nils-herrmann/clean_scirepeval huggingface dataset:
A Novel Algorithm for Extraction of the Layers of the Cornea

Accurate corneal layer boundary extraction from optical coherence tomograms can provide precise layer thickness measurements required in the analysis of corneal disease. This paper establishes a novel approach to precisely obtain the five primary corneal layer boundaries. The proposed method determines correspondence relationships between the layer boundaries to facilitate robust boundary extraction in the presence of noise and artifacts. The first phase of the method applies morphological operators to enhance the prominent structural features of the cornea. The second phase uses a semi-automated segmentation algorithm to extract the upper and lower boundaries of the cornea; these boundaries are used to register the corneal image. The final phase extracts all five boundaries using a global optimization method exploiting the medial correspondence relationship between each layers.The proposed method is tested and verified using a representative set of optical coherence tomography images and compared against several state of the art methods. The proposed method is demonstrated to be more robust to noise, to provide more accurate segmentation results, and to require fewer user interactions than the other published methods.
Remote sensing image synthesis

For remote sensing data, the testing analysis tools is difficult since the ground-truth data are not available in many cases. To address this issue, a novel method for image synthesis is presented for use as a evaluation test-bed. Given the scale-dependent, non-stationary nature of remotely sensed data, a new modeling approach that combines a resolution-oriented hierarchical method with a regional label-oriented binary tree structure is introduced to synthesize such complex data. In this paper, we are proposing on first synthesizing a label field, which contains the complex structural characteristics, then synthesizing the texture based on the generated label field for a more accurate modeling. Experimental results using oper-ational RADARSAT SAR sea-ice image data show that the proposed method is capable of modeling complex, nonstationary scale structures, thus making it well-suitable to produce reliable, realistic remote sensing imagery.
Computationally efficient multiscale estimation of large-scale dynamic systems

Statistical estimation of large-scale dynamic systems governed by stochastic partial differential equations is important in a wide range of scientific applications. However, the realization of computationally efficient algorithms for statistical estimation of such dynamic systems is very difficult. Conventional linear least squares methods are impractical for both computational and storage reasons. A previously-developed multiscale estimation methodology has been successfully applied to a number of large-scale static estimation problems. In this paper we apply the multiscale approach to the more challenging dynamic estimation problems, introducing a recursive procedure that efficiently propagates multiscale models for the estimation errors in a manner analogous to, but more efficient than, the Kalman filter's propagation of the error covariances. We illustrate our research in the context of 1-D and 2-D diffusive processes.
Precise High Speed Multi-Target Multi-Sensor Local Positioning System

When used for tracking, the combination of infrared (IR) and an internal measurement unit (IMU) allows researchers and industry to locate objects to within 1 cm at over 200 Hz with a latency less than 2 ms. This novel tracking  system uses multiple cameras to triangulate an IR LED placed on the object and utilizes IMU data to measure the object's orientation and allow the system to be robust against visual occlusions. The cost-effective IR system is robust against illumination allowing the object to be tracked at over 50 feet from the camera positions. This distance is expected to increase with additional development. This paper describes the preliminary algorithms that utilize the information from both the IR and IMU systems in order to precisely track an object. The algorithms are tested against simulated data generated from profiling the hardware and real data collected from a system prototype.
A probabilistic living cell segmentation model

A better understanding of cell behavior is very important in drug and disease research. Cell size, shape, and motility may play a key role in stem-cell specialization or cancer development. However the traditional method of inferring these values from image sequences manually is such an onerous task that automated methods of cell tracking and segmentation are in high demanded, especially given the increasing amount of cell data being collected. In this paper, a novel probabilistic cell model is designed to segment the individual hematopoietic stem cells (HSCs) extracted from mice bone marrow cells. The proposed cell model has been successfully applied to HSC segmentation, identifying the most probable cell locations in the image on the basis of cell brightness and morphology.
Adaptive multi-resolution CRF-based contour tracking

This paper presents a novel tracker, based on combining a linear chain conditional random field (CRF) adaptive multi-resolution segmentation with an unscented Kalman filter (UKF). Specifically, the proposed method combines multiple features and multiple resolutions to facilitate video tracking. The advantages of our method lie in its speed and robustness. Speed is dramatically improved by taking into account multiple resolutions in one dimensional CRF-based segmentation. Robustness is achieved by using multiple cues. The performance of the proposed method is demonstrated in human head tracking with a non-stationary camera. Results show that we are able to maintain real-time processing on quite generous video sequences. The paper argues that our approach is faster, more efficient and more robust than the conventional UKF.
Model-based tracking: Temporal conditional random fields

We present Temporal Conditional Random Fields, a probabilistic framework for modeling object motion. The state-of-the-art discriminative approach for tracking is known as dynamic conditional random fields. This method models an event based on spatial and temporal relation between pixels in an image sequence without any prediction. To facilitate such a powerful graphical model with prediction and come up with a CRF-based predictor, we propose a set of new temporal relations for object tracking, with feature functions such as optical flow (calculated among consequent frames) and line filed features. We validate our proposed method with real data sequences and will show that the TCRF prediction is nearly equivalent with result of template matching. Experimental results indicate that our TCRF can predict future state of any maneuvering target with nearly zero error during its constant motion. Not only the proposed TCRF has a simple and easy to implement structure, but also it outperforms the state-of-the-art predictors such as Kalman filter.
Vision-based speaker detection using Bayesian networks

The development of user interfaces based on vision and speech requires the solution of a challenging statistical inference problem: The intentions and actions of multiple individuals must be inferred from noisy and ambiguous data. We argue that Bayesian network models are an attractive statistical framework for cue fusion in these applications. Bayes nets combine a natural mechanism for expressing contextual information with efficient algorithms for learning and inference. We illustrate these points through the development of a Bayes net model for detecting when a user is speaking. The model combines four simple vision sensors: face detection, skin color, skin texture, and mouth motion. We present some promising experimental results.
Hierarchical annealing for scientific models

The computational complexity of simulated annealing makes it an impractical tool in many applications, particularly for complex, non-local models on very large 2D and 3D domains as desired in many scientific contexts. In particular, it is very difficult to produce large scale structure from a fine, pixellated lattice. Thus a hierarchical approach is intuitively attractive. However, existing approaches are few and limited. Motivated by a current problem in porous media, we develop a hierarchical approach to complex model sampling. In experiments, this approach results in 1-2 orders of magnitude computational gain, and significant gains in convergence as well.
A Statistical Thresholding Method for Cell Tracking

Tracking the motion of cells in culture is a task, which often still Is undertaken manually, and for which automated methods are strongly desirable. Researchers visually perform cell motion analysis, observe cell movements and cell shape changes for hours to discover when, where and how fast It moves, splits or dies. Hematopoletlc stem cells (HSCs) proliferate and differentiate to different blood cell types continuously during their lifetime, and are of substantial interest in gene therapy, cancer, and stem-cell research. In this paper a statistical method is introduced to track HSCs over time. A statistical thresholding method is combined with joint probabilistic data association in the proposed HSC tracker
Automated analysis and detection of cracks in underground scanned pipes

Closed circuit television (CCTV) surveys are used widely in North America to assess the structural integrity of underground pipes. The video images are examined visually and classified into grades according to degrees of damage. The human eye is extremely effective at recognition and classification, but it is not suitable for assessing pipe defects in thousands of miles of pipeline images due to fatigue, subjectivity and cost. This paper presents ongoing research into the automatic assessment of the structural condition of underground pipes for the purpose of preventive maintenance by municipalities.
Multiresolution model development for overlapping trees via canonical correlation analysis

A class of multiscale stochastic models has been introduced in which Gaussian random processes are described by scale-recursive dynamics that are indexed by the nodes of a tree. One of the primary reasons the framework is useful is that it leads to an extremely fast, statistically optimal algorithm for least-squares estimation in the context of 2-D images. We refine this approach to estimation by eliminating the visually distracting blockiness that has been observed in the previous work. We eliminate the blockiness by discarding the standard assumption that distinct nodes at a given level of our tree correspond to disjoint portions of the image domain; as a consequence of this simple idea, a given image pixel may now correspond to several tree nodes. We develop tools for systematically building overlapping-tree multiscale representations of prespecified statistics, and we develop a corresponding estimation algorithm for this processes. In this way, we achieve nearly optimal estimation results, we generate corresponding error covariance information, and we eliminate blockiness without sacrificing the resolution of fine-scale detail.
Self-similarity measure for multi-modal image registration

In medical image analysis, multi-modal registration has been a challenging task due to the complex intensity relationship between images to be aligned. Conventional multi-modal approaches tend to assess the accuracy of the alignment by measuring a similarity based on statistical dependency of the intensity values between images. However, measuring statistical similarity measures, such as mutual information, is not promising, especially in those cases with complex and spatially dependent intensity relations. A new similarity measure is proposed based on the concept of self-similarity, the similarity of patches within an image, motivated by the fact that similar structures are more probable to undergo similar intensity transformations. The method is applied to the registration framework to align simulated and real brain images from different modalities and compared to the conventional multi-modal registration method. Quantitative evaluation of the method demonstrates that better accuracy can be achieved.
SEC: Stochastic Ensemble Consensus Approach to Unsupervised SAR Sea-Ice Segmentation

The use of synthetic aperture radar (SAR) has become an integral part of sea-ice monitoring and analysis in the polar regions. An important task in sea-ice analysis is to segment SAR sea-ice imagery based on the underlying ice type, which is a challenging task to perform automatically due to various imaging and environmental conditions. A novel stochastic ensemble consensus approach to sea-ice segmentation (SEC) is presented to tackle this challenging task. In SEC, each pixel in the SAR sea-ice image is assigned an initial sub-class based on its tonal characteristics. Ensembles of random samples are generated from a random field representing the SAR sea-ice imagery. The generated ensembles are then used to re-estimate the sub-class of the pixels using a weighted median consensus strategy. Based on the probability distribution of the sub-classes, an expectation maximization (EM) approach is utilized to estimate the final class likelihoods using a Gaussian mixture model (GMM). Finally, maximum likelihood (ML) classification is performed to estimate the final class of each pixel within the SAR sea-ice imagery based on the estimated GMM and the assigned sub-classes. SEC was tested using a variety of operational RADARSAT-1 and RADARSAT-2 SAR sea-ice imagery provided by the Canadian Ice Service (CIS) and was shown to produce successfully segmentation results that were superior to approaches based on K-means clustering, Gamma mixture models, and Markov Random Field (MRF) models for sea-ice segmentation.
Decoupled Active Contour (DAC) for Boundary Detection

The accurate detection of object boundaries via active contours is an ongoing research topic in computer vision. Most active contours converge toward some desired contour by minimizing a sum of internal (prior) and external (image measurement) energy terms. Such an approach is elegant, but suffers from a slow convergence rate and frequently misconverges in the presence of noise or complex contours. To address these limitations, a decoupled active contour (DAC) is developed which applies the two energy terms separately. Essentially, the DAC consists of a measurement update step, employing a Hidden Markov Model (HMM) and Viterbi search, and then a separate prior step, which modifies the updated curve based on the relative strengths of the measurement uncertainty and the nonstationary prior. By separating the measurement and prior steps, the algorithm is less likely to misconverge; furthermore, the use of a Viterbi optimizer allows the method to converge far more rapidly than energy-based iterative solvers. The results clearly demonstrate that the proposed approach is robust to noise, can capture regions of very high curvature, and exhibits limited dependence on contour initialization or parameter settings. Compared to five other published methods and across many image sets, the DAC is found to be faster with better or comparable segmentation accuracy.
Color-based tracking of heads and other mobile objects at video frame rates

We develop a simple and very fast method for object tracking based exclusively on color information in digitized video images. Running on a Silicon Graphics R4600 Indy system with an IndyCam, our algorithm is capable of simultaneously tracking objects at full frame size (640/spl times/480 pixels) and video frame rate (30 fps). Robustness with respect to occlusion is achieved via can explicit hypothesis-tree model of the occlusion process. We demonstrate the efficacy of our technique in the challenging task of tracking people, especially tracking human heads and hands.
Toward an Optimal Solution for Multitarget Tracking

There are ever increasing number of applications of multi-target tracking and considerable research has been conducted to solve this problem. Multi-target tracking is a NP-hard problem and almost all of the present multi-target tracking algorithms are sub-optimal by finding the solution in a reduced hypothesis space. In this paper we introduce a new approach toward finding the optimal single frame solution for general multi-target tracking problem. Our proposed method finds the optimal solution using linear programming optimization method. The proposed method has been successfully applied to synthetic and real data.
Texture CLassification Using Compressed Sensing

This paper presents a simple, novel, yet very powerful approach for texture classification based on compressed sensing and bag of words model, suitable for large texture database applications with images obtained under unknown viewpoint and illumination. At the feature extraction stage, a small set of random features are extracted from local image patches. The random features are embedded into the bag of words model to perform texture classification. Random feature extraction surpasses many conventional feature extraction methods, despite their careful design and complexity. We conduct extensive experiments on the CUReT database to evaluate the performance of the proposed approach. It is demonstrated that excellent performance can be achieved by the proposed approach using a small number of random features, as long as the dimension of the feature space is above certain threshold. Our approach is compared with recent state-of-the-art methods: the Patch method (Varma and Zisserman, TPAMI 09), the MR8 filter bank method (Varma and Zisserman, IJCV 05) and the LBP method (Ojala et al., TPAMI 02). It is shown that the proposed method significantly outperforms MR8 and LBP and is at least as good as the Patch method with drastic reduction in storage and computational complexity.
Mapping and pseudo-inverse algorithms for data assimilation

Among existing ocean data assimilation methodologies, reduced-state Kalman filters are a widely-studied compromise between resolution, optimality, error specification, and computational feasibility. In such reduced-state filters, the measurement update takes place on a coarser grid than that of the general circulation model (GCM); therefore, these filters require mapping operators from the GCM grid to the reduced state and vice-versa. The general requirements are that the state-reduction and interpolation operators be pseudo-inverses of each other, that the coarse state defines a closed dynamical system, that the mapping operations be insensitive to noise, and that they be appropriate for regions with irregular coastlines and bathymetry. In this paper we investigate a variety of approaches, including computing the pseudoinverse by brute force, using the FFT, subsampling methods, implicit methods, and finally develop a novel iterative approach. We also evaluate the mapping performance of eleven interpolation kernels; surprisingly, common kernels such as bilinear, exponential, Gaussian, and sinc, performed only moderately well. This comprehensive study greatly reduces the computational bottleneck and guesswork of pseudo-inverse algorithms, making possible the application of reduced-state filters to global problems at state-of-the-art resolution.
Fractal estimation using models on multiscale trees

We estimate the Hurst parameter H of fractional Brownian motion (or, by extension, the fractal exponent /spl phi/ of stochastic processes having 1/f/sup /spl phi//-like spectra) by applying a multiresolution framework. This framework admits an efficient likelihood function evaluation, allowing us to compute the maximum likelihood estimate of this fractal parameter with relative ease. In addition to yielding results that compare well with other proposed methods, and in contrast with other approaches, our method is directly applicable with, at most, very simple modification in a variety of other contexts including fractal estimation given irregularly sampled data or nonstationary measurement noise and the estimation of fractal parameters for 2-D random fields.
Probabilistic cost functions for network flow phase unwrapping

The well-studied interferometric synthetic aperture radar (InSAR) problem for digital elevation map generation involves the derivation of topography from radar phase. The topography is a function of the full phase, whereas the measured phase is known module 2/spl pi/, necessitating the process of recovering full phase values via phase unwrapping. This mathematical process becomes difficult through the presence of noise and phase discontinuities. The authors' research is motivated by recent research that models phase unwrapping as a network flow minimization problem. The cost function to be optimized is a weighted L/sup 1/-norm of the phase discontinuities. Determining these cost weights is critical, yet past work in the literature does not reflect the statistics of the unwrapping problem. The purpose of this paper is to propose a new method to compute the flow weights from a theoretical foundation. Specifically, they formulate phase unwrapping as a maximum likelihood (ML) estimation problem, which they mathematically rewrite as a network flow problem with a specific choice of weights. The approach is based on estimating the probability of phase discontinuities, which can be derived as a function of coherence and topographic slope from the known statistical properties of SAR phase.
Automatic Skin Lesion Segmentation via Iterative Stochastic Region Merging

An automatic method for segmenting skin lesions in conventional macroscopic images is presented. The images are acquired with conventional cameras, without the use of a dermoscope. Automatic segmentation of skin lesions from macroscopic images is a very challenging problem due to factors such as illumination variations, irregular structural and color variations, the presence of hair, as well as the occurrence of multiple unhealthy skin regions. To address these factors, a novel iterative stochastic region-merging approach is employed to segment the regions corresponding to skin lesions from the macroscopic images, where stochastic region merging is initialized first on a pixel level, and subsequently on a region level until convergence. A region merging likelihood function based on the regional statistics is introduced to determine the merger of regions in a stochastic manner. Experimental results show that the proposed system achieves overall segmentation error of under 10% for skin lesions in macroscopic images, which is lower than that achieved by existing methods.
Deep Randomly-Connected Conditional Random Fields For Image Segmentation

The use of Markov random fields (MRFs) is a common approach for performing image segmentation, where the problem is modeled using MRFs that incorporate priors on neighborhood nodes to allow for efficient Maximum a Posteriori inference. These local MRF models often result in smoothed segmentation boundaries, since they penalize the assignment of different labels to neighboring pixels and are limited in the use of long-range interactions. Although recent work on fully connected random fields and deep random fields has shown to be very promising in addressing these issues, both streams of approaches face certain limitations, which could affect inference performance and computational tractability. In this paper, we introduce the concept of deep randomly connected conditional random fields DRCRF, which fuse fully-connected random fields and deep random fields together to obtain benefits from long-range interactions while allowing for efficient inference using arbitrary potential functions. Leveraging random graph theory, the concept of stochastic cliques is incorporated into a deep CRF structure to take better advantage of long-range interactions while maintaining computational tractability. The experimental results demonstrate that the proposed DRCRF framework outperforms existing fully connected CRF frameworks and provides results comparable to the principled deep random field framework, which is among the state of the art in random field frameworks for image segmentation.