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AuthorTitleYearJournal/ProceedingsReftypeDOI/URL
Ayala, G., Díaz, M.E. and Martínez-Costa, L. Granulometric moments and corneal endothelium status 2001 Pattern Recognition
Vol. 34(6), pp. 1219-1227 
article DOI  
Abstract: Specular microscopy is a common practice in Ophthalmology. The corneal endothelium status is usually evaluated by means of the density, the hexagonality, the mean, the standard deviation and the coefficient of variation of cell areas. We propose to replace the cell area moments by the corresponding moments of a different probability distribution, the granulometric size distribution associated to a disc. All cells touching the frame are ignored by the area moments but used by the granulometric moments. Twenty images have been analyzed. When the size of the focused region is reduced, the area moments show a greater variation than the corresponding granulometric moments.
BibTeX:
@article{Ayala01a,
  author = {Ayala, G. and Díaz, M. E. and Martínez-Costa, L.},
  title = {Granulometric moments and corneal endothelium status},
  journal = {Pattern Recognition},
  year = {2001},
  volume = {34},
  number = {6},
  pages = {1219--1227},
  doi = {https://doi.org/10.1016/S0031-3203(00)00074-1}
}
Ayala, G. and Domingo, J. Spatial size distributions: Applications to shape and texture analysis 2001 IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 23(12), pp. 1430-1442 
article DOI  
Abstract: This paper proposes new descriptors for binary and gray-scale images based on newly defined spatial size distributions (SSD). The main idea consists of combining a granulometric analysis of the image with a comparison between the geometric covariograms for binary images or the auto-correlation function for gray-scale images of the original image and its granulometric transformation; the usual granulometric size distribution then arises as a particular case of this formulation. Examples are given to show that in those cases in which a finer description of the image is required, the more complex descriptors generated from the SSD could be advantageously used. It is also shown that the new descriptors are probability distributions so their intuitive interpretation and properties can be appropriately studied from the probabilistic point of view. The usefulness of these descriptors in shape analysis is illustrated by some synthetic examples and their use in texture analysis is studied. Various cases of SSD and several former methods for texture classification are compared
BibTeX:
@article{Ayala01b,
  author = {G. Ayala and J. Domingo},
  title = {Spatial size distributions: Applications to shape and texture analysis},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year = {2001},
  volume = {23},
  number = {12},
  pages = {1430--1442},
  doi = {https://doi.org/10.1109/34.977566}
}
Ayala, G., Leon, T. and Zapater, V. Different averages of a fuzzy set with an application to vessel segmentation 2005 IEEE Transactions on Fuzzy Systems
Vol. 13(3), pp. 384-393 
article DOI  
Abstract: Image segmentation is a major problem in image processing, particularly in medical image analysis. A great number of segmentation procedures produce intermediate gray-scale images that can be understood as fuzzy sets. Additionally, some segmentation procedures tend to leave free tuning parameters (very influential in the final binary image) for the user. These different binary images can be easily aggregated (into a fuzzy set) by making use of fuzzy set theory. In any case, a single binary image is required so our interest is to associate a crisp set to a given fuzzy set in an intelligent and unsupervised manner. The main idea of this paper is to define the averages of a given fuzzy set by using different definitions of the mean of a random compact set. In particular, the average distance of Baddeley-Molchanov and the mean of Vorob'ev have been used. A theoretical study of some new definitions of fuzzy set averages has been performed. In particular, these averages have been obtained for L-R fuzzy numbers. Finally, we present a medical image application, that of retinal vessel detection. Some recent segmentation procedures have been revisited and modified using these new averages. The experimental results are very promising.
BibTeX:
@article{Ayala05,
  author = {Ayala, G. and Leon, T. and Zapater, V.},
  title = {Different averages of a fuzzy set with an application to vessel segmentation},
  journal = {IEEE Transactions on Fuzzy Systems},
  year = {2005},
  volume = {13},
  number = {3},
  pages = {384--393},
  doi = {https://doi.org/10.1109/TFUZZ.2004.839667}
}
Ayala, G., Epifanio, I., Simó, A. and Zapater, V. Clustering of spatial point patterns 2006 Computational Statistics & Data Analysis
Vol. 50(4), pp. 1016-1032 
article DOI  
Abstract: Spatial point patterns arise as the natural sampling information in many problems. An ophthalmologic problem gave rise to the problem of detecting clusters of point patterns. A set of human corneal endothelium images is given. Each image is described by using a point pattern, the cell centroids. The main problem is to find groups of images corresponding with groups of spatial point patterns. This is interesting from a descriptive point of view and for clinical purposes. A new image can be compared with prototypes of each group and finally evaluated by the physician. Usual descriptors of spatial point patterns such as the empty-space function, the nearest distribution function or Ripley's -function, are used to define dissimilarity measures. Moreover, the relationship between some estimation problems in spatial point processes and survival analysis is used to define dissimilarity measures between point patterns. All the proposed dissimilarities and the cluster procedures are evaluated in a simulation study. Finally, a detailed analysis of the images of corneal endothelia is provided.
BibTeX:
@article{Ayala06,
  author = {G. Ayala and I. Epifanio and A. Simó and V. Zapater},
  title = {Clustering of spatial point patterns},
  journal = {Computational Statistics & Data Analysis},
  year = {2006},
  volume = {50},
  number = {4},
  pages = {1016--1032},
  doi = {https://doi.org/10.1016/j.csda.2004.10.013}
}
Ayala, G., Sebastián, R., Diaz, M., Diaz, E., Zoncu, R. and Toomre, D. Analysis of spatially and temporally overlapping events with application to image sequences 2006 IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 28(10), pp. 1707-1712 
article DOI  
Abstract: Counting spatially and temporally overlapping events in image sequences and estimating their shape-size and duration features are important issues in some applications. We propose a stochastic model, a particular case of the nonisotropic 3D Boolean model, for performing this analysis: the temporal Boolean model. Some probabilistic properties are derived and a methodology for parameter estimation from time-lapse image sequences is proposed using an explicit treatment of the temporal dimension. We estimate the mean number of germs per unit area and time, the mean grain size and the duration distribution. A wide simulation study in order to assess the proposed estimators showed promising results. The model was applied on biological image sequences of invivo cells in order to estimate new parameters such as the mean number and duration distribution of endocytic events. Our results show that the proposed temporal Boolean model is effective for obtaining information about dynamic processes which exhibit short-lived, but spatially and temporally overlapping events
BibTeX:
@article{Ayala06b,
  author = {G. Ayala and R. Sebastián and M.E. Diaz and E. Diaz and R. Zoncu and D. Toomre},
  title = {Analysis of spatially and temporally overlapping events with application to image sequences},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year = {2006},
  volume = {28},
  number = {10},
  pages = {1707--1712},
  doi = {https://doi.org/10.1109/TPAMI.2006.199}
}
Ayala, G. R Code for Hausdorff and Simplex Dispersion Orderings in the 2D Case 2010
Vol. 77Combining Soft Computing and Statistical Methods in Data Analysis, pp. 25-31 
incollection DOI  
BibTeX:
@incollection{ayala10b,
  author = {G. Ayala},
  title = {R Code for Hausdorff and Simplex Dispersion Orderings in the 2D Case},
  booktitle = {Combining Soft Computing and Statistical Methods in Data Analysis},
  publisher = {Springer},
  year = {2010},
  volume = {77},
  pages = {25--31},
  doi = {https://doi.org/10.1007/978-3-642-14746-3_4}
}
Ayala, G., López-Díaz, M.C., López-Díaz, M. and Martínez-Costa, L. Studying hypertension in ocular fundus images using Hausdorff dispersion ordering 2012 Mathematical Medicine and Biology
Vol. 29(2), pp. 131-143 
article DOI URL 
Abstract: Retinal arterial and vein diameters are altered in individuals at risk of cardiovascular events mainly due to high blood pressure. The measurement of retinal vessel diameters has been proved to reflect individuals' vascular health. Dispersion of such measures which are obtained by means of ocular fundus images is a major factor not usually considered in clinical research. In this paper, a method to evaluate if different levels of clinically relevant covariables induce greater dispersion in retinal arterial and vein diameters is proposed. A multivariate dispersion ordering, the Hausdorff dispersion order, is used to compare the level of dispersion in such diameters for different groups of patients. Our statistical conclusions show that dispersion is higher in individuals with long-standing hypertension and in those who need two or more drugs to control hypertension. Hereby, dispersion is increased in the most severely ill persons. However, a greater level of smoking seems to be associated with a lesser dispersion. Dispersion of the vessel diameters must be taken into account in the image analysis of retinal vessel diameters because the comparison between homogeneous groups will produce highly accurate results in medical research.
BibTeX:
@article{Ayala12,
  author = {Ayala, Guillermo and López-Díaz, María Concepción and López-Díaz, Miguel and Martínez-Costa, Lucía},
  title = {Studying hypertension in ocular fundus images using Hausdorff dispersion ordering},
  journal = {Mathematical Medicine and Biology},
  year = {2012},
  volume = {29},
  number = {2},
  pages = {131--143},
  url = {http://imammb.oxfordjournals.org/content/29/2/131.abstract},
  doi = {https://doi.org/10.1093/imammb/dqq019}
}
Ayala, G., Díez, F., Gassó, M.T., Jones, B.E., Martín-Portugués, R. and Ramiro-Aparicio, J. Statistical tools and control of internal lubricant content of inhalation grade HPMC\ capsules during manufacture 2016 International Journal of Pharmaceutics
Vol. 503(1-2), pp. 36-40 
article DOI URL 
Abstract: Abstract The internal lubricant content (ILC) of inhalation grade HPMC\ capsules is a key factor to ensure good powder release when the patient inhales a medicine from a dry powder inhaler (DPI). Powder release from capsules has been shown to be influenced by the ILC. The characteristics used to measure this are the emitted dose, fine particle fraction and mass median aerodynamic diameter. In addition the ILC\ level is critical for capsule shell manufacture because it is an essential part of the process that cannot work without it. An experiment has been applied to the manufacture of inhalation capsules with the required ILC. A full factorial model was used to identify the controlling factors and from this a linear model has been proposed to improve control of the process.
BibTeX:
@article{Ayala16,
  author = {Guillermo Ayala and Fernando Díez and María T. Gassó and Brian E. Jones and Rafael Martín-Portugués and Juan Ramiro-Aparicio},
  title = {Statistical tools and control of internal lubricant content of inhalation grade HPMC\ capsules during manufacture},
  journal = {International Journal of Pharmaceutics},
  year = {2016},
  volume = {503},
  number = {1--2},
  pages = {36--40},
  url = {http://www.sciencedirect.com/science/article/pii/S0378517316301107},
  doi = {https://doi.org/10.1016/j.ijpharm.2016.02.017}
}
Ayala, G., Ferrandiz, J. and Montes, F. Random Set and Coverage Measure 1991 Advances in Applied Probability
Vol. 23(4), pp. 972-974 
article  
BibTeX:
@article{Ayala91,
  author = {G. Ayala and Ferrandiz J. and Montes F.},
  title = {Random Set and Coverage Measure},
  journal = {Advances in Applied Probability},
  year = {1991},
  volume = {23},
  number = {4},
  pages = {972--974}
}
Ayala, G. and Simó, A. Bivariate Random Closed-Sets and Nerve-Fiber Degeneration 1995 Advances in Applied Probability
Vol. 27(2), pp. 293-305 
article  
Abstract: A biphase image, representing the normal and degenerated fibres in a vertical cross-section of a nerve, is considered. A random set model based on a Gibbs point process is proposed for the union of the two phases. A kind of independence between the degeneration process and the original fibres is defined and tested.
BibTeX:
@article{Ayala95,
  author = {G. Ayala and A. Simó},
  title = {Bivariate Random Closed-Sets and Nerve-Fiber Degeneration},
  journal = {Advances in Applied Probability},
  year = {1995},
  volume = {27},
  number = {2},
  pages = {293--305}
}
Ayala, G. and Simó, A. Stochastic labelling of biological images 1998 Statistica Neerlandica
Vol. 52(2), pp. 141-152 
article DOI  
Abstract: Many hypotheses made by experimental researchers can be formulated as a stochastic labelling of a given image. Some stochastic labelling methods for random closed sets are proposed in this paper. Molchanov (I. Molchanov, 1984, Theor. Probability and Math. Statist.29, 113--119) provided the probabilistic background for this problem. However, there is a lack of specific labelling models. Ayala and Simó (G. Ayala and A. Simó, 1995, Advances in Applied Probability27, 293--305) proposed a method in which, given the whole set of connected components, every component is classified in a certain phase or category in a completely random way. Alternative methods are necessary in case the random labelling hypothesis is not reliable. A different kind of labelling method is proposed that considers the environment: the type of every connected component is a function of its location.
BibTeX:
@article{Ayala98,
  author = {G. Ayala and A. Simó},
  title = {Stochastic labelling of biological images},
  journal = {Statistica Neerlandica},
  year = {1998},
  volume = {52},
  number = {2},
  pages = {141--152},
  doi = {https://doi.org/10.1111/1467-9574.00074}
}
Ayala, G., Ferrandiz, J. and Montes, F. Two Methods of Estimation in Boolean Models 1989 Image Analysis and Stereology
Vol. 8(2), pp. 629-634 
article  
BibTeX:
@article{AyalaFerrandizMontes89,
  author = {G. Ayala and J. Ferrandiz and F. Montes},
  title = {Two Methods of Estimation in Boolean Models},
  journal = {Image Analysis and Stereology},
  year = {1989},
  volume = {8},
  number = {2},
  pages = {629--634}
}
Ayala, G., Ferrándiz, J. and Montes, F. Boolean Models: Maximum Likelihood Estimation from Circular Clumps 1990 Biometrical Journal
Vol. 32(1), pp. 73-78 
article DOI  
Abstract: This paper deals with the problem of making inferences on the maximum radius and the intensity of the Poisson point process associated to a Boolean Model of circular primary grains with uniformly distributed random radii. The only sample information used is observed radii of circular clumps (DUPAC, 1980). The behaviour of maximum likelihood estimation has been evaluated by means of Monte Carlo methods.
BibTeX:
@article{AyalaFerrandizMontes90,
  author = {G. Ayala and J. Ferrándiz and F. Montes},
  title = {Boolean Models: Maximum Likelihood Estimation from Circular Clumps},
  journal = {Biometrical Journal},
  year = {1990},
  volume = {32},
  number = {1},
  pages = {73--78},
  doi = {https://doi.org/10.1002/bimj.4710320112}
}
Ayala, G., Ferrandiz, J. and Montes, F. Sparse Sampling and Maximum Likelihood Estimation for Boolean Models 1991 Biometrical Journal
Vol. 33(2), pp. 237-245 
article DOI  
Abstract: A condition for practical independence of contact distribution functions in Boolean models is obtained. This result allows the authors to use maximum likelihcod methods, via sparse sampling, for estimating unknown parameters of an isotropic Boolean model. The second part of this paper is devoted to a simulation study of the proposed method. AMS classification: 60D05
BibTeX:
@article{AyalaFerrandizMontes91,
  author = {G. Ayala and J.R. Ferrandiz and F. Montes},
  title = {Sparse Sampling and Maximum Likelihood Estimation for Boolean Models},
  journal = {Biometrical Journal},
  year = {1991},
  volume = {33},
  number = {2},
  pages = {237--245},
  doi = {https://doi.org/10.1002/bimj.4710330215}
}
Ayala, G., Ferrandiz, J. and Montes, F. On parametric estimation in Boolean models 1993 Rassegna di Metodi Statistici ed Applicazioni
Vol. 8, pp. 1-17 
article  
BibTeX:
@article{AyalaFerrandizMontes93,
  author = {G. Ayala and J.R. Ferrandiz and F. Montes},
  title = {On parametric estimation in Boolean models},
  journal = {Rassegna di Metodi Statistici ed Applicazioni},
  year = {1993},
  volume = {8},
  pages = {1--17}
}
Ayala, G., Gaston, M., Leon, T. and Mallor, F. Measuring Dissimilarity Between Curves by Means of Their Granulometric Size Distributions 2008 , pp. 35-41  inbook  
BibTeX:
@inbook{AyalaGLM08,
  author = {G. Ayala and M. Gaston and T. Leon and F. Mallor},
  title = {Measuring Dissimilarity Between Curves by Means of Their Granulometric Size Distributions},
  publisher = {Springer},
  year = {2008},
  pages = {35--41}
}
Ayala, G., León, T. and Zapater, V. Fuzzy Logic for Medical Engineering: An Application to Vessel Segmentation 2006 , pp. 115-127  inbook DOI  
BibTeX:
@inbook{AyalaLeonZapater06,
  author = {G. Ayala and T. León and V. Zapater},
  title = {Fuzzy Logic for Medical Engineering: An Application to Vessel Segmentation},
  publisher = {Springer},
  year = {2006},
  pages = {115--127},
  doi = {https://doi.org/10.1007/978-1-84628-469-4_8}
}
Ayala, G., López-Díaz, M., López-Díaz, M. and Martínez-Costa, L. Methods and Algorithms to Test the Hausdorff and Simplex Dispersion Orders with an R Package 2015 Methodology and Computing in Applied Probability
Vol. 17(3), pp. 661-675 
article DOI URL 
BibTeX:
@article{AyalaLLM15,
  author = {Ayala, Guillermo and López-Díaz, MaríaConcepción and López-Díaz, Miguel and Martínez-Costa, Lucía},
  title = {Methods and Algorithms to Test the Hausdorff and Simplex Dispersion Orders with an R Package},
  journal = {Methodology and Computing in Applied Probability},
  publisher = {Springer US},
  year = {2015},
  volume = {17},
  number = {3},
  pages = {661--675},
  url = {http://dx.doi.org/10.1007/s11009-013-9386-z},
  doi = {https://doi.org/10.1007/s11009-013-9386-z}
}
Ayala, G. and López-Díaz, M. The simplex dispersion ordering and its application to the evaluation of human corneal endothelia 2009 Journal of Multivariate Analysis
Vol. 100, pp. 1447-1464 
article DOI  
Abstract: A multivariate dispersion ordering based on random simplices is proposed in this paper. Given a View the MathML source-valued random vector, we consider two random simplices determined by the convex hulls of two independent random samples of sizes d+1 of the vector. By means of the stochastic comparison of the Hausdorff distances between such simplices, a multivariate dispersion ordering is introduced. Main properties of the new ordering are studied. Relationships with other dispersion orderings are considered, placing emphasis on the univariate version. Some statistical tests for the new order are proposed. An application of such ordering to the clinical evaluation of human corneal endothelia is provided. Different analyses are included using an image database of human corneal endothelia.
BibTeX:
@article{AyalaLopezDiaz09,
  author = {G. Ayala and M. López-Díaz},
  title = {The simplex dispersion ordering and its application to the evaluation of human corneal endothelia},
  journal = {Journal of Multivariate Analysis},
  year = {2009},
  volume = {100},
  pages = {1447--1464},
  doi = {https://doi.org/10.1016/j.jmva.2008.12.017}
}
Ayala, G. and Montes, F. Random closed sets and Random Processes 1997 Rendiconti del Circolo Matematico di Palermo. Serie II
Vol. 50, pp. 35-41 
article  
BibTeX:
@article{AyalaMontes97,
  author = {G. Ayala and F. Montes},
  title = {Random closed sets and Random Processes},
  journal = {Rendiconti del Circolo Matematico di Palermo. Serie II},
  year = {1997},
  volume = {50},
  pages = {35--41}
}
Ayala, G. and Simó, A. Different dependence measures in spatial point processes 2009 International Journal of Statistics and Management System
Vol. 4(1-2), pp. 1-26 
article URL 
Abstract: A multivariate spatial point pattern consists of the locations of two or more types in a region: different tree or animal species, cases and controls of a disease, centroids of degenerated and non-degenerated nerve fibres in a cross-section of a nerve. The quantification of dependence amongst the different types of points is a basic question. The measure of the dependence has been basically based on the product density or its integrated version, the cross mathbb K function, mathbb K_12 (Cressie93). New measures of local dependence are proposed and studied in this paper. Their estimators and their expressions are considered under two different null hypotheses: independence and random labeling (i.e., one type of points is a random selection of the whole set of points while the other type of points are the remaining). They are compared with the product intensity and its integrated version, the cross mathbb K function. A randomization test for testing the random labeling hypothesis is proposed and applied to two examples. These examples are the locations of maples and oaks in Lansing Woods (Diggle03) and the locations of normal and degenerated fibres in a vertical cross-section of a nerve from a rat.
BibTeX:
@article{AyalaSimo09,
  author = {G. Ayala and A. Simó},
  title = {Different dependence measures in spatial point processes},
  journal = {International Journal of Statistics and Management System},
  year = {2009},
  volume = {4},
  number = {1-2},
  pages = {1--26},
  url = {http://www.math.binghamton.edu/arcones/ijsms/volume-4.html}
}
Ayala, G. and Simó, A. An approximation of the K-function for the study of binary images 1993 Questió
Vol. 17, pp. 235-244 
article  
Abstract: Jensen et al. (1990) gave an exact expression for the cal K-function in non-overlapping Boolean models. The present study proposes and evaluates an approximate expression for the cal K-function in overlapping isotropic Boolean models based on an approximation of the covariogram of the primary grain. We study the suitability of a Boolean model for two binary images using this approximate expression.
BibTeX:
@article{AyalaSimo93,
  author = {G. Ayala and A. Simó},
  title = {An approximation of the K-function for the study of binary images},
  journal = {Questió},
  year = {1993},
  volume = {17},
  pages = {235--244}
}
Benavent, X., Martínez-Costa, L., Ayala, G., Domingo, J. and Marco, P. Semi-automated Evaluation Tool for Retinal Vasculopathy 2009 Computer Methods and Programs in Biomedicine
Vol. 95, pp. 288-299 
article DOI  
Abstract: The ocular fundus is the only area of human body where vascular system is visible using relatively simple instrumentation. Furthermore, there is medical suggestive evidence of a direct relationship between certain measures of vascular characteristics in the ocular fundus (arteriolar and venular calibers and focal arteriolar narrowing) and cardiovascular diseases. In order to establish such relationship on sound statistical basis a method must be provided to measure the needed values in an easy, yet precise and repeatable way. This paper presents a system to assist physicians in signaling and storing the data associated to signs of vascular deterioration and vascular calibers in non-mydriatic ocular fundus images. The system is built around a graphical user interface that, even not fully automatic, guides the practitioner to mark certain anatomic visible features in an easy and precise way. The data are exported in common database formats for further processing and a statistical summary is also presented.
BibTeX:
@article{Benavent09,
  author = {X. Benavent and L. Martínez-Costa and G. Ayala and J. Domingo and P. Marco},
  title = {Semi-automated Evaluation Tool for Retinal Vasculopathy},
  journal = {Computer Methods and Programs in Biomedicine},
  year = {2009},
  volume = {95},
  pages = {288--299},
  doi = {https://doi.org/10.1016/j.cmpb.2009.05.008}
}
Benavent, X., Vegara, F., Domingo, J. and Ayala, G. On the use of Longitudinal Data Techniques for Modeling the Behavior of a Complex System 2002
Vol. 2329, pp. 458-467 
inbook  
Abstract: This work presents the use of longitudinal data analysis techniques to fit the accelerations of a real car in terms of some previous throttle pedal measurements and of the current time. Different repetitions of the same driving maneuvers have been observed in a real car, which constitute the data used to learn the model. The natural statistical framework to analyze these data is to consider it as a particular case of longitudinal data. Different fits are given and tested as a first step in order to explain the relationship between variables describing the control of the car by the driver and the final variables describing the movement of the vehicle. Results show that the approach can be valid in those cases in which a temporal implicit dependency can be assumed and in which several realizations of the experiment in similar conditions are available; in such cases an analytical model of the system can be obtained which has the ability to generalize, i.e. to show a robust behavior when faced to input data not used in the model construction phase.
BibTeX:
@inbook{BenaventVDA02,
  author = {X. Benavent and F. Vegara and J. Domingo and G. Ayala},
  title = {On the use of Longitudinal Data Techniques for Modeling the Behavior of a Complex System},
  publisher = {Springer},
  year = {2002},
  volume = {2329},
  pages = {458--467},
  note = {TY: CHAPTER}
}
de Ves, E., Domingo, J., Ayala, G. and Zuccarello, P. A novel Bayesian framework for relevance feedback in image content-based retrieval systems 2006 Pattern Recognition
Vol. 39(9), pp. 1622-1632 
article DOI  
Abstract: This paper presents a new algorithm for image retrieval in content-based image retrieval systems. The objective of these systems is to get the images which are as similar as possible to a user query from those contained in the global image database without using textual annotations attached to the images. The main problem in obtaining a robust and effective retrieval is the gap between the low level descriptors that can be automatically extracted from the images and the user intention. The algorithm proposed here to address this problem is based on the modeling of user preferences as a probability distribution on the image space. Following a Bayesian methodology, this distribution is the prior distribution and its parameters are modified based on the information provided by the user. This yields the a posteriori from which the predictive distribution is calculated and used to show to the user a new set of images until he/she is satisfied or the target image has been found. Experimental results are shown to evaluate the method on a large image database in terms of precision and recall.
BibTeX:
@article{deVes06,
  author = {E. de Ves and J. Domingo and G. Ayala and P. Zuccarello},
  title = {A novel Bayesian framework for relevance feedback in image content-based retrieval systems},
  journal = {Pattern Recognition},
  year = {2006},
  volume = {39},
  number = {9},
  pages = {1622--1632},
  doi = {https://doi.org/10.1016/j.patcog.2006.01.006}
}
de Ves, E., Benavent, X., Ayala, G. and Domingo, J. Selecting the structuring element for morphological texture classification 2006 Pattern Analysis & Applications
Vol. 9(1), pp. 48-57 
article DOI  
Abstract: Abstract This paper deals with a concrete aspect of texture classification: the choice of a good structuring element (SE) when the texture features used for classification are obtained from morphological granulometries. First, a granulometry is defined from the morphological opening of the texture using a convex and compact subset containing the origin as SE. Then, some usual distributional descriptors (mean, variance, skewness and kurtosis) of the granulometric size distribution are used as texture features. The main point of the paper is the choice of a good SE from the point of view of texture classification. A methodology is explained and software has been developed that helps in such a choice, for any given criterion for the quality of the classification.
BibTeX:
@article{deVes06b,
  author = {E. de Ves and X. Benavent and G. Ayala and J. Domingo},
  title = {Selecting the structuring element for morphological texture classification},
  journal = {Pattern Analysis & Applications},
  year = {2006},
  volume = {9},
  number = {1},
  pages = {48--57},
  doi = {https://doi.org/10.1007/s10044-006-0024-z}
}
de Ves, E., Zuccarello, P., Leon, T. and Ayala, G. IOWA Operators and Its Application to Image Retrieval 2014
Vol. 8621Structural, Syntactic, and Statistical Pattern Recognition. Joint IAPR International Workshop, S+SSPR 2014, Joensuu, Finland, August 20-22, 2014. Proceedings. 
inproceedings  
Abstract: This paper presents a relevance feedback procedure based on logistic regression analysis. Since, the dimension of the feature vector associated to each image is typically larger than the number of evaluated images by the user, different logistic regression models have to be fitted separately. Each fitted model provides us with a relevance probability and a confidence interval for that probability. In order to aggregate these set of probabilities and confidence intervals we use an IOWA operator. The results will show the success of our algorithm and that OWA operators are an efficient and natural way of dealing with this kind of fusion problems.
BibTeX:
@inproceedings{deVes14,
  author = {de Ves, Esther and Zuccarello, Pedro and Leon, Teresa and Ayala, Guillermo},
  title = {IOWA Operators and Its Application to Image Retrieval},
  booktitle = {Structural, Syntactic, and Statistical Pattern Recognition. Joint IAPR International Workshop, S+SSPR 2014, Joensuu, Finland, August 20-22, 2014. Proceedings.},
  publisher = {Springer-Verlag},
  year = {2014},
  volume = {8621}
}
de Ves, E., Benavent, X., Coma, I. and Ayala, G. A novel dynamic multi-model relevance feedback procedure for content-based image retrieval 2016 Neurocomputing
Vol. 208, pp. 99-107 
article DOI URL 
Abstract: Abstract This paper deals with the problem of image retrieval in large databases with a big semantic gap by a relevance feedback procedure. We present a novel algorithm for modelling the users׳s preferences in the content-based image retrieval system. The proposed algorithm considers the probability of an image belonging to the set of those sought by the user, and estimates the parameters of several local logistic regression models whose inputs are the low-level image features. A Principal Component Analysis method is applied to the original vector to reduce its high dimensionality. The relevance probabilities predicted by these local models are combined by means of a weighted average. These weights are obtained according to the variance explained by the group of principal components used for each local model. These models are dynamically estimated in each iteration of the relevance feedback algorithm until the user is satisfied. This novel procedure has been tested in a collection with a large semantic gap, the Wikipedia collection. Two types of experiments have been performed, one with an automatic user and another with a typical user. The method is compared to some recent similar approaches in literature, obtaining very good performance in terms of the MAP\ evaluation measure.
BibTeX:
@article{deVes16,
  author = {de Ves, Esther and Benavent, Xaro and Coma, Inmacula and Ayala, Guillermo},
  title = {A novel dynamic multi-model relevance feedback procedure for content-based image retrieval},
  journal = {Neurocomputing},
  year = {2016},
  volume = {208},
  pages = {99--107},
  note = {SI: BridgingSemantic},
  url = {http://www.sciencedirect.com/science/article/pii/S0925231216304751},
  doi = {https://doi.org/10.1016/j.neucom.2016.02.073}
}
de Ves, E., Ayala, G., Benavent, X., Domingo, J. and Dura, E. Modeling user preferences in content-based image retrieval: A novel attempt to bridge the semantic gap 2015 Neurocomputing
Vol. 168, pp. 829-845 
article DOI URL 
Abstract: Abstract This paper is concerned with content-based image retrieval from a stochastic point of view. The semantic gap problem is addressed in two ways. First, a dimensional reduction is applied using the (pre-calculated) distances among images. The dimension of the reduced vector is the number of preferences that we allow the user to choose from, in this case, three levels. Second, the conditional probability distribution of the random user preference, given this reduced feature vector, is modeled using a proportional odds model. A new model is fitted at each iteration. The score used to rank the image database is based on the estimated probability function of the random preference. Additionally, some memory is incorporated in the procedure by weighting the current and previous scores. Also, a novel evaluation procedure is proposed in this work based on the empirical commutative distribution functions of the relevant and non-relevant retrieved images. Good experimental results are achieved in very different experimental setups and tested in different databases.
BibTeX:
@article{deVes2015,
  author = {Esther de Ves and Guillermo Ayala and Xaro Benavent and Juan Domingo and Esther Dura},
  title = {Modeling user preferences in content-based image retrieval: A novel attempt to bridge the semantic gap},
  journal = {Neurocomputing},
  year = {2015},
  volume = {168},
  pages = {829--845},
  url = {http://www.sciencedirect.com/science/article/pii/S0925231215007171},
  doi = {https://doi.org/10.1016/j.neucom.2015.05.041}
}
de Ves, E., Díaz, M., Ayala, G., Domingo, J. and Simó, A. Robust descriptors of binary shapes with applications 1999 International Journal of Computer Vision
Vol. 34(1), pp. 5-17 
article  
Abstract: The subject of this paper is to propose and test a set of numerical descriptors of 2D binary planar shapes. Given a shape, A, the transformations of A with a given mathematical morphological operation and different structuring elements are considered. The measures of this family of transformed sets provide a numerical description of the original set A.
These descriptors are very robust against noise and maintain a reasonable discriminatory power. The robustness against different levels of contour degradation is tested by simulation. Starting with a clean (without noise) set, Lgr, it is assumed that the observed set, A, is a noisy version (with contour degradation) of Lgr.
The performance of the descriptors, when they are used to compare different shapes or shapes from a scene with models, is studied and compared with related descriptors based on the granulometric analysis of the original set, which are the closest previous alternative to our approach in the literature.
BibTeX:
@article{deVes99,
  author = {E. de Ves and M.E. Díaz and G. Ayala and J. Domingo and A. Simó},
  title = {Robust descriptors of binary shapes with applications},
  journal = {International Journal of Computer Vision},
  year = {1999},
  volume = {34},
  number = {1},
  pages = {5--17}
}
Diaz, M., Ayala, G., Quesada, S. and Martínez-Costa, L. Testing abnormality in the spatial arrangement of cells in the corneal endothelium using spatial point processes 2001 Statistics in Medicine
Vol. 20(22), pp. 3429-3439 
article DOI  
Abstract: The study of central corneal endothelium morphology is important in Ophthalmology. Some of the pathologies that could compromise endothelial cell morphology are trauma, cataract, surgery, use of contact lenses, corneal dystrophies or degenerations. The quantitative analysis of cell shape and cellular pattern is more sensitive in detecting subtle changes in endothelial morphology than cell density measurement or cell area analysis. In this paper, the morphology of the central cornea, the most important area from the point of view of vision, is studied through an associated bivariate spatial point pattern: the centroids of the cells and the triple points, that is, the points where three different cells converge. Nine different summary descriptors (widely used in the statistical analysis of spatial point patterns) have been used: the empty space distribution function; the nearest neighbour distribution function and Ripley's -function for each type of point separately (centroids and triple points), plus the corresponding three versions of these functions in the bivariate case. A control sample with similar age and cell density and no known abnormality is associated to each patient. The above descriptors are calculated for the patient and the controls. Each descriptive of the patient is compared with the corresponding descriptors from the controls by means of a graphical analysis and a formal test. Some patients presenting different pathologies are analysed in detail. Endothelia considered morphologically abnormal by visual inspection, which were not detected by hexagonality or density analysis, could be distinguished from control endothelia by these new descriptors. Copyright 2001 John Wiley & Sons, Ltd.
BibTeX:
@article{Diaz01,
  author = {M.E. Diaz and G. Ayala and S. Quesada and L. Martínez-Costa},
  title = {Testing abnormality in the spatial arrangement of cells in the corneal endothelium using spatial point processes},
  journal = {Statistics in Medicine},
  year = {2001},
  volume = {20},
  number = {22},
  pages = {3429--3439},
  doi = {https://doi.org/10.1002/sim.931}
}
Díaz, M., Ayala, G., Sebastian, R. and Martínez-Costa, L. Granulometric analysis of corneal endothelium specular images by using a germ--grain model 2007 Computers in Biology and Medicine
Vol. 37(3), pp. 364-375 
article DOI  
Abstract: Specular microscopy is widely used to study the human corneal endothelium status in vivo. In this paper, the corneal endothelium is represented as a binary image composed of the cell inscribed circles. The granulometric distribution function of the complement of this image is used as a functional descriptor, which provides information about the shape, size and spatial arrangement of cells. Experimental evaluation using bootstrap techniques shows its ability to discriminate between controls and pathological cases. It represents a reliable and graphical alternative to the classical indices (cell density, hexagonality and coefficient of variation of cell areas), which behave poorly when detecting subtle abnormalities.
BibTeX:
@article{Diaz07,
  author = {M.E. Díaz and G. Ayala and R. Sebastian and L. Martínez-Costa},
  title = {Granulometric analysis of corneal endothelium specular images by using a germ--grain model},
  journal = {Computers in Biology and Medicine},
  year = {2007},
  volume = {37},
  number = {3},
  pages = {364--375},
  doi = {https://doi.org/10.1016/j.compbiomed.2006.04.005}
}
Díaz, E., Sebastian, R., Ayala, G., Díaz, M., Zoncu, R., Toomre, D. and Gasman, S. Measuring Spatio-Temporal Dependencies in Bivariate Temporal Random Sets with Applications to Cell Biology 2008 IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 30(9), pp. 1659-1671 
article DOI  
Abstract: Analyzing spatiotemporal dependencies between different types of events is highly relevant to many biological phenomena (e.g., signaling and trafficking), especially as advances in probes and microscopy have facilitated the imaging of dynamic processes in living cells. For many types of events, the segmented areas can overlap spatially and temporally, forming random clumps. In this paper, we model the binary image sequences of two different event types as a realization of a bivariate temporal random set and propose a nonparametric approach to quantify spatial and spatiotemporal interrelations using the pair correlation, cross-covariance, and the Ripley K functions. Based on these summary statistics, we propose a randomization procedure to test independence between event types by applying random toroidal shifts and Monte Carlo tests. A simulation study assessed the performance of the proposed estimators and showed that these statistics capture the spatiotemporal dependencies accurately. The estimation of the spatiotemporal interval of interactions was also obtained. The method was successfully applied to analyze the interdependencies of several endocytic proteins using image sequences of living cells and validated the procedure as a new way to automatically quantify dependencies between proteins in a formal and robust manner.
BibTeX:
@article{Diaz08,
  author = {E. Díaz and R. Sebastian and G. Ayala and M.E. Díaz and R. Zoncu and D. Toomre and S. Gasman},
  title = {Measuring Spatio-Temporal Dependencies in Bivariate Temporal Random Sets with Applications to Cell Biology},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year = {2008},
  volume = {30},
  number = {9},
  pages = {1659--1671},
  doi = {https://doi.org/10.1109/TPAMI.2007.70821}
}
Díaz, M., Ayala, G., León, T., Zoncu, R. and Toomre, D. Analyzing protein-protein spatial-temporal dependencies from image sequences using fuzzy temporal random sets 2008 Journal of Computational Biology
Vol. 15(9), pp. 1221-1236 
article DOI  
Abstract: Total Internal Reflection Fluorescence Microscopy (TIRFM) allows us to image fluorescent-tagged proteins near the plasma membrane of living cells with high spatial-temporal resolution. Using TIRFM imaging of GFP-tagged clathrin endocytic proteins, areas of fluorescence are observed as overlapping spots of different sizes and durations. Standard procedures to measure protein-protein colocalization of dual labeled samples threshold the original graylevel images to segment areas covered by different proteins. This binary logic is not appropriate as it leaves a free tuning parameter which can influence the conclusions. Moreover, these procedures rely on simple statistical analysis based on correlation coefficients or visual inspection. We propose a probabilistic model to examine spatial-temporal dependencies. Image sequences of two proteins are modeled as a realization of a bivariate fuzzy temporal random set. Spatial-temporal dependencies are described by means of the pair-correlation function and the K-function and are tested using a Monte Carlo test. Five simulated image sequences were used to validate the performance of the procedure. Spatial and spatial-temporal dependencies were generated using a linked pairs model and a Poisson cluster model for the germs. To demonstrate the applicability in addressing current biological questions, we applied the procedure to fluorescent-tagged proteins involved in endocytosis (Clathrin, Hip1R, Epsin, and Caveolin). Results show that this procedure allows biologists to automatically quantify dependencies between molecules in a more formal and robust way. Image sequences and a Matlab toolbox for simulation and testing are available at http://www.uv.es/tracs/.
BibTeX:
@article{Diaz08b,
  author = {M.E. Díaz and G. Ayala and T. León and R. Zoncu and D. Toomre},
  title = {Analyzing protein-protein spatial-temporal dependencies from image sequences using fuzzy temporal random sets},
  journal = {Journal of Computational Biology},
  year = {2008},
  volume = {15},
  number = {9},
  pages = {1221--1236},
  doi = {https://doi.org/10.1089/cmb.2008.0055}
}
Díaz, E., Ayala, G., Díaz, M., Gong, L. and Toomre, D. Automatic detection of dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution 2010 IEEE-ACM Transactions on Computational Biology and Bioinformatics
Vol. 7(1), pp. 2-11 
article DOI  
Abstract: Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual inspection combined with statistical descriptives. Ripley K-functions are used to examine the joint and marginal behavior of locations and fusion times. Semiautomatic detection and mapping of constitutive fusion sites reveals spatial and temporal clustering, but no dependency between the locations and times of fusion events. Our novel approach could be translated to other studies of membrane trafficking in health and diseases such as diabetes.
BibTeX:
@article{Diaz10,
  author = {E. Díaz and G. Ayala and M.E. Díaz and L. Gong and D. Toomre},
  title = {Automatic detection of dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution},
  journal = {IEEE-ACM Transactions on Computational Biology and Bioinformatics},
  year = {2010},
  volume = {7},
  number = {1},
  pages = {2--11},
  doi = {https://doi.org/10.1109/TCBB.2008.30}
}
Díaz, M., Ayala, G. and Díaz, E. Estimating the duration of overlapping events from image sequences using cylindrical temporal Boolean models 2010 Journal of Mathematical Imaging and Vision
Vol. 38(2), pp. 83-94 
article DOI  
Abstract: Recent advances in microscopy jointly to the development of fluorescent probes have enabled to image dynamic processes with very high spatial-temporal resolution, for instance in Cell Biology. In some applications, the segmented areas associated with different events overlap spatially and temporally forming random clumps. In order to study the shape-size features and durations of the events, it is a usual practice to analyze only isolated episodes. However, this sample is biased, because faster and smaller events tend to be isolated. We model the images as a realization of a cylindrical temporal Boolean model. We evaluate the bias introduced when ruling out non-isolated episodes. We propose an estimator of the duration distribution and perform a simulation study to assess its accuracy. The method is applied to fluorescent-tagged proteins image sequences. Results show that this procedure is effective for analyzing dynamic processes where spatial and temporal overlapping occurs.
BibTeX:
@article{Diaz10b,
  author = {M.E. Díaz and G. Ayala and E. Díaz},
  title = {Estimating the duration of overlapping events from image sequences using cylindrical temporal Boolean models},
  journal = {Journal of Mathematical Imaging and Vision},
  year = {2010},
  volume = {38},
  number = {2},
  pages = {83--94},
  doi = {https://doi.org/10.1007/s10851-010-0214-6}
}
Díaz, M., Domingo, J. and Ayala, G. A gray-level 2D feature detector using circular statistics 1997 Pattern Recognition Letters
Vol. 18(11-13), pp. 1083-1089 
article DOI  
Abstract: This paper presents a new method for corner and circular feature detection in gray-level images. It is based on the application of standard statistical techniques to the distribution of gradient orientations in a circular neighborhood of the prospective feature point. An evaluation using standard procedures and a comparison with other approaches is presented. Results show the robustness of this method as compared to the other corner detectors analyzed. The main novelties are the possibility of detecting points that are centers of circular symmetries, and discriminating between junctions, which are classified into corners (two-edge junctions) and multiple edge junctions.
BibTeX:
@article{Diaz97,
  author = {M.E. Díaz and J. Domingo and G. Ayala},
  title = {A gray-level 2D feature detector using circular statistics},
  journal = {Pattern Recognition Letters},
  year = {1997},
  volume = {18},
  number = {11-13},
  pages = {1083--1089},
  doi = {https://doi.org/10.1016/S0167-8655(97)00085-8}
}
Díaz, M., Ayala, G., Albert, J., Ferri, F. and Domingo, J. Accurate detection and characterization of corner points using circular statistics and fuzzy clustering 1998
Vol. 1451, pp. 687-696 
inbook  
Abstract: Accurate detection and characterization of corner points in grey level images is considered as a pattern recognition problem. The method considers circular statistic tests to detect 2D features. A fuzzy clustering algorithm is applied to the edge orientations near the prospective corners to detect and classify them. The method is based on formulating hypotheses about the distribution of these orientations around an edge, corner or other 2-D feature. The method may provide accurate estimates of the direction of the edges that converge in a corner, along with their confidence intervals. Experimental results show the method to be robust enough against noise and contrast changes. Fuzzy membership improves the results of the algorithm and both versions (crisp and fuzzy) give better results than other previously proposed corner detectors.
BibTeX:
@inbook{DiazAAFD98,
  author = {M.E. Díaz and G. Ayala and J. Albert and F. Ferri and J. Domingo},
  title = {Accurate detection and characterization of corner points using circular statistics and fuzzy clustering},
  publisher = {Springer},
  year = {1998},
  volume = {1451},
  pages = {687--696},
  note = {TY: CHAPTER; M3: 10.1007/BFb0033293}
}
Díaz, M. and Ayala, G. Measuring the spatial homogeneity in corneal endotheliums by means of a randomization test 1999
Vol. 1613, pp. 418-423 
inbook  
Abstract: Quantification of regularity of cell sizes and the spatial arrangement of cells in corneal endotheliums becomes of a great importance associated to stress situations such as cataract surgery, corneal transplantation or implantation of intra-ocular lenses. A new index of regularity of the spatial distribution of cell sizes in corneal endotheliums is proposed. The corneal endothelium is described by means of a spatial marked point pattern (the cell centroids marked with the cell areas). The hypothesis of no dependency between mark and locations is tested by a Monte Carlo test. The new index is the p-value of the test validating the hypothesis. Pairs of endotheliums from different eyes of the same person are compared in terms of the traditional measures (density, hexagonality and coefficient of variation) and the new index. Results show how the index proposed can discriminate subtle morphological changes that cannot be detected by the commonly used indices.
BibTeX:
@inbook{DiazAyala99,
  author = {M.E. Díaz and G. Ayala},
  title = {Measuring the spatial homogeneity in corneal endotheliums by means of a randomization test},
  publisher = {Springer},
  year = {1999},
  volume = {1613},
  pages = {418--423},
  note = {PT: S}
}
Domingo, J., Ayala, G. and Díaz, M. Morphometric analysis of human corneal endothelium by means of spatial point patterns 2002 International Journal of Pattern Recognition and Artificial Intelligence
Vol. 16(2), pp. 127-143 
article DOI  
BibTeX:
@article{Domingo02,
  author = {J. Domingo and G. Ayala and M.E. Díaz},
  title = {Morphometric analysis of human corneal endothelium by means of spatial point patterns},
  journal = {International Journal of Pattern Recognition and Artificial Intelligence},
  year = {2002},
  volume = {16},
  number = {2},
  pages = {127--143},
  doi = {https://doi.org/10.1142/S0218001402001605}
}
Domingo, J., Ibáñez, M., Simó, A., Dura, E., Ayala, G. and Alemany, S. Modeling of female human body shapes for apparel design based on cross mean sets 2014 Expert Systems with Applications
Vol. 41(14), pp. 6224-6234 
article DOI URL 
BibTeX:
@article{Domingo14,
  author = {J. Domingo and M.V. Ibáñez and A. Simó and E. Dura and G. Ayala and S. Alemany},
  title = {Modeling of female human body shapes for apparel design based on cross mean sets},
  journal = {Expert Systems with Applications},
  year = {2014},
  volume = {41},
  number = {14},
  pages = {6224--6234},
  url = {http://www.sciencedirect.com/science/article/pii/S0957417414002115},
  doi = {https://doi.org/10.1016/j.eswa.2014.04.014}
}
Domingo, J., Simó, A., Ibáñez, M., Dura, E., Ayala, G. and Alemany, S. Towards a mean body for apparel design 2016 Image and Vision Computing
Vol. 52, pp. 88-96 
article DOI URL 
Abstract: Abstract This paper focuses on shape average with applications to the apparel industry. Apparel industry uses a consensus sizing system; its major concern is to fit most of the population into it. Since anthropometric measures do not grow linearly, it is important to find prototypes to accurately represent each size. This is done using random compact mean sets, obtained from a cloud of 3D points given by a scanner and applying to the sample a previous definition of mean set. Additionally, two approaches to define confidence sets are introduced. The methodology is applied to data obtained from a real anthropometric survey.
BibTeX:
@article{Domingo16,
  author = {J. Domingo and A. Simó and M.V. Ibáñez and E. Dura and G. Ayala and S. Alemany},
  title = {Towards a mean body for apparel design},
  journal = {Image and Vision Computing},
  year = {2016},
  volume = {52},
  pages = {88--96},
  url = {http://www.sciencedirect.com/science/article/pii/S0262885616300944},
  doi = {https://doi.org/10.1016/j.imavis.2016.04.016}
}
Domingo, J., Ayala, G., Simó, A., de Ves, E., Martínez-Costa, L. and Marco, P. Irregular motion recovery in fluorescein angiograms 1997 Pattern Recognition Letters
Vol. 18(8), pp. 805-821 
article DOI  
Abstract: Fluorescein angiography is a common procedure in ophthalmic practice, mainly to evaluate vascular retinopathies and choroidopathies from sequences of ocular fundus images. In order to compare the images, a reliable overlying is essential. This paper proposes some methods for the recovery of irregular motion in fluorescein angiograms (FA). The overlying is done by a three step procedure: detection of relevant points, matching points from different images and estimation of the assumed linear geometric transformation. A stochastic model (closely related to the general linear model) allows to fuse the second and third steps. Two different estimators of the geometric transformation are proposed and tested with real FAs. Images from choroido-retinal diseases have been analysed: diabetic retinopathy, vein occlusions and choroidal neovascular membrane. Results have been evaluated using a different number of relevant points with different spatial arrangements. Registration accuracy is evaluated as the mean squared error between real and transformed relevant point locations for those points not used to estimate the transformation.
BibTeX:
@article{Domingo97,
  author = {J. Domingo and G. Ayala and A. Simó and E. de Ves and L. Martínez-Costa and P. Marco},
  title = {Irregular motion recovery in fluorescein angiograms},
  journal = {Pattern Recognition Letters},
  year = {1997},
  volume = {18},
  number = {8},
  pages = {805--821},
  doi = {https://doi.org/10.1016/S0167-8655(97)00081-0}
}
Domingo, J., Dura, E., Ayala, G. and Ruiz-España, S. Means of 2D and 3D Shapes and Their Application in Anatomical Atlas Building 2015 Computer Analysis of Images and Patterns. 16th International Conference, CAIP 2015 Valletta, Malta, September 2--4, 2015. Proceedings, Part I  inproceedings DOI  
Abstract: This works deals with the concept of mean when applied
to 2D or 3D shapes and with its applicability to the construction of
digital atlases to be used in digital anatomy. Unlike numerical data,
there are several possible definitions of the mean of a shape distribution
and procedures for its estimation from a sample of shapes. Most popular
definitions are based in the distance function or in the coverage function,
each with its strengths and limitations. Closely related to the concept of
mean shape is the concept of atlas, here understood as a probability or
membership map that tells how likely is that a point belongs to a shape
drawn from the shape distribution at hand. We devise a procedure to
build probabilistic atlases from a sample of similar segmented shapes
using information simultaneously from both functions: the distance and
the coverage. Applications of the method in digital anatomy are provided
as well as experiments to show the advantages of the proposed method
regarding state of the art techniques based on the coverage function.
BibTeX:
@inproceedings{DomingoDuraAyalaRuiz2015,
  author = {Domingo, Juan and Dura, Esther and Ayala, Guillermo and Silvia Ruiz-España},
  title = {Means of 2D and 3D Shapes and Their Application in Anatomical Atlas Building},
  booktitle = {Computer Analysis of Images and Patterns. 16th International Conference, CAIP 2015 Valletta, Malta, September 2--4, 2015. Proceedings, Part I},
  year = {2015},
  doi = {https://doi.org/10.1007/978-3-319-23192-144}
}
Domingo, J., Nacher, B., de Ves, E., Alcántara, E., Díaz, M., Ayala, G. and Page, A. Quantifying mean shape and variability of footprints using mean sets 2005
Vol. 30, pp. 455-464 
inbook  
Abstract: This papers presents an application of several definitions of mean set to footwear design. For a given size, footprint pressure images corresponding to different individuals constitute our raw data. Appropriate footwear design needs the knowledge of some kind of typical footprint. Former methods based on contour relevant points are highly sensitive to contour noise; moreover, they lack of repeatability because of the need of a human designer intervention. The method proposed in this paper is based on using mean sets on the thresholded images of the pressure footprints. Three definitions are used, two of them from Vorob'ev and Baddeley-Molchanov and a morphological mean proposed by the authors. Results show that use of mean sets improves previous methodologies in terms of robustness and repeatability.
BibTeX:
@inbook{DomingoNV05,
  author = {J. Domingo and B. Nacher and E. de Ves and E. Alcántara and M.E. Díaz and G. Ayala and A. Page},
  title = {Quantifying mean shape and variability of footprints using mean sets},
  publisher = {Springer},
  year = {2005},
  volume = {30},
  pages = {455--464}
}
Dura, E., Domingo, J., Ayala, G. and Marti-Bonmati, L. Functional statistics based method for the evaluation of the registration of sequences of 3D perfusion MR images 2011 2011 IEEE Nuclear Science Symposium and Medical Imaging Conference, pp. 3149-3152  inproceedings URL 
BibTeX:
@inproceedings{Dura11,
  author = {E. Dura and J. Domingo and G. Ayala and L. Marti-Bonmati},
  title = {Functional statistics based method for the evaluation of the registration of sequences of 3D perfusion MR images},
  booktitle = {2011 IEEE Nuclear Science Symposium and Medical Imaging Conference},
  year = {2011},
  pages = {3149--3152},
  url = {http://www.nss-mic.org/2011/NSSMain.asp}
}
Dura, E., Domingo, J., Ayala, G. and Martí-Bonmatí, L. Evaluation of the registration of temporal series of contrast-enhanced perfusion magnetic resonance 3D images of the liver 2012 Computer Methods and Programs in Biomedicine
Vol. 108(3), pp. 932-945 
article DOI URL 
Abstract: The registration of 2D and 3D images is one of the key tasks in medical image processing and analysis. Accurate registration is a crucial preprocessing step for many tasks; consequently, the evaluation of its accuracy becomes necessary. Unfortunately, this is a difficult task, especially when no golden pattern (true result) is available and when the signal values may have changed between successive images to be registered. This is the case this paper deals with: we have a series of 3D images, magnetic resonance images (MRI) of the liver and adjacent areas that have to be registered. They have been taken while a contrast is diffused through the liver tissue, so intensity of each observed point changes for two reasons: contrast diffusion/perfusion and deformation of the liver (due to body movement and breathing). In this paper, we introduce a new method to automatically compare two or more registration algorithms applied to the same case of a perfusion magnetic resonance dynamic image so that the best of them can be chosen when no ground truth is available. This is done by modeling the function that gives the intensity at a given point as a functional datum, and using statistical techniques to assess its change in comparison with other functions. An example of the application is shown by comparing two parametrizations of a B-spline based registration algorithm. The main result of the proposed method is a suggestive evidence to guide the physician in the process of selecting a registration algorithm, that recommends the algorithm of minimal complexity but still suitable for the case to be analyzed.
BibTeX:
@article{Dura12,
  author = {E. Dura and J. Domingo and G. Ayala and L. Martí-Bonmatí},
  title = {Evaluation of the registration of temporal series of contrast-enhanced perfusion magnetic resonance 3D images of the liver},
  journal = {Computer Methods and Programs in Biomedicine},
  year = {2012},
  volume = {108},
  number = {3},
  pages = {932--945},
  url = {http://www.sciencedirect.com/science/article/pii/S0169260712001290},
  doi = {https://doi.org/10.1016/j.cmpb.2012.04.015}
}
Epifanio, I. and Ayala, G. A random set view of texture classification 2002 IEEE Transactions on Image Processing
Vol. 11(8), pp. 859-867 
article DOI  
Abstract: Texture classification of an image or subimage is an important problem in texture analysis. Many procedures have been proposed. A global framework for texture classification based on random closed set theory is proposed in this paper. In this approach, a binary texture is considered as an outcome of a random closed set. Some distributional descriptors of this stochastic model are used as texture features in order to classify the binary texture, in particular spherical and linear contact distributions and K-functions. If a grayscale texture has to be classified, then the original texture is reduced to a multivariate random closed set where each component (a different random set) corresponds with those pixels verifying a local property. Again, some functional descriptors of the multivariate random closed set defined from the texture can be used as texture features to describe and classify the grayscale texture. Marginal and cross spherical and linear contact distributions and K-functions have been used. Experimental validation is provided by using Brodatz's database and another standard texture database.
BibTeX:
@article{Epifanio02,
  author = {I. Epifanio and G. Ayala},
  title = {A random set view of texture classification},
  journal = {IEEE Transactions on Image Processing},
  year = {2002},
  volume = {11},
  number = {8},
  pages = {859--867},
  doi = {https://doi.org/10.1109/TIP.2002.801119}
}
Esteban, J., de-Hijas, N.Z.M., Kinnari, T.J., Ayala, G., Fernández-Roblas, R. and Gadea, I. Biofilm development by potentially pathogenic non-pigmented rapidly growing mycobacteria 2008 BMC Microbiology
Vol. 8, pp. 184 
article DOI  
BibTeX:
@article{Esteban08,
  author = {Jaime Esteban and Nieves Z. Martín-de-Hijas and Teemu J. Kinnari and Guillermo Ayala and Ricardo Fernández-Roblas and Ignacio Gadea},
  title = {Biofilm development by potentially pathogenic non-pigmented rapidly growing mycobacteria},
  journal = {BMC Microbiology},
  year = {2008},
  volume = {8},
  pages = {184},
  doi = {https://doi.org/10.1186/1471-2180-8-184}
}
Martín-de-Hijas, N., García-Almeida, D., Ayala, G., Fernandez-Roblas, R., Gadea, I., Gómez-Barrena, E. and Esteban, J. Biofilm development by clinical strains of non-pigmented rapidly growing mycobacteria 2009 Clinical Microbiology and Infection
Vol. 15(10), pp. 931-936 
article DOI  
BibTeX:
@article{Esteban09,
  author = {Martín-de-Hijas N. and García-Almeida D. and G. Ayala and Fernandez-Roblas R. and Gadea I. and Gómez-Barrena E. and Esteban J.},
  title = {Biofilm development by clinical strains of non-pigmented rapidly growing mycobacteria},
  journal = {Clinical Microbiology and Infection},
  year = {2009},
  volume = {15},
  number = {10},
  pages = {931--936},
  doi = {https://doi.org/10.1111/j.1469-0691.2009.02882.x}
}
Gadea, I., Ayala, G., Diago, M., Cunat, A. and de Lomas, J. Immunological diagnosis of human hydatid cyst relapse: Utility of the enzyme-linked immunoelectrotransfer blot and discriminant analysis 2000 Clinical and diagnostic laboratory immunology
Vol. 7(4), pp. 549-552 
article  
BibTeX:
@article{Gadea00,
  author = {I. Gadea and G. Ayala and M.T. Diago and A. Cunat and J.G. de Lomas},
  title = {Immunological diagnosis of human hydatid cyst relapse: Utility of the enzyme-linked immunoelectrotransfer blot and discriminant analysis},
  journal = {Clinical and diagnostic laboratory immunology},
  year = {2000},
  volume = {7},
  number = {4},
  pages = {549--552}
}
Gadea, I., Ayala, G., Diago, M., Cunat, A. and de Lomas, J. Immunological diagnosis of human cystic echinococcosis: Utility of discriminant analysis applied to the enzyme-linked immunoelectrotransfer blot 1999 Clinical and diagnostic laboratory immunology
Vol. 6(4), pp. 504-508 
article  
BibTeX:
@article{Gadea99,
  author = {I. Gadea and G. Ayala and M.T. Diago and A. Cunat and J.G. de Lomas},
  title = {Immunological diagnosis of human cystic echinococcosis: Utility of discriminant analysis applied to the enzyme-linked immunoelectrotransfer blot},
  journal = {Clinical and diagnostic laboratory immunology},
  year = {1999},
  volume = {6},
  number = {4},
  pages = {504--508}
}
García-Martínez, J., Ayala, G., Pelechano, V., Chávez, S., Herrero, E. and Pérez-Ortín, J.E. The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast 2012 Transcription
Vol. 3(1), pp. 39-44 
article DOI  
BibTeX:
@article{GarciaMartinez12,
  author = {José García-Martínez and Guillermo Ayala and Vicente Pelechano and Sebastián Chávez and Enrique Herrero and José E. Pérez-Ortín},
  title = {The relative importance of transcription rate, cryptic transcription and mRNA stability on shaping stress responses in yeast},
  journal = {Transcription},
  year = {2012},
  volume = {3},
  number = {1},
  pages = {39--44},
  doi = {https://doi.org/10.4161/trns.3.1.19416}
}
García-Martínez, J., Delgado-Ramos, L., Ayala, G., Pelechano, V., Medina, D.A., Carrasco, F., González, R., Andrés-León, E., Steinmetz, L., Warringer, J., Chávez, S. and Pérez-Ortín, J.E. The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons 2016 Nucleic Acids Research
Vol. 44(8), pp. 3643-3658 
article DOI URL 
Abstract: We analyzed 80 different genomic experiments, and found a positive correlation between both RNA polymerase II transcription and mRNA degradation with growth rates in yeast. Thus, in spite of the marked variation in mRNA turnover, the total mRNA concentration remained approximately constant. Some genes, however, regulated their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. We also detected these regulations within the heterogeneity of a wild-type cell population growing in optimal conditions. The transcriptomic analysis of sorted microcolonies confirmed that the growth rate dictates alternative expression programs by modulating transcription and mRNA decay.The regulation of overall mRNA turnover keeps a constant ratio between mRNA decay and the dilution of [mRNA] caused by cellular growth. This regulation minimizes the indiscriminate transmission of mRNAs from mother to daughter cells, and favors the response capacity of the latter to physiological signals and environmental changes. We also conclude that, by uncoupling mRNA synthesis from decay, cells control the mRNA abundance of those gene regulons that characterize fast and slow growth.
BibTeX:
@article{GarciaMartinez16,
  author = {García-Martínez, José and Delgado-Ramos, Lidia and Ayala, Guillermo and Pelechano, Vicent and Medina, Daniel A. and Carrasco, Fany and González, Ramón and Andrés-León, Eduardo and Steinmetz, Lars and Warringer, Jonas and Chávez, Sebastián and Pérez-Ortín, José E.},
  title = {The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons},
  journal = {Nucleic Acids Research},
  year = {2016},
  volume = {44},
  number = {8},
  pages = {3643--3658},
  url = {http://nar.oxfordjournals.org/content/44/8/3643.abstract},
  doi = {https://doi.org/10.1093/nar/gkv1512}
}
Gutierrez, J., Ayala, G. and Díaz, M. Set Descriptors for Visual Evaluation of Human Corneal Endothelia 2001 Computer Vision and Image Understanding
Vol. 84(2), pp. 249-263 
article DOI  
Abstract: Images of corneal endothelium obtained from specular microscopy are of great importance in the evaluation of the corneal endothelium status. Several commercial tools provide some numerical descriptors to characterize these images in terms of cell density, hexagonality, and some descriptive statistics of the cell areas. However, it is a too simple analysis that only detects severe abnormal endothelia with many irregular and large cells. Detection of subtle abnormalities needs a more refined analysis. This paper proposes a shape-size descriptor based on some modified versions of the geometric covariogram. This descriptor is presented as a valid alternative to the classical analysis that provides a reliable, visual, and easy evaluation of the corneal endothelium. Control images of normal endothelia can be used to classify a given image as normal or abnormal with respect to these controls by means of a graphical test.
BibTeX:
@article{gutierrez01,
  author = {J. Gutierrez and G. Ayala and M.E. Díaz},
  title = {Set Descriptors for Visual Evaluation of Human Corneal Endothelia},
  journal = {Computer Vision and Image Understanding},
  year = {2001},
  volume = {84},
  number = {2},
  pages = {249--263},
  doi = {https://doi.org/10.1006/cviu.2001.0936}
}
Ibáñez, M., Vinué, G., Alemany, S., Simó, A., Epifanio, I., Domingo, J. and Ayala, G. Apparel sizing using trimmed PAM and OWA operators 2012 Expert Systems with Applications
Vol. 39(12), pp. 10512-10520 
article DOI URL 
Abstract: This paper is concerned with apparel sizing system design. One of the most important issues in the apparel development process is to define a sizing system that provides a good fit to the majority of the population. A sizing system classifies a specific population into homogeneous subgroups based on some key body dimensions. Standard sizing systems range linearly from very small to very large. However, anthropometric measures do not grow linearly with size, so they can not accommodate all body types. It is important to determine each class in the sizing system based on a real prototype that is as representative as possible of each class. In this paper we propose a methodology to develop an efficient apparel sizing system based on clustering techniques jointly with OWA operators. Our approach is a natural extension and improvement of the methodology proposed by McCulloch, Paal, and Ashdown (1998), and we apply it to the anthropometric database obtained from a anthropometric survey of the Spanish female population, performed during 2006.
BibTeX:
@article{ibanez12,
  author = {M.V. Ibáñez and G. Vinué and S. Alemany and A. Simó and I. Epifanio and J. Domingo and G. Ayala},
  title = {Apparel sizing using trimmed PAM and OWA operators},
  journal = {Expert Systems with Applications},
  year = {2012},
  volume = {39},
  number = {12},
  pages = {10512--10520},
  url = {http://www.sciencedirect.com/science/article/pii/S0957417412003909},
  doi = {https://doi.org/10.1016/j.eswa.2012.02.127}
}
León, T., Zuccarello, P., Ayala, G., de Ves, E. and Domingo, J. Applying logistic regression to relevance feedback in image retrieval systems 2007 Pattern Recognition
Vol. 40(10), pp. 2621-2632 
article DOI  
Abstract: This paper deals with the problem of image retrieval from large image databases. A particularly interesting problem is the retrieval of all images which are similar to one in the user's mind, taking into account his/her feedback which is expressed as positive or negative preferences for the images that the system progressively shows during the search. Here we present a novel algorithm for the incorporation of user preferences in an image retrieval system based exclusively on the visual content of the image, which is stored as a vector of low-level features. The algorithm considers the probability of an image belonging to the set of those sought by the user, and models the logit of this probability as the output of a generalized linear model whose inputs are the low-level image features. The image database is ranked by the output of the model and shown to the user, who selects a few positive and negative samples, repeating the process in an iterative way until he/she is satisfied. The problem of the small sample size with respect to the number of features is solved by adjusting several partial generalized linear models and combining their relevance probabilities by means of an ordered averaged weighted operator. Experiments were made with 40 users and they exhibited good performance in finding a target image (4 iterations on average) in a database of about 4700 images. The mean number of positive and negative examples is of 4 and 6 per iteration. A clustering of users into sets also shows consistent patterns of behavior.
BibTeX:
@article{Leon07,
  author = {T. León and P. Zuccarello and G. Ayala and E. de Ves and J. Domingo},
  title = {Applying logistic regression to relevance feedback in image retrieval systems},
  journal = {Pattern Recognition},
  year = {2007},
  volume = {40},
  number = {10},
  pages = {2621--2632},
  doi = {https://doi.org/10.1016/j.patcog.2007.02.002}
}
León, T., Ayala, G., Gastón, M. and Mallor, F. Using Mathematical Morphology for unsupervised classification of functional data 2011 Journal of Statistical Computation and Simulation
Vol. 81(8), pp. 1001-1016 
article DOI  
Abstract: This paper is concerned with the unsupervised classification of functional data by using mathematical
morphology. Different morphological operators are used to extract relevant structures of the functions
(considered as sets through their subgraph representations). These operators can be considered as prepro-
cessing tools whose outputs are also functional data. We explore some dissimilarity measures and clustering
methods for the classification of the transformed data. Our approach is illustrated through a detailed analy-
sis of two data sets. These techniques, which have mainly been used in image processing, provide a flexible
and robust toolbox for improving the results in unsupervised functional data classification.
BibTeX:
@article{Leon10,
  author = {T. León and G. Ayala and M. Gastón and F. Mallor},
  title = {Using Mathematical Morphology for unsupervised classification of functional data},
  journal = {Journal of Statistical Computation and Simulation},
  year = {2011},
  volume = {81},
  number = {8},
  pages = {1001--1016},
  doi = {https://doi.org/10.1080/00949651003596099}
}
Martínez-Costa, L., Marco, P., Ayala, G., de Ves, E., Domingo, J. and Simó, A. Macular Edema Computer-Aided Evaluation in Ocular Vein Occlusions 1998 Computers and Biomedical Research
Vol. 31(5), pp. 374-384 
article DOI  
Abstract: This paper is concerned with the use of digital fundus imaging to detect, quantify, and follow up macular angiographic leakage due to retinal vein occlusions. Images were matched automatically. We detected those pixels with a high increment in gray level within the closest area to the foveal center. Binary images displaying leakage were obtained. The procedure was checked against two observers' agreement. Twenty-one angiographic studies were collected. Two images of each sequence were selected for digitalization. Numerical descriptors of the leakage were proposed and quantification plots were designed for each pair of images. Interobserver concordance ranged between 82 and 98% when manually detected leakage was compared with computer segmented areas. The detection and quantification of leakage areas may serve as a guide for severity evaluation and treatment planning. Moreover, they permit a precise follow-up of macular edema.
BibTeX:
@article{MartinezCosta98,
  author = {L. Martínez-Costa and P. Marco and G. Ayala and E. de Ves and J. Domingo and A. Simó},
  title = {Macular Edema Computer-Aided Evaluation in Ocular Vein Occlusions},
  journal = {Computers and Biomedical Research},
  year = {1998},
  volume = {31},
  number = {5},
  pages = {374--384},
  doi = {https://doi.org/10.1006/cbmr.1998.1487}
}
Martín-Sanchez, A., McLean, L., Beynon, R.L., Hurst, J.L., Ayala, G., Lanuza, E. and Martinez-García, F. From sexual attraction to maternal aggression: When pheromones change their behavioural significance 2015 Hormones and Behavior
Vol. 68, pp. 65-76 
article DOI  
Abstract: This article is part of a Special Issue "Chemosignals and Reproduction". This paper reviews the role of chemosignals in the socio-sexual interactions of female mice, and reports two experiments testing the role of pup-derived chemosignals and the male sexual pheromone darcin in inducing and promoting maternal aggression. Female mice are attracted to urine-borne male pheromones. Volatile and non-volatile urine fractions have been proposed to contain olfactory and vomeronasal pheromones. In particular, the male-specific major urinary protein (MUP) MUP20, darcin, has been shown to be rewarding and attractive to females. Non-urinary male chemosignals, such as the lacrimal protein ESP1, promote lordosis in female mice, but its attractive properties are still to be tested. There is evidence indicating that ESP1 and MUPs are detected by vomeronasal type 2 receptors (V2R). When a female mouse becomes pregnant, she undergoes dramatic changes in her physiology and behaviour. She builds a nest for her pups and takes care of them. Dams also defend the nest against conspecific intruders, attacking especially gonadally intact males. Maternal behaviour is dependent on a functional olfactory system, thus suggesting a role of chemosignals in the development of maternal behaviour. Our first experiment demonstrates, however, that pup chemosignals are not sufficient to induce maternal aggression in virgin females. In addition, it is known that vomeronasal stimuli are needed for maternal aggression. Since MUPs (and other molecules) are able to promote intermale aggression, in our second experiment we test if the attractive MUP darcin also promotes attacks on castrated male intruders by lactating dams. Our findings demonstrate that the same chemosignal, darcin, promotes attraction or aggression according to female reproductive state.
BibTeX:
@article{MartinSanchez15,
  author = {Ana Martín-Sanchez and Lynn McLean and Robert L. Beynon and Jane L. Hurst and Ayala, Guillermo and Lanuza, Enrique and Fernando Martinez-García},
  title = {From sexual attraction to maternal aggression: When pheromones change their behavioural significance},
  journal = {Hormones and Behavior},
  year = {2015},
  volume = {68},
  pages = {65--76},
  doi = {https://doi.org/10.1016/j.yhbeh.2014.08.007}
}
Ortigosa, N., Cano, Ó., Ayala, G., Galbis, A. and Fernández, C. Atrial fibrillation subtypes classification using the General Fourier-family Transform 2014 Medical Engineering & Physics
Vol. 36, pp. 554-560 
article DOI URL 
Abstract: Abstract Atrial fibrillation patients can be classified into paroxysmal, persistent and permanent attending to the temporal pattern of this arrhythmia. The surface electrocardiogram hides this differentiation. A classification method to discriminate between the different subtypes of atrial fibrillation by using short segments of electrocardiograms recordings is presented. We will process the electrocardiograms (ECGs) using time--frequency techniques with a global accuracy of 80%. Real cases are evaluated showing promising results for an implementation in a semiautomated diagnostic system.
BibTeX:
@article{Ortigosa14,
  author = {Nuria Ortigosa and Óscar Cano and Guillermo Ayala and Antonio Galbis and Carmen Fernández},
  title = {Atrial fibrillation subtypes classification using the General Fourier-family Transform},
  journal = {Medical Engineering & Physics},
  year = {2014},
  volume = {36},
  pages = {554--560},
  url = {http://www.sciencedirect.com/science/article/pii/S1350453313002713},
  doi = {https://doi.org/10.1016/j.medengphy.2013.12.005}
}
Page, A., Ayala, G., Leon, M., Peydro, M. and Prat, J. Normalizing temporal patterns to analyze sit-to-stand movements by using registration of functional data 2006 Journal of Biomechanics
Vol. 39(13), pp. 2526-2534 
article DOI  
Abstract: Functional data analysis techniques provide an alternative way of representing movement and movement variability as a function of time. In particular, the registration of functional data provides a local normalization of time functions. This normalization transforms a set of curves, records of repeated trials, yielding a new set of curves that only vary in terms of amplitude. Therefore, main events occur at the “same time” for all transformed curves and interesting features of individual recordings remain after averaging processes.
This paper presents an application of the registration process to the analysis of the vertical forces exerted on the ground by both feet during the sit-to-stand movement. This movement is particularly interesting in functional evaluations related to balance control, lower extremity dysfunction or low-back pain.
BibTeX:
@article{Page06,
  author = {A. Page and G. Ayala and M.T. Leon and M.F. Peydro and J.M. Prat},
  title = {Normalizing temporal patterns to analyze sit-to-stand movements by using registration of functional data},
  journal = {Journal of Biomechanics},
  year = {2006},
  volume = {39},
  number = {13},
  pages = {2526--2534},
  doi = {https://doi.org/10.1016/j.jbiomech.2005.07.032}
}
Zoncu, R., Perera, R., Sebastián, R., F. Nakatsu, F., Chen, H., Balla, T., Ayala, G., D. Toomre, D. and Camilli, P.D. Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate 2007 Proceedings of the National Academy of Sciences of the United States of America
Vol. 104(10), pp. 3793-3798 
article DOI  
BibTeX:
@article{PNAS07,
  author = {R. Zoncu and R.M. Perera and R. Sebastián and F. Nakatsu F. and H. Chen and T. Balla and G. Ayala and D. Toomre D. and P.V. De Camilli},
  title = {Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  year = {2007},
  volume = {104},
  number = {10},
  pages = {3793--3798},
  doi = {https://doi.org/10.1073/pnas.0611733104}
}
RIFFO-CAMPOS, Á.L., CASTILLO, J., AYALA, G., CERVANTES, A., LÓPEZ-RODAS, G. and FRANCO, L. An RNA-seq analysis reveals that the EPDR1 and ZNF518B genes and their alternative splicing isoforms are differentially expressed in colorectal cancer cells depending on G13D KRAS mutation 2016 Oncology Reports
Vol. 36, pp. 3627-3634 
article DOI  
BibTeX:
@article{Riffo16,
  author = {ÁNGELA L. RIFFO-CAMPOS and JOSEFA CASTILLO and GUILLERMO AYALA and ANDRÉS CERVANTES and GERARDO LÓPEZ-RODAS and LUIS FRANCO},
  title = {An RNA-seq analysis reveals that the EPDR1 and ZNF518B genes and their alternative splicing isoforms are differentially expressed in colorectal cancer cells depending on G13D KRAS mutation},
  journal = {Oncology Reports},
  year = {2016},
  volume = {36},
  pages = {3627--3634},
  doi = {https://doi.org/10.3892/or.2016.5210}
}
Sebastián, R., Díaz, M., Ayala, G., Letinic, K., Moncho-Bogani, J. and Toomre, D. Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells 2006 IEEE/ACM Transactions on Computational Biology and Bioinformatics
Vol. 3(1), pp. 17-32 
article DOI  
Abstract: Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis of fusion of constitutive vesicular traffic with the plasma membrane has not been systematically performed. Also, the spatial sites and times of vesicle fusion have not yet been analyzed together. In addition, more formal tests are required in testing biological hypotheses, rather than visual inspection combined with statistical descriptives. Ripley K-functions are used to examine the joint and marginal behavior of locations and fusion times. Semiautomatic detection and mapping of constitutive fusion sites reveals spatial and temporal clustering, but no dependency between the locations and times of fusion events. Our novel approach could be translated to other studies of membrane trafficking in health and diseases such as diabetes.
BibTeX:
@article{Sebastian2006,
  author = {R. Sebastián and M.E. Díaz and G. Ayala and K. Letinic and J. Moncho-Bogani and D. Toomre},
  title = {Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year = {2006},
  volume = {3},
  number = {1},
  pages = {17--32},
  doi = {https://doi.org/10.1109/TCBB.2006.11}
}
Sebastián, R., Díaz, E., Ayala, G., Díaz, M., Zoncu, R. and Toomre, D. Studying endocytosis in space and time by means of temporal Boolean models 2006 Pattern Recognition
Vol. 39(11), pp. 2175-2185 
article DOI  
Abstract: Endocytosis is a process by which cells carry traffic from the extracellular space into various intracellular compartments. Visualization of fluorescently tagged clathrin proteins (mediators of endocytosis) allows us to image endocytosis in real time. When imaging the plasma membrane, areas of fluorescence generated by different endocytic processes overlap spatially and temporally, forming random clumps. Here, a sequence of segmented clathrin spots is considered a realization of a non-isotropic 3D Boolean model. Estimates of the intensity, the mean perimeter and the density function of the durations of endocytic events are obtained.
BibTeX:
@article{SebastianPR2006,
  author = {R. Sebastián and E. Díaz and G. Ayala and M.E. Díaz and R. Zoncu and D. Toomre},
  title = {Studying endocytosis in space and time by means of temporal Boolean models},
  journal = {Pattern Recognition},
  year = {2006},
  volume = {39},
  number = {11},
  pages = {2175--2185},
  doi = {https://doi.org/10.1016/j.patcog.2006.04.030}
}
Simó, A., Ves, E.D. and Ayala, G. Resuming shapes with applications 2004 Journal of Mathematical Imaging and Vision
Vol. 20(3), pp. 209-222 
article DOI  
Abstract: Many image processing tasks need some kind of average of different shapes. Frequently, different shapes obtained from several images have to be summarized. If these shapes can be considered as different realizations of a given random compact set, then the natural summaries are the different mean sets proposed in the literature. In this paper, new mean sets are defined by using the basic transformations of Mathematical Morphology (dilation, erosion, opening and closing). These new definitions can be considered, under some additional assumptions, as particular cases of the distance average of Baddeley and Molchanov. The use of the former and new mean sets as summary descriptors of shapes is illustrated with two applications: the analysis of human corneal endothelium images and the segmentation of the fovea in a fundus image. The variation of the random compact sets is described by means of confidence sets for the mean and by using set intervals (a generalization of confidence intervals for random sets). Finally, a third application is proposed: a procedure for denoising a single image by using mean sets.
BibTeX:
@article{Simo04,
  author = {A. Simó and E. De Ves and G. Ayala},
  title = {Resuming shapes with applications},
  journal = {Journal of Mathematical Imaging and Vision},
  year = {2004},
  volume = {20},
  number = {3},
  pages = {209--222},
  doi = {https://doi.org/10.1023/B:JMIV.0000024039.27561.b9}
}
Simó, A., Ves, E.D., Díaz, M., Ayala, G. and Domingo, J. Bayesian estimation of edge orientations in junctions 1999 Pattern Recognition Letters
Vol. 20(11-13), pp. 1113-1122 
article DOI  
Abstract: Junctions, defined as those points of an image where two or more edges meet, play a significant role in many computer vision applications. Junction detection is a widely treated problem, and some detectors can provide even the directions of the edges that meet in a junction. The main objective of this paper is the precise estimation of such directions. It is supposed that the junction point has been previously found by some detector. Also, it is assumed that samples, possibly noisy, of orientations of the edges found in a circular window surrounding the point are available. A mixture of von Mises distributions is assumed for these data, and then a Bayesian methodology is applied to estimate its parameters, some of which are precisely the searched edge orientations. The Bayesian methodology requires the calculation of the mean value of expectation of a posterior distribution which is too complicated to be analytically solved; consequently, a Markov Chain Monte Carlo Method is used for this purpose. Tests have been performed on both a synthetic and a real image. They show that the procedure converges to the expected value for the orientations, and moreover, can provide reliable confidence intervals for these quantities. Since computational cost is high, this method should be used when precision is preferred to speed.
BibTeX:
@article{Simo99,
  author = {A. Simó and E. De Ves and M.E. Díaz and G. Ayala and J. Domingo},
  title = {Bayesian estimation of edge orientations in junctions},
  journal = {Pattern Recognition Letters},
  year = {1999},
  volume = {20},
  number = {11-13},
  pages = {1113--1122},
  doi = {https://doi.org/10.1016/S0167-8655(99)00078-1}
}
Torres-Gimeno, A., Martínez-Costa, L. and Ayala, G. Preoperative factors influencing success in pterygium surgery 2012 BMC Ophthalmology
Vol. 12(38) 
article DOI  
BibTeX:
@article{Torres12,
  author = {Ana Torres-Gimeno and Lucía Martínez-Costa and Guillermo Ayala},
  title = {Preoperative factors influencing success in pterygium surgery},
  journal = {BMC Ophthalmology},
  year = {2012},
  volume = {12},
  number = {38},
  doi = {https://doi.org/10.1186/1471-2415-12-38}
}
García-Aguado, R., Viñoles, J., Brimacombe, J., Vivo, M., Lopez-Estudillo, R. and Ayala, G. Suction catheter guided insertion of the ProSeal (TM) laryngeal mask airway is superior to the digital technique 2006 Canadian Journal of Anaesthesia-Journal Canadien D Anesthesie
Vol. 53(4), pp. 398-403 
article  
BibTeX:
@article{Vinoles06,
  author = {R. García-Aguado and J. Viñoles and J. Brimacombe and M. Vivo and R. Lopez-Estudillo and G. Ayala},
  title = {Suction catheter guided insertion of the ProSeal (TM) laryngeal mask airway is superior to the digital technique},
  journal = {Canadian Journal of Anaesthesia-Journal Canadien D Anesthesie},
  year = {2006},
  volume = {53},
  number = {4},
  pages = {398--403}
}
Vinoles, J., Ibanez, M. and Ayala, G. Predicting recovery at home after Ambulatory Surgery 2011 BMC Health Services Research
Vol. 11(1), pp. 269 
article DOI URL 
Abstract: The correct implementation of Ambulatory Surgery must be accompanied by an accurate monitoring of the patient post-discharge state. We fit different statistical models to predict the first hours postoperative status of a discharged patient. We will also be able to predict, for any discharged patient, the probability of needing a closer follow-up, or of having a normal progress at home. BACKGROUND:The status of a discharged patient is predicted during the first 48 hours after discharge by using variables routinely used in Ambulatory Surgery. The models fitted will provide the physician with an insight into the post-discharge progress. These models will provide valuable information to assist in educating the patient and their carers about what to expect after discharge as well as to improve their overall level of satisfaction.METHODS:A total of 922 patients from the Ambulatory Surgery Unit of the Dr. Peset University Hospital (Valencia, Spain) were selected for this study. Their post-discharge status was evaluated through a phone questionnaire. We pretend to predict four variables which were self-reported via phone interviews with the discharged patient: sleep, pain, oral tolerance of fluid/food and bleeding status. A fifth variable called phone score will be built as the sum of these four ordinal variables. The number of phone interviews varies between patients, depending on the evolution. The proportional odds model was used. The predictors were age, sex, ASA status, surgical time, discharge time, type of anaesthesia, surgical specialty and ambulatory surgical incapacity (ASI). This last variable reflects, before the operation, the state of incapacity and severity of symptoms in the discharged patient.RESULTS:Age, ambulatory surgical incapacity and the surgical specialty are significant to explain the level of pain at the first call. For the first two phone calls, ambulatory surgical incapacity is significant as a predictor for all responses except for sleep at the first call.CONCLUSIONS:The variable ambulatory surgical incapacity proved to be a good predictor of the patient's status at home. These predictions could be used to assist in educating patients and their carers about what to expect after discharge, as well as to improve their overall level of satisfaction.
BibTeX:
@article{vinoles11,
  author = {Vinoles, Juan and Ibanez, Maria and Ayala, Guilllermo},
  title = {Predicting recovery at home after Ambulatory Surgery},
  journal = {BMC Health Services Research},
  year = {2011},
  volume = {11},
  number = {1},
  pages = {269},
  url = {http://www.biomedcentral.com/1472-6963/11/269},
  doi = {https://doi.org/10.1186/1472-6963-11-269}
}
Vinué, G., León, T., Alemany, S. and Ayala, G. Looking for representative fit models for apparel sizing 2014 Decision Support Systems
Vol. 57(0), pp. 22-33 
article DOI URL 
Abstract: Abstract This paper is concerned with the generation of optimal fit models for use in apparel design. Representative fit models or prototypes are important for defining a meaningful sizing system. However, there is no agreement among apparel manufacturers and each one has their own prototypes and size charts i.e. there is a lack of standard sizes in garments from different apparel manufacturers. We propose two algorithms based on a new hierarchical partitioning around medoids clustering method originally developed for gene expression data. We are concerned with a different application; therefore, the dissimilarity between the objects has to be different and must be designed to deal with anthropometric features. Furthermore, one of the algorithms incorporates a different rule to split the clusters, which, in our case, provides better results. Our procedures not only make it possible to obtain optimal prototypes, but also to detect outliers. These outliers should be removed before defining prototypes so that the companies' market share can be optimized. All the analyses are performed using the anthropometric database obtained from a survey of the Spanish female population.
BibTeX:
@article{Vinue14,
  author = {G. Vinué and T. León and S. Alemany and G. Ayala},
  title = {Looking for representative fit models for apparel sizing},
  journal = {Decision Support Systems},
  year = {2014},
  volume = {57},
  number = {0},
  pages = {22--33},
  url = {http://www.sciencedirect.com/science/article/pii/S0167923613001929},
  doi = {https://doi.org/10.1016/j.dss.2013.07.007}
}
Zapater, V., Martínez-Costa, L. and Ayala, G. Classifying human endothelial cells based on individual granulometric size distributions 2002 Image and Vision Computing
Vol. 20(11), pp. 783-791 
article DOI  
Abstract: This paper presents an application to a medical problem of methods of shape analysis based on mathematical morphology. The medical problem consists on the detection of abnormalities in the corneal endothelium, a tissue composed by quasi-planar cells of ideally regular hexagonal shape. Images of this tissue are taken by a specular microscope and used to evaluate the corneal endothelium status. Up to now, cell density, hexagonality and an analysis of cell areas are the usual descriptors of a corneal endothelium. These parameters are not sensitive enough to detect subtle lesions. What this paper proposes is an analysis based on granulometries, which are size-shape descriptors widely used in Mathematical Morphology. Applications of granulometries lead to distribution functions whose moments are used as shape descriptors. Former approaches proposed a global evaluation of the whole corneal endothelium but irregularities affecting to a few cells could be ignored. Differently to that approach, this paper uses the granulometric size distribution of each cell. A group of normal cells is chosen as controls and a given cell is classified as normal or abnormal by comparing its granulometric size distribution with the corresponding distributions of the controls. The technique is illustrated with the analysis of some images of corneal endothelia.
BibTeX:
@article{Zapater02,
  author = {V. Zapater and L. Martínez-Costa and G. Ayala},
  title = {Classifying human endothelial cells based on individual granulometric size distributions},
  journal = {Image and Vision Computing},
  year = {2002},
  volume = {20},
  number = {11},
  pages = {783--791},
  doi = {https://doi.org/10.1016/S0262-8856(02)00087-2}
}
Zapater, V., Martínez-Costa, L. and Ayala, G. A granulometric analysis of specular microscopy images of human corneal endothelia 2005 Computer Vision and Image Understanding
Vol. 97(3), pp. 297-314 
article DOI  
Abstract: The inner layer of the human cornea, called the corneal endothelium, plays an important role in the maintenance of corneal transparency. Specular microscopy is the most widely used technique to study the corneal endothelium in vivo. Improvements in technology have allowed us to obtain good quality specular images, but the detection and quantification of small size--shape cell changes is not obvious, specially when the physician wants to evaluate endothelial cell changes after some surgical procedures. This paper proposes a methodology to analyze specular microscopy images. Every corneal endothelium is described by means of different cumulative distribution functions or some moments (mean, standard deviation, kurtosis, and skewness) of these distribution functions. These distributions are defined from different granulometries based on successive structural openings of the corneal endothelium. Changes in cell morphology are pointed out by comparing the cumulative distribution function (or the corresponding moments) of a given patient with the corresponding cumulative distribution functions (or their moments) of a group of age-matched controls. Different comparison procedures are given, providing us with different numerical evaluations of the corneal endothelium status. These new indices are compared with the classic descriptors used in commercial packages (density, hexagonality, and coefficient of variation of cell areas). Detailed analysis of different images of corneal endothelia are given using the classic and new indices jointly.
BibTeX:
@article{Zapater05,
  author = {V. Zapater and L. Martínez-Costa and G. Ayala},
  title = {A granulometric analysis of specular microscopy images of human corneal endothelia},
  journal = {Computer Vision and Image Understanding},
  year = {2005},
  volume = {97},
  number = {3},
  pages = {297--314},
  doi = {https://doi.org/10.1016/j.cviu.2004.09.001}
}
Dura, E., Domingo, J., Ayala, G., Marti-Bonmati, L. and Goceri, E. Probabilistic Liver Atlas Construction 2017 BioMedical Engineering OnLine  article  
BibTeX:
@article{Dura17,
  author = {Dura, E. and Domingo, J. and Ayala, G. and Marti-Bonmati, L. and Goceri, E.},
  title = {Probabilistic Liver Atlas Construction},
  journal = {BioMedical Engineering OnLine},
  year = {2017}
}
Ayala, G. Estadística Básica 2015   electronic URL 
BibTeX:
@electronic{nmr13,
  author = {Guillermo Ayala},
  title = {Estadística Básica},
  year = {2015},
  url = {https://www.uv.es/ayala/docencia/nmr/nmr13.pdf}
}
Berral-Gonzalez, A., Riffo-Campos, A.L. and Ayala, G. OMICfpp: a fuzzy approach for paired RNA-Seq counts 2019 BMC Genomics
Vol. 20(1), pp. 259 
article URL 
Abstract: RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. In addition, experimental design must be taken into account and few tools consider it.
BibTeX:
@article{Berral-Gonzalez2019,
  author = {Berral-Gonzalez, Alberto and Riffo-Campos, Angela L. and Ayala, Guillermo},
  title = {OMICfpp: a fuzzy approach for paired RNA-Seq counts},
  journal = {BMC Genomics},
  year = {2019},
  volume = {20},
  number = {1},
  pages = {259},
  url = {https://doi.org/10.1186/s12864-019-5496-5}
}
Ortigosa, N., Ayala, G. and Cano, O. Functional Data Analysis for ECG Recordings of Paroxysmal Atrial Fibrillation Patients before and after Pulmonary Vein Isolation 2018 Computing in Cardiology
Vol. 2018-September 
conference DOI URL 
BibTeX:
@conference{Ortigosa2018,
  author = {Ortigosa, N. and Ayala, G. and Cano, O.},
  title = {Functional Data Analysis for ECG Recordings of Paroxysmal Atrial Fibrillation Patients before and after Pulmonary Vein Isolation},
  journal = {Computing in Cardiology},
  year = {2018},
  volume = {2018-September},
  note = {cited By 0},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068749249&doi=10.22489%2fCinC.2018.306&partnerID=40&md5=caf2e918a794b301c8c3b88823252105},
  doi = {https://doi.org/10.22489/CinC.2018.306}
}
Riffo-Campos, A., Montes, F. and Ayala, G. Working with (too) Few Samples 2018 Studies in Systems, Decision and Control
Vol. 142, pp. 337-346 
article DOI URL 
BibTeX:
@article{Riffo-Campos2018337,
  author = {Riffo-Campos, A.L. and Montes, F. and Ayala, G.},
  title = {Working with (too) Few Samples},
  journal = {Studies in Systems, Decision and Control},
  year = {2018},
  volume = {142},
  pages = {337--346},
  note = {cited By 0},
  url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042905658&doi=10.1007%2f978-3-319-73848-2_32&partnerID=40&md5=3f2ec089b3fe62d2555e275921b9840d},
  doi = {https://doi.org/10.1007/978-3-319-73848-2_32}
}
Gimeno-Valiente, F., Riffo-Campos, Á.L., Ayala, G., Tarazona, N., Gambardella, V., Rodr\iguez, F.M., Huerta, M., Mart\inez-Ciarpaglini, C., Montón-Bueno, J., Roselló, S., Roda, D., Cervantes, A., Franco, L., López-Rodas, G. and Castillo, J. EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness 2020 Scientific Reports
Vol. 10(1) 
article DOI  
BibTeX:
@article{Gimeno20,
  author = {Gimeno-Valiente, F. and Riffo-Campos, Á. L. and Ayala, G. and Tarazona, N. and Gambardella, V. and Rodr\iguez, F. M. and Huerta, M. and Mart\inez-Ciarpaglini, C. and Montón-Bueno, J. and Roselló, S. and Roda, D. and Cervantes, A. and Franco, L. and López-Rodas, G. and Castillo, J.},
  title = {EPDR1 up-regulation in human colorectal cancer is related to staging and favours cell proliferation and invasiveness},
  journal = {Scientific Reports},
  publisher = {Springer Science and Business Media LLC},
  year = {2020},
  volume = {10},
  number = {1},
  doi = {https://doi.org/10.1038/s41598-020-60476-7}
}
Ayala, G. and Galbis-Gramage, E. Comprehensive Foodomics 2020
Vol. 2, pp. 313-323 
inbook  
BibTeX:
@inbook{AyalaGalbis20,
  author = {Ayala, G. and Galbis-Gramage, E.},
  title = {Comprehensive Foodomics},
  publisher = {Elsevier},
  year = {2020},
  volume = {2},
  pages = {313--323}
}
de Ves, E., Benavent, X., Ayala, G. and Cerverón, V. Image Retrieval System for Citizen Services Using Penalized Logistic Regression Models 2020 Proceedings of the 10th Euro-American Conference on Telematics and Information Systems  inproceedings DOI URL 
Abstract: This paper describes a procedure to deal with large image collections obtained by smart city services based on interaction with citizens providing pictures. The semantic gap between the low-level image features and represented concepts and situations has been addressed using image retrieval techniques. A relevance feedback procedure is proposed for Content-Based Image Retrieval (CBIR) based on the modelling of user responses. One of the novelties of the proposal is that the feedback learning procedure can use the information that citizens themselves can provide when using these services.The proposed algorithm considers the probability of an image belonging to the set of those sought by the user, by selecting a set of relevant and irrelevant images to the query, and by adjusting a penalized logistic regression model to the information provided by the user. The Wikipedia2011 image collection has been used for testing purposes. The procedure has been compared to other retrieval relevance feedback procedures in recent literature. Good results have been obtained with just one global model fitted with high dimensionality data.
BibTeX:
@inproceedings{deVes20,
  author = {de Ves, E. and Benavent, X. and Ayala, G. and Cerverón, V.},
  title = {Image Retrieval System for Citizen Services Using Penalized Logistic Regression Models},
  booktitle = {Proceedings of the 10th Euro-American Conference on Telematics and Information Systems},
  publisher = {Association for Computing Machinery},
  year = {2020},
  url = {https://doi.org/10.1145/3401895.3402084},
  doi = {https://doi.org/10.1145/3401895.3402084}
}
Ortigosa, N., Ayala, G. and Cano, Ó. Variation of P-wave indices in paroxysmal atrial fibrillation patients before and after catheter ablation 2021 Biomedical Signal Processing and Control
Vol. 66, pp. 102500 
article DOI URL 
Abstract: The effects of pulmonary vein isolation in the surface electrocardiogram of patients with paroxysmal atrial fibrillation are analyzed in this paper using non-invasive markers for early detection of the arrhythmia recurrences. Several features have been extracted on P-waves of V1 lead for paroxysmal atrial fibrillation patients who underwent catheter ablation of pulmonary veins for restoring sinus rhythm permanently. Surface ECG was simultaneously recorded along with intracardiac recordings starting from the beginning of the intervention until half an hour after the catheter ablation successfully ended. Significant difference between the means before and after catheter ablation have been observed for the cross-correlation index, kurtosis and amplitude dispersion of P-waves. A logistic regression has been applied to all the descriptors and pointed to the amplitude dispersion index, as well as the minimum gradient joint with kurtosis of P-waves prior to catheter ablation as good predictors of recurrence of atrial fibrillation (78% accuracy). It is important to note how using a few descriptors good classification results are achieved. This study opens a door to early detection of atrial fibrillation recurrences using markers obtained by non-invasive methods.
BibTeX:
@article{Ortigosa21,
  author = {Nuria Ortigosa and Guillermo Ayala and Óscar Cano},
  title = {Variation of P-wave indices in paroxysmal atrial fibrillation patients before and after catheter ablation},
  journal = {Biomedical Signal Processing and Control},
  year = {2021},
  volume = {66},
  pages = {102500},
  url = {https://www.sciencedirect.com/science/article/pii/S1746809421000975},
  doi = {https://doi.org/10.1016/j.bspc.2021.102500}
}
Riffo-Campos, A.L., Ayala, G. and Montes, F. Gene Set Analysis Using Spatial Statistics 2021 Mathematics
Vol. 9(5) 
article DOI URL 
Abstract: Gene differential expression consists of the study of the possible association between the gene expression, evaluated using different types of data as DNA microarray or RNA-Seq technologies, and the phenotype. This can be performed marginally for each gene (differential gene expression) or using a gene set collection (gene set analysis). A previous (marginal) per-gene analysis of differential expression is usually performed in order to obtain a set of significant genes or marginal p-values used later in the study of association between phenotype and gene expression. This paper proposes the use of methods of spatial statistics for testing gene set differential expression analysis using paired samples of RNA-Seq counts. This approach is not based on a previous per-gene differential expression analysis. Instead, we compare the paired counts within each sample/control using a binomial test. Each pair per gene will produce a p-value so gene expression profile is transformed into a vector of p-values which will be considered as an event belonging to a point pattern. This would be the first component of a bivariate point pattern. The second component is generated by applying two different randomization distributions to the correspondence between samples and treatment. The self-contained null hypothesis considered in gene set analysis can be formulated in terms of the associated point pattern as a random labeling of the considered bivariate point pattern. The gene sets were defined by the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The proposed methodology was tested in four RNA-Seq datasets of colorectal cancer (CRC) patients and the results were contrasted with those obtained using the edgeR-GOseq pipeline. The proposed methodology has proved to be consistent at the biological and statistical level, in particular using Cuzick and Edwards test with one realization of the second component and between-pair distribution.
BibTeX:
@article{RiffoCampos21,
  author = {Riffo-Campos, Angela L. and Ayala, Guillermo and Montes, Francisco},
  title = {Gene Set Analysis Using Spatial Statistics},
  journal = {Mathematics},
  year = {2021},
  volume = {9},
  number = {5},
  url = {https://www.mdpi.com/2227-7390/9/5/521},
  doi = {https://doi.org/10.3390/math9050521}
}
Riffo-Campos, A.L., Ayala, G. and Domingo, J. Ordering of Omics Features Using Beta Distributions on Montecarlo p-Values 2021 Mathematics
Vol. 9(11), pp. 1307 
article DOI  
BibTeX:
@article{RiffoCampos2021,
  author = {Angela L. Riffo-Campos and Guillermo Ayala and Juan Domingo},
  title = {Ordering of Omics Features Using Beta Distributions on Montecarlo p-Values},
  journal = {Mathematics},
  publisher = {MDPI AG},
  year = {2021},
  volume = {9},
  number = {11},
  pages = {1307},
  doi = {https://doi.org/10.3390/math9111307}
}
Abellán-Álvaro, M., Ayala, G., Barneo-Muñoz, M., Martínez-García, F., Agustín-Pavón, C. and Lanuza, E. Motherhood-induced gene expression in the mouse medial amygdala: Changes induced by pregnancy and lactation but not by pup stimuli 2021 The FASEB Journal
Vol. 35(9), pp. e21806 
article DOI URL 
Abstract: Abstract During lactation, adult female mice display aggressive responses toward male intruders, triggered by male-derived chemosensory signals. This aggressive behavior is not shown by pup-sensitized virgin females sharing pup care with dams. The genetic mechanisms underlying the switch from attraction to aggression are unknown. In this work, we investigate the differential gene expression in lactating females expressing maternal aggression compared to pup-sensitized virgin females in the medial amygdala (Me), a key neural structure integrating chemosensory and hormonal information. The results showed 197 genes upregulated in dams, including genes encoding hormones such as prolactin, growth hormone, or follicle-stimulating hormone, neuropeptides such as galanin, oxytocin, and pro-opiomelanocortin, and genes related to catecholaminergic and cholinergic neurotransmission. In contrast, 99 genes were downregulated in dams, among which we find those encoding for inhibins and transcription factors of the Fos and early growth response families. The gene set analysis revealed numerous Gene Ontology functional groups with higher expression in dams than in pup-sensitized virgin females, including those related with the regulation of the Jak/Stat cascade. Of note, a number of olfactory and vomeronasal receptor genes was expressed in the Me, although without differences between dams and virgins. For prolactin and growth hormone, a qPCR experiment comparing dams, pup-sensitized, and pup-naïve virgin females showed that dams expressed higher levels of both hormones than pup-naïve virgins, with pup-sensitized virgins showing intermediate levels. Altogether, the results show important gene expression changes in the Me, which may underlie some of the behavioral responses characterizing maternal behavior.
BibTeX:
@article{Abellan2021,
  author = {Abellán-Álvaro, María and Ayala, Guillermo and Barneo-Muñoz, Manuela and Martínez-García, Fernando and Agustín-Pavón, Carmen and Lanuza, Enrique},
  title = {Motherhood-induced gene expression in the mouse medial amygdala: Changes induced by pregnancy and lactation but not by pup stimuli},
  journal = {The FASEB Journal},
  year = {2021},
  volume = {35},
  number = {9},
  pages = {e21806},
  url = {https://faseb.onlinelibrary.wiley.com/doi/abs/10.1096/fj.202100163RR},
  doi = {https://doi.org/10.1096/fj.202100163RR}
}
Ayala G. and Montes, F. Probabilidad Básica 2022   electronic URL 
BibTeX:
@electronic{AyalaMontes22,
  author = {Ayala, G. and Montes, F.},
  title = {Probabilidad Básica},
  year = {2022},
  url = {https://www.uv.es/ayala/docencia/probabilidad/prob.pdf}
}
Melero, R., Quiroz-Rodríguez, M.E., Lara-Hernández, F., Redón, J., Sáez, G., Briongos-Figuero, L.S., Abadía-Otero, J., Martín-Escudero, J.C., Chaves, F.J., Ayala, G. and García-García, A.-B. Genetic interaction in the association between oxidative stress and diabetes in the Spanish population 2023 Free Radical Biology and Medicine
Vol. 205, pp. 62-68 
article DOI URL 
Abstract: Oxidative stress (OS) is a relevant intermediate mechanism involved in Type 2 Diabetes Mellitus (T2D) development. To date, the interaction between OS parameters and variations in genes related to T2D has not been analyzed.
Aims
To study the genetic interaction of genes potentially related to OS levels (redox homeostasis, renin-angiotensin-aldosterone system, endoplasmic stress response, dyslipidemia, obesity and metal transport) and OS and T2D risk in a general population from Spain (the Hortega Study) in relation to the risk of suffering from T2D.
Materials and methods
One thousand five hundred and two adults from the University Hospital Rio Hortega area were studied and 900 single nucleotide polymorphisms (SNPs) from 272 candidate genes were analyzed.
Results
There were no differences in OS levels between cases and controls. Some polymorphisms were associated with T2D and with OS levels. Significant interactions were observed between OS levels and two polymorphisms in relation to T2D presence: rs196904 (ERN1 gene) and rs2410718 (COX7C gene); and between OS levels and haplotypes of the genes: SP2, HFF1A, ILI8R1, EIF2AK2, TXNRD2, PPARA, NDUFS2 and ERN1.
Conclusions
Our results indicate that genetic variations of the studied genes are associated with OS levels and that their interaction with OS parameters may contribute to the risk of developing T2D in the Spanish general population. These data support the importance of analyzing the influence of OS levels and their interaction with genetic variations in order to establish their real impact in T2D risk. Further studies are required to identify the real relevance of interactions between genetic variations and OS levels and the mechanisms involved in them.
BibTeX:
@article{Melero2023,
  author = {Melero, Rebeca and Quiroz-Rodríguez, Maria Elena and Lara-Hernández, Francisco and Redón, Josep and Sáez, Guillermo and Briongos-Figuero, Laisa S. and Abadía-Otero, Jessica and Martín-Escudero, Juan Carlos and Chaves, F. Javier and Ayala, Guillermo and García-García, Ana-Bárbara},
  title = {Genetic interaction in the association between oxidative stress and diabetes in the Spanish population},
  journal = {Free Radical Biology and Medicine},
  year = {2023},
  volume = {205},
  pages = {62--68},
  url = {https://www.sciencedirect.com/science/article/pii/S0891584923004719},
  doi = {https://doi.org/10.1016/j.freeradbiomed.2023.05.030}
}
Domingo, J., Kutsyr-Kolesnyk, O., Leon, T., Perez-Moraga, R., Ayala, G. and Roson, B. A cell abundance analysis based on efficient PAM clustering for a better understanding of the dynamics of endometrial remodelling 2023 BMC Bioinformatics
Vol. 24(1), pp. 440 
article DOI URL 
Abstract: Single-cell RNA sequencing (scRNA-seq) is a powerful tool for investigating cell abundance changes during tissue regeneration and remodeling processes. Differential cell abundance supports the initial clustering of all cells; then, the number of cells per cluster and sample are evaluated, and the dependence of these counts concerning the phenotypic covariates of the samples is studied. Analysis heavily depends on the clustering method. Partitioning Around Medoids (PAM or k-medoids) represents a well-established clustering procedure that leverages the downstream interpretation of clusters by pinpointing real individuals in the dataset as cluster centers (medoids) without reducing dimensions. Of note, PAM suffers from high computational costs and memory requirements.
BibTeX:
@article{Domingo2023,
  author = {Domingo, Juan and Kutsyr-Kolesnyk, Oleksandra and Leon, Teresa and Perez-Moraga, Raul and Ayala, Guillermo and Roson, Beatriz},
  title = {A cell abundance analysis based on efficient PAM clustering for a better understanding of the dynamics of endometrial remodelling},
  journal = {BMC Bioinformatics},
  year = {2023},
  volume = {24},
  number = {1},
  pages = {440},
  url = {https://doi.org/10.1186/s12859-023-05569-6},
  doi = {https://doi.org/10.1186/s12859-023-05569-6}
}
Aragón-Basanta, E., Venegas, W., Ayala, G., Page, A. and Serra-Añó, P. Relationship between neck kinematics and neck dissability index. An approach based on functional regression 2024 Scientific Reports
Vol. 14(1) 
article DOI  
BibTeX:
@article{AragonBasanta2024,
  author = {Aragón-Basanta, Elisa and Venegas, William and Ayala, Guillermo and Page, Alvaro and Serra-Añó, Pilar},
  title = {Relationship between neck kinematics and neck dissability index. An approach based on functional regression},
  journal = {Scientific Reports},
  publisher = {Springer Science and Business Media LLC},
  year = {2024},
  volume = {14},
  number = {1},
  doi = {https://doi.org/10.1038/s41598-023-50562-x}
}