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David Roche, Debora Gil, & Jesus Giraldo. (2014). Mathematical modeling of G protein-coupled receptor function: What can we learn from empirical and mechanistic models? In G Protein-Coupled Receptors – Modeling and Simulation Advances in Experimental Medicine and Biology (Vol. 796, pp. 159–181). Springer Netherlands.
Abstract: Empirical and mechanistic models differ in their approaches to the analysis of pharmacological effect. Whereas the parameters of the former are not physical constants those of the latter embody the nature, often complex, of biology. Empirical models are exclusively used for curve fitting, merely to characterize the shape of the E/[A] curves. Mechanistic models, on the contrary, enable the examination of mechanistic hypotheses by parameter simulation. Regretfully, the many parameters that mechanistic models may include can represent a great difficulty for curve fitting, representing, thus, a challenge for computational method development. In the present study some empirical and mechanistic models are shown and the connections, which may appear in a number of cases between them, are analyzed from the curves they yield. It may be concluded that systematic and careful curve shape analysis can be extremely useful for the understanding of receptor function, ligand classification and drug discovery, thus providing a common language for the communication between pharmacologists and medicinal chemists.
Keywords: β-arrestin; biased agonism; curve fitting; empirical modeling; evolutionary algorithm; functional selectivity; G protein; GPCR; Hill coefficient; intrinsic efficacy; inverse agonism; mathematical modeling; mechanistic modeling; operational model; parameter optimization; receptor dimer; receptor oligomerization; receptor constitutive activity; signal transduction; two-state model
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H. Martin Kjer, Jens Fagertun, Sergio Vera, & Debora Gil. (2017). Medial structure generation for registration of anatomical structures. In Skeletonization, Theory, Methods and Applications (Vol. 11).
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Aura Hernandez-Sabate, & Debora Gil. (2012). The Benefits of IVUS Dynamics for Retrieving Stable Models of Arteries. In Yasuhiro Honda (Ed.), Intravascular Ultrasound (pp. 185–206). Intech.
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Debora Gil, Oriol Ramos Terrades, & Raquel Perez. (2021). Topological Radiomics (TOPiomics): Early Detection of Genetic Abnormalities in Cancer Treatment Evolution. In Extended Abstracts GEOMVAP 2019, Trends in Mathematics 15 (Vol. 15, 89–93). Springer Nature.
Abstract: Abnormalities in radiomic measures correlate to genomic alterations prone to alter the outcome of personalized anti-cancer treatments. TOPiomics is a new method for the early detection of variations in tumor imaging phenotype from a topological structure in multi-view radiomic spaces.
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Debora Gil, F. Javier Sanchez, Gloria Fernandez Esparrach, & Jorge Bernal. (2015). 3D Stable Spatio-temporal Polyp Localization in Colonoscopy Videos. In Computer-Assisted and Robotic Endoscopy. Revised selected papers of Second International Workshop, CARE 2015, Held in Conjunction with MICCAI 2015 (Vol. 9515, pp. 140–152). LNCS.
Abstract: Computational intelligent systems could reduce polyp miss rate in colonoscopy for colon cancer diagnosis and, thus, increase the efficiency of the procedure. One of the main problems of existing polyp localization methods is a lack of spatio-temporal stability in their response. We propose to explore the response of a given polyp localization across temporal windows in order to select
those image regions presenting the highest stable spatio-temporal response.
Spatio-temporal stability is achieved by extracting 3D watershed regions on the
temporal window. Stability in localization response is statistically determined by analysis of the variance of the output of the localization method inside each 3D region. We have explored the benefits of considering spatio-temporal stability in two different tasks: polyp localization and polyp detection. Experimental results indicate an average improvement of 21:5% in polyp localization and 43:78% in polyp detection.
Keywords: Colonoscopy, Polyp Detection, Polyp Localization, Region Extraction, Watersheds
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Enric Marti, Jordi Regincos, Juan Jose Villanueva, & Jaime Lopez-Krahe. (1994). Line drawing interpretation as polyhedral objects to man-machine interaction in CAD systems. In Advances in Pattern Recognition and Image Analysis, (pp. 158–169). World Scientific Pub.
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Jaume Garcia, Petia Radeva, & Francesc Carreras. (2004). Combining Spectral and Active Shape methods to Track Tagged MRI. In Recent Advances in Artificial Intelligence Research and Development (pp. 37–44). IOS Press.
Abstract: Tagged magnetic resonance is a very usefull and unique tool that provides a complete local and global knowledge of the left ventricle (LV) motion. In this article we introduce a method capable of tracking and segmenting the LV. Spectral methods are applied in order to obtain the so called HARP images which encode information about movement and are the base for LV point-tracking. For segmentation we use Active Shapes (ASM) that model LV shape variation in order to overcome possible local misplacements of the boundary. We finally show experiments on both synthetic and real data which appear to be very promising.
Keywords: MR; tagged MR; ASM; LV segmentation; motion estimation.
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Debora Gil, & Petia Radeva. (2004). Inhibition of False Landmarks. In J. V. et al (Ed.), Recent Advances in Artificial Intelligence Research and Development (pp. 233–244). Barcelona (Spain): IOS Press.
Abstract: We argue that a corner detector should be based on the degree of continuity of the tangent vector to the image level sets, work on the image domain and need no assumptions on neither the image local structure nor the particular geometry of the corner/junction. An operator measuring the degree of differentiability of the projection matrix on the image gradient fulfills the above requirements. Its high sensitivity to changes in vector directions makes it suitable for landmark location in real images prone to need smoothing to reduce the impact of noise. Because using smoothing kernels leads to corner misplacement, we suggest an alternative fake response remover based on the receptive field inhibition of spurious details. The combination of both orientation discontinuity detection and noise inhibition produce our Inhibition Orientation Energy (IOE) landmark locator.
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Debora Gil, & Petia Radeva. (2003). Curvature Vector Flow to Assure Convergent Deformable Models for Shape Modelling. In B. Springer (Ed.), Energy Minimization Methods In Computer Vision And Pattern Recognition (Vol. 2683, pp. 357–372). LNCS. Lisbon, PORTUGAL: Springer, Berlin.
Abstract: Poor convergence to concave shapes is a main limitation of snakes as a standard segmentation and shape modelling technique. The gradient of the external energy of the snake represents a force that pushes the snake into concave regions, as its internal energy increases when new inexion points are created. In spite of the improvement of the external energy by the gradient vector ow technique, highly non convex shapes can not be obtained, yet. In the present paper, we develop a new external energy based on the geometry of the curve to be modelled. By tracking back the deformation of a curve that evolves by minimum curvature ow, we construct a distance map that encapsulates the natural way of adapting to non convex shapes. The gradient of this map, which we call curvature vector ow (CVF), is capable of attracting a snake towards any contour, whatever its geometry. Our experiments show that, any initial snake condition converges to the curve to be modelled in optimal time.
Keywords: Initial condition; Convex shape; Non convex analysis; Increase; Segmentation; Gradient; Standard; Standards; Concave shape; Flow models; Tracking; Edge detection; Curvature
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Debora Gil, Oriol Rodriguez-Leor, Petia Radeva, & Aura Hernandez-Sabate. (2007). Assessing Artery Motion Compensation in IVUS. In Computer Analysis Of Images And Patterns (Vol. 4673, pp. 213–220). Lecture Notes in Computer Science. Heidelberg: Springerlink.
Abstract: Cardiac dynamics suppression is a main issue for visual improvement and computation of tissue mechanical properties in IntraVascular UltraSound (IVUS). Although in recent times several motion compensation techniques have arisen, there is a lack of objective evaluation of motion reduction in in vivo pullbacks. We consider that the assessment protocol deserves special attention for the sake of a clinical applicability as reliable as possible. Our work focuses on defining a quality measure and a validation protocol assessing IVUS motion compensation. On the grounds of continuum mechanics laws we introduce a novel score measuring motion reduction in in vivo sequences. Synthetic experiments validate the proposed score as measure of motion parameters accuracy; while results in in vivo pullbacks show its reliability in clinical cases.
Keywords: validation standards; quality measures; IVUS motion compensation; conservation laws; Fourier development
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Misael Rosales, Petia Radeva, Oriol Rodriguez, & Debora Gil. (2005). Suppression of IVUS Image Rotation. A Kinematic Approach. In Monica Andres and Hernandez Petia and Santos A. and R. Frangi (Ed.), Functional Imaging and Modeling of the Heart (Vol. 3504, pp. 889–892). LNCS, 3504. Springer Berlin / Heidelberg.
Abstract: IntraVascular Ultrasound (IVUS) is an exploratory technique used in interventional procedures that shows cross section images of arteries and provides qualitative information about the causes and severity of the arterial lumen narrowing. Cross section analysis as well as visualization of plaque extension in a vessel segment during the catheter imaging pullback are the technique main advantages. However, IVUS sequence exhibits a periodic rotation artifact that makes difficult the longitudinal lesion inspection and hinders any segmentation algorithm. In this paper we propose a new kinematic method to estimate and remove the image rotation of IVUS images sequences. Results on several IVUS sequences show good results and prompt some of the clinical applications to vessel dynamics study, and relation to vessel pathology.
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Sergio Vera, Debora Gil, Agnes Borras, F. Javier Sanchez, Frederic Perez, Marius G. Linguraru, et al. (2012). Computation and Evaluation of Medial Surfaces for Shape Representation of Abdominal Organs. In H. Yoshida et al (Ed.), Workshop on Computational and Clinical Applications in Abdominal Imaging (Vol. 7029, 223–230). LNCS. Berlin: Springer Link.
Abstract: Medial representations are powerful tools for describing and parameterizing the volumetric shape of anatomical structures. Existing 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 avoid degenerated medial axis segments; second, we introduce an energy based method which performs independently of the dimension. We evaluate quantitatively the performance of our
method with respect to existing approaches, by applying them to synthetic shapes of known medial geometry. Finally, we show results on shape representation of multiple abdominal organs,
exploring the use of medial manifolds for the representation of multi-organ relations.
Keywords: medial manifolds, abdomen.
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Ignasi Rius, Dani Rowe, Jordi Gonzalez, & Xavier Roca. (2005). A 3D Dynamic Model of Human Actions for Probabilistic Image Tracking. In Pattern Recognition and Image Analysis (IbPRIA 2005), LNCS 3522: 529–536.
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Dani Rowe, Ignasi Rius, Jordi Gonzalez, Xavier Roca, & Juan J. Villanueva. (2005). Probabilistic Image-Based Tracking: Improving Particle Filtering. In Pattern Recognition and Image Analysis (IbPRIA 2005), LNCS 3522: 85–92.
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Mikhail Mozerov. (2006). An Effective Stereo Matching Algorithm with Optimal Path Cost Aggregation. In 28th Annual Symposium of the German Association for Pattern Recognition, LNCS 4174: 617–626.
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