nils-herrmann/clean_scirepeval huggingface dataset:
Image segmentation using clustering with saddle point detection

We discuss a novel statistical framework for image segmentation based on nonparametric clustering. By employing the mean shift procedure for analysis, image regions are identified as clusters in the joint color-spatial domain. To measure the significance of each cluster we use a test statistics that compares the estimated density of the cluster mode with the estimated density on the cluster boundary. The cluster boundary in the color domain is defined by saddle points lying on the cluster borders defined in the spatial domain. The proposed technique compares favorably to other segmentation methods described in literature.
A probabilistic framework for object recognition in video

We propose a solution to the problem of object recognition given a continuous video sequence containing multiple views of an object. Initially, object models are acquired from images of the objects taken from different views. Recognition is achieved from the video sequences by employing a multiple hypothesis approach. Appearance similarity, and pose transition smoothness constraints are used to estimate the probability of the measurement being generated from a certain model hypothesis at each time instant. A smooth gradient direction feature that is quasiinvariant to illumination changes and noise is used to represent the appearance of object. The pose of the object at each time instant is modelled as a von Mises-Fisher distribution. Recognition is achieved by choosing the hypothesis set that has accumulated the maximum evidence at the end of the sequence. We have performed detailed experiments demonstrating the viability of the proposed approach.
Personalized learning-based segmentation of thoracic aorta and main branches for diagnosis and treatment planning

Coarctation of the aorta (CoA), is an obstruction of the aortic arch present in 5-8% of congenital heart diseases. For children older than a year, CoA is increasingly treated by aortic stenting instead of surgical repair. In pediatric cardiology, CMR is accepted as the standard non-invasive imaging modality to assess the aortic arch in it's entire spatial context . Interpreting such 3D datasets are required to assess the underlying anatomy during both diagnosis and therapy planning phases. However this process is time consuming and varies with operator skills. Within this study we propose - for the first time in our knowledge - a method of automatic segmentation of the lumen of thoracic aorta and main branches. The personalized model of the aorta and the supra-aortic arteries, automatically estimated from 3D CMR data, will provide better understanding of the complexity of pathology and assist the cardiologist to choose the best treatment and timing of repair. A hierarchical framework based on robust machine-learning algorithms is proposed to estimate the personalized model parameters. Experiments throughout 212 3D CMR volumes demonstrate model estimation error of 3.24 mm and average computation time of 8 sec. combined with clinical evaluation on 32 patients.
Smart cameras with real-time video object generation

The paper presents a system for video object generation and selective encoding with applications in surveillance, mobile videophones, and the automotive industry. Object tracking and MPEG-4 compression are performed in real-time. The system belongs to a new generation of intelligent vision sensors called smart cameras, which execute autonomous vision tasks and report events and data to a remote base-station. A detection module signals the presence of an object of interest within the camera field of view, while the tracking part follows the target to generate temporal trajectories. The compression is MPEG-4 compliant and implements the simple profile of the standard, which is capable of encoding up to four video objects. At the same time, the compression is selective, maintaining a higher quality for foreground objects and a lower quality for background representation. This property contributes to bandwidth reduction while preserving the essential information of foreground objects. The system performance is demonstrated in experiments that involve objects representing faces and vehicles seen from both static and moving cameras.
Automatic ovarian follicle quantification from 3D ultrasound data using global/local context with database guided segmentation

In this paper, we present a novel probabilistic framework for automatic follicle quantification in 3D ultrasound data. The proposed framework robustly estimates size and location of each individual ovarian follicle by fusing the information from both global and local context. Follicle candidates at detected locations are then segmented by a novel database guided segmentation method. To efficiently search hypothesis in a high dimensional space for multiple object detection, a clustered marginal space learning approach is introduced. Extensive evaluations conducted on 501 volumes containing 8108 follicles showed that our method is able to detect and segment ovarian follicles with high robustness and accuracy. It is also much faster than the current ultrasound manual workflow. The proposed method is able to streamline the clinical workflow and improve the accuracy of existing follicular measurements.
Kernel-Based Object Tracking

A new approach toward target representation and localization, the central component in visual tracking of nonrigid objects, is proposed. The feature histogram-based target representations are regularized by spatial masking with an isotropic kernel. The masking induces spatially-smooth similarity functions suitable for gradient-based optimization, hence, the target localization problem can be formulated using the basin of attraction of the local maxima. We employ a metric derived from the Bhattacharyya coefficient as similarity measure, and use the mean shift procedure to perform the optimization. In the presented tracking examples, the new method successfully coped with camera motion, partial occlusions, clutter, and target scale variations. Integration with motion filters and data association techniques is also discussed. We describe only a few of the potential applications: exploitation of background information, Kalman tracking using motion models, and face tracking.
Patient-specific modeling of left heart anatomy, dynamics and hemodynamics from high resolution 4D CT

There is a growing need for patient-specific cardiac models for intervention planning, outcome prediction or assessment of cardiac disease progression. However, most of the recent work in cardiovascular simulation relies on generic heart models built from at most one cardiac phase with simplified motion, driven by fluid dynamics equations. We propose to advance the state-of-the-art by exploiting a comprehensive, patient-specific left heart model extracted from 4D Computed Tomography (CT) data. Explicit physiological constrains are captured in the modeling of the left ventricle (including outflow tract), left atrium (including pulmonary veins), mitral valve, and aortic valve (including ascending aorta). By using this patient-specific model as an input to a 3D Navier-Stokes solver we derive realistic hemodynamics, constrained by the local anatomy, along the entire heart cycle. We present a differential assessment of the flow dynamics corresponding to specific heart conditions. The simulation results shed light upon the functional differences between one normal and two diseased hearts - one with a dilated aortic root and one with a bicuspid aortic valve.
Database-guided segmentation of anatomical structures with complex appearance

The segmentation of anatomical structures has been traditionally formulated as a perceptual grouping task, and solved through clustering and variational approaches. However, such strategies require the a priori knowledge to be explicitly defined in the optimization criterion, e.g., "high-gradient border", "smoothness"', or "similar intensity or texture". This approach is limited by the validity of underlying assumptions and cannot capture complex structure appearance. This paper introduces database-guided segmentation as a new data-driven paradigm that directly exploits expert annotation of interest structures in large medical databases. Segmentation is formulated as a two-step learning problem. The first step is structure detection where we learn how to discriminate between the object of interest and background. The resulting classifier based on a boosted cascade of simple features also provides a global rigid transformation of the structure. The second step is shape inference where we use a sample-based representation of the joint distribution of appearance and shape annotations. To learn the association between the complex appearance and shape we propose a feature selection mechanism and the corresponding metric. We show that the selected features are better than using directly the appearance and illustrate the performance of the proposed method on a large set of ultrasound heart images.
Joint Real-time Object Detection and Pose Estimation Using Probabilistic Boosting Network

In this paper, we present a learning procedure called probabilistic boosting network (PBN) for joint real-time object detection and pose estimation. Grounded on the law of total probability, PBN integrates evidence from two building blocks, namely a multiclass boosting classifier for pose estimation and a boosted detection cascade for object detection. By inferring the pose parameter, we avoid the exhaustive scanning for the pose, which hampers real time requirement. In addition, we only need one integral image/volume with no need of image/volume rotation. We implement PBN using a graph-structured network that alternates the two tasks of foreground/background discrimination and pose estimation for rejecting negatives as quickly as possible. Compared with previous approaches, we gain accuracy in object localization and pose estimation while noticeably reducing the computation. We invoke PBN to detect the left ventricle from a 3D ultrasound volume, processing about 10 volumes per second, and the left atrium from 2D images in real time.
A fast and accurate tracking algorithm of left ventricles in 3D echocardiography

Tracking of left ventricles in 3D echocardiography is a challenging topic because of the poor quality of ultrasound images and the speed consideration. In this paper, a fast and accurate learning based 3D tracking algorithm is presented. A novel one-step forward prediction is proposed to generate the motion prior using motion manifold learning. Collaborative trackers are introduced to achieve both temporal consistence anproc biomedical optical ima image segmentation cellular biophys fluores biology comd tracking robustness. The algorithm is completely automatic and computationally efficient. The mean point-to-mesh error of our algorithm is 1.28 mm. It requires less than 1.5 seconds to process a 3D volume (160 x 148 x 208 voxels).
Robust discriminative wire structure modeling with application to stent enhancement in fluoroscopy

Learning-based methods have been widely used in detecting landmarks or anatomical structures in various medical imaging applications. The performance of discriminative learning techniques has been demonstrated superior to traditional low-level filtering in robustness and scalability. Nevertheless, some structures and patterns are more difficult to be defined by such methods and complicated and ad-hoc methods still need to be used, e.g. a non-rigid and highly deformable wire structure. In this paper, we propose a novel scheme to train classifiers to detect the markers and guide wire segment anchored by markers. The classifier utilizes the markers as the end point and parameterizes the wire in-between them. The probabilities of the markers and the wire are integrated in a Bayesian framework. As a result, both the marker and the wire detection are improved by such a unified approach. Promising results are demonstrated by quantitative evaluation on 263 fluoroscopic sequences with 12495 frames. Our training scheme can further be generalized to localize longer guidewire with higher degrees of parameterization.
Prediction Based Collaborative Trackers (PCT): A Robust and Accurate Approach Toward 3D Medical Object Tracking

Robust and fast 3D tracking of deformable objects, such as heart, is a challenging task because of the relatively low image contrast and speed requirement. Many existing 2D algorithms might not be directly applied on the 3D tracking problem. The 3D tracking performance is limited due to dramatically increased data size, landmarks ambiguity, signal drop-out or complex nonrigid deformation. In this paper, we present a robust, fast, and accurate 3D tracking algorithm: prediction based collaborative trackers (PCT). A novel one-step forward prediction is introduced to generate the motion prior using motion manifold learning. Collaborative trackers are introduced to achieve both temporal consistency and failure recovery. Compared with tracking by detection and 3D optical flow, PCT provides the best results. The new tracking algorithm is completely automatic and computationally efficient. It requires less than 1.5 s to process a 3D volume which contains millions of voxels. In order to demonstrate the generality of PCT, the tracker is fully tested on three large clinical datasets for three 3D heart tracking problems with two different imaging modalities: endocardium tracking of the left ventricle (67 sequences, 1134 3D volumetric echocardiography data), dense tracking in the myocardial regions between the epicardium and endocardium of the left ventricle (503 sequences, roughly 9000 3D volumetric echocardiography data), and whole heart four chambers tracking (20 sequences, 200 cardiac 3D volumetric CT data). Our datasets are much larger than most studies reported in the literature and we achieve very accurate tracking results compared with human experts' annotations and recent literature.
Four-Chamber Heart Modeling and Automatic Segmentation for 3-D Cardiac CT Volumes Using Marginal Space Learning and Steerable Features

We propose an automatic four-chamber heart segmentation system for the quantitative functional analysis of the heart from cardiac computed tomography (CT) volumes. Two topics are discussed: heart modeling and automatic model fitting to an unseen volume. Heart modeling is a nontrivial task since the heart is a complex nonrigid organ. The model must be anatomically accurate, allow manual editing, and provide sufficient information to guide automatic detection and segmentation. Unlike previous work, we explicitly represent important landmarks (such as the valves and the ventricular septum cusps) among the control points of the model. The control points can be detected reliably to guide the automatic model fitting process. Using this model, we develop an efficient and robust approach for automatic heart chamber segmentation in 3D CT volumes. We formulate the segmentation as a two-step learning problem: anatomical structure localization and boundary delineation. In both steps, we exploit the recent advances in learning discriminative models. A novel algorithm, marginal space learning (MSL), is introduced to solve the 9-D similarity transformation search problem for localizing the heart chambers. After determining the pose of the heart chambers, we estimate the 3D shape through learning-based boundary delineation. The proposed method has been extensively tested on the largest dataset (with 323 volumes from 137 patients) ever reported in the literature. To the best of our knowledge, our system is the fastest with a speed of 4.0 s per volume (on a dual-core 3.2-GHz processor) for the automatic segmentation of all four chambers.
Performance analysis in content-based retrieval with textures

The features employed in content-based retrieval are most often simple low-level representations, while a human observer judges similarity between images based on high-level semantic properties. Using textures as an example, we show that a more accurate description of the underlying distribution of low-level features does not improve the retrieval performance. We also introduce the simplified multiresolution symmetric autoregressive model for textures, and the Bhattacharyya distance based similarity measure. Experiments are performed with four texture representations and four similarity measures over the Brodatz and Vis Tex databases.
Fractal Clustering and Knowledge-driven Validation Assessment for Gene Expression Profiling

DNA microarray experiments generate a substantial amount of information about the global gene expression. Gene expression profiles can be represented as points in multi-dimensional space. It is essential to identify relevant groups of genes in biomedical research. Clustering is helpful in pattern recognition in gene expression profiles. A number of clustering techniques have been introduced. However, these traditional methods mainly utilize shape-based assumption or some distance metric to cluster the points in multi-dimension linear Euclidean space. Their results shows poor consistence with the functional annotation of genes in previous validation study. From a novel different perspective, we propose fractal clustering method to cluster genes using intrinsic (fractal) dimension from modern geometry. This method clusters points in such a way that points in the same clusters are more self-affine among themselves than to the points in other clusters. We assess this method using annotation-based validation assessment for gene clusters. It shows that this method is superior in identifying functional related gene groups than other traditional methods
Density estimation-based information fusion for multiple motion computation

Vision tasks, such as motion analysis, object tracking, robot localization, and 3D modeling, often require the fusion of estimates coming from different sources. Most of the fusion algorithms, however, are not robust with respect to outliers and only consider one source models. Their performance deteriorates when initial assumptions are not valid (e.g., the presence of outliers in the data or data corresponding to multiple motions). The paper presents a statistical solution to the fusion problem based on variable-bandwidth kernel density estimation. The fusion estimate is represented by the mode of a density function that exploits the uncertainty of the estimates to be fused. We show that the fusion estimate is consistent and conservative. Since our construction is founded on density estimation, it handles naturally outliers and multiple source models. We test the density-based fusion for the task of multiple motion computation. Superior experimental results validate our theory.
Probabilistic 3D Polyp Detection in CT Images: The Role of Sample Alignment

Automatic polyp detection is an increasingly important task in medical imaging with virtual colonoscopy [15] being widely used. In this paper, we present a 3D object detection algorithm and show its application on polyp detection from CT images. We make the following contributions: (1) The system adopts Probabilistic Boosting Tree (PBT) to probabilistically detect polyps. Integral volume and 3D Haar filters are introduced to achieve fast feature computation. (2) We give an explicit convergence rate analysis for the AdaBoost algorithm  and prove that the error at each step \in t+1. is tightly bounded by the previous error \in t. (3) For a 3D polyp template, a generative model is defined. Given the bound and convergence analysis, we analyze the role of "sample alignment" in the template design and devise a robust and efficient algorithm for polyp detection. The overall system has been tested on 150 volumes and the results obtained are very encouraging.
Lymph node detection in 3-D chest CT using a spatial prior probability

Lymph nodes have high clinical relevance but detection is challenging as they are hard to see due to low contrast and irregular shape. In this paper, a method for fully automatic mediastinal lymph node detection in 3-D computed tomography (CT) images of the chest area is proposed. Discriminative learning is used to detect lymph nodes based on their appearance. Because lymph nodes can easily be confused with other structures, it is vital to incorporate as much anatomical knowledge as possible to achieve good detection rates. Here, a learned prior of the spatial distribution is proposed to model this knowledge. As atlas matching is generally inaccurate in the chest area because of anatomical variations, this prior is not learned in the space of a single atlas, but in the space of multiple ones that are attached to anatomical structures. During test, the priors are weighted and merged according to spatial distances. Cross-validation on 54 CT datasets showed that the prior based detector yields a true positive rate of 52.3% for seven false positives per volume image, which is about two times better than without a spatial prior.
A probabilistic, hierarchical, and discriminant framework for rapid and accurate detection of deformable anatomic structure

We propose a probabilistic, hierarchical, and discriminant (PHD) framework for fast and accurate detection of deformable anatomic structures from medical images. The PHD framework has three characteristics. First, it integrates distinctive primitives of the anatomic structures at global, segmental, and landmark levels in a probabilistic manner. Second, since the configuration of the anatomic structures lies in a high-dimensional parameter space, it seeks the best configuration via a hierarchical evaluation of the detection probability that quickly prunes the search space. Finally, to separate the primitive from the background, it adopts a discriminative boosting learning implementation. We apply the PHD framework for accurately detecting various deformable anatomic structures from M- mode and Doppler echocardiograms in about a second.
BoostMotion: Boosting a Discriminative Similarity Function for Motion Estimation

Motion estimation for applications where appearance undergoes complex changes is challenging due to lack of an appropriate similarity function. In this paper, we propose to learn a discriminative similarity function based on an annotated database that exemplifies the appearance variations. We invoke the LogitBoost algorithm to selectively combine weak learners into one strong similarity function. The weak learners based on local rectangle features are constructed as nonparametric 2D piecewise constant functions, using the feature responses from both images, to strengthen the modeling power and accommodate fast evaluation. Because the negatives possess a location parameter measuring their closeness to the positives, we present a locationsensitive cascade training procedure, which bootstraps negatives for later stages of the cascade from the regions closer to the positives. This allows viewing a large number of negatives and steering the training process to yield lower training and test errors. In experiments of estimating the motion for the endocardial wall of the left ventricle in echocardiography, we compare the learned similarity function with conventional ones and obtain improved performances. We also contrast the proposed method with a learning-based detection algorithm to demonstrate the importance of temporal information in motion estimation. Finally, we insert the learned similarity function into a simple contour tracking algorithm and find that it reduces drifting.