3D protein structure matching by patch signatures

For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches. As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein against a large protein database. In this paper, we address a vector space based representation for protein structures, where a patch is formed by the vectors within the region. Based on our previews work, a compact representation of the patch named patch signature is applied here. A similarity measure of two patches is then derived based on their signatures. To achieve fast patch matching in large protein databases, a match-and-expand strategy is proposed. Given a query patch, a set of small k-sized matching patches, called candidate patches, is generated in match stage. The candidate patches are further filtered by enlarging k in expand stage. Our extensive experimental results demonstrate encouraging performances with respect to this biologically critical but previously computationally prohibitive problem.

Specification matching of object-oriented components

Object-orientation supports software reuse via features such as abstraction, information hiding, polymorphism, inheritance and redefinition. However, while libraries of classes do exist, one of the challenges that still remains is to locate suitable classes and adapt them to meet the specific requirements of the software developer. Traditional approaches to library retrieval are text-based; it is therefore difficult for the developer to express their requirements in a precise and unambiguous manner. A more promising approach is specification-based retrieval, where library component interfaces and requirements are expressed using a formal specification language. In this case retrieval is based on matching formal specifications. In this paper we describe how existing approaches to specification matching can be extended to handle object-oriented components.

Mirror neurons in the tree of life, development and evolution of sensorimotor matching responses

Mirror neurons in the tree of life rappresenta lo sviluppo e l' evoluzione del sistema dei neuroni specchio nei primati umani, non - umani e di alcune specie di uccelli, utilizzando metodi cooptati dalla filosofia della biologia e la biologia teorica, per integrare dati relativi al sistema nervoso e al comportamento delle specie in esame.

Semi-global techniques in image matching and change detection with applications to civil and environmental engineering.

This work of thesis wants to present a dissertation of the wide range of modern dense matching algorithms, which are spreading in different application and research fields, with a particular attention to the innovative “Semi-Global” matching techniques. The choice of develop a semi-global numerical code was justified by the need of getting insight on the variables and strategies that affect the algorithm performances with the primary objective of maximizing the method accuracy and efficiency, and the results level of completeness. The dissertation will consist in the metrological characterization of the proprietary implementation of the semi-global matching algorithm, evaluating the influence of several matching variables and functions implemented in the process and comparing the accuracy and completeness of different results (digital surface models, disparity maps and 2D displacement fields) obtained using our code and other commercial and open-source matching programs in a wide variety of application fields.

Co-registration of magnetoencephalography with magnetic resonance imaging using bite-bar-based fiducials and surface-matching

Objective: To introduce a new technique for co-registration of Magnetoencephalography (MEG) with magnetic resonance imaging (MRI). We compare the accuracy of a new bite-bar with fixed fiducials to a previous technique whereby fiducial coils were attached proximal to landmarks on the skull. Methods: A bite-bar with fixed fiducial coils is used to determine the position of the head in the MEG co-ordinate system. Co-registration is performed by a surface-matching technique. The advantage of fixing the coils is that the co-ordinate system is not based upon arbitrary and operator dependent fiducial points that are attached to landmarks (e.g. nasion and the preauricular points), but rather on those that are permanently fixed in relation to the skull. Results: As a consequence of minimizing coil movement during digitization, errors in localization of the coils are significantly reduced, as shown by a randomization test. Displacement of the bite-bar caused by removal and repositioning between MEG recordings is minimal (∼0.5 mm), and dipole localization accuracy of a somatosensory mapping paradigm shows a repeatability of ∼5 mm. The overall accuracy of the new procedure is greatly improved compared to the previous technique. Conclusions: The test-retest reliability and accuracy of target localization with the new design is superior to techniques that incorporate anatomical-based fiducial points or coils placed on the circumference of the head. © 2003 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Binocular interaction:Contrast matching and contrast discrimination are predicted by the same model

How do signals from the 2 eyes combine and interact? Our recent work has challenged earlier schemes in which monocular contrast signals are subject to square-law transduction followed by summation across eyes and binocular gain control. Much more successful was a new 'two-stage' model in which the initial transducer was almost linear and contrast gain control occurred both pre- and post-binocular summation. Here we extend that work by: (i) exploring the two-dimensional stimulus space (defined by left- and right-eye contrasts) more thoroughly, and (ii) performing contrast discrimination and contrast matching tasks for the same stimuli. Twenty-five base-stimuli made from 1 c/deg patches of horizontal grating, were defined by the factorial combination of 5 contrasts for the left eye (0.3-32%) with five contrasts for the right eye (0.3-32%). Other than in contrast, the gratings in the two eyes were identical. In a 2IFC discrimination task, the base-stimuli were masks (pedestals), where the contrast increment was presented to one eye only. In a matching task, the base-stimuli were standards to which observers matched the contrast of either a monocular or binocular test grating. In the model, discrimination depends on the local gradient of the observer's internal contrast-response function, while matching equates the magnitude (rather than gradient) of response to the test and standard. With all model parameters fixed by previous work, the two-stage model successfully predicted both the discrimination and the matching data and was much more successful than linear or quadratic binocular summation models. These results show that performance measures and perception (contrast discrimination and contrast matching) can be understood in the same theoretical framework for binocular contrast vision. © 2007 VSP.

The role of texture amplitude in shape from shading: evidence from a haptic matching task

The pattern of illumination on an undulating surface can be used to infer its 3-D form (shape from shading). But the recovery of shape would be invalid if the shading actually arose from reflectance variation. When a corrugated surface is painted with an albedo texture, the variation in local mean luminance (LM) due to shading is accompanied by a similar modulation in texture amplitude (AM). This is not so for reflectance variation, nor for roughly textured surfaces. We used a haptic matching technique to show that modulations of texture amplitude play a role in the interpretation of shape from shading. Observers were shown plaid stimuli comprising LM and AM combined in-phase (LM+AM) on one oblique and in anti-phase (LM-AM) on the other. Stimuli were presented via a modified ReachIN workstation allowing the co-registration of visual and haptic stimuli. In the first experiment, observers were asked to adjust the phase of a haptic surface, which had the same orientation as the LM+AM combination, until its peak in depth aligned with the visually perceived peak. The resulting alignments were consistent with the use of a lighting-from-above prior. In the second experiment, observers were asked to adjust the amplitude of the haptic surface to match that of the visually perceived surface. Observers chose relatively large amplitude settings when the haptic surface was oriented and phase-aligned with the LM+AM cue. When the haptic surface was aligned with the LM-AM cue, amplitude settings were close to zero. Thus the LM/AM phase relation is a significant visual depth cue, and is used to discriminate between shading and reflectance variations. [Supported by the Engineering and Physical Sciences Research Council, EPSRC].

Grayscale and colour image Codec based on matching pursuit in the spatio-frequency domain

This report presents and evaluates a novel idea for scalable lossy colour image coding with Matching Pursuit (MP) performed in a transform domain. The benefits of the idea of MP performed in the transform domain are analysed in detail. The main contribution of this work is extending MP with wavelets to colour coding and proposing a coding method. We exploit correlations between image subbands after wavelet transformation in RGB colour space. Then, a new and simple quantisation and coding scheme of colour MP decomposition based on Run Length Encoding (RLE), inspired by the idea of coding indexes in relational databases, is applied. As a final coding step arithmetic coding is used assuming uniform distributions of MP atom parameters. The target application is compression at low and medium bit-rates. Coding performance is compared to JPEG 2000 showing the potential to outperform the latter with more sophisticated than uniform data models for arithmetic coder. The results are presented for grayscale and colour coding of 12 standard test images.

Interocular suppression is gated by interocular feature matching

We present a new form of contrast masking in which the target is a patch of low spatial frequency grating (0.46 c/deg) and the mask is a dark thin ring that surrounds the centre of the target patch. In matching and detection experiments we found little or no effect for binocular presentation of mask and test stimuli. But when mask and test were presented briefly (33 or 200 ms) to different eyes (dichoptic presentation), masking was substantial. In a 'half-binocular' condition the test stimulus was presented to one eye, but the mask stimulus was presented to both eyes with zero-disparity. This produced masking effects intermediate to those found in dichoptic and full-binocular conditions. We suggest that interocular feature matching can attenuate the potency of interocular suppression, but unlike in previous work (McKee, S. P., Bravo, M. J., Taylor, D. G., & Legge, G. E. (1994) Stereo matching precedes dichoptic masking. Vision Research, 34, 1047) we do not invoke a special role for depth perception. © 2004 Elsevier Ltd. All rights reserved.