Lossless and low-cost integer-based lifting wavelet transform

Discrete wavelet transform (DWT) is a powerful tool for analyzing real-time signals, including aperiodic, irregular, noisy, and transient data, because of its capability to explore signals in both the frequency- and time-domain in different resolutions. For this reason, they are used extensively in a wide number of applications in image and signal processing. Despite the wide usage, the implementation of the wavelet transform is usually lossy or computationally complex, and it requires expensive hardware. However, in many applications, such as medical diagnosis, reversible data-hiding, and critical satellite data, lossless implementation of the wavelet transform is desirable. It is also important to have more hardware-friendly implementations due to its recent inclusion in signal processing modules in system-on-chips (SoCs). To address the need, this research work provides a generalized implementation of a wavelet transform using an integer-based lifting method to produce lossless and low-cost architecture while maintaining the performance close to the original wavelets. In order to achieve a general implementation method for all orthogonal and biorthogonal wavelets, the Daubechies wavelet family has been utilized at first since it is one of the most widely used wavelets and based on a systematic method of construction of compact support orthogonal wavelets. Though the first two phases of this work are for Daubechies wavelets, they can be generalized in order to apply to other wavelets as well. Subsequently, some techniques used in the primary works have been adopted and the critical issues for achieving general lossless implementation have solved to propose a general lossless method. The research work presented here can be divided into several phases. In the first phase, low-cost architectures of the Daubechies-4 (D4) and Daubechies-6 (D6) wavelets have been derived by applying the integer-polynomial mapping. A lifting architecture has been used which reduces the cost by a half compared to the conventional convolution-based approach. The application of integer-polynomial mapping (IPM) of the polynomial filter coefficient with a floating-point value further decreases the complexity and reduces the loss in signal reconstruction. Also, the “resource sharing” between lifting steps results in a further reduction in implementation costs and near-lossless data reconstruction. In the second phase, a completely lossless or error-free architecture has been proposed for the Daubechies-8 (D8) wavelet. Several lifting variants have been derived for the same wavelet, the integer mapping has been applied, and the best variant is determined in terms of performance, using entropy and transform coding gain. Then a theory has been derived regarding the impact of scaling steps on the transform coding gain (GT). The approach results in the lowest cost lossless architecture of the D8 in the literature, to the best of our knowledge. The proposed approach may be applied to other orthogonal wavelets, including biorthogonal ones to achieve higher performance. In the final phase, a general algorithm has been proposed to implement the original filter coefficients expressed by a polyphase matrix into a more efficient lifting structure. This is done by using modified factorization, so that the factorized polyphase matrix does not include the lossy scaling step like the conventional lifting method. This general technique has been applied on some widely used orthogonal and biorthogonal wavelets and its advantages have been discussed. Since the discrete wavelet transform is used in a vast number of applications, the proposed algorithms can be utilized in those cases to achieve lossless, low-cost, and hardware-friendly architectures

Combinatorial Algorithms for String Sanitization

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we consider the problem of sanitizing a string by concealing the occurrences of sensitive patterns, while maintaining data utility, in two settings that are relevant to many common string processing tasks. In the first setting, we aim to generate the minimal-length string that preserves the order of appearance and frequency of all non-sensitive patterns. Such a string allows accurately performing tasks based on the sequential nature and pattern frequencies of the string. To construct such a string, we propose a time-optimal algorithm, TFS-ALGO. We also propose another time-optimal algorithm, PFS-ALGO, which preserves a partial order of appearance of non-sensitive patterns but produces a much shorter string that can be analyzed more efficiently. The strings produced by either of these algorithms are constructed by concatenating non-sensitive parts of the input string. However, it is possible to detect the sensitive patterns by ``reversing'' the concatenation operations. In response, we propose a heuristic, MCSR-ALGO, which replaces letters in the strings output by the algorithms with carefully selected letters, so that sensitive patterns are not reinstated, implausible patterns are not introduced, and occurrences of spurious patterns are prevented. In the second setting, we aim to generate a string that is at minimal edit distance from the original string, in addition to preserving the order of appearance and frequency of all non-sensitive patterns. To construct such a string, we propose an algorithm, ETFS-ALGO, based on solving specific instances of approximate regular expression matching.Comment: Extended version of a paper accepted to ECML/PKDD 201

String Sanitization: A Combinatorial Approach

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge (e.g., trips to mental health clinics from a string representing a user’s loc

Optimisation via encodings: a renormalisation group perspective

The traditional way of tackling discrete optimization problems is by using local search on suitably defined cost or fitness landscapes. Such approaches are however limited by the slowing down that occurs when local minima, that are a feature of the typically rugged landscapes encountered, arrest the progress of the search process. Another way of tackling optimization problems is by the use of heuristic approximations to estimate a global cost minimum. Here we present a combination of these two approaches by using cover-encoding maps which map processes from a larger search space to subsets of the original search space. The key idea is to construct cover-encoding maps with the help of suitable heuristics that single out near-optimal solutions and result in landscapes on the larger search space that no longer exhibit trapping local minima. The processes that are typically employed involve some form of coarse-graining, and we suggest here that they can be viewed as avatars of renormalisation group transformations.Comment: 17 pages, 2 figures. arXiv admin note: text overlap with arXiv:1806.0524

The Origin of Basaltic Lava Flow Textures

This study addresses the links between the surface morphologies, internal structure, and microtexture of basaltic lava flows. The AD 1783-84 Laki eruption in south Iceland produced a 600 km2 basaltic lava flow-field dominated by rubbly pāhoehoe surface morphology. Field observations and aerial photograph interpretation show that the lava surface gradually changed from spiny to slabby and then to rubbly along single flows through repetitive crust disruption at the active front. The rubble was compressed into ridges when lava advance was obstructed and during large lava surges that coincided with the opening of new eruptive fissures. Fluid lava was transported in an extensive network of tubes that formed within the flows. Petrological study of Laki near-vent tephra and lava surface samples shows that, during the eruption, the magma lost ~ 1 wt. % of water during ascent, which induced melt undercooling and triggered groundmass crystallization. This caused an ~ 10% anorthite gap across plagioclase phenocrysts and drove considerable microlite formation (up to 30 vol.%) in the early stages of flow. It is estimated that fluid lava was transported from the vent to the most distal active front, 60 km from the vent, with cooling rates of < 0.5°C/km. Young lava flow-fields in the Reykjanes Peninsula (Iceland), and some flows from the flood basalts of the Columbia River Province (USA), have surface and internal structures intermediate between rubbly pāhoehoe and 'a'ā. The increasing size and decreasing number density of plagioclase microlites with increasing depth in these flows, as in the Laki lavas, indicate that solidification rates decreased sharply inwards. Differences between sections are attributed to variations in lava bulk composition and the transport mode, duration of emplacement, and interaction with surface water of the fluid lava. Pāhoehoe and 'a'ā have low and high plagioclase number densities respectively, with an inverse correlation with the average size and aspect ratio of plagioclases. Rubbly pāhoehoe lavas have intermediate characteristics. This correlation between lava surface morphologies and plagioclase textural characteristics provides a tool that may be useful for inferring eruption and emplacement processes from textural measurements of flow interiors in ancient basaltic lava flow-fields

Mapping the genotype-phenotype relationship in complex disease.

Computational methods to identify harmful variations in humans perform well for rare diseases such as Huntington\u27s but not for common diseases like hypertension or diabetes. A modelling approach that takes protein context into account was illustrated to identify harmful variants involved in complex diseases

The N-terminal Domain of the Y-box Binding Protein YB-1 Plays a Major Role in Cell Proliferation and Apoptosis

Y-box binding protein, YB-1, is a member of the cold shock domain superfamily of proteins. It is involved in a plethora of cellular functions, including cell proliferation. The molecular mechanisms governing the involvement of YB-1 in cell proliferation are still unclear. Earlier studies done in chicken pre-B lymphocyte DT-40 cells in our laboratory have shown that a targeted disruption in one allele of chicken YB-1 (Chk-Yb-1b) gene at its N-terminal domain resulted in multiple abnormalities in the heterozygous mutants, including slower growth rate, abnormal cell morphology, increased cell size, increased genomic DNA content and significant changes in levels of cell cycle specific genes like the cyclin dependent kinase inhibitor - p21. The current study is based on the hypothesis that the defects seen in the heterozygous mutant DT-40 cells were due to a dominant negative effect of the potential YB-1 N-terminal truncated protein. The goal of this study is to determine if the introduction of the N-terminal region of YB-1 mimics the defects seen in the mutant DT-40 cells and to identify cell cycle specific proteins that interact with YB-1. Using rat hepatoma cells (H411E) as a model system, we introduced three different YB-1 N-terminal fusion proteins, i) APYB77GFP, the 77 amino acid long full length YB-1 N-terminal sequence containing clone, ii) APYB36GFP, the 36 amino acid long peptide with the internal deletion Δ12-52 (APYB36Δ12-52GFP represented as APYB36GFP) and iii) APYB26GFP, the 26 amino acid proline rich YB-1 N-terminal sequence containing clone and investigated their effects on incubated cells. Our findings show that introduction of the APYB26GFP and APYB77GFP proteins resulted in cell cycle arrest at the G2/M phase. In contrast, incubation with the APYB36GFP protein showed a lower proportion of G2/M phase cells. APYB26GFP and APYB77GFP protein incubations also resulted in significant apoptosis, which was confirmed by Annexin V staining, DNA fragmentation analysis and nuclear breakdown analysis. The APYB36GFP incubation showed lesser percentage of apoptotic cells. We conclude that the YB-1 amino-end sequence plays an important role in cell proliferation and apoptosis. We also demonstrate that YB-1 interacts with the cell cycle protein - cyclin D1, predominantly in the cytoplasm of G2/M phase blocked cells and the YB-1 N-terminus is involved in this interaction. We propose that the proline alanine rich PPAAPPAAPALSAADTK sequence present in APYB26GFP and APYB77GFP, but not in APYB36GFP is involved in this interaction, as cyclin D1 did not immunoprecipitate with APYB36GFP. We conclude that the YB-1 N-terminus interacts with Cyclin D1 in the cytoplasm of G2/M phase cells and this interaction probably sequesters the cyclin D1 in the cytoplasm leading to cell cycle arrest and apoptosis. In summary, this study demonstrates that the amino-end domain of YB-1 plays a role in cell proliferation and apoptosis probably by sequestering cyclin D1 in the cell cytoplasm. It is likely that this process is mediated through the proline alanine rich sequence PPAAPPAAPALSAADTK, present in the N-terminus of YB-1

Molecular mechanisms of folding of intrinsically disordered proteins

In this thesis, we studied the interaction between the intrinsically disordered domain of the nucleoprotein (N) of Measles virus (MeV), NTAIL, and its partner XD, the X domain of the MeV phosphoprotein (P). It had been previously shown that the α-MoRE (residues 489-506) of NTAIL undergoes an α-helical folding after binding to XD (induced fit mechanism) while regions flanking the α-MoRE remain disordered (fuzzy) in the complex. The fuzzy appendage preceding the α-MoRE was shown to decrease the binding affinities towards XD and the rate of folding of the α-MoRE. In this thesis, by producing NTAIL variants (single-site variants, truncation variants, artificial variants) and performing kinetic experiments of the interaction with XD, we studied the folding after binding mechanism of NTAIL at the single residue level, and investigated the mechanisms through which the fuzzy region hampers the binding affinity and the folding rate of the α-MoRE. We concluded that the central part of the helix is responsible for the initial interactions driving the binding with XD. Moreover, we found that the fuzzy region causes a decrease in the folding rate of the α-MoRE through a combination of entropic and enthalpic effects. We also studied the interaction between NTAIL and a variant of XD, I504A, that populates only the native state. These studies showed that both the binding and the folding steps of the NTAIL-XD interaction are highly dependent on the shape of XD, suggesting that this IDP folds by heterogeneous nucleation via a mechanism induced by the shape of the partner (templated folding)