Thomas J. Naughton

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

BackgroundIn recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner.ResultsWe start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. We have investigated patterns of amino acid substitution among homologous sequences from the three Domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. Perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral Pol proteins.ConclusionThis demonstrates that choosing protein models based on their source or method of construction may not be appropriate.

Resistance of the double random phase encryption against various attacks

Several attacks are proposed against the double random phase encryption scheme. These attacks are demonstrated on computer-generated ciphered images. The scheme is shown to be resistant against brute force attacks but susceptible to chosen and known plaintext attacks. In particular, we describe a technique to recover the exact keys with only two known plain images. We compare this technique to other attacks proposed in the literature.

Real-time three-dimensional object reconstruction by use of a phase-encoded digital hologram.

A three-dimensional (3D) object reconstruction technique that uses only phase information of a phase-shifting digital hologram and a phase-only spatial-light modulator is proposed. It is well known that a digital hologram can store both amplitude and phase information of an optical electric field and can reconstruct the original 3D object in a computer. We demonstrate that it is possible to reconstruct optically 3D objects using only phase information of the optical field calculated from phase-shifting digital holograms. The use of phase-only information enables us to reduce the amount of data in the digital hologram and reconstruct optically the 3D objects using a liquid-crystal spatial light modulator without optical power loss. Numerical evaluation of the reconstructed 3D object is presented.

Three-Dimensional Imaging and Processing Using Computational Holographic Imaging

Digital holography is a technique that permits digital capture of holograms and subsequent processing on a digital computer. This paper reviews various applications of this technique. The presented applications cover three-dimensional (3-D) imaging as well as several associated problems. For the case of 3-D imaging, optical and digital methods to reconstruct and visualize the recorded objects are described. In addition, techniques to compress and encrypt 3-D information in the form of digital holograms are presented. Lastly, 3-D pattern recognition applications of digital holography are discussed. The described techniques constitute a comprehensive approach to 3-D imaging and processing.

Compression of digital holograms for three-dimensional object reconstruction and recognition

We present the results of applying lossless and lossy data compression to a three-dimensional object reconstruction and recognition technique based on phase-shift digital holography. We find that the best lossless (Lempel-Ziv, Lempel-Ziv-Welch, Huffman, Burrows-Wheeler) compression rates can be expected when the digital hologram is stored in an intermediate coding of separate data streams for real and imaginary components. The lossy techniques are based on subsampling, quantization, and discrete Fourier transformation. For various degrees of speckle reduction, we quantify the number of Fourier coefficients that can be removed from the hologram domain, and the lowest level of quantization achievable, without incurring significant loss in correlation performance or significant error in the reconstructed object domain.

A known-plaintext heuristic attack on the Fourier plane encryption algorithm

The Fourier plane encryption algorithm is subjected to a known-plaintext attack. The simulated annealing heuristic algorithm is used to estimate the key, using a known plaintext-ciphertext pair, which decrypts the ciphertext with arbitrarily low error. The strength of the algorithm is tested by using this estimated key to decrypt a different ciphertext which was also encrypted using the same original key. We assume that the plaintext is amplitude-encoded real-valued image, and analyze only the mathematical algorithm rather than a real optical system that can be more secure. The Fourier plane encryption algorithm is found to be susceptible to a known-plaintext heuristic attack.

Dynamic task scheduling using genetic algorithms for heterogeneous distributed computing

An algorithm has been developed to dynamically schedule heterogeneous tasks on heterogeneous processors in a distributed system. The scheduler operates in an environment with dynamically changing resources and adapts to variable system resources. It operates in a batch fashion and utilises a genetic algorithm to minimise the total execution time. We have compared our scheduler to six other schedulers, three batch-mode and three immediate-mode schedulers. We have performed simulations with randomly generated task sets, using uniform, normal, and Poisson distributions, whilst varying the communication overheads between the clients and scheduler. We have achieved more efficient results than all other schedulers across a range of different scenarios while scheduling 10,000 tasks on up to 50 heterogeneous processors.

Compression of encrypted three-dimensional objects using digital holography

We present the results of applying data compression techniques to encrypted three-dimensional objects. The objects are captured using phase-shift digital holography and encrypted using a random phase mask in the Fresnel domain. Lossy quantization is combined with lossless coding techniques to quantify compression ratios. Lossless compression alone applied to the encrypted holographic data achieves compression ratios lower than 1.05. When combined with quantization and an integer encoding scheme, this rises to between 12 and 65 (depending on the hologram chosen and the method of measuring compression ratio), with good decryption and reconstruction quality. Our techniques are suitable for a range of secure three-dimensional object storage and transmission applications.

Reduction of speckle in digital holography by discrete Fourier filtering

We present a digital signal processing technique that reduces the speckle content in reconstructed digital holograms. The method is based on sequential sampling of the discrete Fourier transform of the reconstructed image field. Speckle reduction is achieved at the expense of a reduced intensity and resolution, but this trade-off is shown to be greatly superior to that imposed by the traditional mean and median filtering techniques. In particular, we show that the speckle can be reduced by half with no loss of resolution (according to standard definitions of both metrics).

Efficient compression of Fresnel fields for internet transmission of three-dimensional images

We compress phase-shift digital holograms (whole Fresnel fields) for the transmission of three-dimensional images. For real-time networking applications, the time required to compress can be as critical as the compression rate. We achieve lossy compression through quantization of both the real and imaginary streams, followed by a bit packing operation. Compression losses in the reconstructed objects were quantified. We define a speedup metric that combines space gains due to compression with temporal overheads due to the compression routine and the transmission serialization. We empirically verify transmission speedup due to compression using a special-purpose Internet-based networking application.