A View of P Systems from Information Theory

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-54072-6_22In this work we propose new view of P systems by using the framework of Information Theory. Given a cell-like P system with communication and evolution rules, we analyze the amount of information that it holds as the result of symbol movements across the membranes. Under this approach, we propose new definitions and results related to the information of P systems and their entropy. In addition, we propose a new working manner for P systems based only in the entropy evolution during the computation time.Work partially supported by the Spanish Ministry of Economy and Competitiveness under EXPLORA Research Project SAF2013-49788-EXP.Sempere Luna, JM. (2017). A View of P Systems from Information Theory. En International Conference on Membrane Computing. Springer Verlag (Germany). 352-362. https://doi.org/10.1007/978-3-319-54072-6 22S35236

On Compensation Loops in Genomic Duplications

Electronic version of an article published as International Journal of Foundations of Computer Science 2020 31:01, 133-142, DOI: 10.1142/S0129054120400092 © World Scientific Publishing Company https://www.worldscientific.com/worldscinet/ijfcs[EN] In this paper, we investigate the compensation loops, a DNA rearrangement in chromosomes due to unequal crossing over. We study the e fect of compensation loops over the gene duplication, and we formalize it as a restricted case of gene duplication in general. We study this biological process under the point of view of formal languages, and we provide some results about the languages de fined in this way.Sempere Luna, JM. (2020). On Compensation Loops in Genomic Duplications. International Journal of Foundations of Computer Science. 31(1):133-142. https://doi.org/10.1142/S0129054120400092S133142311Bovet, D. P., & Varricchio, S. (1992). On the regularity of languages on a binary alphabet generated by copying systems. Information Processing Letters, 44(3), 119-123. doi:10.1016/0020-0190(92)90050-6Dassow, J., Mitrana, V., & Salomaa, A. (1997). Context-free evolutionary grammars and the structural language of nucleic acids. Biosystems, 43(3), 169-177. doi:10.1016/s0303-2647(97)00036-1Ehrenfeucht, A., & Rozenberg, G. (1984). On regularity of languages generated by copying systems. Discrete Applied Mathematics, 8(3), 313-317. doi:10.1016/0166-218x(84)90129-xLeupold, P., Martín-Vide, C., & Mitrana, V. (2005). Uniformly bounded duplication languages. Discrete Applied Mathematics, 146(3), 301-310. doi:10.1016/j.dam.2004.10.003Leupold, P., & Mitrana, V. (2007). Uniformly bounded duplication codes. RAIRO - Theoretical Informatics and Applications, 41(4), 411-424. doi:10.1051/ita:2007021Leupold, P., Mitrana, V., & Sempere, J. M. (2003). Formal Languages Arising from Gene Repeated Duplication. Lecture Notes in Computer Science, 297-308. doi:10.1007/978-3-540-24635-0_22Rozenberg, G., & Salomaa, A. (Eds.). (1997). Handbook of Formal Languages. doi:10.1007/978-3-642-59126-

Modeling of Decision Trees Through P systems

[EN] In this paper, we propose a decision-tree modeling in the framework of membrane computing. We propose an algorithm to obtain a P system that is equivalent to any decision tree taken as input. In our case, and unlike previous proposals, we formulate the concepts of decision trees endogenously, since there is no external agent involved in the modeling. The tree structure can be defined naturally by the topology of the regions in the P system and the decision rules are defined by communication rules of the P system.Sempere Luna, JM. (2019). Modeling of Decision Trees Through P systems. New Generation Computing. 37(3):325-337. https://doi.org/10.1007/s00354-019-00052-4325337373Breiman, L., Friedman, J., Olshen, R., Stone, C.: Classification and Regression Trees. Chapman & Hall, Boca Raton (1984)Cardona, M., Colomer, M.A., Margalida, A., Palau, A., Pérez-Hurtado, I., Pérez-Jiménez, M.J., Sanuy, D.: A computational modeling for real ecosystems based on P systems. Nat. Comput. 10(1), 39–53 (2011)Cecilia, J.M., García, J.M., Guerrero, G.D., Martínez-del-Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J.: Simulation of P systems with active membranes on CUDA. Brief. Bioinform. 11(3), 313–322 (2010)Díaz-Pernil, D., Peña-Cantillana, F., Gutiérrez-Naranjo, M.A.: Self-constructing Recognizer P Systems. In: Proceedings of the Thirteenth Brainstorming Week on Membrane Computing. Fénix Editora, pp. 137–154 (2014)Fayyad, U.M., Irani, K.B.: On the handling of continuous-valued attributes in decision tree generation. Mach. Learn. 8, 87–102 (1992)Kingsford, C., Salzberg, S.L.: What are decision trees ? Nat. Biotechnol. 26(9), 1011–1013 (2008)Martín-Vide, C., Păun, Gh, Pazos, J., Rodríguez-Patón, A.: Tissue P systems. Theor. Comput. Sci. 296, 295–326 (2003)Martínez-del-Amor, M.A., García-Quismondo, M., Macías-Ramos, L.F., Valencia-Cabrera, L., Riscos-Núñez, A., Pérez-Jiménez, M.J.: Simulating P systems on GPU devices: a survey. Fund. Inf. 136(3), 269–284 (2015)Mitchell, T.: Machine Learning. McGraw-Hill, New York City (1997)Păun, Gh: Membrane Computing, An Introduction. Springer, Berlin (2002)Păun, Gh, Rozenberg, G., Salomaa, A. (eds.): The Oxford Handbook of Membrane Computing. Oxford University Press, Oxford (2010)Quinlan, J.R.: C4.5: Programs for Machine Learning. Morgan Kaufmann, Burlington (1993)Sempere, J.M.: A View of P systems from information theory. In: Proceedings of the 17th international conference on membrane computing (CMC 2016) LNCS vol. 10105. Springer, pp. 352–362 (2017)Sammut, C., Webb, G.I. (eds.): Encyclopedia of Machine Learning. Springer, Berlin (2011)Wang, J., Hu, J., Peng, H., Pérez-Jiménez, M.J., Riscos-Núñez, A.: Decision tree models induced by membrane systems. Rom. J. Inf. Sci. Technol. 18(3), 228–239 (2015)Zhang, C., Ma, Y. (eds.): Ensemble Machine Learning, Methods and Applications. Springer, Berlin (2012)Zhang, X., Wang, B., Ding, Z., Tang, J., He, J.: Implementation of membrane algorithms on GPU. J. Appl. Math. 2014, 7 (2014

On the Languages Accepted by Watson-Crick Finite Automata with Delays

[EN] In this work, we analyze the computational power of Watson-Crick finite automata (WKFA) if some restrictions over the transition function in the model are imposed. We consider that the restrictions imposed refer to the maximum length difference between the two input strands which is called the delay. We prove that the language class accepted by WKFA with such restrictions is a proper subclass of the languages accepted by arbitrary WKFA in general. In addition, we initiate the study of the language classes characterized by WKFAs with bounded delays. We prove some of the results by means of various relationships between WKFA and sticker systems.This work has been developed with the financial support of the European Union's Horizon 2020 research and innovation programme under grant agreement No. 952215 corresponding to the TAILOR project.Sempere Luna, JM. (2021). On the Languages Accepted by Watson-Crick Finite Automata with Delays. Mathematics. 9(8):1-12. https://doi.org/10.3390/math9080813S1129

- DUOPOLY PRICE COMMUNICATION

We investigate the role of price communication in imperfect information environments by setting up a dynamic differentiated duopoly where actions are not observable and where firms decide, before pricing, whether to communicate their choices to the rivals. When firms play simultaneously in the pricing stages, communication across them is a dominant strategy allowing firms to coordinate prices, thus reducing competition. However, when communication takes place within pricing stages, this meaning that firms are given the opportunity to choose roles, the above firms coordination in prices is mitigated. This is because of the existence of a second mover advantage effect. Communication by the leader acts as a pre-commitment device to a price umbrella that the follower will undercut. As a result, we end up with a more competitive situation although price levels will not go down to those without communication.commitment, price communication

Preface: 11th Workshop on Non-classical Models of Automata and Applications (NCMA 2019)

Holzer, M.; Sempere Luna, JM. (2021). Preface: 11th Workshop on Non-classical Models of Automata and Applications (NCMA 2019). RAIRO - Theoretical Informatics and Applications. 55:1-2. https://doi.org/10.1051/ita/2021009S125

Generating networks of genetic processors

[EN] The Networks of Genetic Processors (NGPs) are non-conventional models of computation based on genetic operations over strings, namely mutation and crossover operations as it was established in genetic algorithms. Initially, they have been proposed as acceptor machines which are decision problem solvers. In that case, it has been shown that they are universal computing models equivalent to Turing machines. In this work, we propose NGPs as enumeration devices and we analyze their computational power. First, we define the model and we propose its definition as parallel genetic algorithms. Once the correspondence between the two formalisms has been established, we carry out a study of the generation capacity of the NGPs under the research framework of the theory of formal languages. We investigate the relationships between the number of processors of the model and its generative power. Our results show that the number of processors is important to increase the generative capability of the model up to an upper bound, and that NGPs are universal models of computation if they are formulated as generation devices. This allows us to affirm that parallel genetic algorithms working under certain restrictions can be considered equivalent to Turing machines and, therefore, they are universal models of computation.This research was partially supported by TAILOR, a project funded by EU Horizon 2020 research and innovation programme under GA No 952215.Campos Frances, M.; Sempere Luna, JM. (2022). Generating networks of genetic processors. Genetic Programming and Evolvable Machines. 23(1):133-155. https://doi.org/10.1007/s10710-021-09423-713315523

Recomendaciones para la determinación de HER2 en cáncer de mama. Consenso Nacional de la Sociedad Española de Anatomía Patológica ( SEAP ) y de la Sociedad Española de Oncología Médica ( SEOM )

La identificación de los carcinomas de mama con amplificación/sobreexpresión de HER2 es crítica en la práctica clínica diaria ya que estas neoplasias requieren un tratamiento específico que incluye el uso de terapias dirigidas. Tanto las técnicas de hibridación in situ como las técnicas inmunohistoquímicas son métodos apropiados para la identificación de cánceres de mama HER2 positivos. Sin embargo, numerosos estudios, incluidos los desarrollados por la Asociación para la Garantía de Calidad en Patología de la SEAP (AGCP) y la experiencia de centros de referencia nacionales en la determinación de HER2 han puesto de manifiesto importantes problemas de reproducibilidad entre laboratorios. Por estos motivos, patólogos expertos en la determinación de HER2 de estos centros de referencia, así como oncólogos médicos con una contrastada actividad en cáncer de mama, en representación de las sociedades respectivas (SEAP y SEOM), han trabajado para debatir y consensuar las recomendaciones nacionales de determinación de HER2. Estas recomendaciones se basan no sólo en la experiencia de los participantes en el consenso, sino también en la experiencia internacional publicada en recientes guías de distintos países, tales como Estados Unidos, Reino Unido y Canadá. En este consenso, se recomiendan los requisitos mínimos que un laboratorio de Anatomía Patológica debe cumplir para garantizar la adecuada determinación de HER2 en la práctica diaria. Aquellos laboratorios que carezcan de los estándares mínimos expuestos en esta guía deberían trabajar en alcanzarlos y durante este proceso remitir a laboratorios de referencia las muestras en las que la determinación de HER2 tenga implicaciones clínicas para las pacientes.Breast cancers with HER2 alterations are critical to identify because such tumors require unique treatment, including the use of targeted therapies. HER2 alterations at the DNA (amplification) and protein (overexpression) level usually occur in concert, and both in situ hybridization and immunohistochemistry can be accurate methods to assess these alterations. However, recent studies including those conducted by the Association for Quality Assessment of the Spanish Society of Pathology and the experience of several national reference centres for HER2 testing have suggested that serious reproducibility issues exist with both techniques. To address this, a joint committee of both the Spanish Society of Pathology and the Spanish Society of Medical Oncology has met to review guidelines for HER2 testing. Consensus recommendation are based not only on panellist’s experience but also in those consensus guidelines previously reported in several countries, such as United Stated, United Kingdom and Canada. These guidelines include minimal requirements that Pathology Department must meet in order to guarantee appropriate HER2 testing in breast cancer. Pathology laboratories that do not meet these standards must put effort to reach them and, in the meantime, send clinical cases to reference [email protected]

Análisis del polimorfismo cromosómico en matrimonios con descendencia normal

Tesis Univ. Complutense de Madrid, 1982.Depto. de Genética, Fisiología y MicrobiologíaFac. de Ciencias BiológicasTRUEProQuestpu

Análisis del polimorfismo cromosómico en matrimonios con descendencia normal

Tesis Univ. Complutense de Madrid, 1982.Depto. de Genética, Fisiología y MicrobiologíaFac. de Ciencias BiológicasTRUEProQuestpu