic pulse with a common start time. The resulting waveform shows a maximum variation between the rising-edges of the pulses of approximately 39¥ìs, well below its target of 1ms.

Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

An extension to the rank constraint for improving the reliability of stereo matching algorithms using the rank transform

The rank transform is one non-parametric transform which has been applied to the stereo matching problem The advantages of this transform include its invariance to radio metric distortion and its amenability to hardware implementation. This paper describes the derivation of the rank constraint for matching using the rank transform Previous work has shown that this constraint was capable of resolving ambiguous matches thereby improving match reliability A new matching algorithm incorporating this constraint was also proposed. This paper extends on this previous work by proposing a matching algorithm which uses a dimensional match surface in which the match score is computed for every possible template and match window combination. The principal advantage of this algorithm is that the use of the match surface enforces the left�right consistency and uniqueness constraints thus improving the algorithms ability to remove invalid matches Experimental results for a number of test stereo pairs show that the new algorithm is capable of identifying and removing a large number of in incorrect matches particularly in the case of occlusions

Fast and robust stereo matching algorithms for mining automation

The mining environment, being complex, irregular, and time-varying, presents a challenging prospect for stereo vision. For this application, speed, reliability, and the ability to produce a dense depth map are of foremost importance. This paper evaluates a number of matching techniques for possible use in a stereo vision sensor for mining automation applications. Area-based techniques have been investigated because they have the potential to yield dense maps, are amenable to fast hardware implementation, and are suited to textured scenes. In addition, two nonparametric transforms, namely, rank and census, have been investigated. Matching algorithms using these transforms were found to have a number of clear advantages, including reliability in the presence of radiometric distortion, low computational complexity, and amenability to hardware implementation.

Fast and robust stereo matching algorithms for mining automation

The mining environment, being complex, irregular and time varying, presents a challenging prospect for stereo vision. The objective is to produce a stereo vision sensor suited to close-range scenes consisting primarily of rocks. This sensor should be able to produce a dense depth map within real-time constraints. Speed and robustness are of foremost importance for this investigation. A number of area based matching metrics have been implemented, including the SAD, SSD, NCC, and their zero-meaned versions. The NCC and the zero meaned SAD and SSD were found to produce the disparity maps with the highest proportion of valid matches. The plain SAD and SSD were the least computationally expensive, due to all their operations taking place in integer arithmetic, however, they were extremely sensitive to radiometric distortion. Non-parametric techniques for matching, in particular, the rank and the census transform, have also been investigated. The rank and census transforms were found to be robust with respect to radiometric distortion, as well as being able to produce disparity maps with a high proportion of valid matches. An additional advantage of both the rank and the census transform is their amenability to fast hardware implementation.

A generic implementation framework for stereo matching algorithms

Traditional area-based matching techniques make use of similarity metrics such as the Sum of Absolute Differences(SAD), Sum of Squared Differences (SSD) and Normalised Cross Correlation (NCC). Non-parametric matching algorithms such as the rank and census rely on the relative ordering of pixel values rather than the pixels themselves as a similarity measure. Both traditional area-based and non-parametric stereo matching techniques have an algorithmic structure which is amenable to fast hardware realisation. This investigation undertakes a performance assessment of these two families of algorithms for robustness to radiometric distortion and random noise. A generic implementation framework is presented for the stereo matching problem and the relative hardware requirements for the various metrics investigated.

Fast and robust stereo matching algorithms for mining automation

The mining environment, being complex, irregular and time varying, presents a challenging prospect for stereo vision. For this application, speed, reliability, and the ability to produce a dense depth map are of foremost importance. This paper evaluates a number of matching techniques for possible use in a stereo vision sensor for mining automation applications. Area-based techniques have been investigated because they have the potential to yield dense maps, are amenable to fast hardware implementation, and are suited to textured scenes. In addition, two non-parametric transforms, namely, the rank and census, have been investigated. Matching algorithms using these transforms were found to have a number of clear advantages, including reliability in the presence of radiometric distortion, low computational complexity, and amenability to hardware implementation.

Frame-rate stereopsis using non-parametric transforms and programmable logic

A frame-rate stereo vision system, based on non-parametric matching metrics, is described. Traditional metrics, such as normalized cross-correlation, are expensive in terms of logic. Non-parametric measures require only simple, parallelizable, functions such as comparators, counters and exclusive-or, and are thus very well suited to implementation in reprogrammable logic.

Estimating the probability of an invalid match for matching using the rank transform

A fundamental problem faced by stereo matching algorithms is the matching or correspondence problem. A wide range of algorithms have been proposed for the correspondence problem. For all matching algorithms, it would be useful to be able to compute a measure of the probability of correctness, or reliability of a match. This paper focuses in particular on one class for matching algorithms, which are based on the rank transform. The interest in these algorithms for stereo matching stems from their invariance to radiometric distortion, and their amenability to fast hardware implementation. This work differs from previous work in that it derives, from first principles, an expression for the probability of a correct match. This method was based on an enumeration of all possible symbols for matching. The theoretical results for disparity error prediction, obtained using this method, were found to agree well with experimental results. However, disadvantages of the technique developed in this chapter are that it is not easily applicable to real images, and also that it is too computationally expensive for practical window sizes. Nevertheless, the exercise provides an interesting and novel analysis of match reliability.

Solving tri-diagonal linear systems using field programmable gate arrays

In this paper, we present the outcomes of a project on the exploration of the use of Field Programmable Gate Arrays (FPGAs) as co-processors for scientific computation. We designed a custom circuit for the pipelined solving of multiple tri-diagonal linear systems. The design is well suited for applications that require many independent tri-diagonal system solves, such as finite difference methods for solving PDEs or applications utilising cubic spline interpolation. The selected solver algorithm was the Tri-Diagonal Matrix Algorithm (TDMA or Thomas Algorithm). Our solver supports user specified precision thought the use of a custom floating point VHDL library supporting addition, subtraction, multiplication and division. The variable precision TDMA solver was tested for correctness in simulation mode. The TDMA pipeline was tested successfully in hardware using a simplified solver model. The details of implementation, the limitations, and future work are also discussed.

Ironmongeries life cycle costing and quality satisfaction

Most commonly, residents are always arguing about the satisfaction of sustainability and quality of their high rise residential property. This paper aim is to maintain the best quality satisfaction of the door hardware by introducing the whole life cycle costing approach to the property manager of the public housing in Johor. This paper looks into the current situation of ironmongeries (door hardware) of 2 public housings in Johor, Malaysia and testing the whole life cycle costing approach towards them. The calculation and the literature review are conducted. The questionnaire surveys of 2 public housings were conducted to make clear the occupants’ evaluation about the actual quality conditions of the ironmongeries in their house. As a result, the quality of door hardware based on the whole life cycle costing approach is one of the best among their previous decision making tool that have been applied. Practitioners can benefit from this paper as it provides information on calculating the whole life costing and making the decisions about ironmongeries selection of their properties.