A Spectrum of TCP-Friendly Window-Based Congestion Control Algorithms

The increased diversity of Internet application requirements has spurred recent interests in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The parameterization of these control rules is done so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. In this paper, we define a new spectrum of window-based congestion control algorithms that are TCP-friendly as well as TCP-compatible under RED. Contrary to previous memory-less controls, our algorithms utilize history information in their control rules. Our proposed algorithms have two salient features: (1) They enable a wider region of TCP-friendliness, and thus more flexibility in trading off among smoothness, aggressiveness, and responsiveness; and (2) they ensure a faster convergence to fairness under a wide range of system conditions. We demonstrate analytically and through extensive ns simulations the steady-state and transient behaviors of several instances of this new spectrum of algorithms. In particular, SIMD is one instance in which the congestion window is increased super-linearly with time since the detection of the last loss. Compared to recently proposed TCP-friendly AIMD and binomial algorithms, we demonstrate the superiority of SIMD in: (1) adapting to sudden increases in available bandwidth, while maintaining competitive smoothness and responsiveness; and (2) rapidly converging to fairness and efficiency.

A Spectrum of TCP-friendly Window-Based Congestion Control Algorithms

The increasing diversity of Internet application requirements has spurred recent interest in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The control rules are parameterized so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. This paper presents a comprehensive study of a new spectrum of window-based congestion controls, which are TCP-friendly as well as TCP-compatible under RED. Our controls utilize history information in their control rules. By doing so, they improve the transient behavior, compared to recently proposed slowly-responsive congestion controls such as general AIMD and binomial controls. Our controls can achieve better tradeoffs among smoothness, aggressiveness, and responsiveness, and they can achieve faster convergence. We demonstrate analytically and through extensive ns simulations the steady-state and transient behavior of several instances of this new spectrum.

Popularity-Aware GreedyDual-Size Web Proxy Caching Algorithms

Web caching aims to reduce network traffic, server load, and user-perceived retrieval delays by replicating "popular" content on proxy caches that are strategically placed within the network. While key to effective cache utilization, popularity information (e.g. relative access frequencies of objects requested through a proxy) is seldom incorporated directly in cache replacement algorithms. Rather, other properties of the request stream (e.g. temporal locality and content size), which are easier to capture in an on-line fashion, are used to indirectly infer popularity information, and hence drive cache replacement policies. Recent studies suggest that the correlation between these secondary properties and popularity is weakening due in part to the prevalence of efficient client and proxy caches (which tend to mask these correlations). This trend points to the need for proxy cache replacement algorithms that directly capture and use popularity information. In this paper, we (1) present an on-line algorithm that effectively captures and maintains an accurate popularity profile of Web objects requested through a caching proxy, (2) propose a novel cache replacement policy that uses such information to generalize the well-known GreedyDual-Size algorithm, and (3) show the superiority of our proposed algorithm by comparing it to a host of recently-proposed and widely-used algorithms using extensive trace-driven simulations and a variety of performance metrics.

Some Considerations on a Calculus with Weak References

Weak references are references that do not prevent the object they point to from being garbage collected. Most realistic languages, including Java, SML/NJ, and OCaml to name a few, have some facility for programming with weak references. Weak references are used in implementing idioms like memoizing functions and hash-consing in order to avoid potential memory leaks. However, the semantics of weak references in many languages are not clearly specified. Without a formal semantics for weak references it becomes impossible to prove the correctness of implementations making use of this feature. Previous work by Hallett and Kfoury extends λgc, a language for modeling garbage collection, to λweak, a similar language with weak references. Using this previously formalized semantics for weak references, we consider two issues related to well-behavedness of programs. Firstly, we provide a new, simpler proof of the well-behavedness of the syntactically restricted fragment of λweak defined previously. Secondly, we give a natural semantic criterion for well-behavedness much broader than the syntactic restriction, which is useful as principle for programming with weak references. Furthermore we extend the result, proved in previously of λgc, which allows one to use type-inference to collect some reachable objects that are never used. We prove that this result holds of our language, and we extend this result to allow the collection of weakly-referenced reachable garbage without incurring the computational overhead sometimes associated with collecting weak bindings (e.g. the need to recompute a memoized function). Lastly we use extend the semantic framework to model the key/value weak references found in Haskell and we prove the Haskell is semantics equivalent to a simpler semantics due to the lack of side-effects in our language.

Towards Formalizing Java's Weak References

Weak references provide the programmer with limited control over the process of memory management. By using them, a programmer can make decisions based on previous actions that are taken by the garbage collector. Although this is often helpful, the outcome of a program using weak references is less predictable due to the nondeterminism they introduce in program evaluation. It is therefore desirable to have a framework of formal tools to reason about weak references and programs that use them. We present several calculi that formalize various aspects of weak references, inspired by their implementation in Java. We provide a calculus to model multiple levels of non-strong references, where a different garbage collection policy is applied to each level. We consider different collection policies such as eager collection and lazy collection. Similar to the way they are implemented in Java, we give the semantics of eager collection to weak references and the semantics of lazy collection to soft references. Moreover, we condition garbage collection on the availability of time and space resources. While time constraints are used in order to restrict garbage collection, space constraints are used in order to trigger it. Finalizers are a problematic feature in Java, especially when they interact with weak references. We provide a calculus to model finalizer evaluation. Since finalizers have little meaning in a language without side-effect, we introduce a limited form of side effect into the calculus. We discuss determinism and the separate notion of uniqueness of (evaluation) outcome. We show that in our calculus, finalizer evaluation does not affect uniqueness of outcome.

Construction of Neural Network Classification Expert Systems Using Switching Theory Algorithms

A new family of neural network architectures is presented. This family of architectures solves the problem of constructing and training minimal neural network classification expert systems by using switching theory. The primary insight that leads to the use of switching theory is that the problem of minimizing the number of rules and the number of IF statements (antecedents) per rule in a neural network expert system can be recast into the problem of minimizing the number of digital gates and the number of connections between digital gates in a Very Large Scale Integrated (VLSI) circuit. The rules that the neural network generates to perform a task are readily extractable from the network's weights and topology. Analysis and simulations on the Mushroom database illustrate the system's performance.

Combining and choosing case base maintenance algorithms

Case-Based Reasoning (CBR) uses past experiences to solve new problems. The quality of the past experiences, which are stored as cases in a case base, is a big factor in the performance of a CBR system. The system's competence may be improved by adding problems to the case base after they have been solved and their solutions verified to be correct. However, from time to time, the case base may have to be refined to reduce redundancy and to get rid of any noisy cases that may have been introduced. Many case base maintenance algorithms have been developed to delete noisy and redundant cases. However, different algorithms work well in different situations and it may be difficult for a knowledge engineer to know which one is the best to use for a particular case base. In this thesis, we investigate ways to combine algorithms to produce better deletion decisions than the decisions made by individual algorithms, and ways to choose which algorithm is best for a given case base at a given time. We analyse five of the most commonly-used maintenance algorithms in detail and show how the different algorithms perform better on different datasets. This motivates us to develop a new approach: maintenance by a committee of experts (MACE). MACE allows us to combine maintenance algorithms to produce a composite algorithm which exploits the merits of each of the algorithms that it contains. By combining different algorithms in different ways we can also define algorithms that have different trade-offs between accuracy and deletion. While MACE allows us to define an infinite number of new composite algorithms, we still face the problem of choosing which algorithm to use. To make this choice, we need to be able to identify properties of a case base that are predictive of which maintenance algorithm is best. We examine a number of measures of dataset complexity for this purpose. These provide a numerical way to describe a case base at a given time. We use the numerical description to develop a meta-case-based classification system. This system uses previous experience about which maintenance algorithm was best to use for other case bases to predict which algorithm to use for a new case base. Finally, we give the knowledge engineer more control over the deletion process by creating incremental versions of the maintenance algorithms. These incremental algorithms suggest one case at a time for deletion rather than a group of cases, which allows the knowledge engineer to decide whether or not each case in turn should be deleted or kept. We also develop incremental versions of the complexity measures, allowing us to create an incremental version of our meta-case-based classification system. Since the case base changes after each deletion, the best algorithm to use may also change. The incremental system allows us to choose which algorithm is the best to use at each point in the deletion process.

Secure architectures for pairing based public key cryptography

Along with the growing demand for cryptosystems in systems ranging from large servers to mobile devices, suitable cryptogrophic protocols for use under certain constraints are becoming more and more important. Constraints such as calculation time, area, efficiency and security, must be considered by the designer. Elliptic curves, since their introduction to public key cryptography in 1985 have challenged established public key and signature generation schemes such as RSA, offering more security per bit. Amongst Elliptic curve based systems, pairing based cryptographies are thoroughly researched and can be used in many public key protocols such as identity based schemes. For hardware implementions of pairing based protocols, all components which calculate operations over Elliptic curves can be considered. Designers of the pairing algorithms must choose calculation blocks and arrange the basic operations carefully so that the implementation can meet the constraints of time and hardware resource area. This thesis deals with different hardware architectures to accelerate the pairing based cryptosystems in the field of characteristic two. Using different top-level architectures the hardware efficiency of operations that run at different times is first considered in this thesis. Security is another important aspect of pairing based cryptography to be considered in practically Side Channel Analysis (SCA) attacks. The naively implemented hardware accelerators for pairing based cryptographies can be vulnerable when taking the physical analysis attacks into consideration. This thesis considered the weaknesses in pairing based public key cryptography and addresses the particular calculations in the systems that are insecure. In this case, countermeasures should be applied to protect the weak link of the implementation to improve and perfect the pairing based algorithms. Some important rules that the designers must obey to improve the security of the cryptosystems are proposed. According to these rules, three countermeasures that protect the pairing based cryptosystems against SCA attacks are applied. The implementations of the countermeasures are presented and their performances are investigated.

Artefact detection and removal algorithms for EEG diagnostic systems

The electroencephalogram (EEG) is a medical technology that is used in the monitoring of the brain and in the diagnosis of many neurological illnesses. Although coarse in its precision, the EEG is a non-invasive tool that requires minimal set-up times, and is suitably unobtrusive and mobile to allow continuous monitoring of the patient, either in clinical or domestic environments. Consequently, the EEG is the current tool-of-choice with which to continuously monitor the brain where temporal resolution, ease-of- use and mobility are important. Traditionally, EEG data are examined by a trained clinician who identifies neurological events of interest. However, recent advances in signal processing and machine learning techniques have allowed the automated detection of neurological events for many medical applications. In doing so, the burden of work on the clinician has been significantly reduced, improving the response time to illness, and allowing the relevant medical treatment to be administered within minutes rather than hours. However, as typical EEG signals are of the order of microvolts (μV ), contamination by signals arising from sources other than the brain is frequent. These extra-cerebral sources, known as artefacts, can significantly distort the EEG signal, making its interpretation difficult, and can dramatically disimprove automatic neurological event detection classification performance. This thesis therefore, contributes to the further improvement of auto- mated neurological event detection systems, by identifying some of the major obstacles in deploying these EEG systems in ambulatory and clinical environments so that the EEG technologies can emerge from the laboratory towards real-world settings, where they can have a real-impact on the lives of patients. In this context, the thesis tackles three major problems in EEG monitoring, namely: (i) the problem of head-movement artefacts in ambulatory EEG, (ii) the high numbers of false detections in state-of-the-art, automated, epileptiform activity detection systems and (iii) false detections in state-of-the-art, automated neonatal seizure detection systems. To accomplish this, the thesis employs a wide range of statistical, signal processing and machine learning techniques drawn from mathematics, engineering and computer science. The first body of work outlined in this thesis proposes a system to automatically detect head-movement artefacts in ambulatory EEG and utilises supervised machine learning classifiers to do so. The resulting head-movement artefact detection system is the first of its kind and offers accurate detection of head-movement artefacts in ambulatory EEG. Subsequently, addtional physiological signals, in the form of gyroscopes, are used to detect head-movements and in doing so, bring additional information to the head- movement artefact detection task. A framework for combining EEG and gyroscope signals is then developed, offering improved head-movement arte- fact detection. The artefact detection methods developed for ambulatory EEG are subsequently adapted for use in an automated epileptiform activity detection system. Information from support vector machines classifiers used to detect epileptiform activity is fused with information from artefact-specific detection classifiers in order to significantly reduce the number of false detections in the epileptiform activity detection system. By this means, epileptiform activity detection which compares favourably with other state-of-the-art systems is achieved. Finally, the problem of false detections in automated neonatal seizure detection is approached in an alternative manner; blind source separation techniques, complimented with information from additional physiological signals are used to remove respiration artefact from the EEG. In utilising these methods, some encouraging advances have been made in detecting and removing respiration artefacts from the neonatal EEG, and in doing so, the performance of the underlying diagnostic technology is improved, bringing its deployment in the real-world, clinical domain one step closer.

Profiling side-channel attacks on cryptographic algorithms

Traditionally, attacks on cryptographic algorithms looked for mathematical weaknesses in the underlying structure of a cipher. Side-channel attacks, however, look to extract secret key information based on the leakage from the device on which the cipher is implemented, be it smart-card, microprocessor, dedicated hardware or personal computer. Attacks based on the power consumption, electromagnetic emanations and execution time have all been practically demonstrated on a range of devices to reveal partial secret-key information from which the full key can be reconstructed. The focus of this thesis is power analysis, more specifically a class of attacks known as profiling attacks. These attacks assume a potential attacker has access to, or can control, an identical device to that which is under attack, which allows him to profile the power consumption of operations or data flow during encryption. This assumes a stronger adversary than traditional non-profiling attacks such as differential or correlation power analysis, however the ability to model a device allows templates to be used post-profiling to extract key information from many different target devices using the power consumption of very few encryptions. This allows an adversary to overcome protocols intended to prevent secret key recovery by restricting the number of available traces. In this thesis a detailed investigation of template attacks is conducted, along with how the selection of various attack parameters practically affect the efficiency of the secret key recovery, as well as examining the underlying assumption of profiling attacks in that the power consumption of one device can be used to extract secret keys from another. Trace only attacks, where the corresponding plaintext or ciphertext data is unavailable, are then investigated against both symmetric and asymmetric algorithms with the goal of key recovery from a single trace. This allows an adversary to bypass many of the currently proposed countermeasures, particularly in the asymmetric domain. An investigation into machine-learning methods for side-channel analysis as an alternative to template or stochastic methods is also conducted, with support vector machines, logistic regression and neural networks investigated from a side-channel viewpoint. Both binary and multi-class classification attack scenarios are examined in order to explore the relative strengths of each algorithm. Finally these machine-learning based alternatives are empirically compared with template attacks, with their respective merits examined with regards to attack efficiency.

Algorithms for indoor localization based on IEEE 802.15.4-2011 UWB and inertial sensors

In this thesis, extensive experiments are firstly conducted to characterize the performance of using the emerging IEEE 802.15.4-2011 ultra wideband (UWB) for indoor localization, and the results demonstrate the accuracy and precision of using time of arrival measurements for ranging applications. A multipath propagation controlling technique is synthesized which considers the relationship between transmit power, transmission range and signal-to-noise ratio. The methodology includes a novel bilateral transmitter output power control algorithm which is demonstrated to be able to stabilize the multipath channel, and enable sub 5cm instant ranging accuracy in line of sight conditions. A fully-coupled architecture is proposed for the localization system using a combination of IEEE 802.15.4-2011 UWB and inertial sensors. This architecture not only implements the position estimation of the object by fusing the UWB and inertial measurements, but enables the nodes in the localization network to mutually share positional and other useful information via the UWB channel. The hybrid system has been demonstrated to be capable of simultaneous local-positioning and remote-tracking of the mobile object. Three fusion algorithms for relative position estimation are proposed, including internal navigation system (INS), INS with UWB ranging correction, and orientation plus ranging. Experimental results show that the INS with UWB correction algorithm achieves an average position accuracy of 0.1883m, and gets 83% and 62% improvements on the accuracy of the INS (1.0994m) and the existing extended Kalman filter tracking algorithm (0.5m), respectively.

Novel Computational Protein Design Algorithms with Applications to Cystic Fibrosis and HIV

Proteins are essential components of cells and are crucial for catalyzing reactions, signaling, recognition, motility, recycling, and structural stability. This diversity of function suggests that nature is only scratching the surface of protein functional space. Protein function is determined by structure, which in turn is determined predominantly by amino acid sequence. Protein design aims to explore protein sequence and conformational space to design novel proteins with new or improved function. The vast number of possible protein sequences makes exploring the space a challenging problem.

Computational structure-based protein design (CSPD) allows for the rational design of proteins. Because of the large search space, CSPD methods must balance search accuracy and modeling simplifications. We have developed algorithms that allow for the accurate and efficient search of protein conformational space. Specifically, we focus on algorithms that maintain provability, account for protein flexibility, and use ensemble-based rankings. We present several novel algorithms for incorporating improved flexibility into CSPD with continuous rotamers. We applied these algorithms to two biomedically important design problems. We designed peptide inhibitors of the cystic fibrosis agonist CAL that were able to restore function of the vital cystic fibrosis protein CFTR. We also designed improved HIV antibodies and nanobodies to combat HIV infections.

Design of Scheduling Algorithms Using Game Theoretic Ideas

Scheduling a set of jobs over a collection of machines to optimize a certain quality-of-service measure is one of the most important research topics in both computer science theory and practice. In this thesis, we design algorithms that optimize {\em flow-time} (or delay) of jobs for scheduling problems that arise in a wide range of applications. We consider the classical model of unrelated machine scheduling and resolve several long standing open problems; we introduce new models that capture the novel algorithmic challenges in scheduling jobs in data centers or large clusters; we study the effect of selfish behavior in distributed and decentralized environments; we design algorithms that strive to balance the energy consumption and performance.

The technically interesting aspect of our work is the surprising connections we establish between approximation and online algorithms, economics, game theory, and queuing theory. It is the interplay of ideas from these different areas that lies at the heart of most of the algorithms presented in this thesis.

The main contributions of the thesis can be placed in one of the following categories.

1. Classical Unrelated Machine Scheduling: We give the first polygorithmic approximation algorithms for minimizing the average flow-time and minimizing the maximum flow-time in the offline setting. In the online and non-clairvoyant setting, we design the first non-clairvoyant algorithm for minimizing the weighted flow-time in the resource augmentation model. Our work introduces iterated rounding technique for the offline flow-time optimization, and gives the first framework to analyze non-clairvoyant algorithms for unrelated machines.

2. Polytope Scheduling Problem: To capture the multidimensional nature of the scheduling problems that arise in practice, we introduce Polytope Scheduling Problem (\psp). The \psp problem generalizes almost all classical scheduling models, and also captures hitherto unstudied scheduling problems such as routing multi-commodity flows, routing multicast (video-on-demand) trees, and multi-dimensional resource allocation. We design several competitive algorithms for the \psp problem and its variants for the objectives of minimizing the flow-time and completion time. Our work establishes many interesting connections between scheduling and market equilibrium concepts, fairness and non-clairvoyant scheduling, and queuing theoretic notion of stability and resource augmentation analysis.

3. Energy Efficient Scheduling: We give the first non-clairvoyant algorithm for minimizing the total flow-time + energy in the online and resource augmentation model for the most general setting of unrelated machines.

4. Selfish Scheduling: We study the effect of selfish behavior in scheduling and routing problems. We define a fairness index for scheduling policies called {\em bounded stretch}, and show that for the objective of minimizing the average (weighted) completion time, policies with small stretch lead to equilibrium outcomes with small price of anarchy. Our work gives the first linear/ convex programming duality based framework to bound the price of anarchy for general equilibrium concepts such as coarse correlated equilibrium.

Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.

Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, but differences in CNV call thresholds and characteristics exist. We evaluated the relative performance of seven methods: circular binary segmentation, CNVFinder, cnvPartition, gain and loss of DNA, Nexus algorithms, PennCNV and QuantiSNP. Tested data included real and simulated Illumina HumHap 550 data from the Singapore cohort study of the risk factors for Myopia (SCORM) and simulated data from Affymetrix 6.0 and platform-independent distributions. The normalized singleton ratio (NSR) is proposed as a metric for parameter optimization before enacting full analysis. We used 10 SCORM samples for optimizing parameter settings for each method and then evaluated method performance at optimal parameters using 100 SCORM samples. The statistical power, false positive rates, and receiver operating characteristic (ROC) curve residuals were evaluated by simulation studies. Optimal parameters, as determined by NSR and ROC curve residuals, were consistent across datasets. QuantiSNP outperformed other methods based on ROC curve residuals over most datasets. Nexus Rank and SNPRank have low specificity and high power. Nexus Rank calls oversized CNVs. PennCNV detects one of the fewest numbers of CNVs.

Approximation algorithms for two-machine flow shop scheduling with batch setup times

In many practical situations, batching of similar jobs to avoid setups is performed while constructing a schedule. This paper addresses the problem of non-preemptively scheduling independent jobs in a two-machine flow shop with the objective of minimizing the makespan. Jobs are grouped into batches. A sequence independent batch setup time on each machine is required before the first job is processed, and when a machine switches from processing a job in some batch to a job of another batch. Besides its practical interest, this problem is a direct generalization of the classical two-machine flow shop problem with no grouping of jobs, which can be solved optimally by Johnson's well-known algorithm. The problem under investigation is known to be NP-hard. We propose two O(n logn) time heuristic algorithms. The first heuristic, which creates a schedule with minimum total setup time by forcing all jobs in the same batch to be sequenced in adjacent positions, has a worst-case performance ratio of 3/2. By allowing each batch to be split into at most two sub-batches, a second heuristic is developed which has an improved worst-case performance ratio of 4/3. © 1998 The Mathematical Programming Society, Inc. Published by Elsevier Science B.V.