nils-herrmann/clean_scirepeval huggingface dataset:
An Inner-Product Calculus for Periodic Functions and Curves

Our motivation is the design of efficient algorithms to process closed curves represented by basis functions or wavelets. To that end, we introduce an inner-product calculus to evaluate correlations and L2 distances between such curves. In particular, we present formulas for the direct and exact evaluation of correlation matrices in the case of closed (i.e., periodic) parametric curves and periodic signals. We give simplifications for practical cases that involve B-splines. To illustrate this approach, we also propose a least-squares approximation scheme that is able to resample curves while minimizing aliasing artifacts. Another application is the exact calculation of the enclosed area.
The fractional Hilbert transform and dual-tree Gabor-like wavelet analysis

We provide an amplitude-phase representation of the dual-tree complex wavelet transform by extending the fixed quadrature relationship of the dual-tree wavelets to arbitrary phase-shifts using the fractional Hilbert transform (fHT). The fHT is a generalization of the Hilbert transform that extends the quadrature phase-shift action of the latter to arbitrary phase-shifts—a real shift parameter controls this phase-shift action. Next, based on the proposed representation and the observation that the fHT operator maps well-localized B-spline wavelets (that resemble Gaussian-windowed sinusoids) into B-spline wavelets of the same order but different shift, we relate the corresponding dual-tree scheme to the paradigm of multiresolution windowed Fourier analysis.
Optimality of Operator-Like Wavelets for Representing Sparse AR(1) Processes

The discrete cosine transform (DCT) is known to be asymptotically equivalent to the Karhunen-Loève transform (KLT) of Gaussian first-order auto-regressive (AR(1)) processes. Since being uncorrelated under the Gaussian hypothesis is synonymous with independence, it also yields an independent-component analysis (ICA) of such signals. In this paper, we present a constructive non-Gaussian generalization of this result: the characterization of the optimal orthogonal transform (ICA) for the family of symmetric-stable AR(1) processes. The degree of sparsity of these processes is controlled by the stability parameter 0 <; α ≤ 2 with the only non-sparse member of the family being the classical Gaussian AR(1) process with α = 2. Specifically, we prove that, for α <; 2, a fixed family of operator-like wavelet bases systematically outperforms the DCT in terms of compression and denoising ability. The effect is quantified with the help of two performance criteria (one based on the Kullback-Leibler divergence, and the other on Stein's formula for the minimum estimation error) that can also be viewed as statistical measures of independence. Finally, we observe that, for the sparser kind of processes with 0 <; α ≤ 1, the operator-like wavelet basis, as dictated by linear system theory, is undistinguishable from the ICA solution obtained through numerical optimization. Our framework offers a unified view that encompasses sinusoidal transforms such as the DCT and a family of orthogonal Haar-like wavelets that is linked analytically to the underlying signal model.
Optimized steerable wavelets for texture analysis of lung tissue in 3-D CT: Classification of usual interstitial pneumonia

Our aim is to optimize wavelet-based feature extraction for differentiating between the classical versus atypical pattern of usual interstitial pneumonia (UIP) in volumetric CT. Our proposal is to act on the bandwidth of steerable wavelets while maintaining their tight frame property. To that end, we designed a family of maximally localized wavelet pyramids in 3-D for a continuously adjustable radial bandwidth [Ω,π], Ω G [π/4, π/2]. The proposed wavelets are coupled with a rotation-covariant directional operator based on the Riesz transform, which provides characterizations of the organization image directions independently from their local orientations. The influence of the wavelet bandwidth on the classification performance was found to be large with area under the receiver operating characteristic curve (AUC) values in [0.784,0.921]. This demonstrated the importance of finding the minimum spatial support of the wavelet required to leverage the wealth of morphological tissue properties in the vicinity of the lung boundaries.
Generalized poisson summation formula for tempered distributions

The Poisson summation formula (PSF), which relates the sampling of an analog signal with the periodization of its Fourier transform, plays a key role in the classical sampling theory. In its current forms, the formula is only applicable to a limited class of signals in L1. However, this assumption on the signals is too strict for many applications in signal processing that require sampling of non-decaying signals. In this paper we generalize the PSF for functions living in weighted Sobolev spaces that do not impose any decay on the functions. The only requirement is that the signal to be sampled and its weak derivatives up to order 1/2+ ε for arbitrarily small ε > 0, grow slower than a polynomial in the L2 sense. The generalized PSF will be interpreted in the language of distributions.
Steerable Pyramids and Tight Wavelet Frames in $L_{2}({\BBR}^{d})$

We present a functional framework for the design of tight steerable wavelet frames in any number of dimensions. The 2-D version of the method can be viewed as a generalization of Simoncelli's steerable pyramid that gives access to a larger palette of steerable wavelets via a suitable parametrization. The backbone of our construction is a primal isotropic wavelet frame that provides the multiresolution decomposition of the signal. The steerable wavelets are obtained by applying a one-to-many mapping (N th-order generalized Riesz transform) to the primal ones. The shaping of the steerable wavelets is controlled by an M × M unitary matrix (where M is the number of wavelet channels) that can be selected arbitrarily; this allows for a much wider range of solutions than the traditional equiangular configuration (steerable pyramid). We give a complete functional description of these generalized wavelet transforms and derive their steering equations. We describe some concrete examples of transforms, including some built around a Mallat-type multiresolution analysis of L2(Rd), and provide a fast Fourier transform-based decomposition algorithm. We also propose a principal-component-based method for signal adapted wavelet design. Finally, we present some illustrative examples together with a comparison of the denoising performance of various brands of steerable transforms. The results are in favor of an optimized wavelet design (equalized principal component analysis), which consistently performs best.
Resolution-invariant separable ARMA modeling of images

We suggest a continuous-domain stochastic modeling of images that is invariant to spatial resolution. Specifically, we are proposing an estimator that is calibrated with respect to the sampling step, and that can potentially handle aliased data. Motivated by Markov random fields, we assume a continuous-domain ARMA model and suggest an algorithm for estimating the continuous-domain parameters from the sampled data. The continuous-domain parameters we estimate provide features that can further be used for image classification, segmentation and interpolation, regardless of sampling interval values and of aliasing effects that may appear in the digital image. Experimental results indicate that the proposed approach is preferable over a discrete-domain ARMA modeling.
Splines: a perfect fit for signal and image processing

The article provides arguments in favor of an alternative approach that uses splines, which is equally justifiable on a theoretical basis, and which offers many practical advantages. To reassure the reader who may be afraid to enter new territory, it is emphasized that one is not losing anything because the traditional theory is retained as a particular case (i.e., a spline of infinite degree). The basic computational tools are also familiar to a signal processing audience (filters and recursive algorithms), even though their use in the present context is less conventional. The article also brings out the connection with the multiresolution theory of the wavelet transform. This article attempts to fulfil three goals. The first is to provide a tutorial on splines that is geared to a signal processing audience. The second is to gather all their important properties and provide an overview of the mathematical and computational tools available; i.e., a road map for the practitioner with references to the appropriate literature. The third goal is to give a review of the primary applications of splines in signal and image processing.
Is Uniqueness Lost for Under-Sampled Continuous-Time Auto-Regressive Processes?

We consider the problem of sampling continuous-time auto-regressive processes on a uniform grid. We investigate whether a given sampled process originates from a single continuous-time model, and address this uniqueness problem by introducing an alternative description of poles in the complex plane. We then utilize Kronecker's approximation theorem and prove that the set of non-unique continuous-time AR(2) models has Lebesgue measure zero in this plane. This is a key aspect in current estimation algorithms that use sampled data, as it allows one to remove the sampling rate constraint that is imposed currently.
Efficient Reconstruction of Hexagonally Sampled Data using Three-Directional Box-Splines

Three-directional box-splines are particularly well-suited to interpolate and approximate hexagonally sampled data. In this paper, we propose a computationally efficient end-to-end reconstruction process. First, we introduce a prefiltering step that is based on a quasi-interpolation scheme using low-complexity finite-impulse-response (FIR) filters. Second, we derive a closed analytical expression for three-directional box-splines of any order that leads to a fast evaluation of the spline surface. All operations act locally on the data, and thus are well adapted to applications dealing with large images. To demonstrate the feasibility of our method, we implemented the complete procedure and we present experimental results.
Optimal Interpolation of Fractional Brownian Motion Given Its Noisy Samples

We consider the problem of estimating a fractional Brownian motion known only from its noisy samples at the integers. We show that the optimal estimator can be expressed using a digital Wiener-like filter followed by a simple time-variant correction accounting for nonstationarity. Moreover, we prove that this estimate lives in a symmetric fractional spline space and give a practical implementation for optimal upsampling of noisy fBm samples by integer factors
Sampling and (sparse) stochastic processes: A tale of splines and innovation

The commonality between splines and Gaussian or sparse stochastic processes is that they are ruled by the same type of differential equations. Our purpose here is to demonstrate that this has profound implications for the three primary forms of sampling: uniform, nonuniform, and compressed sensing. The connection with classical sampling is that there is a one-to-one correspondence between spline interpolation and the minimum-mean-square-error reconstruction of a Gaussian process from its uniform or nonuniform samples. The caveat, of course, is that the spline type has to be matched to the operator that whitens the process. The connection with compressed sensing is that the non-Gaussian processes that are ruled by linear differential equations generally admit a parsimonious representation in a wavelet-like basis. There is also a construction based on splines that yields a wavelet-like basis that is matched to the underlying differential operator. It has been observed that expansions in such bases provide excellent M-term approximations of sparse processes. This property is backed by recent estimates of the local Besov regularity of sparse processes.
Anisotropic Interpolation of Sparse Generalized Image Samples

Practical image-acquisition systems are often modeled as a continuous-domain prefilter followed by an ideal sampler, where generalized samples are obtained after convolution with the impulse response of the device. In this paper, our goal is to interpolate images from a given subset of such samples. We express our solution in the continuous domain, considering consistent resampling as a data-fidelity constraint. To make the problem well posed and ensure edge-preserving solutions, we develop an efficient anisotropic regularization approach that is based on an improved version of the edge-enhancing anisotropic diffusion equation. Following variational principles, our reconstruction algorithm minimizes successive quadratic cost functionals. To ensure fast convergence, we solve the corresponding sequence of linear problems by using multigrid iterations that are specifically tailored to their sparse structure. We conduct illustrative experiments and discuss the potential of our approach both in terms of algorithmic design and reconstruction quality. In particular, we present results that use as little as 2% of the image samples.
Innovation modelling and wavelet analysis of fractal processes in bio-imaging

Growth and form in biology are often associated with some level of fractality. Fractal characteristics have also been noted in a number of imaging modalities. These observations make fractal modelling relevant in the context of bio-imaging. In this paper, we introduce a simple and yet rigorous innovation model for multi-dimensional fractional Brownian motion (fBm) and provide the computational tools for the analysis of such processes in a multi-resolution framework. The key point is that these processes can be whitened by application of the appropriate fractional Lapla-cian operator which has a corresponding polyharmonic wavelet. We examine the case of MRI and mammography images through comparison with theoretical results, which underline the suitability of fractal models in the study of bio-textures.
Multiresolution Monogenic Signal Analysis Using the Riesz–Laplace Wavelet Transform

The monogenic signal is the natural 2D counterpart of the 1D analytic signal. We propose to transpose the concept to the wavelet domain by considering a complexified version of the Riesz transform which has the remarkable property of mapping a real-valued (primary) wavelet basis of L2(R2) into a complex one. The Riesz operator is also steerable in the sense that it give access to the Hilbert transform of the signal along any orientation. Having set those foundations, we specify a primary polyharmonic spline wavelet basis of L2(R2) that involves a single Mexican-hat-like mother wavelet (Laplacian of a B-spline). The important point is that our primary wavelets are quasi-isotropic: they behave like multiscale versions of the fractional Laplace operator from which they are derived, which ensures steerability. We propose to pair these real-valued basis functions with their complex Riesz counterparts to specify a multiresolution monogenic signal analysis. This yields a representation where each wavelet index is associated with a local orientation, an amplitude and a phase. We give a corresponding wavelet-domain method for estimating the underlying instantaneous frequency. We also provide a mechanism for improving the shift and rotation-invariance of the wavelet decomposition and show how to implement the transform efficiently using perfect-reconstruction filterbanks. We illustrate the specific feature-extraction capabilities of the representation and present novel examples of wavelet-domain processing; in particular, a robust, tensor-based analysis of directional image patterns, the demodulation of interferograms, and the reconstruction of digital holograms.
Bimodal myocardial motion analysis from B-mode and tissue Doppler ultrasound

We present a new method for estimating heart motion from two-dimensional echocardiographic sequences by exploiting two ultrasound modalities: B-mode and tissue Doppler. The algorithm estimates a two-dimensional velocity field locally by using a spatial affine velocity model inside a sliding window. Within each window, we minimize a local cost function that is composed of two quadratic terms: an optical flow constraint that involves the B-mode data and a constraint that enforces the agreement of the velocity field with the directional tissue Doppler measurements. The relative influence of the two different modalities to the resulting solution is controlled by an adjustable weighting parameter. Robustness is achieved by a coarse-to-fine multi-scale approach.
Generalized Daubechies wavelets

We present a generalization of the Daubechies wavelet family. The context is that of a non-stationary multiresolution analysis - i.e., a sequence of embedded approximation spaces generated by scaling functions that are not necessarily dilates of one another. The constraints that we impose on these scaling functions are: (1) orthogonality with respect to translation; (2) reproduction of a given set of exponential polynomials; and (3) minimal support. These design requirements lead to the construction of a general family of compactly-supported, orthonormal wavelet-like bases of L/sub 2/. If the exponential parameters are all zero, then one recovers Daubechies wavelets, which are orthogonal to the polynomials of degree (N-1) where N is the order (vanishing-moment property). A fast filterbank implementation of the generalized wavelet transform follows naturally; it is similar to Mallat's algorithm, except that the filters are now scale-dependent. The new transforms offer increased flexibility and are tunable to the spectral characteristics of a wide class of signals.
Snakes on a Plane: A perfect snap for bioimage analysis

In recent years, there has been an increasing interest in getting a proper quantitative understanding of cellular and molecular processes [1], . One of the major challenges of current biomedical research is to characterize not only the spatial organization of these complex systems but also their spatiotemporal relationships , . Microscopy has matured to the point that it enables sensitive time-lapse imaging of cells in vivo and even of single molecules , . Making microscopy more quantitative brings important scientific benefits in the form of improved performance and reproducibility. This has been fostered by the development of technological achievements such as high-throughput microscopy. A direct consequence is that the size and complexity of image data are increasing. Time-lapse experiments commonly generate hundreds to thousands of images, each containing hundreds of objects to be analyzed [7]. These data often cannot be analyzed manually because the manpower required would be too extensive, which calls for automated methods for the analysis of biomedical images. Such computerized extraction of quantitative information out of the rapidly expanding amount of acquired data remains a major challenge. The development of the related algorithms is nontrivial and is one of the most active fronts in the new field of bioimage informatics [8]?[11]. Segmenting thousands of individual biological objects and tracking them over time is remarkably difficult. A typical algorithm will need to be tuned to the imaging modality and will have to cope with the fact that cells can be tightly packed and may appear in various configurations, making them difficult to segregate.
The fractional spline wavelet transform: definition end implementation

We define a new wavelet transform that is based on a previously defined family of scaling functions: the fractional B-splines. The interest of this family is that they interpolate between the integer degrees of polynomial B-splines and that they allow a fractional order of approximation. The orthogonal fractional spline wavelets essentially behave as fractional differentiators. This property seems promising for the analysis of 1/f/sup /spl alpha// noise that can be whitened by an appropriate choice of the degree of the spline transform. We present a practical FFT-based algorithm for the implementation of these fractional wavelet transforms, and give some examples of processing.
MOMS: maximal-order interpolation of minimal support

We consider the problem of interpolating a signal using a linear combination of shifted versions of a compactly-supported basis function phi(x). We first give the expression for the cases of phi's that have minimal support for a given accuracy (also known as "approximation order"). This class of functions, which we call maximal-order-minimal-support functions (MOMS) is made of linear combinations of the B-spline of the same order and of its derivatives. We provide an explicit form of the MOMS that maximizes the approximation accuracy when the step-size is small enough. We compute the sampling gain obtained by using these optimal basis functions over the splines of the same order. We show that it is already substantial for small orders and that it further increases with the approximation order L. When L is large, this sampling gain becomes linear; more specifically, its exact asymptotic expression is 2/(pie)L. Since the optimal functions are continuous, but not differentiable, for even orders, and even only piecewise continuous for odd orders, our result implies that regularity has little to do with approximating performance. These theoretical findings are corroborated by experimental evidence that involves compounded rotations of images.
Design of Steerable Wavelets to Detect Multifold Junctions

We propose a framework for the detection of junctions in images. Although the detection of edges and key points is a well examined and described area, the multiscale detection of junction centers, especially for odd orders, poses a challenge in pattern analysis. The goal of this paper is to build optimal junction detectors based on 2D steerable wavelets that are polar-separable in the Fourier domain. The approaches we develop are general and can be used for the detection of arbitrary symmetric and asymmetric junctions. The backbone of our construction is a multiscale pyramid with a radial wavelet function where the directional components are represented by circular harmonics and encoded in a shaping matrix. We are able to detect M-fold junctions in different scales and orientations. We provide experimental results on both simulated and real data to demonstrate the effectiveness of the algorithm.
Digital phase reconstruction via iterative solutions of transport-of-intensity equation

We develop a variational algorithm for reconstructing phase objects from a series of bright field micrographs. Our mathematical model is based on the transport-of-intensity equation (TIE), which links the phase of a complex field to the axial derivative of its intensity. To reduce reconstruction artifacts, we formulate TIE in a regularized fashion by introducing a family of penalty functionals based on the eigenvalues of the structure tensor. To solve the arising optimization problem, we propose an algorithm based on the alternating direction method of multipliers (ADMM). We apply our method on simulated data and illustrate improved performance compared to the conventional methods such as Tikhonov and total variation (TV) regularizations. We further demonstrate the applicability of the proposed approach by applying it to experimentally-acquired bright field data.