[{"oa_version":"None","status":"public","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"intvolume":"        29","author":[{"last_name":"Monk","first_name":"Travis","full_name":"Monk, Travis"},{"last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"},{"full_name":"Lücke, Jörg","first_name":"Jörg","last_name":"Lücke"}],"title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","ec_funded":1,"acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","publisher":"Neural Information Processing Systems","quality_controlled":"1","month":"01","alternative_title":["Advances in Neural Information Processing Systems"],"publist_id":"6469","date_updated":"2021-01-12T08:22:08Z","citation":{"apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016."},"conference":{"location":"Barcelona, Spaine","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","end_date":"2016-12-10"},"language":[{"iso":"eng"}],"page":"4285 - 4293","volume":29,"department":[{"_id":"GaTk"}],"type":"conference","day":"01","date_published":"2016-01-01T00:00:00Z","publication_status":"published","year":"2016","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"948","date_created":"2018-12-11T11:49:21Z","abstract":[{"lang":"eng","text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations."}]},{"date_published":"2016-12-30T00:00:00Z","type":"journal_article","department":[{"_id":"GaTk"}],"day":"30","volume":2016,"article_number":"123502","language":[{"iso":"eng"}],"citation":{"mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>.","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &#38;amp; Growth.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience, 2016. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>.","short":"D. De Martino, D. Masoero,  Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth.  Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2016, no. 12. IOPscience, 2016.","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2016;2016(12). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">10.1088/1742-5468/aa4e8f</a>","apa":"De Martino, D., &#38; Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &#38;amp; growth. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience. <a href=\"https://doi.org/10.1088/1742-5468/aa4e8f\">https://doi.org/10.1088/1742-5468/aa4e8f</a>"},"abstract":[{"text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations.","lang":"eng"}],"date_created":"2018-12-11T11:50:37Z","publication":" Journal of Statistical Mechanics: Theory and Experiment","_id":"1188","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"year":"2016","publication_status":"published","title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth","issue":"12","doi":"10.1088/1742-5468/aa4e8f","author":[{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino"},{"full_name":"Masoero, Davide","first_name":"Davide","last_name":"Masoero"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"intvolume":"      2016","status":"public","oa_version":"Preprint","date_updated":"2021-01-12T06:48:57Z","publist_id":"6165","month":"12","quality_controlled":"1","publisher":"IOPscience","acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","oa":1,"ec_funded":1},{"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"9709","relation":"research_data"}]},"status":"public","intvolume":"        12","author":[{"last_name":"Prentice","full_name":"Prentice, Jason","first_name":"Jason"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Ioffe","full_name":"Ioffe, Mark","first_name":"Mark"},{"full_name":"Loback, Adrianna","first_name":"Adrianna","last_name":"Loback"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Berry","full_name":"Berry, Michael","first_name":"Michael"}],"ddc":["570"],"doi":"10.1371/journal.pcbi.1005148","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Error-robust modes of the retinal population code","issue":"11","oa":1,"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:44:38Z","date_created":"2019-01-25T10:35:00Z","file_size":4492021,"content_type":"application/pdf","file_name":"2016_PLOS_Prentice.pdf","file_id":"5884","creator":"kschuh","relation":"main_file","checksum":"47b08cbd4dbf32b25ba161f5f4b262cc"}],"acknowledgement":"JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript.","publisher":"Public Library of Science","quality_controlled":"1","month":"11","publist_id":"6153","date_updated":"2023-02-23T14:05:40Z","file_date_updated":"2020-07-14T12:44:38Z","citation":{"mla":"Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” <i>PLoS Computational Biology</i>, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">10.1371/journal.pcbi.1005148</a>.","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” <i>PLoS Computational Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">https://doi.org/10.1371/journal.pcbi.1005148</a>.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” <i>PLoS Computational Biology</i>, vol. 12, no. 11. Public Library of Science, 2016.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2016). Error-robust modes of the retinal population code. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">https://doi.org/10.1371/journal.pcbi.1005148</a>","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. <i>PLoS Computational Biology</i>. 2016;12(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">10.1371/journal.pcbi.1005148</a>"},"language":[{"iso":"eng"}],"volume":12,"article_number":"e1005855","type":"journal_article","department":[{"_id":"GaTk"}],"day":"17","date_published":"2016-11-17T00:00:00Z","publication_status":"published","year":"2016","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes"}],"_id":"1197","has_accepted_license":"1","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:50:40Z","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}]},{"abstract":[{"lang":"eng","text":"Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae."}],"date_created":"2018-12-11T11:50:41Z","publication":"Journal of Clinical Microbiology","_id":"1203","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"year":"2016","publication_status":"published","date_published":"2016-12-01T00:00:00Z","day":"01","department":[{"_id":"GaTk"}],"type":"journal_article","volume":54,"page":"3010 - 3017","language":[{"iso":"eng"}],"citation":{"short":"F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.","chicago":"Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” <i>Journal of Clinical Microbiology</i>. American Society for Microbiology, 2016. <a href=\"https://doi.org/10.1128/JCM.01511-16\">https://doi.org/10.1128/JCM.01511-16</a>.","mla":"Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” <i>Journal of Clinical Microbiology</i>, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:<a href=\"https://doi.org/10.1128/JCM.01511-16\">10.1128/JCM.01511-16</a>.","ista":"Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.","ieee":"F. Hu <i>et al.</i>, “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” <i>Journal of Clinical Microbiology</i>, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.","ama":"Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. <i>Journal of Clinical Microbiology</i>. 2016;54(12):3010-3017. doi:<a href=\"https://doi.org/10.1128/JCM.01511-16\">10.1128/JCM.01511-16</a>","apa":"Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. <i>Journal of Clinical Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/JCM.01511-16\">https://doi.org/10.1128/JCM.01511-16</a>"},"date_updated":"2021-01-12T06:49:04Z","publist_id":"6146","month":"12","quality_controlled":"1","publisher":"American Society for Microbiology","acknowledgement":"We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support.","oa":1,"title":"Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination","issue":"12","doi":"10.1128/JCM.01511-16","author":[{"full_name":"Hu, Fang","first_name":"Fang","last_name":"Hu"},{"first_name":"Lavanya","full_name":"Rishishwar, Lavanya","last_name":"Rishishwar"},{"full_name":"Sivadas, Ambily","first_name":"Ambily","last_name":"Sivadas"},{"last_name":"Mitchell","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel","first_name":"Gabriel"},{"last_name":"King","full_name":"King, Jordan","first_name":"Jordan"},{"full_name":"Murphy, Timothy","first_name":"Timothy","last_name":"Murphy"},{"full_name":"Gilsdorf, Janet","first_name":"Janet","last_name":"Gilsdorf"},{"first_name":"Leonard","full_name":"Mayer, Leonard","last_name":"Mayer"},{"full_name":"Wang, Xin","first_name":"Xin","last_name":"Wang"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/"}],"intvolume":"        54","oa_version":"Submitted Version"},{"_id":"1214","publist_id":"6121","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"date_updated":"2021-01-12T06:49:08Z","date_created":"2018-12-11T11:50:45Z","publication_status":"published","year":"2016","publisher":"IEEE","acknowledgement":"RD thanks for the hospitality at the Max-Planck-Institute and for helpful discussions with Nihat Ay and Keyan Zahedi.","month":"11","scopus_import":1,"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/IROS.2016.7759138","title":"Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm","article_number":"7759138","volume":"2016-November","date_published":"2016-11-28T00:00:00Z","type":"conference","day":"28","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"conference":{"start_date":"2016-09-09","end_date":"2016-09-14","name":"IEEE RSJ International Conference on Intelligent Robots and Systems IROS ","location":"Daejeon, Korea"},"citation":{"ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS  vol. 2016–November, 7759138.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.","mla":"Martius, Georg S., et al. <i>Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm</i>. Vol. 2016–November, 7759138, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/IROS.2016.7759138\">10.1109/IROS.2016.7759138</a>.","chicago":"Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. <a href=\"https://doi.org/10.1109/IROS.2016.7759138\">https://doi.org/10.1109/IROS.2016.7759138</a>.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/IROS.2016.7759138\">10.1109/IROS.2016.7759138</a>","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. <a href=\"https://doi.org/10.1109/IROS.2016.7759138\">https://doi.org/10.1109/IROS.2016.7759138</a>","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November."},"oa_version":"None","status":"public","author":[{"last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"full_name":"Hostettler, Raphael","first_name":"Raphael","last_name":"Hostettler"},{"full_name":"Knoll, Alois","first_name":"Alois","last_name":"Knoll"},{"full_name":"Der, Ralf","first_name":"Ralf","last_name":"Der"}],"language":[{"iso":"eng"}]},{"page":"1 - 19","doi":"10.2514/6.2016-3764","title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","day":"01","type":"conference","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_published":"2016-06-01T00:00:00Z","oa_version":"Preprint","citation":{"ieee":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.","apa":"Mikić, G., Stoll, A., Bevirt, J., Grah, R., &#38; Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA. <a href=\"https://doi.org/10.2514/6.2016-3764\">https://doi.org/10.2514/6.2016-3764</a>","ama":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:<a href=\"https://doi.org/10.2514/6.2016-3764\">10.2514/6.2016-3764</a>","chicago":"Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. <a href=\"https://doi.org/10.2514/6.2016-3764\">https://doi.org/10.2514/6.2016-3764</a>.","mla":"Mikić, Gregor, et al. <i>Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency</i>. AIAA, 2016, pp. 1–19, doi:<a href=\"https://doi.org/10.2514/6.2016-3764\">10.2514/6.2016-3764</a>.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.","ista":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19."},"conference":{"location":"Washington, D.C., USA","start_date":"2016-06-13","end_date":"2016-06-17","name":"AIAA: Aviation Technology, Integration, and Operations Conference"},"status":"public","main_file_link":[{"url":"https://ntrs.nasa.gov/search.jsp?R=20160010167&amp;hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&amp;qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA","open_access":"1"}],"author":[{"first_name":"Gregor","full_name":"Mikić, Gregor","last_name":"Mikić"},{"last_name":"Stoll","full_name":"Stoll, Alex","first_name":"Alex"},{"last_name":"Bevirt","full_name":"Bevirt, Joe","first_name":"Joe"},{"last_name":"Grah","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560"},{"last_name":"Moore","first_name":"Mark","full_name":"Moore, Mark"}],"language":[{"iso":"eng"}],"_id":"1220","publist_id":"6114","date_created":"2018-12-11T11:50:47Z","date_updated":"2023-02-21T10:17:50Z","abstract":[{"lang":"eng","text":"Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system."}],"publication_status":"published","oa":1,"year":"2016","publisher":"AIAA","scopus_import":1,"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06"},{"oa":1,"quality_controlled":"1","month":"02","acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","publisher":"American Institute of Physics","publist_id":"6088","date_updated":"2021-01-12T06:49:20Z","intvolume":"        93","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.02562"}],"status":"public","oa_version":"Preprint","author":[{"first_name":"Thomas R","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski"},{"last_name":"Walczak","full_name":"Walczak, Aleksandra","first_name":"Aleksandra"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"title":"Extending the dynamic range of transcription factor action by translational regulation","issue":"2","doi":"10.1103/PhysRevE.93.022404","year":"2016","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","_id":"1242","date_created":"2018-12-11T11:50:54Z","abstract":[{"lang":"eng","text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression."}],"citation":{"apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>","ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American Institute of Physics, 2016.","ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>.","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>.","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016)."},"language":[{"iso":"eng"}],"article_number":"022404","volume":93,"type":"journal_article","day":"04","department":[{"_id":"GaTk"}],"date_published":"2016-02-04T00:00:00Z"},{"oa_version":"Submitted Version","intvolume":"       113","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/"}],"status":"public","author":[{"last_name":"Recouvreux","full_name":"Recouvreux, Pierre","first_name":"Pierre"},{"last_name":"Sokolowski","first_name":"Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R"},{"full_name":"Grammoustianou, Aristea","first_name":"Aristea","last_name":"Grammoustianou"},{"last_name":"Tenwolde","first_name":"Pieter","full_name":"Tenwolde, Pieter"},{"full_name":"Dogterom, Marileen","first_name":"Marileen","last_name":"Dogterom"}],"doi":"10.1073/pnas.1419248113","issue":"7","title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","oa":1,"acknowledgement":"We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”","publisher":"National Academy of Sciences","quality_controlled":"1","month":"02","publist_id":"6085","date_updated":"2021-01-12T06:49:21Z","citation":{"short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","chicago":"Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>.","mla":"Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>.","ista":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.","ieee":"P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” <i>PNAS</i>, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.","ama":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. 2016;113(7):1811-1816. doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>","apa":"Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &#38; Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>"},"language":[{"iso":"eng"}],"page":"1811 - 1816","volume":113,"day":"16","department":[{"_id":"GaTk"}],"type":"journal_article","date_published":"2016-02-16T00:00:00Z","publication_status":"published","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"_id":"1244","publication":"PNAS","date_created":"2018-12-11T11:50:55Z","abstract":[{"lang":"eng","text":"Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns."}]},{"oa":1,"month":"03","quality_controlled":"1","publisher":"Annual Reviews","acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","publist_id":"6080","date_updated":"2021-01-12T06:49:23Z","intvolume":"         7","main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"status":"public","oa_version":"Preprint","author":[{"first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"}],"title":"Information processing in living systems","doi":"10.1146/annurev-conmatphys-031214-014803","year":"2016","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes"}],"publication":"Annual Review of Condensed Matter Physics","_id":"1248","abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"date_created":"2018-12-11T11:50:56Z","citation":{"apa":"Tkačik, G., &#38; Bialek, W. (2016). Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>","ama":"Tkačik G, Bialek W. Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. 2016;7:89-117. doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” <i>Annual Review of Condensed Matter Physics</i>, vol. 7. Annual Reviews, pp. 89–117, 2016.","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>.","chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>."},"language":[{"iso":"eng"}],"volume":7,"page":"89 - 117","date_published":"2016-03-10T00:00:00Z","department":[{"_id":"GaTk"}],"type":"journal_article","day":"10"},{"citation":{"ama":"De Martino D. The dual of the space of interactions in neural network models. <i>International Journal of Modern Physics C</i>. 2016;27(6). doi:<a href=\"https://doi.org/10.1142/S0129183116500674\">10.1142/S0129183116500674</a>","apa":"De Martino, D. (2016). The dual of the space of interactions in neural network models. <i>International Journal of Modern Physics C</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129183116500674\">https://doi.org/10.1142/S0129183116500674</a>","ieee":"D. De Martino, “The dual of the space of interactions in neural network models,” <i>International Journal of Modern Physics C</i>, vol. 27, no. 6. World Scientific Publishing, 2016.","ista":"De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.","mla":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” <i>International Journal of Modern Physics C</i>, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:<a href=\"https://doi.org/10.1142/S0129183116500674\">10.1142/S0129183116500674</a>.","chicago":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” <i>International Journal of Modern Physics C</i>. World Scientific Publishing, 2016. <a href=\"https://doi.org/10.1142/S0129183116500674\">https://doi.org/10.1142/S0129183116500674</a>.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016)."},"article_processing_charge":"No","language":[{"iso":"eng"}],"article_number":"1650067","volume":27,"date_published":"2016-06-01T00:00:00Z","day":"01","department":[{"_id":"GaTk"}],"type":"journal_article","publication_status":"published","year":"2016","external_id":{"arxiv":["1505.02963"]},"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1260","publication":"International Journal of Modern Physics C","article_type":"original","arxiv":1,"abstract":[{"lang":"eng","text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way."}],"date_created":"2018-12-11T11:51:00Z","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.02963"}],"intvolume":"        27","status":"public","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"doi":"10.1142/S0129183116500674","issue":"6","title":"The dual of the space of interactions in neural network models","oa":1,"publisher":"World Scientific Publishing","month":"06","quality_controlled":"1","publist_id":"6065","date_updated":"2021-01-12T06:49:28Z"},{"publist_id":"6056","date_updated":"2021-01-12T06:49:30Z","oa":1,"month":"07","quality_controlled":"1","publisher":"eLife Sciences Publications","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","file":[{"creator":"system","relation":"main_file","checksum":"dc52d967dc76174477bb258d84be2899","file_id":"4874","file_size":2819055,"content_type":"application/pdf","file_name":"IST-2016-700-v1+1_e13824-download.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:11:20Z"}],"issue":"2016JULY","title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.7554/eLife.13824","intvolume":"         5","status":"public","oa_version":"Published Version","ddc":["571"],"author":[{"last_name":"Chalk","first_name":"Matthew J","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436"},{"last_name":"Gutkin","full_name":"Gutkin, Boris","first_name":"Boris"},{"last_name":"Denève","full_name":"Denève, Sophie","first_name":"Sophie"}],"publication":"eLife","has_accepted_license":"1","_id":"1266","abstract":[{"lang":"eng","text":"Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code."}],"date_created":"2018-12-11T11:51:02Z","year":"2016","publication_status":"published","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":5,"article_number":"e13824","date_published":"2016-07-01T00:00:00Z","day":"01","department":[{"_id":"GaTk"}],"type":"journal_article","pubrep_id":"700","citation":{"short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","mla":"Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” <i>ELife</i>, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.13824\">10.7554/eLife.13824</a>.","chicago":"Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.13824\">https://doi.org/10.7554/eLife.13824</a>.","ista":"Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.","ieee":"M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” <i>eLife</i>, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","ama":"Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. <i>eLife</i>. 2016;5(2016JULY). doi:<a href=\"https://doi.org/10.7554/eLife.13824\">10.7554/eLife.13824</a>","apa":"Chalk, M. J., Gutkin, B., &#38; Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.13824\">https://doi.org/10.7554/eLife.13824</a>"},"file_date_updated":"2020-07-14T12:44:42Z","language":[{"iso":"eng"}]},{"pubrep_id":"696","type":"journal_article","day":"27","department":[{"_id":"GaTk"}],"date_published":"2016-09-27T00:00:00Z","article_number":"e0163628","volume":11,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:42Z","citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” <i>PLoS One</i>, vol. 11, no. 9. Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628\">https://doi.org/10.1371/journal.pone.0163628</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. <i>PLoS One</i>. 2016;11(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628\">10.1371/journal.pone.0163628</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628\">https://doi.org/10.1371/journal.pone.0163628</a>.","mla":"Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” <i>PLoS One</i>, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628\">10.1371/journal.pone.0163628</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628."},"date_created":"2018-12-11T11:51:03Z","abstract":[{"text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic &quot;French Flag&quot; model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call &quot;Counter&quot; patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.","lang":"eng"}],"has_accepted_license":"1","_id":"1270","publication":"PLoS One","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","year":"2016","doi":"10.1371/journal.pone.0163628","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","issue":"9","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"ddc":["571"],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9869"},{"id":"9870","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9871"}]},"intvolume":"        11","status":"public","date_updated":"2023-02-23T14:11:37Z","publist_id":"6050","file":[{"relation":"main_file","creator":"system","checksum":"3d0d55d373096a033bd9cf79288c8586","file_id":"4837","content_type":"application/pdf","file_size":4950415,"file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","date_created":"2018-12-12T10:10:47Z","date_updated":"2020-07-14T12:44:42Z","access_level":"open_access"}],"publisher":"Public Library of Science","acknowledgement":"The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program \"Nanosystems Initiative Munich\" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 \"Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions\" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).","quality_controlled":"1","month":"09","oa":1},{"doi":"10.1038/nchembio.2176","issue":"11","title":"Compounds that select against the tetracycline-resistance efflux pump","author":[{"last_name":"Stone","first_name":"Laura","full_name":"Stone, Laura"},{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"first_name":"Tami","full_name":"Lieberman, Tami","last_name":"Lieberman"},{"last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Clardy","full_name":"Clardy, Jon","first_name":"Jon"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"oa_version":"Preprint","intvolume":"        12","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"status":"public","date_updated":"2021-01-12T06:49:39Z","publist_id":"6026","publisher":"Nature Publishing Group","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","month":"11","quality_controlled":"1","oa":1,"date_published":"2016-11-01T00:00:00Z","day":"01","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"type":"journal_article","page":"902 - 904","volume":12,"language":[{"iso":"eng"}],"citation":{"ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” <i>Nature Chemical Biology</i>, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., &#38; Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. 2016;12(11):902-904. doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>.","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904."},"abstract":[{"lang":"eng","text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline."}],"date_created":"2018-12-11T11:51:10Z","_id":"1290","publication":"Nature Chemical Biology","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2016"},{"publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"09","year":"2016","date_created":"2021-08-10T08:53:48Z","date_updated":"2023-02-21T16:56:40Z","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"_id":"9869","author":[{"first_name":"Patrick","full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","first_name":"Ulrich","full_name":"Gerland, Ulrich"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"1270","status":"public"}]},"citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>."},"article_processing_charge":"No","status":"public","department":[{"_id":"GaTk"}],"type":"research_data_reference","day":"27","date_published":"2016-09-27T00:00:00Z","doi":"10.1371/journal.pone.0163628.s001","title":"Error bound on an estimator of position"},{"year":"2016","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"09","_id":"9870","date_created":"2021-08-10T09:23:45Z","date_updated":"2023-02-21T16:56:40Z","abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"oa_version":"Published Version","citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in an Ising Model</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>."},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1270"}]},"article_processing_charge":"No","status":"public","author":[{"last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick","first_name":"Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"doi":"10.1371/journal.pone.0163628.s002","title":"Computation of positional information in an Ising model","type":"research_data_reference","department":[{"_id":"GaTk"}],"day":"27","date_published":"2016-09-27T00:00:00Z"},{"abstract":[{"lang":"eng","text":"The positional information in a discrete morphogen field with Gaussian noise is computed."}],"date_created":"2021-08-10T09:27:35Z","date_updated":"2023-02-21T16:56:40Z","_id":"9871","month":"09","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","year":"2016","department":[{"_id":"GaTk"}],"type":"research_data_reference","day":"27","title":"Computation of positional information in a discrete morphogen field","doi":"10.1371/journal.pone.0163628.s003","author":[{"first_name":"Patrick","full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"status":"public","article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1270"}]},"citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in a Discrete Morphogen Field</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>."},"oa_version":"Published Version"},{"ddc":["000","570"],"author":[{"first_name":"Francesca","full_name":"Parise, Francesca","last_name":"Parise"},{"first_name":"John","full_name":"Lygeros, John","last_name":"Lygeros"},{"orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess"}],"intvolume":"         3","status":"public","oa_version":"Published Version","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.3389/fenvs.2015.00042","month":"06","quality_controlled":"1","publisher":"Frontiers","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","file":[{"date_updated":"2022-02-25T11:55:26Z","date_created":"2022-02-25T11:55:26Z","access_level":"open_access","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","file_size":1371201,"content_type":"application/pdf","success":1,"file_id":"10795","checksum":"26c222487564e1be02a11d688d6f769d","creator":"dernst","relation":"main_file"}],"oa":1,"ec_funded":1,"date_updated":"2022-02-25T11:59:23Z","keyword":["General Environmental Science"],"language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>.","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015)."},"file_date_updated":"2022-02-25T11:55:26Z","date_published":"2015-06-10T00:00:00Z","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"day":"10","type":"journal_article","publication_identifier":{"issn":["2296-665X"]},"article_number":"42","volume":3,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"year":"2015","publication_status":"published","abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"date_created":"2022-02-25T11:42:25Z","article_type":"original","publication":"Frontiers in Environmental Science","_id":"10794","has_accepted_license":"1"},{"oa_version":"Published Version","status":"public","intvolume":"        17","author":[{"last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"},{"last_name":"Olbrich","full_name":"Olbrich, Eckehard","first_name":"Eckehard"}],"ddc":["000"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.3390/e17107266","issue":"10","title":"Quantifying emergent behavior of autonomous robots","ec_funded":1,"oa":1,"publisher":"MDPI","acknowledgement":"This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","file":[{"checksum":"945d99631a96e0315acb26dc8541dcf9","creator":"system","relation":"main_file","file_id":"4943","file_name":"IST-2016-464-v1+1_entropy-17-07266.pdf","file_size":6455007,"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:08Z","date_created":"2018-12-12T10:12:25Z"}],"month":"10","quality_controlled":"1","publist_id":"5495","date_updated":"2023-10-17T11:42:00Z","citation":{"short":"G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” <i>Entropy</i>, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:<a href=\"https://doi.org/10.3390/e17107266\">10.3390/e17107266</a>.","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” <i>Entropy</i>. MDPI, 2015. <a href=\"https://doi.org/10.3390/e17107266\">https://doi.org/10.3390/e17107266</a>.","ista":"Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297.","ieee":"G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” <i>Entropy</i>, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015.","apa":"Martius, G. S., &#38; Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. <i>Entropy</i>. MDPI. <a href=\"https://doi.org/10.3390/e17107266\">https://doi.org/10.3390/e17107266</a>","ama":"Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. <i>Entropy</i>. 2015;17(10):7266-7297. doi:<a href=\"https://doi.org/10.3390/e17107266\">10.3390/e17107266</a>"},"file_date_updated":"2020-07-14T12:45:08Z","article_processing_charge":"No","language":[{"iso":"eng"}],"page":"7266 - 7297","volume":17,"pubrep_id":"464","date_published":"2015-10-23T00:00:00Z","type":"journal_article","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"day":"23","publication_status":"published","year":"2015","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","_id":"1655","has_accepted_license":"1","publication":"Entropy","abstract":[{"lang":"eng","text":"Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration."}],"date_created":"2018-12-11T11:53:17Z"},{"abstract":[{"text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space.","lang":"eng"}],"date_created":"2018-12-11T11:53:18Z","_id":"1658","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"year":"2015","publication_status":"published","date_published":"2015-09-01T00:00:00Z","type":"conference","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"day":"01","volume":9308,"page":"77 - 89","language":[{"iso":"eng"}],"series_title":"Lecture Notes in Computer Science","citation":{"ieee":"S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015.","ama":"Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. Adaptive moment closure for parameter inference of biochemical reaction networks. 2015;9308:77-89. doi:<a href=\"https://doi.org/10.1007/978-3-319-23401-4_8\">10.1007/978-3-319-23401-4_8</a>","apa":"Bogomolov, S., Henzinger, T. A., Podelski, A., Ruess, J., &#38; Schilling, C. (2015). Adaptive moment closure for parameter inference of biochemical reaction networks. Presented at the CMSB: Computational Methods in Systems Biology, Nantes, France: Springer. <a href=\"https://doi.org/10.1007/978-3-319-23401-4_8\">https://doi.org/10.1007/978-3-319-23401-4_8</a>","mla":"Bogomolov, Sergiy, et al. <i>Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks</i>. Vol. 9308, Springer, 2015, pp. 77–89, doi:<a href=\"https://doi.org/10.1007/978-3-319-23401-4_8\">10.1007/978-3-319-23401-4_8</a>.","chicago":"Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-23401-4_8\">https://doi.org/10.1007/978-3-319-23401-4_8</a>.","short":"S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89.","ista":"Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89."},"conference":{"location":"Nantes, France","name":"CMSB: Computational Methods in Systems Biology","start_date":"2015-09-16","end_date":"2015-09-18"},"date_updated":"2023-02-21T16:17:24Z","publist_id":"5492","alternative_title":["LNCS"],"month":"09","quality_controlled":"1","publisher":"Springer","ec_funded":1,"title":"Adaptive moment closure for parameter inference of biochemical reaction networks","doi":"10.1007/978-3-319-23401-4_8","author":[{"last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess"},{"last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"}],"intvolume":"      9308","status":"public","related_material":{"record":[{"status":"public","id":"1148","relation":"later_version"}]},"oa_version":"None"},{"oa":1,"ec_funded":1,"month":"11","quality_controlled":"1","publisher":"Public Library of Science","file":[{"file_size":2580778,"content_type":"application/pdf","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:07:58Z","access_level":"open_access","relation":"main_file","creator":"system","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","file_id":"4657"}],"publist_id":"5483","date_updated":"2023-09-07T11:53:49Z","status":"public","intvolume":"        11","related_material":{"record":[{"status":"public","id":"9712","relation":"research_data"},{"relation":"dissertation_contains","id":"1131","status":"public"}]},"oa_version":"Published Version","ddc":["576"],"author":[{"orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","last_name":"Tugrul"},{"first_name":"Tiago","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"issue":"11","title":"Dynamics of transcription factor binding site evolution","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi":"10.1371/journal.pgen.1005639","year":"2015","publication_status":"published","scopus_import":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PLoS Genetics","_id":"1666","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"date_created":"2018-12-11T11:53:21Z","citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11)."},"file_date_updated":"2020-07-14T12:45:10Z","language":[{"iso":"eng"}],"volume":11,"date_published":"2015-11-06T00:00:00Z","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"day":"06","type":"journal_article","pubrep_id":"463"}]