David Roche, Debora Gil, & Jesus Giraldo. (2013). Multiple active receptor conformation, agonist efficacy and maximum effect of the system: the conformation-based operational model of agonism,. DDT - Drug Discovery Today, 18(7-8), 365–371.
Abstract: The operational model of agonism assumes that the maximum effect a particular receptor system can achieve (the Em parameter) is fixed. Em estimates are above but close to the asymptotic maximum effects of endogenous agonists. The concept of Em is contradicted by superagonists and those positive allosteric modulators that significantly increase the maximum effect of endogenous agonists. An extension of the operational model is proposed that assumes that the Em parameter does not necessarily have a single value for a receptor system but has multiple values associated to multiple active receptor conformations. The model provides a mechanistic link between active receptor conformation and agonist efficacy, which can be useful for the analysis of agonist response under different receptor scenarios.
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Mikhail Mozerov. (2013). Constrained Optical Flow Estimation as a Matching Problem. TIP - IEEE Transactions on Image Processing, 22(5), 2044–2055.
Abstract: In general, discretization in the motion vector domain yields an intractable number of labels. In this paper we propose an approach that can reduce general optical flow to the constrained matching problem by pre-estimating a 2D disparity labeling map of the desired discrete motion vector function. One of the goals of the proposed paper is estimating coarse distribution of motion vectors and then utilizing this distribution as global constraints for discrete optical flow estimation. This pre-estimation is done with a simple frame-to-frame correlation technique also known as the digital symmetric-phase-only-filter (SPOF). We discover a strong correlation between the output of the SPOF and the motion vector distribution of the related optical flow. The two step matching paradigm for optical flow estimation is applied: pixel accuracy (integer flow), and subpixel accuracy estimation. The matching problem is solved by global optimization. Experiments on the Middlebury optical flow datasets confirm our intuitive assumptions about strong correlation between motion vector distribution of optical flow and maximal peaks of SPOF outputs. The overall performance of the proposed method is promising and achieves state-of-the-art results on the Middlebury benchmark.
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Sergio Vera, Debora Gil, Agnes Borras, Marius George Linguraru, & Miguel Angel Gonzalez Ballester. (2013). Geometric Steerable Medial Maps. MVA - Machine Vision and Applications, 24(6), 1255–1266.
Abstract: In order to provide more intuitive and easily interpretable representations of complex shapes/organs, medial manifolds should reach a compromise between simplicity in geometry and capability for restoring the anatomy/shape of the organ/volume. Existing morphological methods show excellent results when applied to 2D objects, but their quality drops across dimensions.
This paper contributes to the computation of medial manifolds in two aspects. First, we provide a standard scheme for the computation of medial manifolds that avoids degenerated medial axis segments. Second, we introduce a continuous operator for accurate and efficient computation of medial structures of arbitrary dimension. We evaluate quantitatively the performance of our method with respect to existing approaches, by applying them to syn- thetic shapes of known medial geometry. We also show its higher performance for medical imaging applications in terms of simplicity of medial structures and capability for reconstructing the anatomical volume.
Keywords: Medial Representations ,Medial Manifolds Comparation , Surface , Reconstruction
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Gemma Roig, Xavier Boix, R. de Nijs, Sebastian Ramos, K. Kühnlenz, & Luc Van Gool. (2013). Active MAP Inference in CRFs for Efficient Semantic Segmentation. In 15th IEEE International Conference on Computer Vision (pp. 2312–2319).
Abstract: Most MAP inference algorithms for CRFs optimize an energy function knowing all the potentials. In this paper, we focus on CRFs where the computational cost of instantiating the potentials is orders of magnitude higher than MAP inference. This is often the case in semantic image segmentation, where most potentials are instantiated by slow classifiers fed with costly features. We introduce Active MAP inference 1) to on-the-fly select a subset of potentials to be instantiated in the energy function, leaving the rest of the parameters of the potentials unknown, and 2) to estimate the MAP labeling from such incomplete energy function. Results for semantic segmentation benchmarks, namely PASCAL VOC 2010 [5] and MSRC-21 [19], show that Active MAP inference achieves similar levels of accuracy but with major efficiency gains.
Keywords: Semantic Segmentation
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David Vazquez, Antonio Lopez, Daniel Ponsa, & David Geronimo. (2013). Interactive Training of Human Detectors. In Multiodal Interaction in Image and Video Applications (Vol. 48, pp. 169–182). Springer Berlin Heidelberg.
Abstract: Image based human detection remains as a challenging problem. Most promising detectors rely on classifiers trained with labelled samples. However, labelling is a manual labor intensive step. To overcome this problem we propose to collect images of pedestrians from a virtual city, i.e., with automatic labels, and train a pedestrian detector with them, which works fine when such virtual-world data are similar to testing one, i.e., real-world pedestrians in urban areas. When testing data is acquired in different conditions than training one, e.g., human detection in personal photo albums, dataset shift appears. In previous work, we cast this problem as one of domain adaptation and solve it with an active learning procedure. In this work, we focus on the same problem but evaluating a different set of faster to compute features, i.e., Haar, EOH and their combination. In particular, we train a classifier with virtual-world data, using such features and Real AdaBoost as learning machine. This classifier is applied to real-world training images. Then, a human oracle interactively corrects the wrong detections, i.e., few miss detections are manually annotated and some false ones are pointed out too. A low amount of manual annotation is fixed as restriction. Real- and virtual-world difficult samples are combined within what we call cool world and we retrain the classifier with this data. Our experiments show that this adapted classifier is equivalent to the one trained with only real-world data but requiring 90% less manual annotations.
Keywords: Pedestrian Detection; Virtual World; AdaBoost; Domain Adaptation
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Ferran Poveda, Debora Gil, Enric Marti, Albert Andaluz, Manel Ballester, & Francesc Carreras Costa. (2013). Helical structure of the cardiac ventricular anatomy assessed by Diffusion Tensor Magnetic Resonance Imaging multi-resolution tractography. REC - Revista Española de Cardiología, 66(10), 782–790.
Abstract: Deep understanding of myocardial structure linking morphology and function of the heart would unravel crucial knowledge for medical and surgical clinical procedures and studies. Several conceptual models of myocardial fiber organization have been proposed but the lack of an automatic and objective methodology prevented an agreement. We sought to deepen in this knowledge through advanced computer graphic representations of the myocardial fiber architecture by diffusion tensor magnetic resonance imaging (DT-MRI).
We performed automatic tractography reconstruction of unsegmented DT-MRI canine heart datasets coming from the public database of the Johns Hopkins University. Full scale tractographies have been build with 200 seeds and are composed by streamlines computed on the vectorial field of primary eigenvectors given at the diffusion tensor volumes. Also, we introduced a novel multi-scale visualization technique in order to obtain a simplified tractography. This methodology allowed to keep the main geometric features of the fiber tracts, making easier to decipher the main properties of the architectural organization of the heart.
On the analysis of the output from our tractographic representations we found exact correlation with low-level details of myocardial architecture, but also with the more abstract conceptualization of a continuous helical ventricular myocardial fiber array.
Objective analysis of myocardial architecture by an automated method, including the entire myocardium and using several 3D levels of complexity, reveals a continuous helical myocardial fiber arrangement of both right and left ventricles, supporting the anatomical model of the helical ventricular myocardial band described by Torrent-Guasp.
Keywords: Heart;Diffusion magnetic resonance imaging;Diffusion tractography;Helical heart;Myocardial ventricular band.
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David Roche, Debora Gil, & Jesus Giraldo. (2013). Mechanistic analysis of the function of agonists and allosteric modulators: Reconciling two-state and operational models. BJP - British Journal of Pharmacology, 169(6), 1189–202.
Abstract: Two-state and operational models of both agonism and allosterism are compared to identify and characterize common pharmacological parameters. To account for the receptor-dependent basal response, constitutive receptor activity is considered in the operational models. By arranging two-state models as the fraction of active receptors and operational models as the fractional response relative to the maximum effect of the system, a one-by-one correspondence between parameters is found. The comparative analysis allows a better understanding of complex allosteric interactions. In particular, the inclusion of constitutive receptor activity in the operational model of allosterism allows the characterization of modulators able to lower the basal response of the system; that is, allosteric modulators with negative intrinsic efficacy. Theoretical simulations and overall goodness of fit of the models to simulated data suggest that it is feasible to apply the models to experimental data and constitute one step forward in receptor theory formalism.
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Joan M. Nuñez, Debora Gil, & Fernando Vilariño. (2013). Finger joint characterization from X-ray images for rheymatoid arthritis assessment. In 6th International Conference on Biomedical Electronics and Devices (pp. 288–292). SciTePress.
Abstract: In this study we propose amodular systemfor automatic rheumatoid arthritis assessment which provides a joint space width measure. A hand joint model is proposed based on the accurate analysis of a X-ray finger joint image sample set. This model shows that the sclerosis and the lower bone are the main necessary features in order to perform a proper finger joint characterization. We propose sclerosis and lower bone detection methods as well as the experimental setup necessary for its performance assessment. Our characterization is used to propose and compute a joint space width score which is shown to be related to the different degrees of arthritis. This assertion is verified by comparing our proposed score with Sharp Van der Heijde score, confirming that the lower our score is the more advanced is the patient affection.
Keywords: Rheumatoid Arthritis; X-Ray; Hand Joint; Sclerosis; Sharp Van der Heijde
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Joan M. Nuñez, Jorge Bernal, F. Javier Sanchez, & Fernando Vilariño. (2013). Blood Vessel Characterization in Colonoscopy Images to Improve Polyp Localization. In Proceedings of the International Conference on Computer Vision Theory and Applications (Vol. 1, pp. 162–171). SciTePress.
Abstract: This paper presents an approach to mitigate the contribution of blood vessels to the energy image used at different tasks of automatic colonoscopy image analysis. This goal is achieved by introducing a characterization of endoluminal scene objects which allows us to differentiate between the trace of 2-dimensional visual objects,such as vessels, and shades from 3-dimensional visual objects, such as folds. The proposed characterization is based on the influence that the object shape has in the resulting visual feature, and it leads to the development of a blood vessel attenuation algorithm. A database consisting of manually labelled masks was built in order to test the performance of our method, which shows an encouraging success in blood vessel mitigation while keeping other structures intact. Moreover, by extending our method to the only available polyp localization
algorithm tested on a public database, blood vessel mitigation proved to have a positive influence on the overall performance.
Keywords: Colonoscopy; Blood vessel; Linear features; Valley detection
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Angel Sappa, & Jordi Vitria. (2013). Multimodal Interaction in Image and Video Applications (Vol. 48). Springer Berlin Heidelberg.
Abstract: Book Series Intelligent Systems Reference Library
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Jiaolong Xu, David Vazquez, Antonio Lopez, Javier Marin, & Daniel Ponsa. (2013). Learning a Multiview Part-based Model in Virtual World for Pedestrian Detection. In IEEE Intelligent Vehicles Symposium (pp. 467–472). IEEE.
Abstract: State-of-the-art deformable part-based models based on latent SVM have shown excellent results on human detection. In this paper, we propose to train a multiview deformable part-based model with automatically generated part examples from virtual-world data. The method is efficient as: (i) the part detectors are trained with precisely extracted virtual examples, thus no latent learning is needed, (ii) the multiview pedestrian detector enhances the performance of the pedestrian root model, (iii) a top-down approach is used for part detection which reduces the searching space. We evaluate our model on Daimler and Karlsruhe Pedestrian Benchmarks with publicly available Caltech pedestrian detection evaluation framework and the result outperforms the state-of-the-art latent SVM V4.0, on both average miss rate and speed (our detector is ten times faster).
Keywords: Pedestrian Detection; Virtual World; Part based
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Marina Alberti. (2013). Detection and Alignment of Vascular Structures in Intravascular Ultrasound using Pattern Recognition Techniques (Simone Balocco, & Petia Radeva, Eds.). Ph.D. thesis, Ediciones Graficas Rey, .
Abstract: In this thesis, several methods for the automatic analysis of Intravascular Ultrasound
(IVUS) sequences are presented, aimed at assisting physicians in the diagnosis, the assessment of the intervention and the monitoring of the patients with coronary disease.
The basis for the developed frameworks are machine learning, pattern recognition and
image processing techniques.
First, a novel approach for the automatic detection of vascular bifurcations in
IVUS is presented. The task is addressed as a binary classi cation problem (identifying bifurcation and non-bifurcation angular sectors in the sequence images). The
multiscale stacked sequential learning algorithm is applied, to take into account the
spatial and temporal context in IVUS sequences, and the results are re ned using
a-priori information about branching dimensions and geometry. The achieved performance is comparable to intra- and inter-observer variability.
Then, we propose a novel method for the automatic non-rigid alignment of IVUS
sequences of the same patient, acquired at dierent moments (before and after percutaneous coronary intervention, or at baseline and follow-up examinations). The
method is based on the description of the morphological content of the vessel, obtained by extracting temporal morphological pro les from the IVUS acquisitions, by
means of methods for segmentation, characterization and detection in IVUS. A technique for non-rigid sequence alignment – the Dynamic Time Warping algorithm -
is applied to the pro les and adapted to the speci c clinical problem. Two dierent robust strategies are proposed to address the partial overlapping between frames
of corresponding sequences, and a regularization term is introduced to compensate
for possible errors in the pro le extraction. The bene ts of the proposed strategy
are demonstrated by extensive validation on synthetic and in-vivo data. The results
show the interest of the proposed non-linear alignment and the clinical value of the
method.
Finally, a novel automatic approach for the extraction of the luminal border in
IVUS images is presented. The method applies the multiscale stacked sequential
learning algorithm and extends it to 2-D+T, in a rst classi cation phase (the identi-
cation of lumen and non-lumen regions of the images), while an active contour model
is used in a second phase, to identify the lumen contour. The method is extended
to the longitudinal dimension of the sequences and it is validated on a challenging
data-set.
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Juan Ramon Terven Salinas, Joaquin Salas, & Bogdan Raducanu. (2013). Estado del Arte en Sistemas de Vision Artificial para Personas Invidentes. KS - Komputer Sapiens, 20–25.
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Patricia Marquez, Debora Gil, Aura Hernandez-Sabate, & Daniel Kondermann. (2013). When Is A Confidence Measure Good Enough? In 9th International Conference on Computer Vision Systems (Vol. 7963, pp. 344–353). LNCS. Springer Link.
Abstract: Confidence estimation has recently become a hot topic in image processing and computer vision.Yet, several definitions exist of the term “confidence” which are sometimes used interchangeably. This is a position paper, in which we aim to give an overview on existing definitions,
thereby clarifying the meaning of the used terms to facilitate further research in this field. Based on these clarifications, we develop a theory to compare confidence measures with respect to their quality.
Keywords: Optical flow, confidence measure, performance evaluation
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David Vazquez, Jiaolong Xu, Sebastian Ramos, Antonio Lopez, & Daniel Ponsa. (2013). Weakly Supervised Automatic Annotation of Pedestrian Bounding Boxes. In CVPR Workshop on Ground Truth – What is a good dataset? (pp. 706–711). IEEE.
Abstract: Among the components of a pedestrian detector, its trained pedestrian classifier is crucial for achieving the desired performance. The initial task of the training process consists in collecting samples of pedestrians and background, which involves tiresome manual annotation of pedestrian bounding boxes (BBs). Thus, recent works have assessed the use of automatically collected samples from photo-realistic virtual worlds. However, learning from virtual-world samples and testing in real-world images may suffer the dataset shift problem. Accordingly, in this paper we assess an strategy to collect samples from the real world and retrain with them, thus avoiding the dataset shift, but in such a way that no BBs of real-world pedestrians have to be provided. In particular, we train a pedestrian classifier based on virtual-world samples (no human annotation required). Then, using such a classifier we collect pedestrian samples from real-world images by detection. After, a human oracle rejects the false detections efficiently (weak annotation). Finally, a new classifier is trained with the accepted detections. We show that this classifier is competitive with respect to the counterpart trained with samples collected by manually annotating hundreds of pedestrian BBs.
Keywords: Pedestrian Detection; Domain Adaptation
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