Items where Subject is "neural networks"

Paper

Adesnik, H., Bruns, W., Taniguchi, H., Huang, Z. J., Scanziani, M. (October 2012) A neural circuit for spatial summation in visual cortex. Nature, 490 (7419). pp. 226-231. ISSN 0028-0836

Allegra, N., Bamieh, B., Mitra, P., Sire, C. (January 2018) Phase transitions in distributed control systems with multiplicative noise. Journal of Statistical Mechanics-Theory and Experiment. ISSN 1742-5468

Bamieh, B., Jovanović, M. R., Mitra, P., Patterson, S. (2012) Coherence in large-scale networks: Dimension-dependent limitations of local feedback. IEEE Transactions on Automatic Control, 57 (9). pp. 2235-2249.

Barabási, Dániel L, Bianconi, Ginestra, Bullmore, Ed, Burgess, Mark, Chung, SueYeon, Eliassi-Rad, Tina, George, Dileep, Kovács, István A, Makse, Hernán, Nichols, Thomas E, Papadimitriou, Christos, Sporns, Olaf, Stachenfeld, Kim, Toroczkai, Zoltán, Towlson, Emma K, Zador, Anthony M, Zeng, Hongkui, Barabási, Albert-László, Bernard, Amy, Buzsáki, György (August 2023) Neuroscience Needs Network Science. The Journal of Neuroscience, 43 (34). pp. 5989-5995. ISSN 0270-6474

Bartley, A. F., Huang, Z. J., Huber, K. M., Gibson, J. R. (October 2008) Differential Activity-Dependent, Homeostatic Plasticity of Two Neocortical Inhibitory Circuits. J Neurophysiol, 100 (4). pp. 1983-1994.

Bokil, H., Pesaran, B., Andersen, R. A., Mitra, P. P. (2005) A framework for detection and classification of events in neural activity. arXiv.

Bokil, H. S., Mitra, P. P. (2007) Non-parametric methods for the analysis of neurobiological time-series data. 46th IEEE Conference on Decision and Control, 2007. pp. 5833-5838.

Brauth, S. E., Heaton, J. T., Shea, S. D., Durand, S. E., Hall, W. S. (January 1997) Functional anatomy of forebrain vocal control pathways in the budgerigar (Melopsittacus undulatus). Annals of the New York Academy of Sciences, 807. pp. 368-85. ISSN 0077-8923 (Print)0077-8923

Brody, C. D., Hopfield, J. J. (March 2003) Simple networks for spike-timing-based computation, with application to olfactory processing. Neuron, 37 (5). pp. 843-852. ISSN 0896-6273

Chattopadhyaya, B., Baho, E., Huang, Z. J., Schachner, M., Di Cristo, G. (2013) Neural cell adhesion molecule-mediated fyn activation promotes GABAergic synapse maturation in postnatal mouse cortex. Journal of Neuroscience, 33 (14). pp. 5957-68. ISSN 0270-6474

Chattopadhyaya, B., Di Cristo, G., Higashiyama, H., Knott, G. W., Kuhlman, S. J., Welker, E., Huang, Z. J. (October 2004) Experience and activity-dependent maturation of perisomatic GABAergic innervation in primary visual cortex during a postnatal critical period. Journal of Neuroscience, 24 (43). pp. 9598-611. ISSN 0270-6474

Chklovskii, D. B., Koulakov, A. A. (September 2000) A wire length minimization approach to ocular dominance patterns in mammalian visual cortex. Physica A-Statistical Mechanics and Its Applications, 284 (1-4). pp. 318-334. ISSN 0378-4371

Cohen, Yarden, Engel, Tatiana A, Langdon, Christopher, Lindsay, Grace W, Ott, Torben, Peters, Megan AK, Shine, James M, Breton-Provencher, Vincent, Ramaswamy, Srikanth (November 2022) Recent Advances at the Interface of Neuroscience and Artificial Neural Networks. The Journal of Neuroscience, 42 (45). pp. 8514-8523. ISSN 1529-2401

Cowley, Benjamin R, Stan, Patricia L, Pillow, Jonathan W, Smith, Matthew A (November 2023) Compact deep neural network models of visual cortex. bioRxiv. (Submitted)

Cowley, B. R., Kaufman, M. T., Butler, Z. S., Churchland, M. M., Ryu, S. I., Shenoy, K. V., Yu, B. M. (December 2013) DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural activity. Journal of Neural Engineering, 10 (6). ISSN 17412560 (ISSN)

Cox, C. L., Denk, W., Tank, D. W., Svoboda, K. (August 2000) Action potentials reliably invade axonal arbors of rat neocortical neurons. Proceedings of the National Academy of Sciences of the United States of America, 97 (17). pp. 9724-9728. ISSN 0027-8424

Daruwalla, Kyle, Lipasti, Mikko (May 2024) Information bottleneck-based Hebbian learning rule naturally ties working memory and synaptic updates. Frontiers in Computational Neuroscience, 18. p. 1240348. ISSN 1662-5188

Dasgupta, S., Stevens, C. F., Navlakha, S. (November 2017) A neural algorithm for a fundamental computing problem. Science, 358 (6364). pp. 793-796. ISSN 0036-8075 (Public Dataset)

DeWeese, M. R., Zador, A. M. (February 2006) Neurobiology: Efficiency measures. Nature, 439 (7079). pp. 920-921. ISSN 00280836

Delevich, K., Tucciarone, J., Huang, Z. J., Li, B. (April 2015) The Mediodorsal Thalamus Drives Feedforward Inhibition in the Anterior Cingulate Cortex via Parvalbumin Interneurons. Journal of Neuroscience , 35 (14). pp. 5743-53. ISSN 0270-6474

Dunn, Timothy W., Koo, Peter K. (2017) Inferring Functional Neural Connectivity with Deep Residual Convolutional Networks. bioRxiv. p. 141010. (Unpublished)

Eban-Rothschild, Ada, Borniger, Jeremy C., Rothschild, Gideon, Giardino, William J., Morrow, Joshua G., de Lecea, Luis (2019) Arousal-State Dependent Alterations in VTA-GABAergic Neural Activity. bioRxiv.

Engel, T. A., Helbig, B., Russell, D. F., Schimansky-Geier, L., Neiman, A. B. (August 2009) Coherent stochastic oscillations enhance signal detection in spiking neurons. Phys Rev E Stat Nonlin Soft Matter Phys, 80 (2 Pt 1). 021919. ISSN 1539-3755 (Print)1539-3755 (Linking)

Engel, T. A., Schimansky-Geier, L., Herz, A. V., Schreiber, S., Erchova, I. (September 2008) Subthreshold membrane-potential resonances shape spike-train patterns in the entorhinal cortex. J Neurophysiol, 100 (3). pp. 1576-89. ISSN 0022-3077 (Print)0022-3077 (Linking)

Engel, T. A., Wang, X. J. (May 2011) Same or different? A neural circuit mechanism of similarity-based pattern match decision making. J Neurosci, 31 (19). pp. 6982-96. ISSN 1529-2401 (Electronic)0270-6474 (Linking)

Goodhill, G., Baker, C., Balasubramanian, V., Bazhenov, M., Beck, J., Becker, S., Bethge, M., Boahen, K., Boden, M., Bonin, V., Bouret, S., Fairhall, A., Flash, T., French, R., Gillies, A., Gollisch, T., Gurney, K., Gutkin, B., Hayhoe, M., Hunt, J., Ibbotson, M., Kepecs, A., Kingdom, F., Kropff, E., Longden, K., Marder, E., Miikkulainen, R., Oliva, A., Olshausen, B., Pillow, J., Prenger, R., Redish, D., Rolls, E., Rucci, M., Breakspear, M., Bressloff, P., Bulthoff, H., Burgess, N., Burkitt, A., Butts, D., Carreira-Perpinan, M., Chklovskii, D., Eden, U., Ermentrout, B., Schmidhuber, J., Semyanov, A., Sharpee, T., Smith, A., Sommer, F., Srinivasan, M., Stanley, G., Stopfer, M., Tanaka, H., Theunissen, F., Tranchina, D., Treves, A., Van Ooyen, A., Verschure, P., Vorobyev, M., Wachtler, T., Wallis, G., Willmore, B., Wiskott, L., Wyeth, G., Zanker, J., Zetzsche, C., Zhaoping, L. (2008) Network: Computation in Neural Systems: Editorial. Network: Computation in Neural Systems, 19 (1). pp. 1-2. ISSN 0954898X (ISSN)

Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, JA, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-Ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-Sueki, H, Frith, MC, Abugessaisa, I, Aitken, S, Aken, BL, Alam, I, Alam, T, Alasiri, R, Alhendi, AMN, Alinejad-Rokny, H, Alvarez, MJ, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, AL, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, JK, Bajic, VB, Bajpai, A, Baker, S, Baldarelli, RM, Balic, A, Bansal, M, Batagov, AO, Batzoglou, S, Beckhouse, AG, Beltrami, AP, Beltrami, CA, Bertin, N, Bhattacharya, S, Bickel, PJ, Blake, JA, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, JB, Bult, CJ, Burroughs, AM, Burt, DW, Busch, A, Caglio, G, Califano, A, Cameron, CJ, Cannistraci, CV, Carbone, A, Carlisle, AJ, Carninci, P, Carter, KW, Cesselli, D, Chang, JC, Chen, JC, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, EL, Coskun, M, Dalby, M, Dalla, E, Daub, CO, Davis, CA, de Hoon, MJL, de Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, AD, Dieterich, LC (June 2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1). ISSN 2041-1723 (In Press)

Hopfield, J. J., Brody, C. D. (February 2003) Separating objects and 'neural' computation. Comptes Rendus Biologies, 326 (2). pp. 219-222. ISSN 1631-0691

How, Javier J, Navlakha, Saket, Chalasani, Sreekanth H (November 2021) Neural network features distinguish chemosensory stimuli in Caenorhabditis elegans. PLoS Computational Biology, 17 (11). e1009591. ISSN 1553-7358

Huang, E. P. (July 1999) A meeting of minds: learning and memory in 1999. Learning & Memory, 6 (4). pp. 341-6. ISSN 1072-0502

Huang, Z. J., Satterlie, R. A. (1990) Neuronal mechanisms underlying behavioral switching in a pteropod mollusc. Journal of Comparative Physiology - A Sensory, Neural, and Behavioral Physiology, 166 (6). pp. 875-887. ISSN 03407594 (ISSN)

Kaczmarzyk, Jakub R, Gupta, Rajarsi, Kurc, Tahsin M, Abousamra, Shahira, Saltz, Joel H, Koo, Peter K (September 2023) ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification. Computer Methods and Programs in Biomedicine, 239. p. 107631. ISSN 0169-2607

Karnani, Mahesh M, Jackson, Jesse, Ayzenshtat, Inbal, Tucciarone, Jason, Manoocheri, Kasra, Snider, William G, Yuste, Rafael (April 2016) Cooperative Subnetworks of Molecularly Similar Interneurons in Mouse Neocortex. Neuron, 90 (1). pp. 86-100. ISSN 0896-6273

Kaufman, M. T., Churchland, M. M., Ryu, S. I., Shenoy, K. V. (February 2014) Cortical activity in the null space: permitting preparation without movement. Nature Neuroscience, 17 (3). pp. 440-448. ISSN 1097-6256

Kepecs, A., Fishell, G. (January 2014) Interneuron cell types are fit to function. Nature, 505 (7483). pp. 318-326. ISSN 0028-0836

Kepecs, A., Lisman, J. (February 2003) Information encoding and computation with spikes and bursts. Network, 14 (1). pp. 103-18. ISSN 0954-898X (Print)

Kepecs, A., Van Rossum, M. C. W., Song, S., Tegner, J. (2002) Spike-timing-dependent plasticity: Common themes and divergent vistas. Biological Cybernetics, 87 (5-6). pp. 446-458. ISSN 03401200 (ISSN)

Kepecs, A., Wang, X. J. (2000) Analysis of complex bursting in cortical pyramidal neuron models. Neurocomputing, 32-33. pp. 181-187. ISSN 09252312 (ISSN)

Kepple, Daniel, Giaffar, Hamza, Rinberg, Dmitry, Koulakov, Alexei (September 2016) Deconstructing Odorant Identity via Primacy in Dual Networks. arXiv. (Submitted)

Kepple, D. R., Giaffar, H., Rinberg, D., Koulakov, A. A. (October 2018) Primacy coding in dual olfactory networks. 51st Asilomar Conference on Signals, Systems, and Computers, 2017-O. pp. 587-592.

Kiyani, E, Silber, S, Kooshkbaghi, M, Karttunen, M (December 2022) Machine-learning-based data-driven discovery of nonlinear phase-field dynamics. Physical Review E, 106 (6). ISSN 2470-0045

Klindt, David, Sanborn, Sophia, Acosta, Francisco, Poitevin, Frédéric, Miolane, Nina (October 2023) Identifying Interpretable Visual Features in Artificial and Biological Neural Systems. arXiv. (Submitted)

Knott, S., Mostafavi, S., Mousavi, P. (2010) A neural network based modeling and validation approach for identifying gene regulatory networks. Neurocomputing, 73 (13-15). pp. 2419-2429.

Koo, Peter K, Ploenzke, Matt (February 2020) Interpreting Deep Neural Networks Beyond Attribution Methods: Quantifying Global Importance of Genomic Features. bioRxiv. (Submitted)

Koo, Peter K., Ploenzke, Matt (2019) Improving Convolutional Network Interpretability with Exponential Activations. bioRxiv. p. 650804. (Unpublished)

Koo, Peter K., Qian, Sharon, Kaplun, Gal, Volf, Verena, Kalimeris, Dimitris (2019) Robust Neural Networks are More Interpretable for Genomics. bioRxiv. p. 657437. (Unpublished)

Koulakov, A. A., Chklovskii, D. B. (February 2001) Orientation preference patterns in mammalian visual cortex: A wire length minimization approach. Neuron, 29 (2). pp. 519-527. ISSN 0896-6273

Koulakov, A. A., Raghavachari, S., Kepecs, A., Lisman, J. E. (2002) Model for a robust neural integrator. Nature Neuroscience, 5 (8). pp. 775-782. ISSN 10976256 (ISSN)

Kvitsiani, D., Ranade, S., Hangya, B., Taniguchi, H., Huang, J. Z., Kepecs, A. (May 2013) Distinct behavioural and network correlates of two interneuron types in prefrontal cortex. Nature, 498 (7454). pp. 363-366. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter (2022) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. bioRxiv. (Submitted)

Lee, Nicholas Keone, Tang, Ziqi, Toneyan, Shushan, Koo, Peter K (May 2023) EvoAug: improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations. Genome Biology, 24 (1). p. 105. ISSN 1474-760X

Lee, Hassal, Ciabatti, Ernesto, González-Rueda, Ana, Williams, Elena, Nugent, Fiona, Mookerjee, Souradip, Morgese, Fabio, Tripodi, Marco (March 2023) Combining long-term circuit mapping and network transcriptomics with SiR-N2c. Nature Methods. ISSN 1548-7091 (Public Dataset)

Lin, H., Hangya, B., Fox, S. E., Muller, R. U. (March 2012) Repetitive convulsant-induced seizures reduce the number but not precision of hippocampal place cells. Journal of Neuroscience, 32 (12). pp. 4163-78. ISSN 0270-6474

Liu, J., Lee, H. J., Weitz, A. J., Fang, Z., Lin, P., Choy, M., Fisher, R., Pinskiy, V., Tolpygo, A., Mitra, P., Schiff, N., Lee, J. H. (December 2015) Frequency-selective control of cortical and subcortical networks by central thalamus. Elife, 4. e09215. ISSN 2050-084X (Electronic)2050-084X (Linking)

Lu, J., Tucciarone, J., Padilla-Coreano, N., He, M., Gordon, J. A., Huang, Z. J. (October 2017) Selective inhibitory control of pyramidal neuron ensembles and cortical subnetworks by chandelier cells. Nat Neurosci, 20 (10). pp. 1377-1383. ISSN 1097-6256

Machens, C. K. (June 2002) Adaptive sampling by information maximization. Physical Review Letters, 88 (22). ISSN 0031-9007

Machens, C. K., Brody, C. D. (February 2008) Design of continuous attractor networks with monotonic tuning using a symmetry principle. Neural Comput, 20 (2). pp. 452-85.

Majdandzic, Antonio, Rajesh, Chandana, Koo, Peter K (May 2023) Correcting gradient-based interpretations of deep neural networks for genomics. Genome Biology, 24 (1). p. 109. ISSN 1474-760X

Majdandzic, Antonio, Rajesh, Chandana, Tang, Amber, Toneyan, Shushan, Labelson, Ethan, Tripathy, Rohit, Koo, Peter K (November 2022) Selecting deep neural networks that yield consistent attribution-based interpretations for genomics. Proc Mach Learn Res, 200. pp. 131-149. ISSN 2640-3498

Masse, N. Y., Turner, G. C., Jefferis, G. S. X. E. (August 2009) Olfactory Information Processing in Drosophila. Current Biology, 19 (16). R700-R713. ISSN 0960-9822

Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., Alon, U. (October 2002) Network motifs: Simple building blocks of complex networks. Science, 298 (5594). pp. 824-827. ISSN 0036-8075

Mitra, Partha P, Sire, Clément (December 2023) AI without networks. bioRxiv. (Submitted)

Mo, Ziyi, Siepel, Adam (September 2023) Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. bioRxiv. (Submitted)

Mo, Ziyi, Siepel, Adam (November 2023) Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. PLoS Genetics, 19 (11). e1011032. ISSN 1553-7390

Mohan, Hemanth, An, Xu, Kondo, Hideki, Zhao, Shengli, Matho, Katherine, Musall, Simon, Mitra, Partha, Huang, Z Josh (March 2022) Cortical glutamatergic projection neuron types contribute to distinct functional subnetworks. Research Square. (Unpublished)

Mohan, Hemanth, An, Xu, Xu, X Hermione, Kondo, Hideki, Zhao, Shengli, Matho, Katherine S, Wang, Bor-Shuen, Musall, Simon, Mitra, Partha, Huang, Z Josh (January 2023) Cortical glutamatergic projection neuron types contribute to distinct functional subnetworks. Nature Neuroscience. ISSN 1097-6256

Musall, S., Urai, A. E., Sussillo, D., Churchland, A. K. (October 2019) Harnessing behavioral diversity to understand neural computations for cognition. Curr Opin Neurobiol, 58. pp. 229-238. ISSN 0959-4388

Navlakha, S., Bar-Joseph, Z., Barth, A. L. (January 2018) Network Design and the Brain. Trends Cogn Sci, 22 (1). pp. 64-78. ISSN 1364-6613

Navlakha, S., Barth, A. L., Bar-Joseph, Z. (July 2015) Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks. PLoS Comput Biol, 11 (7). e1004347. ISSN 1553-734x

Neiman, Alexander, Engel, Tatiana (2008) Information transfer in ampullary electroreceptors. APS Meeting Abstracts.

Neiman, Alexander, Engel, Tatiana, Russell, David, Helbig, Brian, Schimansky-Geier, Lutz (2009) Epithelial oscillations enhance signal detection in a peripheral sensory system. APS Meeting Abstracts.

Nikitchenko, M., Koulakov, A. A. (October 2008) Neural Integrator: A Sandpile Model. Neural Comput, 20 (10). pp. 2379-2417.

Perez-Orive, J., Mazor, O., Turner, G. C., Cassenaer, S., Wilson, R. I., Laurent, G. (2002) Oscillations and sparsening of odor representations in the mushroom body. Science, 297 (5580). pp. 359-365. ISSN 00368075 (ISSN)

Poucet, B., Sargolini, F., Song, E. Y., Hangya, B., Fox, S., Muller, R. U. (January 2014) Independence of landmark and selfmotion-guided navigation: A different role for grid cells. Philosophical Transactions of the Royal Society B: Biological Sciences, 369 (1635). ISSN 09628436 (ISSN)

Pouget, A., Drugowitsch, J., Kepecs, A. (February 2016) Confidence and certainty: distinct probabilistic quantities for different goals. Nat Neurosci, 19 (3). pp. 366-74. ISSN 1546-1726 (Electronic)1097-6256 (Linking)

Ramanan, K., Sengupta, A., Ziedins, I., Mitra, P. P. (2002) Markov random field models of multicasting in tree networks. Advances in Applied Probability, 34 (1). pp. 58-84. ISSN 00018678 (ISSN)

Roach, James, Churchland, Anne, Engel, Tatiana (2022) Two roles for choice selective inhibition in decision-making circuits. bioRxiv. (Submitted)

Roach, James P, Churchland, Anne K, Engel, Tatiana A (January 2023) Choice selective inhibition drives stability and competition in decision circuits. Nature Communications, 14 (1). p. 147. ISSN 2041-1723

Rockland, K. S. (May 2015) About connections. Front Neuroanat, 9. p. 61. ISSN 1662-5129 (Electronic)1662-5129 (Linking)

Sanders, H., Kolterman, B. E., Shusterman, R., Rinberg, D., Koulakov, A., Lisman, J. (September 2014) A network that performs brute-force conversion of a temporal sequence to a spatial pattern: relevance to odor recognition. Frontiers in Computational Neuroscience, 8. Article no.108. ISSN 1662-5188

Seitz, Evan E, McCandlish, David M, Kinney, Justin B, Koo, Peter K (November 2023) Interpreting cis -regulatory mechanisms from genomic deep neural networks using surrogate models. bioRxiv. (Submitted)

Shao, L., Lu, B., Wen, Z., Teng, S., Wang, L., Zhao, Y., Wang, L., Ishizuka, K., Xu, X., Sawa, A., Song, H., Ming, G., Zhong, Y. (July 2017) Disrupted-in-Schizophrenia-1 (DISC1) protein disturbs neural function in multiple disease-risk pathways. Hum Mol Genet, 26 (14). pp. 2634-2648. ISSN 0964-6906

Shen, Yang, Wang, Julia, Navlakha, Saket (August 2021) A Correspondence between Normalization Strategies in Artificial and Biological Neural Networks. Neural Computation. pp. 1-25. ISSN 0899-7667

Shenoy, K. V., Meeker, D., Cao, S., Kureshi, S. A., Pesaran, B., Buneo, C. A., Batista, A. P., Mitra, P. P., Burdick, J. W., Andersen, R. A. (2003) Neural prosthetic control signals from plan activity. NeuroReport, 14 (4). pp. 591-596. ISSN 09594965 (ISSN)

Sheppard, J. P., Wang, J. P., Wong, P. C. M. (May 2012) Large-scale cortical network properties predict future sound-to-word learning success. Journal of Cognitive Neuroscience, 24 (5). pp. 1087-1103. ISSN 0898-929X

Shi, Yan-Liang, Zeraati, Roxana, Levina, Anna, Engel, Tatiana A (July 2022) Spatial and temporal correlations in neural networks with structured connectivity. arXiv. (Submitted)

Shi, YL, Zeraati, R, Levina, A, Engel, TA (January 2023) Spatial and temporal correlations in neural networks with structured connectivity. Physical Review Research, 5 (1). ISSN 2643-1564

Shuvaev, Sergey, Giaffar, Hamza, Koulakov, Alexei A (December 2017) Representations of Sound in Deep Learning of Audio Features from Music. arXiv. (Submitted)

Shuvaev, Sergey A, Başerdem, Batuhan, Zador, Anthony, Koulakov, Alexei A (November 2016) Network cloning using DNA barcodes. arXiv. (Submitted)

Shuvaev, S. A., Baserdem, B., Zador, A. M., Koulakov, A. A. (April 2019) Network cloning using DNA barcodes. Proc Natl Acad Sci U S A, 116 (19). pp. 9610-9615. ISSN 0027-8424

Sussillo, David, Churchland, Mark M., Kaufman, Matthew T., Shenoy, Krishna V. (June 2015) A neural network that finds a naturalistic solution for the production of muscle activity. Nat Neurosci, 18 (7). pp. 1025-1033. ISSN 1097-6256

Svoboda, K., Ugurbil, K. (October 2003) New technologies: probing neurons and their networks - Editorial Overview. Current Opinion in Neurobiology, 13 (5). pp. 568-569. ISSN 0959-4388

Tareen, Ammar, Posfai, Anna, Ireland, William, McCandlish, David, Kinney, Justin (July 2020) MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. BioRxiv. (Unpublished)

Toneyan, Shushan, Koo, Peter K (July 2023) Interpreting Cis -Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics. bioRxiv. (Submitted)

Triplett, J. W., Pfeiffenberger, C., Yamada, J., Stafford, B. K., Sweeney, N. T., Litke, A. M., Sher, A., Koulakov, A. A., Feldheim, D. A. (November 2011) Competition is a driving force in topographic mapping. Proceedings of the National Academy of Sciences of the United States of America, 108 (47). pp. 19060-19065. ISSN 00278424

Turner, G. C., Bazhenov, M., Laurent, G. (February 2008) Olfactory Representations by Drosophila Mushroom Body Neurons. Journal of Neurophysiology, 99. 734 - 746. ISSN 0022-3077

Tyree, S. M., Borniger, J. C., de Lecea, L. (2018) Hypocretin as a Hub for Arousal and Motivation. Front Neurol, 9. p. 413. ISSN 1664-2295 (Print)1664-2295 (Linking)

Utama, R., Piekarewicz, J. (January 2018) Validating neural-network refinements of nuclear mass models. Physical Review C, 97 (1). article no. 014306.

Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H., Chklovskii, D. B. (February 2011) Structural Properties of the Caenorhabditis elegans Neuronal Network. Plos Computational Biology, 7 (2). ISSN 1553-734X

Verechtchaguina, T., Schimansky-Geier, L., Sokolov, I. M. (September 2004) Spectra and waiting-time densities in firing resonant and nonresonant neurons. Phys Rev E Stat Nonlin Soft Matter Phys, 70 (3 Pt 1). 031916. ISSN 1539-3755 (Print)1539-3755 (Linking)

Verechtchaguina, T., Sokolov, I. M., Schimansky-Geier, L. (March 2006) First passage time densities in non-Markovian models with subthreshold oscillations. Europhysics Letters, 73 (5). pp. 691-697. ISSN 0295-5075

Verechtchaguina, T., Sokolov, I. M., Schimansky-Geier, L. (March 2006) First passage time densities in resonate-and-fire models. Phys Rev E Stat Nonlin Soft Matter Phys, 73 (3 Pt 1). 031108. ISSN 1539-3755 (Print)1539-3755 (Linking)

Verechtchaguina, T., Sokolov, I. M., Schimansky-Geier, L. (May 2007) Interspike interval densities of resonate and fire neurons. Biosystems, 89 (1-3). pp. 63-8. ISSN 0303-2647 (Print)0303-2647 (Linking)

Vidne, M., Ahmadian, Y., Shlens, J., Pillow, J. W., Kulkarni, J., Litke, A. M., Chichilnisky, E. J., Simoncelli, E., Paninski, L. (August 2012) Modeling the impact of common noise inputs on the network activity of retinal ganglion cells. Journal of Computational Neuroscience, 33 (1). pp. 97-121. ISSN 09295313 (ISSN)

Wei, Y. (2012) Eigenvalue spectra of asymmetric random matrices for multicomponent neural networks. Physical Review E , 85 (6-2).

Wei, Y., Tsigankov, D., Koulakov, A. (December 2013) The molecular basis for the development of neural maps. Annals of the New York Academy of Sciences, 1305. pp. 44-60. ISSN 0077-8923

Wilson, C. D., Serrano, G. O., Koulakov, A. A., Rinberg, D. (November 2017) A primacy code for odor identity. Nat Commun, 8 (1). p. 1477. ISSN 2041-1723

Wilson, R. I., Turner, G. C., Laurent, G. (2004) Transformation of Olfactory Representations in the Drosophila Antennal Lobe. Science, 303 (5656). pp. 366-370. ISSN 00368075 (ISSN)

Wu, M. V., Manoli, D. S., Fraser, E. J., Coats, J. K., Tollkuhn, J., Honda, S., Harada, N., Shah, N. M. (October 2009) Estrogen masculinizes neural pathways and sex-specific behaviors. Cell, 139 (1). pp. 61-72. ISSN 1097-4172 (Electronic)0092-8674 (Linking)

Zador, A. M. (August 2019) A critique of pure learning and what artificial neural networks can learn from animal brains. Nat Commun, 10 (1). p. 3770. ISSN 2041-1723

Zador, A. M., Pearlmutter, B. A. (1996) VC Dimension of an Integrate-and-Fire Neuron Model. Neural Computation, 8 (3). pp. 611-624.

Zeraati, Roxana, Shi, Yan-Liang, Steinmetz, Nicholas A, Gieselmann, Marc A, Thiele, Alexander, Moore, Tirin, Levina, Anna, Engel, Tatiana A (April 2023) Intrinsic timescales in the visual cortex change with selective attention and reflect spatial connectivity. Nature Communications, 14 (1). p. 1858. ISSN 2041-1723

Zhou, Jessica, Rizzo, Kaeli, Tang, Ziqi, Koo, Peter K (November 2024) Uncertainty-aware genomic deep learning with knowledge distillation. bioRxiv. ISSN 2692-8205 (Public Dataset) (Submitted)

Zhu, Jiening, Oh, Jung Hun, Simhal, Anish K, Elkin, Rena, Norton, Larry, Deasy, Joseph O, Tannenbaum, Allen (September 2023) Geometric graph neural networks on multi-omics data to predict cancer survival outcomes. Computers in Biology and Medicine, 163. p. 107117. ISSN 0010-4825

Book Section

Chklovskii, D. B., Stevens, C. F. (2000) Wiring Optimization in the Brain. In: Advances in neural information processing systems 12 : proceedings of the 1999 conference. MIT Press, Cambridge, Mass., pp. 103-107. ISBN 0262194503

Conference or Workshop Item

Koo, P. K., Ploenzke, Matt (June 2019) Improving Convolutional Network Interpretability with Exponential Activations. In: ICML Workshop for Computational Biology, Long Beach, CA.

Koo, Peter K., Qian, Sharon, Volf, Verena, Kalimeris, Dimitris (June 2019) Robust Neural Networks are More Interpretable for Genomics. In: ICML Workshop for Computational Biology, Long Beach, CA.

Thesis

Chakraborty, S. (November 2005) Analysis and Modeling of Neural Connectivity in a Short Term Memory System. PhD thesis, Cold Spring Harbor Laboratory.

Chen, B. L. (2007) Neuronal Network of C. elegans: from Anatomy to Behavior. PhD thesis, Cold Spring Harbor Laboratory.

Engel, Tatiana (2007) Firing statistics in neurons as non-Markovian first passage time problem. PhD thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I.

Video

Albeanu, D. F. (November 2012) Talk from Florin Albeanu at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Kepecs, A. (November 2011) Talk from Adam Kepecs at the Cold Spring Harbor Laboratory In-House Symposium (2011). [Video] (Unpublished)

Koulakov, A. A. (November 2012) Talk from Alex Koulakov at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)

Turner, G. C. (November 2012) Talk from Glenn Turner at the Cold Spring Harbor Laboratory In-House Symposium (2012). [Video] (Unpublished)