Article

Knight, James C and Nowotny, Thomas (2020) Larger GPU-accelerated brain simulations with procedural connectivity. Nature Computational Science. ISSN 2662-8457 (Accepted)

Stimberg, Marcel, Goodman, Dan F M and Nowotny, Thomas (2020) Brian2GeNN: accelerating spiking neural network simulations with graphics hardware. Scientific Reports, 10 (a410). ISSN 2045-2322

Pannunzi, Mario and Nowotny, Thomas (2019) Odor stimuli: not just chemical identity. Frontiers in Physiology, 10. ISSN 1664-042X

Diamand, Alan, Schmuker, Michael and Nowotny, Thomas (2019) An unsupervised neuromorphic clustering algorithm. Biological Cybernetics. ISSN 0340-1200

Knight, James C and Nowotny, Thomas (2018) GPUs outperform current HPC and neuromorphic solutions in terms of speed and energy when simulating a highly-connected cortical model. Frontiers in Neuroscience, 12 (941). pp. 1-19. ISSN 1662-453X

Chan, Ho Ka, Hersperger, Fabian, Marachlian, Emiliano, Smith, Brian H, Locatelli, Fernando, Szyszka, Paul and Nowotny, Thomas (2018) Odorant mixtures elicit less variable and faster responses than pure odorants. PLoS Computational Biology, 14 (12). e1006536 1-27. ISSN 1553-734X

Blundell, Inga, Brette, Romain, Cleland, Thomas A, Close, Thomas G, Coca, Daniel, Davison, Andrew P, Diaz-Pier, Sandra, Fernandez Musoles, Carlos, Gleeson, Padraig, Goodman, Dan F M, Hines, Michael, Hopkins, Michael W, Kumbhar, Pramod, Lester, David R, Marin, Boris, Morrison, Abigail, Müller, Eric, Nowotny, Thomas, Peyser, Alexander, Plotnikov, Dimitri, Richmond, Paul, Rowley, Andrew, Rumpe, Bernhard, Stimberg, Marcel, Stokes, Alan B, Tomkins, Adam, Trensch, Guido, Woodman, Marmaduke and Eppler, Jochen Martin (2018) Code generation in computational neuroscience: a review of tools and techniques. Frontiers in Neuroinformatics, 12 (68). pp. 1-35. ISSN 1662-5196

Perez, Margot, Nowotny, Thomas, d'Ettore, Patrizia and Giurfa, Martin (2016) Olfactory experience shapes the evaluation of odour similarity in ants - a behavioural and computational analysis. Proceedings of the Royal Society B: Biological Sciences, 283 (1837). p. 20160551. ISSN 0962-8452

Wu, Gang, Nowotny, Thomas, Zhang, Yongliang, Yu, Hong-Qi and Li, David Day-Uei (2016) Artificial neural network approaches for fluorescence lifetime imaging techniques. Optics Letters, 41 (11). pp. 2561-2564. ISSN 0146-9592

Chan, Ho Ka, Yang, Dong-Ping, Zhou, Changsong and Nowotny, Thomas (2016) Burst firing enhances neural ouput correlation. Frontiers in Computational Neuroscience, 10. a42. ISSN 1662-5188

Diamond, A, Schmuker, M, Berna, A Z, Trowell, S and Nowotny, Thomas (2016) Classifying continuous, real-time e-nose sensor data using a bio-inspired spiking network modelled on the insect olfactory system. Bioinspiration and Biomimetics, 11 (2). ISSN 1748-3190

Diamond, Alan, Nowotny, Thomas and Schmuker, Michael (2016) Comparing neuromorphic solutions in action: implementing a bio-inspired solution to a benchmark classification task on three parallel-computing platforms. Frontiers in Neuroscience, 9 (a491). pp. 1-14. ISSN 1662-4548

Yavuz, Esin, Turner, James and Nowotny, Thomas (2016) GeNN: a code generation framework for accelerated brain simulations. Scientific Reports, 6. p. 18854. ISSN 2045-2322

Wu, Gang, Nowotny, Thomas, Chen, Yu and Li, David Day-Uei (2016) GPU acceleration of time-domain fluorescence lifetime imaging. Journal of Biomedical Optics, 21 (1). 017001. ISSN 1083-3668

Nowotny, Thomas, de Bruyne, Marien, Berna, Amalia Z, Warr, Coral G and Trowell, Stephen C (2014) Drosophila olfactory receptors as classifiers for volatiles from disparate real world applications. Bioinspiration and Biomimetics, 9 (4). a046007 1-13. ISSN 1748-3190

Nowotny, Thomas (2014) Two challenges of correct validation in pattern recognition. Frontiers in Robotics and AI, 1 (5). pp. 1-6. ISSN 2296-9144

Samu, David, Seth, Anil K and Nowotny, Thomas (2014) Influence of wiring cost on the large-scale architecture of human cortical connectivity. PLoS Computational Biology, 10 (4). e1003557. ISSN 1553-734X

Wang, X Rosalind, Lizier, Joseph T, Nowotny, Thomas, Berna, Amalia Z, Prokopenko, Mikhail and Trowell, Stephen C (2014) Feature selection for chemical sensor arrays using mutual information. PLoS ONE, 9 (3). e89840. ISSN 1932-6203

Nowotny, Thomas, Rospars, Jean-Pierre, Martinez, Dominique, Elbanna, Shereen and Anton, Sylvia (2013) Machine learning for automatic prediction of the quality of electrophysiological recordings. PLoS ONE, 8 (12). e80838. ISSN 1932-6203

Nowotny, Thomas, Stierle, Jacob S, Galizia, C Giovanni and Szyszka, Paul (2013) Data-driven honeybee antennal lobe model suggests how stimulus-onset asynchrony can aid odour segregation. Brain Research, 1536. pp. 119-134. ISSN 0006-8993

Nowotny, Thomas, Berna, Amalia Z, Binions, Russell and Trowell, Stephen (2013) Optimal feature selection for classifying a large set of chemicals using metal oxide sensors. Sensors and Actuators B: Chemical, 187. pp. 471-480. ISSN 0925-4005

Serrano, Eduardo, Nowotny, Thomas, Levi, Rafael, Smith, Brian H and Huerta, Ramón (2013) Gain control network conditions in early sensory coding. PLoS Computational Biology, 9 (7). e1003133. ISSN 1553-7358

Samu, David, Marra, Vincenzo, Kemenes, Ildiko, Crossley, Michael, Kemenes, György, Staras, Kevin and Nowotny, Thomas (2012) Single electrode dynamic clamp with StdpC. Journal of Neuroscience Methods, 211 (1). pp. 11-21. ISSN 0165-0270

Huerta, Ramón, Vembu, Shankar, Amigó, José M, Nowotny, Thomas and Elkan, Charles (2012) Inhibition in multiclass classification. Neural Computation, 24 (9). pp. 2473-2507. ISSN 0899-7667

Harris, Christopher A, Buckley, Christopher L, Nowotny, Thomas, Passaro, Peter A, Seth, Anil K, Kemenes, György and O'Shea, Michael (2012) Multi-neuronal refractory period adapts centrally generated behaviour to reward. PLoS ONE, 7 (7). e42493. ISSN 1932-6203

Grémiaux, Alexandre, Nowotny, Thomas, Martinez, Dominique, Lucas, Philippe and Rospars, Jean-Pierre (2012) Modelling the signal delivered by a population of first-order neurons in a moth olfactory system. Brain Research, 1434. pp. 123-135. ISSN 0006-8993

Buckley, Christopher L and Nowotny, Thomas (2012) Transient dynamics between displaced fixed points: an alternate nonlinear dynamical framework for olfaction. Brain Research, 1434. pp. 62-72. ISSN 0006-8993

Belmabrouk, Hana, Nowotny, Thomas, Rospars, Jean-Pierre and Martinez, Dominique (2011) Interaction of cellular and network mechanisms for efficient pheromone coding in moths. Proceedings of the National Academy of Sciences of the United States of America, 108 (49). pp. 19790-19795. ISSN 1091-6490

Buckley, Christopher L and Nowotny, Thomas (2011) Multi-scale model of an inhibitory network shows optimal properties near bifurcation. Physical Review Letters, 106 (23). p. 238109. ISSN 0031-9007

Papadopoulou, Maria, Cassenaer, Stijn, Nowotny, Thomas and Laurent, Gilles (2011) Normalization for sparse encoding of odors by a wide-field interneuron. Science, 332 (6030). pp. 721-725. ISSN 0036-8075

Kemenes, Ildikó, Marra, Vincenzo, Crossley, Michael, Samu, Dávid, Staras, Kevin, Kemenes, György and Nowotny, Thomas (2011) Dynamic clamp with StdpC software. Nature Protocols, 6 (3). pp. 405-417. ISSN 1754-2189

Zavada, Andrei, Buckley, Christopher, Martinez, D, Rospars, J P and Nowotny, Thomas (2011) Competition-based model of pheromone component ratio detection in the moth. PLoS ONE, 6 (2). e16308.

Nowotny, Thomas, Muezzinoglu, Mehmet K and Huerta, Ramon (2011) Bio-mimetic classification on modern parallel hardware: realizations in NVidia CUDA and OpenMP. International Journal of Innovative Computing, Information and Control, 7 (7A). pp. 3825-3838.

Ashwin, Peter, Nowotny, Thomas and Karabacak, Özkan (2011) Criteria for robustness of heteroclinic cycles in neural microcircuits. Journal of Mathematical Neuroscience, 1 (13). pp. 1-18. ISSN 0929-5313

Szücs, Attila, Berton, Fulvia, Nowotny, Thomas, Sanna, Pietro and Francesconi, Walter (2010) Consistency and diversity of spike dynamics in the neurons of bed nucleus of Stria Terminalis of the rat: a dynamic clamp study. PLoS ONE, 5 (8). ISSN 1932-6203

Huerta, Ramón and Nowotny, Thomas (2009) Fast and robust learning by reinforcement signals: explorations in the insect brain. Neural Computation, 21 (8). pp. 2123-2151. ISSN 0899-7667

Nowotny, Thomas, Huerta, Ramon and Rabinovich, Mikhail I (2008) Neuronal synchrony: peculiarity and generality. Chaos, 18 (3). 037119. ISSN 1054-1500

Ivanchenko, Mikhail V, Nowotny, Thomas, Selverston, Allen I and Rabinovich, Mikhail I (2008) Pacemaker and network mechanisms of neural rhythm generation. Journal of Theoretical Biology, 253 (3). pp. 452-461. ISSN 0022-5193

Nowotny, Thomas, Levi, Rafael and Selverston, Allen I (2008) Probing the dynamics of identified neurons with a data-driven modeling approach. PLoS ONE, 3 (7). ISSN 1932-6203

Nowotny, Thomas and Requardt, Manford (2007) Emergent properties in structurally dynamic disordered cellular networks. Journal of Cellular Automata, 2 (4). pp. 273-289. ISSN 1557-5969

Nowotny, Thomas and Rabinovich, Mikhail I (2007) Dynamical origin of independent spiking and bursting activity in neural microcircuits. Physical Review Letters, 98 (12). p. 128106. ISSN 0031-9007

Nowotny, Thomas, Szucs, Attila, Levi, Rafael and Selverston, Allen I. (2007) Models wagging the dog: are circuits constructed with disparate parameters? Neural Computation, 19 (8). pp. 1985-2003. ISSN 0899-7667

Nowotny, Thomas, Szűcs, Attila, Pinto, Reynaldo D and Selverston, Allen I (2006) StdpC: a modern dynamic clamp. Journal of Neuroscience Methods, 158 (2). pp. 287-299. ISSN 0165-0270

Haas, Julie S, Nowotny, Thomas and Abarbanel, H D I (2006) Spike-timing-dependent plasticity of inhibitory synapses in the entorhinal cortex. Journal of Neurophysiology, 96 (6). 3305 - 3313. ISSN 0022-3077

Nowotny, Thomas, Huerta, Ramon, Abarbanel, Henry D I and Rabinovich, Mikhail I (2005) Self-organization in the olfactory system: one shot odor recognition in insects. Biological Cybernetics, 93 (6). pp. 436-446. ISSN 1432-0770

Huerta, Ramón, Nowotny, Thomas, Garcia-Sanchez, Marta, Abarbanel, H D I and Rabinovich, M I (2004) Learning classification in the olfactory system of insects. Neural Computation, 16 (8). pp. 1601-1640. ISSN 0899-7667

Nowotny, Thomas, Zhigulin, Valentin P, Selverston, Allan I, Abarbanel, Henry D I and Rabinovich, Mikhail I (2003) Enhancement of synchronization in a hybrid neural circuit by spike timing dependent plasticity. Journal of Neuroscience, 23 (30). pp. 9776-9785. ISSN 0270-6474

Nowotny, T and Huerta, R (2003) Explaining synchrony in feedforward networks: are McCulloch-Pitts neurons good enough? Biological Cybernetics, 89 (4). pp. 237-241.

Nowotny, Thomas, Rabinovich, Mikhail I, Huerta, Ramón and Abarbanel, Henry D I (2003) Decoding temporal information through slow lateral excitation in the olfactory system of insects. Journal of Computational Neuroscience, 15 (2). pp. 271-281. ISSN 0929-5313

Nowotny, Thomas, Rabinovich, Misha I and Abarbanel, Henry D I (2003) Spatial representation of temporal information through spike timing dependent plasticity. Physical Review E, 68 (1). 011908. ISSN 1539-3755

Nowotny, Thomas, Patzlaff, Heiko and Behn, Ulrich (2002) Phase diagram of the random field Ising model on the Bethe lattice. Physical Review E, 65 (1). 016127.

Nowotny, Thomas and Behn, Ulrich (2001) Convolution of multifractals and the local magnetization in a random field Ising chain. Journal of Physics A: Mathematical and General, 34 (39). pp. 8057-8079. ISSN 8057–8079

Nowotny, Thomas, Patzlaff, Heiko and Behn, Ulrich (2001) Orbits and phase transitions in the multifractal spectrum. Journal of Physics A: Mathematical and General, 34 (1). pp. 1-23. ISSN 8057–8079

Requardt, Manfred and Nowotny, Thomas (1999) Pregeometric concepts on graphs and cellular networks as possible models of space-time at the Planck-scale. Chaos, Solitons & Fractals, 10 (2-3). pp. 469-481.

Nowotny, Thomas and Requardt, Manfred (1998) Dimension theory of graphs and networks. Journal of Physics A, 31. pp. 2447-2463.

Book Section

Yavuz, Esin and Nowotny, Thomas (2016) Input-modulation as an alternative to conventional learning strategies. In: Proceedings of the ICANN 2016 Conference. Lecture Notes in Computer Science, 9886 . Springer, pp. 54-62. ISBN 0302-9743

Nowotny, Thomas and Benjamin, Paul (2013) Gap junctions in small networks. In: Jaeger, Dieter and Jung, Ranu (eds.) Encyclopedia of Computational Neuroscience. Springer-Verlag. ISBN 9781461466741

Nowotny, Thomas and Rabinovich, MI (2011) Pacemaker and network mechanisms of neural rhythm generation. In: Kumar Das, M (ed.) Modern Pacemakers - Present and Future. InTech, pp. 405-425. ISBN 978-953-307-214-2

Nowotny, Thomas (2009) "Sloppy engineering" and the olfactory system of insects. In: Marco, S and Gutierrez, A (eds.) Biologically Inspired Signal Processing for Chemical Sensing. Springer, pp. 3-32. ISBN 9783642001758

Conference or Workshop Item

Kogo, Naoki, Kern, Felix, Nowotny, Thomas, van Ee, Raymond, van Wezel, Richard and Aihara, Takeshi (2018) Effect of noise on mutually inhibiting pyramidal cells in visual cortex: foundation of stochasticity in bi-stable perception. In: Computational and Mathematical Models in Vision (MODVIS), 16-18 May 2018, Tradewinds Island Resorts in St. Pete Beach, FL.

Turner, James P and Nowotny, Thomas (2015) Estimating numerical error in neural network simulations on Graphics Processing Units. In: CNS 2015, 18-23 July 2015, Prague, Czech Republic.

Nowotny, Thomas, Turner, James and Yavuz, Esin (2015) More flexibility for code generation with GeNN v2.1. In: CNS 2015, 18-23 July 2015, Prague, Czech Republic.

Yavuz, Esin, Maul, Pascale and Nowotny, Thomas (2015) Spiking neural network model of reinforcement learning in the honeybee implemented on the GPU. In: CNS 2015, 18-23 July 2015, Prague, Czech Republic.

Diamond, Alan, Schmuker, Michael, Berna, Amalia Z, Trowell, Stephen and Nowotny, Thomas (2014) Classifying chemical sensor data using GPU-accelerated bio-mimetic neuronal networks based on the insect olfactory system. In: CNS 2014, 26-31 July 2014, Québec City, Canada.

Nowotny, Thomas, Cope, Alexander J, Yavuz, Esin, Stimberg, Marcel, Goodman, Dan FM, Marshall, James and Gurney, Kevin (2014) SpineML and Brian 2.0 interfaces for using GPU enhanced Neuronal Networks (GeNN). In: CNS 2014, 26-31 July 2014, Québec City, Canada.

Wu, Gang, Nowotny, Thomas and Li, David (2014) GPU enhanced fluorescence lifetime imaging processors with non-iterative and iterative algorithms. In: The Microscience Microscopy Congress 2014 (MMC2014), 30 June - 3 July, 2014, Manchester, UK.

Yavuz, Esin, Turner, James and Nowotny, Thomas (2014) Simulating spiking neural networks on massively parallel graphical processing units using a code generation approach with GeNN. In: CNS 2014, 26-31 July, 2014, Québec City, Canada.

Nowotny, Thomas, Galizia, C Giovanni and Szyszka, Paul (2013) Data-driven honeybee antennal lobe model demonstrates how stimulus-onset asynchrony can aid odor segregation. In: CNS 2013, 13-18 July 2013, Paris, France.

Corcoran, Thomas Greg, Phillipedes, Andrew and Nowotny, Thomas (2013) A numerical renormalisation group method for the analysis of critical spreading activity in spiking neural networks. In: CNS 2013, 13-18 July 2013, Paris, France.

Nowotny, Thomas, Trowell, Stephen and de Bruyne, Marien (2012) Benchmarking Drosophila receptor neurons for technical applications. In: CNS 2012, 21-26 July 2012, Decatur, Atlanta.

Nowotny, Thomas and Huerta, Ramón (2012) On the equivalence of Hebbian learning and the SVM formalism. In: Information Sciences and Systems (CISS), 2012 46th Annual Conference on, 21-23 March 2012, Princeton, NJ.

Corcoran, Thomas Gregory, Philippides, Andy and Nowotny, Thomas (2011) Coarse-grained statistics for attributing criticality to heterogeneous neural networks. In: CNS 2011, 23-28 July 2011, Stockholm, Sweden.

Drix, Damien and Nowotny, Thomas (2011) Dynamic observer: ion channel measurement beyond voltage clamp. In: CNS 2011, 23-28 July 2011, Stockholm, Sweden.

Nowotny, Thomas (2011) Flexible neuronal network simulation framework using code generation for NVidia® CUDA™. In: CNS 2011, 23-28 July 2011, Stockholm.

Buckley, Christopher L and Nowotny, Thomas (2011) Transient dynamics between displaced fixed points: an alternate nonlinear dynamical framework for olfaction. In: CNS 2011, 23-28 July 2011, Stockholm, Sweden.

Baroni, Fabiano and Nowotny, Thomas (2011) The effect of intrinsic subthreshold oscillations on the spontaneous dynamics of a ring network with distance-dependent delays. In: CNS 2011, 23-28 July 2011, Stockholm, Sweden.

Nowotny, Thomas (2009) Divergence alone cannot guarantee stable sparse activity patterns if connections are dense. In: CNS 2009, 18-23 July 2009, Berlin.

Buckley, Christopher L and Nowotny, Thomas (2009) Moving beyond convergence in the pheromone system of the moth. In: CNS 2009, 18-23 July 2009, Berlin.

Nowotny, Thomas, Szücs, Attila, Levi, Rafael and Selverston, Allen I (2009) Homeostasis versus neuronal variability: models and experiments in crustaceans. In: Annual Meeting of the Society-for-Experimental-Biology, Glasgow, SCOTLAND.

Conference Proceedings

Knight, James C, Sakhapov, Daniil, Domcsek, Norbert, Dewar, Alexander D M, Graham, Paul, Nowotny, Thomas and Philippides, Andrew (2019) Insect-inspired visual navigation on-board an autonomous robot: real-world routes encoded in a single layer network. ALife 2019: the 2019 conference on Artificial Life, Newcastle, July 29 - August 2, 2019. Published in: Proceedings of ALIFE 2019: The 2019 Conference on Artificial Life. (31) 60-67. MIT Press ISBN 9780262358446

Chan, Ho Ka and Nowotny, Thomas (2017) A biophysical model of the early olfactory system of honeybees. ICONIP: International Conference on Neural Information Processing (2017), Guangzhou, China, 14-18 November 2017. Published in: International Conference on Neural Information Processing. 10637 639-647. Springer Verlag ISSN 0302-9743 ISBN 9783319700922