Do androids dream of electric chimera?

This paper describes the use of the Chimera Architecture as the basis for a generative rhythmic improvisation system that is intended for use in ensemble contexts. This interactive soft- ware system learns in real time based on an audio input from live performers. The paper describes the components of the Chimera Architecture including a novel analysis engine that uses prediction to robustly assess the rhythmic salience of the input stream. Analytical results are stored in a hierarchical structure that includes multiple scenarios which allow ab- stracted and alternate interpretations of the current metrical context. The system draws upon this Chimera Architecture when generating a musical response. The generated rhythms are intended to have a particular ambiguity in relation to the music performance by other members of the ensemble. Ambi- guity is controlled through alternate interpretations of the Chimera. We describe an implementation of the Chimera Ar- chitecture that focuses on rhythmic material, and present and discuss initial experimental results of the software system playing along with recordings of a live performance.

The educational affordances of generative media in arts education

Network Jamming systems provide real-time collaborative media performance experiences for novice or inexperienced users. In this paper we will outline the theoretical and developmental drivers for our Network Jamming software, called jam2jam. jam2jam employs generative algorithmic techniques with particular implications for accessibility and learning. We will describe how theories of engagement have directed the design and development of jam2jam and show how iterative testing cycles in numerous international sites have informed the evolution of the system and its educational potential. Generative media systems present an opportunity for users to leverage computational systems to make sense of complex media forms through interactive and collaborative experiences. Generative music and art are a relatively new phenomenon that use procedural invention as a creative technique to produce music and visual media. These kinds of systems present a range of affordances that can facilitate new kinds of relationships with music and media performance and production. Early systems have demonstrated the potential to provide access to collaborative ensemble experiences to users with little formal musical or artistic expertise.This presentation examines the educational affordances of these systems evidenced by field data drawn from the Network Jamming Project. These generative performance systems enable access to a unique kind of music/media’ ensemble performance with very little musical/ media knowledge or skill and they further offer the possibility of unique interactive relationships with artists and creative knowledge through collaborative performance. Through the process of observing, documenting and analysing young people interacting with the generative media software jam2jam a theory of meaningful engagement has emerged from the need to describe and codify how users experience creative engagement with music/media performance and the locations of meaning. In this research we observed that the musical metaphors and practices of ‘ensemble’ or collaborative performance and improvisation as a creative process for experienced musicians can be made available to novice users. The relational meanings of these musical practices afford access to high level personal, social and cultural experiences. Within the creative process of collaborative improvisation lie a series of modes of creative engagement that move from appreciation through exploration, selection, direction toward embodiment. The expressive sounds and visions made in real-time by improvisers collaborating are immediate and compelling. Generative media systems let novices access these experiences with simple interfaces that allow them to make highly professional and expressive sonic and visual content simply by using gestures and being attentive and perceptive to their collaborators. These kinds of experiences present the potential for highly complex expressive interactions with sound and media as a performance. Evidence that has emerged from this research suggest that collaborative performance with generative media is transformative and meaningful. In this presentation we draw out these ideas around an emerging theory of meaningful engagement that has evolved from the development of network jamming software. Primarily we focus on demonstrating how these experiences might lead to understandings that may be of educational and social benefit.

Network jamming : distributed performance using generative music

Generative music systems can be performed by manipulating the values of their algorithmic parameters, and their semi-autonomous nature provides an opportunity for coordinated interaction amongst a network of systems, a practice we call Network Jamming. This paper outlines the characteristics of this networked performance practice and discusses the types of mediated musical relationships and ensemble configurations that can arise. We have developed and tested the jam2jam network jamming software over recent years. We describe this system, draw from our experiences with it, and use it to illustrate some characteristics of Network Jamming.

An analysis of the RC4 family of stream ciphers against algebraic attacks

To date, most applications of algebraic analysis and attacks on stream ciphers are on those based on lin- ear feedback shift registers (LFSRs). In this paper, we extend algebraic analysis to non-LFSR based stream ciphers. Specifically, we perform an algebraic analysis on the RC4 family of stream ciphers, an example of stream ciphers based on dynamic tables, and inves- tigate its implications to potential algebraic attacks on the cipher. This is, to our knowledge, the first pa- per that evaluates the security of RC4 against alge- braic attacks through providing a full set of equations that describe the complex word manipulations in the system. For an arbitrary word size, we derive alge- braic representations for the three main operations used in RC4, namely state extraction, word addition and state permutation. Equations relating the inter- nal states and keystream of RC4 are then obtained from each component of the cipher based on these al- gebraic representations, and analysed in terms of their contributions to the security of RC4 against algebraic attacks. Interestingly, it is shown that each of the three main operations contained in the components has its own unique algebraic properties, and when their respective equations are combined, the resulting system becomes infeasible to solve. This results in a high level of security being achieved by RC4 against algebraic attacks. On the other hand, the removal of an operation from the cipher could compromise this security. Experiments on reduced versions of RC4 have been performed, which confirms the validity of our algebraic analysis and the conclusion that the full RC4 stream cipher seems to be immune to algebraic attacks at present.

Analysis of linear relationships in block ciphers

This thesis is devoted to the study of linear relationships in symmetric block ciphers. A block cipher is designed so that the ciphertext is produced as a nonlinear function of the plaintext and secret master key. However, linear relationships within the cipher can still exist if the texts and components of the cipher are manipulated in a number of ways, as shown in this thesis. There are four main contributions of this thesis. The first contribution is the extension of the applicability of integral attacks from word-based to bitbased block ciphers. Integral attacks exploit the linear relationship between texts at intermediate stages of encryption. This relationship can be used to recover subkey bits in a key recovery attack. In principle, integral attacks can be applied to bit-based block ciphers. However, specific tools to define the attack on these ciphers are not available. This problem is addressed in this thesis by introducing a refined set of notations to describe the attack. The bit patternbased integral attack is successfully demonstrated on reduced-round variants of the block ciphers Noekeon, Present and Serpent. The second contribution is the discovery of a very small system of equations that describe the LEX-AES stream cipher. LEX-AES is based heavily on the 128-bit-key (16-byte) Advanced Encryption Standard (AES) block cipher. In one instance, the system contains 21 equations and 17 unknown bytes. This is very close to the upper limit for an exhaustive key search, which is 16 bytes. One only needs to acquire 36 bytes of keystream to generate the equations. Therefore, the security of this cipher depends on the difficulty of solving this small system of equations. The third contribution is the proposal of an alternative method to measure diffusion in the linear transformation of Substitution-Permutation-Network (SPN) block ciphers. Currently, the branch number is widely used for this purpose. It is useful for estimating the possible success of differential and linear attacks on a particular SPN cipher. However, the measure does not give information on the number of input bits that are left unchanged by the transformation when producing the output bits. The new measure introduced in this thesis is intended to complement the current branch number technique. The measure is based on fixed points and simple linear relationships between the input and output words of the linear transformation. The measure represents the average fraction of input words to a linear diffusion transformation that are not effectively changed by the transformation. This measure is applied to the block ciphers AES, ARIA, Serpent and Present. It is shown that except for Serpent, the linear transformations used in the block ciphers examined do not behave as expected for a random linear transformation. The fourth contribution is the identification of linear paths in the nonlinear round function of the SMS4 block cipher. The SMS4 block cipher is used as a standard in the Chinese Wireless LAN Wired Authentication and Privacy Infrastructure (WAPI) and hence, the round function should exhibit a high level of nonlinearity. However, the findings in this thesis on the existence of linear relationships show that this is not the case. It is shown that in some exceptional cases, the first four rounds of SMS4 are effectively linear. In these cases, the effective number of rounds for SMS4 is reduced by four, from 32 to 28. The findings raise questions about the security provided by SMS4, and might provide clues on the existence of a flaw in the design of the cipher.

Developing a theatre of the integrated actor : the application of the Suzuki actor training method within three theatrical contexts

This research project examines the application of the Suzuki Actor Training Method (the Suzuki Method) within the work ofTadashi Suzuki's company in Japan, the Shizuoka Performing Arts Complex (SPAC), within the work of Brisbane theatre company Frank:Austral Asian Performance Ensemble (Frank:AAPE), and as related to the development of the theatre performance Surfacing. These three theatrical contexts have been studied from the viewpoint of a "participant- observer". The researcher has trained in the Suzuki Method with Frank:AAPE and SP AC, performed with Frank:AAPE, and was the solo performer and collaborative developer in the performance Surfacing (directed by Leah Mercer). Observations of these three groups are based on a phenomenological definition of the "integrated actor", an actor who is able to achieve a totality or unity between the body and the mind, and between the body and the voice, through a powerful sense of intention. The term "integrated actor" has been informed by the philosophy of Merleau-Ponty and his concept of the "lived body". Three main hypotheses are presented in this study: that the Suzuki Method focuses on actors learning through their body; that the Suzuki Method presents an holistic approach to the body and the voice; and that the Suzuki Method develops actors with a strong sense of intention. These three aspects of the Suzuki Method are explored in relation to the stylistic features of the work of SPAC, Frank:AAPE and the performance Surfacing.

Unsupervised alignment of thousands of images

The task addressed in this thesis is the automatic alignment of an ensemble of misaligned images in an unsupervised manner. This application is especially useful in computer vision applications where annotations of the shape of an object of interest present in a collection of images is required. Performing this task manually is a slow, tedious, expensive and error prone process which hinders the progress of research laboratories and businesses. Most recently, the unsupervised removal of geometric variation present in a collection of images has been referred to as congealing based on the seminal work of Learned-Miller [21]. The only assumption made in congealing is that the parametric nature of the misalignment is known a priori (e.g. translation, similarity, a�ne, etc) and that the object of interest is guaranteed to be present in each image. The capability to congeal an ensemble of misaligned images stemming from the same object class has numerous applications in object recognition, detection and tracking. This thesis concerns itself with the construction of a congealing algorithm titled, least-squares congealing, which is inspired by the well known image to image alignment algorithm developed by Lucas and Kanade [24]. The algorithm is shown to have superior performance characteristics when compared to previously established methods: canonical congealing by Learned-Miller [21] and stochastic congealing by Z�ollei [39].

Access to meaningful relationships through virtual instruments and ensembles

This workshop focuses upon research about the qualities of community in music and of music in community facilitated by technologically supported relationships. Generative media systems present an opportunity for users to leverage computational systems to form new relationships through interactive and collaborative experiences. Generative music and art are a relatively new phenomenon that use procedural invention as a creative technique to produce music and visual media. Early systems have demonstrated the potential to provide access to collaborative ensemble experiences for users with little formal musical or artistic expertise. This workshop examines the relational affordances of these systems evidenced by selected field data drawn from the Network Jamming Project. These generative performance systems enable access to unique ensembles with very little musical knowledge or skill and offer the possibility of interactive relationships with artists and musical knowledge through collaborative performance. In this workshop we will focus on data that highlights how these simulated experiences might lead to understandings that may be of social benefit. Conference participants will be invited to jam in real time using virtual interfaces and to evaluate purposively selected video artifacts that demonstrate different kinds of interactive relationship with artists, peers, and community and that enrich the sense of expressive self. Theoretical insights about meaningful engagement drawn from the longitudinal and cross cultural experiences will underpin the discussion and practical presentation.

Collaborative digital media performance with generative music systems

Music is inherently active and interactive. Like technologies before them, digital systems provide a range of enhanced music performance opportunities. In this paper we outline the educational advantages of ensemble performance in which generative media systems are integrated. As a concrete example, we focus on our work with the jam2jam system which uses generative music processes to enhance collaborative music making. We suggest that our research points toward a new class of activities that maintain the well established benefits of ensemble performance while adding cultural and pedagogical value by leveraging the capabilities and cachet of digital media practices.

Assembling dynamic repertoires of literate practices : teaching that makes a difference

This chapter considers how teachers can make a difference to the kinds of literacy young people take up. Increasingly, researchers and policy-makers see literacy as an ensemble of socio-cultural situated practices rather than as a unitary skill. Accordingly, the differences in what young people come to do with literacy, in and out of school, confront us more directly. If literacy development involves assembling dynamic repertoires of practices, it is crucial to consider what different groups of children growing up and going to school in different places have access to and make investments in over time; the kinds of literate communities from which some are excluded or included; and how educators make a difference to the kinds of literate trajectories and identities young people put together.

Boosting the margin: A new explanation for the effectiveness of voting methods

One of the surprising recurring phenomena observed in experiments with boosting is that the test error of the generated classifier usually does not increase as its size becomes very large, and often is observed to decrease even after the training error reaches zero. In this paper, we show that this phenomenon is related to the distribution of margins of the training examples with respect to the generated voting classification rule, where the margin of an example is simply the difference between the number of correct votes and the maximum number of votes received by any incorrect label. We show that techniques used in the analysis of Vapnik's support vector classifiers and of neural networks with small weights can be applied to voting methods to relate the margin distribution to the test error. We also show theoretically and experimentally that boosting is especially effective at increasing the margins of the training examples. Finally, we compare our explanation to those based on the bias-variance decomposition.

Least-squares congealing for large numbers of images

In this paper we pursue the task of aligning an ensemble of images in an unsupervised manner. This task has been commonly referred to as “congealing” in literature. A form of congealing, using a least-squares criteria, has been recently demonstrated to have desirable properties over conventional congealing. Least-squares congealing can be viewed as an extension of the Lucas & Kanade (LK)image alignment algorithm. It is well understood that the alignment performance for the LK algorithm, when aligning a single image with another, is theoretically and empirically equivalent for additive and compositional warps. In this paper we: (i) demonstrate that this equivalence does not hold for the extended case of congealing, (ii) characterize the inherent drawbacks associated with least-squares congealing when dealing with large numbers of images, and (iii) propose a novel method for circumventing these limitations through the application of an inverse-compositional strategy that maintains the attractive properties of the original method while being able to handle very large numbers of images.

Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.

A comparative study of algorithms for the flowshop scheduling problem

In this paper, we propose three meta-heuristic algorithms for the permutation flowshop (PFS) and the general flowshop (GFS) problems. Two different neighborhood structures are used for these two types of flowshop problem. For the PFS problem, an insertion neighborhood structure is used, while for the GFS problem, a critical-path neighborhood structure is adopted. To evaluate the performance of the proposed algorithms, two sets of problem instances are tested against the algorithms for both types of flowshop problems. The computational results show that the proposed meta-heuristic algorithms with insertion neighborhood for the PFS problem perform slightly better than the corresponding algorithms with critical-path neighborhood for the GFS problem. But in terms of computation time, the GFS algorithms are faster than the corresponding PFS algorithms.