On the performance and programming of reversible molecular computers

If the 20th century was known for the computational revolution, what will the 21st be known for? Perhaps the recent strides in the nascent fields of molecular programming and biological computation will help bring about the ‘Coming Era of Nanotechnology’ promised in Drexler’s ‘Engines of Creation’. Though there is still far to go, there is much reason for optimism. This thesis examines the underlying principles needed to realise the computational aspects of such ‘engines’ in a performant way. Its main body focusses on the ways in which thermodynamics constrains the operation and design of such systems, and it ends with the proposal of a model of computation appropriate for exploiting these constraints. These thermodynamic constraints are approached from three different directions. The first considers the maximum possible aggregate performance of a system of computers of given volume, V, with a given supply of free energy. From this perspective, reversible computing is imperative in order to circumvent the Landauer limit. A result of Frank is refined and strengthened, showing that the adiabatic regime reversible computer performance is the best possible for any computer—quantum or classical. This therefore shows a universal scaling law governing the performance of compact computers of ~V^(5/6), compared to ~V^(2/3) for conventional computers. For the case of molecular computers, it is shown how to attain this bound. The second direction extends this performance analysis to the case where individual computational particles or sub-units can interact with one another. The third extends it to interactions with shared, non-computational parts of the system. It is found that accommodating these interactions in molecular computers imposes a performance penalty that undermines the earlier scaling result. Nonetheless, scaling superior to that of irreversible computers can be preserved, and appropriate mitigations and considerations are discussed. These analyses are framed in a context of molecular computation, but where possible more general computational systems are considered. The proposed model, the א-calculus, is appropriate for programming reversible molecular computers taking into account these constraints. A variety of examples and mathematical analyses accompany it. Moreover, abstract sketches of potential molecular implementations are provided. Developing these into viable schemes suitable for experimental validation will be a focus of future work

A computer-aided design for digital filter implementation

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Homogeneous vector capsules and their application to sufficient and complete data

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonCapsules (vector-valued neurons) have recently become a more active area of research in neural networks. However, existing formulations have several drawbacks including the large number of trainable parameters that they require as well as the reliance on routing mechanisms between layers of capsules. The primary aim of this project is to demonstrate the benefits of a new formulation of capsules called Homogeneous Vector Capsules (HVCs) that overcome these drawbacks. Using HVCs, new state-of-the-art accuracies for the MNIST dataset are established for multiple individual models as well as multiple ensembles. This work additionally presents a dataset consisting of high-resolution images of 13 micro-PCBs captured in various rotations and perspectives relative to the camera, with each sample labeled for PCB type, rotation category, and perspective categories. Experiments performed and elucidated in this work examine classification accuracy of rotations and perspectives that were not trained on as well as the ability to artificially generate missing rotations and perspectives during training. The results of these experiments include showing that using HVCs is superior to using fully connected layers. This work also showed that certain training samples are more informative of class membership than others. These samples can be identified prior to training by analyzing their position in reduced dimensional space relative to the classes’ centroids in that space. And a definition and calculation both for class density and dataset completeness based on the distribution of data in the reduced dimensional space has been put forth. Experimentation using the dataset completeness calculation shows that those datasets that meet a certain completeness threshold can be trained on a subset of the total dataset, based on each class’s density, while improving upon or maintaining validation accuracy

Exploiting primitive grouping constraints for noise robust automatic speech recognition : studies with simultaneous speech.

Significant strides have been made in the field of automatic speech recognition over the past three decades. However, the systems are not robust; their performance degrades in the presence of even moderate amounts of noise. This thesis presents an approach to developing a speech recognition system that takes inspiration firom the approach of human speech recognition

Compilers for portable programming of heterogeneous parallel & approximate computing systems

Programming heterogeneous systems such as the System-on-chip (SoC) processors in modern mobile devices can be extremely complex because a single system may include multiple different parallelism models, instruction sets, memory hierarchies, and systems use different combinations of these features. This is further complicated by software and hardware approximate computing optimizations. Different compute units on an SoC use different approximate computing methods and an application would usually be composed of multiple compute kernels, each one specialized to run on a different hardware. Determining how best to map such an application to a modern heterogeneous system is an open research problem. First, we propose a parallel abstraction of heterogeneous hardware that is a carefully chosen combination of well-known parallel models and is able to capture the parallelism in a wide range of popular parallel hardware. This abstraction uses a hierarchical dataflow graph with side effects and vector SIMD instructions. We use this abstraction to define a parallel program representation called HPVM that aims to address both functional portability and performance portability across heterogeneous systems. Second, we further extend HPVM representation to enable accuracy-aware performance and energy tuning on heterogeneous systems with multiple compute units and approximation methods. We call it ApproxHPVM, and it automatically translates end-to-end application-level accuracy constraints into accuracy requirements for individual operations. ApproxHPVM uses a hardware-agnostic accuracy-tuning phase to do this translation, which greatly speeds up the analysis, enables greater portability, and enables future capabilities like accuracy-aware dynamic scheduling and design space exploration. We have implemented a prototype HPVM system, defining the HPVM IR as an extension of the LLVM compiler IR, compiler optimizations that operate directly on HPVM graphs, and code generators that translate the virtual ISA to NVIDIA GPUs, Intel’s AVX vector units, and to multicore X86-64 processors. Experimental results show that HPVM optimizations achieve significant performance improvements, HPVM translators achieve performance competitive with manually developed OpenCL code for both GPUs and vector hardware, and that runtime scheduling policies can make use of both program and runtime information to exploit the flexible compilation capabilities. Furthermore, our evaluation of ApproxHPVM shows that our framework can offload chunks of approximable computations to special purpose accelerators that provide significant gains in performance and energy, while staying within a user-specified application-level accuracy constraint with high probability

Genetic evolution and equivalence of some complex systems: fractals, cellular automata and lindenmayer systems

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid. Escuela Politécnica Superior, Departamento de Ingeniería informática.26-04-200