Publications 2023

Journal papers

• Hata, J., Nakae, K., Tsukada, H., Woodward, A., Haga, Y., Iida, M., Uematsu, A., Seki, F., Ichinohe, N., Gong, R., Kaneko, T., Yoshimaru, D., Watakabe, A., Abe, H., Tani, T., Hamada, T., Gutierrez, C. E., Skibbe, H., Maeda, M., Papazian, F., Hagiya, K., Kishi, N., Ishii, S., Doya, K., Shimogori, T., Yamamori, T., Okano, H. J., & Okano, H. (2023).
  Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range. Scientific Data, 10(1), 211, https://doi.org/10.1038/s41597-023-02121-2
• Callan, D. E., Fukada, T., Dehais, F., & Ishii, S. (2023).
  The role of brain localized gamma and alpha oscillations in inattentional deafness: implications for understanding human attention. Frontiers in Human Neuroscience, section Cognitive Neuroscience, 17, https://doi.org/10.3389/fn-hum.2023.1168108
• Watakabe, A., Skibbe, H., Nakae, K., Abe, H., Ichinohe, N., Rachmadi, F. M., Wang, J., Takaji, M., Mizukami, H., Woodward, A., Gong, R., Hata, J., Okano, H., Ishii, S., & Yamamori, T. (2023).
  Local and long-distance organization of prefrontal cortex circuits in the marmoset brain. Neuron, 111, 1-16.
• Skibbe, H., Rachmadi, M. F., Nakae, K., Gutierrez, C. E., Hata, J., Tsukada, H., Poon, C., Doya, K., Majka, P., Rosa, M. G., Okano, H., Yamamori, T., Ishii, S., Reisert, M., & Watakabe, A. (2023).
  The Brain/MINDS marmoset connectivity resource: an open access platform for cellular-level tracing and tractography in the primate brain. PLoS Biology, 21(6), e3002158
• Ohashi, K., Nakanishi, K., Yasui, Y., & Ishii, S. (2023).
  Deep adversarial reinforcement learning to make policy robust against worst-case value prediction. IEEE Access, 11, 100798-100809.
• Mitsuhashi, S., & Ishii, S. (2023)
  Triangle inequality for inverse optimal control. IEEE Access, 11, 119187-119199.
• Shomali, SR., Ahmadabadi, MN., Rasuli, SN., & Shimazaki, H. (2023)
  Uncovering hidden network architecture from spiking activities using an exact statistical input-output relation of neurons.
  Communications Biology, 6: 169 s42003-023-04511-z
• Higashi, H. (2023)
  Dimension-wise Sequential Update for Learning a Multidimensional Environment in Human.
  Journal of Cognitive Neuroscience, 10.1162/jocn_a_01975

Publications 2022

Journal papers

• Lee, S., Kume, H., Urakubo, H., Kasai, H., & Ishii, S. (2022)
  Tri-view two-photon microscopic image registration and deblurring with convolutional neural networks.
  Neural Networks, 152: 57-69
• Katayama, R., Yoshida, Y., & Ishii, S. (2022)
  Confidence modulates the decodability of scene prediction during partially-observable maze exploration in humans.
  Communications Biology, 5: 367
• Yamaguchi, K., Maeda, Y., Sawada, T., Iino, Y., Tajiri, M., Nakazato, R., Tajiri, M., Nakazato, R., Ishii, S., Kasai, H., & Yagishita, S. (2022)
  A behavioural correlate of the synaptic eligibility trace in the nucleus accumbens.
  Scientific Reports, 12, 1921
• Hwang, J., Park, G., Kwon, T. & Ishii, S. (2022)
  Transition Motion Synthesis for Object Interaction based on Learning Transition Strategies. Computer Graphics Forum.
  https://doi.org/10.1111/cgf.14499
• Nakauchi, S., Kondo, T., Kinzuka, Y., Taniyama, Y., Tamura, H., Higashi, H., Hine, K., Minami, T., Linhares, J. M. M., & Naschimento, S. M. C. (2022)
  Universality and superiority in preference for chromatic composition of art paintings.
  Scientific Reports, 12: 4294.
• Shinomoto, S., Tsubo, Y., & Marunaka Y. (2022)
  Detection and categorization of severe cardiac disorders based solely on heart period measurements.
  Scientific Reports, 12: 17019

Conference papers

• Parmas, P., & Seno, T. (2022)
  Proppo: a Message Passing Framework for Customizable and Composable Learning Algorithms.
  Advances in Neural Information Processing Systems (NeurIPS). New Orleans, USA.

Publications 2021

Journal papers

• Urakubo, H.,Yagishita, S., Kasai, H., Kubota, Y., & Ishii, S. (2021)
  The critical balance between dopamine D2 receptor and RGS for the sensitive detection of a transient decay in dopamine signal.
  PLOS Computational Biology.17(9): e1009364. https://doi.org/10.1371/journal.pcbi.1009364
• Kubo, A., Meshgi, K., & Ishii, S. (2021)
  A meta-Q-learning approach to discriminative correlation filter based visual tracking.
  Journal of Intelligence and Robotic Systems, 101(1), 1-11.
• Liang, Z., Zhou, R., Zhang, L., Li, L., Huang, G., Zhang, Z., & Ishii, S. (2021)
  EEGFuseNet: hybrid unsupervised deep feature characterization and fusion for high-dimensional EEG with an application to emotion recognition
  IEEE Transactions on Neural Systems and Rehabilitation Engineering, 29, 1913-1925, https://doi.org/10.1109/TNSRE.2021.3111689
• Ohashi, K., Nakanishi, K., Sasaki, W., Yasui, Y., & Ishii, S. (2021)
  Deep adversarial reinforcement learning with noise compensation by auto-encoder
  IEEE Access, 9:143901-143912 https://doi.org/10.1109/access.2021.3121751
• Kita, Y., Nishibe, H.,Wang, Y.,Hashikawa, T., Kikuchi, S., Mami, U., Yoshida, A., Yoshida, C.,Kawase, T., Ishii, S., Skibbe, H., & Shimogori, T., (2021)
  Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences.
  Proceedings of the National Academy of the USA, 118(18):e2020125118 https://doi.org/10.1073/pnas.2020125118
• Bonci, A., Fiori, S., Higashi, H., Tanaka, T., & Verdini, F. (2021)
  An introductory tutorial on brain–computer interfaces and their applications.
  Electronics, 10(560).
• Endo, D., Kobayashi, R., Bartolo, R., Averbeck, B.B., Sugase-Miyamoto, Y., Hayashi, K., Kawano, K., Richmond, B.J. & Shinomoto, S. (2021)
  A convolutional neural network for estimating synaptic connectivity from spike trains.
  Scientific Reports, 11(1), pp.1-18.
• Koyama, S., Horie, T. & Shinomoto, S. (2021)
  Estimating the time-varying reproduction number of COVID-19 with a state-space method.
  PLoS Computational Biology, 17(1): e1008679.

Conference papers

• Parmas, P., and Sugiyama, M. (2021)
  A unified view of likelihood ratio and reparameterization gradients.
  International Conference on Artificial Intelligence and Statistics (AISTATS), pp. 4078-4086, Virtual Conference.

Publications 2020

Journal papers

• Hwang J., Ishii, S., Kwon, T., & Oba, S. (2020)
  Modularized predictive codingbased online motion sysnthesis combining environmental constraints and motion data.
  IEEE Access, 8, 10.1109/ACCESS.2020.3036449
• Urakubo, H., Yagishita, S., Kasai, H., & Ishii, S. (2020)
  Signaling models for dopamine-dependent temporal contiguity in striatal synaptic plasticity.
  PLoS Computational Biology, 16(7): e1008078, https://doi.org/10.1371/journal.pcbi.1008078
• Ishii, S., Lee, S., Urakubo, H., Kume, H., & Kasai, H. (2020)
  Generative and discriminative model-based approaches to microscopic image restoration and segmentation.
  Microscopy, 69(2): 79-91, https://doi.org/10.1093/jmicro/dfaa007.
• Liang, Z., Li, F., Hu, W., Huang, G., Oba, S., Zhang, Z., & Ishii, S. (2020)
  A generalized encoding system of alpha oscillations through visual saliency analysis.
  IEEE Transactions on Neural Systems and Rehabilitation Engineering, 28(12): 2731-2743
• Gutierrez, C. E., Skibbe, H., Nakae, K., Tsukada, H., Lienard, J., Watakabe, A., Hata, J., Reisert, M., Woodward A., Yamaguchi, Y., Yamamori, T., Okano, H., Ishii, S. & Doya, K. (2020)
  Optimization and validation of diffusion MRIbased fiber tracking with neural tracer data.
  Scientific Reports, 10, 21285, https://doi.org/10.1038/s41598-020-78284-4
• Parajuli, L. K., Urakubo, H., Takahashi-Nakazato, A., Ogelman, R., Iwasaki, H., Koike, M., Kwon, H. B., Ishii, S., Oh, W. C., Fukazawa, Y., & Okabe, S. (2020)
  Geometry and the organization principle of spine synapses along a dendrite.
  eNeuro, 0248-20, https://doi.org/10.1523/ENEURO.0248-20.2020
• Fujita, Y., Yagishita, S., Kasai, H., Ishii, S. (2020)
  Computational characteristics of the striatal dopamine system described by reinforcement learning with fast generalization.
  Frontiers in Computational Neuroscience. https://doi.org/10.1101/2019.12.12.873950
• Woodward, A., Gong, R., Abe, H., Nakae, K., Hata, J., Skibbe, H., Yamaguchi, Y., Ishii, S., Okano, H., Yamamori, T., & Ichinohe, N. (2020)
  The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain.
  Brain Structure and Function, 225, 1225-1243, https://doi.org/10.1007/s00429-020-02073-y
• Iino, Y., Sawada, T., Yamaguchi, K., Tajiri, M., Ishii, S., Kasai, H., & Yagishita, S. (2020)
  Dopamine D2 receptors in discrimination learning and spine enlargement.
  Nature, 579: 555-560, doi: 10.1038/s41586-020-2115-1
• Lee, S., Negishi, M., Urakubo, H., Kasai, H., & Ishii, S. (2020)
  Mu-net: multi-scale U-net for two-photon microscopy image denoising and restoration.
  Neural Networks, 125: 92-103, doi: 10.1016/j.neunet.2020.01.026
• Nishimoto, T., Higashi, H., Morioka, H., & Ishii, S. (2020)
  An EEG-based personal identification method using unsupervised feature extraction and its robustness against intra-subject variability.
  Journal of Neural Engineering, 17(2): 026007.
• Nakakoga, S., Higashi, H., Muramatsu, J., Nakauchi, S., & Minami, T. (2020)
  Asymmetrical characteristics of emotional responses to pictures and sounds: Evidence from pupillometry.
  PLOS ONE, 15: e0230775..
• Higashi, H., Bui, M.V., Syahir, A., Nakauchi, S. (2020)
  Computational lighting for extracting optical features from RGB images.
  Measurement, 151:107183 doi: 10.1016/j.measurement.2019.107183

Publications 2019

Journal papers

• Skibbe, H., Reisert, M., Nakae, K., Watakabe, A., Hata, J., Okano, H., Yamamori, T., & Ishii, S.(2019)
  PAT: Probabilistic axon tracking for densely labeled neurons in large 3D micrographs.
  IEEE Transactions on Medical Imaging, 38(1):69-78. doi: 10.1109/TMI.2018.2855736.
• Ito, R., Nakae, K., Hata, J., Okano, H., & Ishii, S. (2019)
  Semi-Supervised Deep Learning of Brain Tissue Segmentation.
  Neural Networks, 116: 25-34
• Liang, Z., Oba, S., & Ishii, S. (2019)
  An unsupervised EEG decoding system for human emotion recognition.
  Neural Networks, 116: 257-268
• Ohnishi, S., Uchibe, E., Yamaguchi, Y., Nakanishi, K., Yasui, Y., & Ishii, S. (2019)
  Constrained Deep Q-Learning Gradually Approaching Ordinary Q-Learning.
  Frontiers in Neurorobotics, 13: 103 https://doi.org/10.3389/fnbot.2019.00103
• Urakubo, H., Bullmann, T., Kubota, Y., Oba, S., & Ishii, S. (2019)
  UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images.
  Scientific Reports, 9(1):19413 https://doi.org/10.1038/s41598-019-55431-0
• Yoon, Y., Park, J., Taniguchi, A., Kohsaka, H., Nakae, K., Nonaka, S., Ishii, S., & Nose, A. (2019)
  System level analyses of motor-related neural activities in larval Drosophila.
  Journal of Neurogenetics, 33(3), 179-189, doi: 10.1080/01677063.2019.1605365.
• Higashi, H., Minami, T., Nakauchi, S. (2019)
  Cooperative update of beliefs and state-transition functions in human reinforcement learning.
  Scientific Reports, 9:17794 doi: 10.1038/s41598-019-53600-9
• Nakae K. (2019)
  Statistical Estimation of Phase Response Curves Using Data Transformation.
  Journal of the Physical Society of Japan, 88.8: 084003 doi: 10.7566/JPSJ.88.084003

Conference papers

• Nakae, K., Hata. J., Skibbe, H., Alexander, W., Carlos, G.E., Tsukada, H., Gong, R., Okano, H., & Ishii, S. (2019)
  Macro-scale connectome by diffusion MRI of exvivo marmoset brain with a pipeline of global fiber reconstruction.
  ISBM 2019, Tokyo, 2019.1.29
• Katayama, R., Ishii, S., and Yoshida, W. (2019)
  Decoding scene prediction and its confidence during maze exploration.
  Joint Meeting of International Brain Research Organization (IBRO2019), Daegu, Korea, 2019.9.22
• Liang, Z., Higashi, H., Oba, S., & Ishii, S. (2019)
  Brain dynamics encoding from visual input during free viewing of natural videos.
  The 2019 International Joint Conference on Neural Networks (IJCNN2019), Budapest, Hungary, 2019/7/14
• Hwang, J., Ishii, S., & Oba, S. (2019).
  Online motion synthesis framework using a simple mass model based on predictive coding.
  Proceedings of the 18th annual ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 2019/07/30 https://dl.acm.org/doi/abs/10.1145/3309486.3339894
• Meshgi, K., Mirzaei, M. S., Oba, S. (2019).
  Long and Short Memory Balancing in Visual Co-Tracking Using Q-Learning..
  IEEE International Conference on Image Processing (ICIP), pp. 3970-3974, Taipei, Taiwan 2019/10/22-25 https://ieeexplore.ieee.org/abstract/document/8803577
• Nakae, K. (2019)
  Data assimilation on a whole brain using Brain/MINDS database..
  Workshop: Theory towards Brains, Machines and Minds, Wako, RIKEN CBS, 2019/10/15 (invited)

Publications 2018

Journal papers

• Fuchigami,T., Shikauchi, Y., Nakae, K., Shikauchi, M., Ogawa, T., Ishii, S. (2018)
  Zero-shot fMRI decoding with three-dimensional registration based on diffusion tensor imaging.
  Scientific Reports, 2018;8(1):12342. doi:10.1038/s41598-018-30676-3
• Liang, Z., Hamada, Y., Oba, S. & Ishii, S. (2018)
  Characterization of electroencephalog- raphy signals for estimating saliency features in videos.
  Neural Networks,105: 52-64.
• Yamaguchi, S., Naoki, H., Ikeda, M., Tsukada, Y., Nakano, S., Mori, I., & Ishii,S. (2018)
  Thermotactic behavioral strategy of C. elegans identified using inverse reinforcement learning.
  PLoS Computational Biology,14(5): e1006122. https://doi.org/10.1371/journal.pcbi.1006122.
• Kondo, Y., Aoki, K., & Ishii, S. (2018)
  Inverse tissue mechanics of cell monolayer expansion.
  PLoS Computational Biology,14(3): e1006029. https://doi.org/10.1371/journal.pcbi.1006029.
• Yamada, T., Nishiyama, M., Oba, S., Jimbo, H. C., Ikeda, K., Ishii, S., Hong, K., & Sakumura, Y. (2018)
  Computational methods for estimating molecular system from membrane potential reordings in neuronal growth cone.
  Scientific Reports, 8, 4559, doi: 10.1038/s41598-018-22506-3
• Muta, Y., Fujita, Y., Sumiyama, K., Sakurai, A,. Taketo, M,. Chiba T,. Seno, H,. Aoki, K,. Matsuda, M,. & Imajo,M. (2018)
  Composite regulation of ERK activity dynamics underlies tumour-specific traits in the intestine.
  Nature Communications, 9(1):2174.
• Kobayashi, C., Okamoto, K., Mochizuki, Y., Urakubo, H., Funayama, K., Ishikawa, T., Kashima, T., Ouchi, A., Szymanska, A.F., Ishii, S., Ikegaya, Y. (2018)
  GABAergic inhibition reduces the impact of synaptic excitation on somatic excitation.
  Neuroscience Research, 146: 22-35

Conference papers

• Fujita, Y. & Ishii, S. (2018)
  Reproducing the cognitive function with the robustness against the brain structure and with the efficient learning algorithm.
  CNS2018, Seattle, USA, 2018.7.15
• Liang, Z., Oba, S. & Ishii, S. (2018)
  Inherent Feature Connection (I-Con) Map for Liking Emotion Detection: an EEG Study.
  32nd British Human Computer Interaction Conference (BHCI 2018): Workshop on Affective Computing, pp. 1-5, http://dx.doi.org/10.14236/ewic/HCI2018.209, Belfast, UK, 2018.07.03.
• Meshgi, K., Oba, S., & Ishii, S. (2018)
  Efficient diverse ensemble for discriminative co-tracking.
  Computer Vision and Pattern Recoginition 2018(CVPR), 2018.06.07.
• Nakae, K., Hata. J., Skibbe, H., Alexander, W., Carlos, G.E., Tsukada, H., Gong, R., Okano, H., & Ishii, S. (2018)
  Individuality of macro-scale connectome of common marmoset with global fiber reconstruction by diffusion MRI.
  AINI 2018, Wako, 2018.12.21
• Urakubo, H.，Ishii, S. (2018)
  Improvement of a proof reading software in EM connectomics and its application to the simulation of extracellular DA signaling.
  Joint symposium of 10th optogenetics research conference and second international symposium on brain information dynamics 2018, Tokyo, 2018.7.5
• Urakubo, H.，Ishii, S. (2018)
  Development of a unified environment for automated neuronal network reconstruction from EM images
  AINI 2018, Wako, 2018.12.21

Publications 2017

Journal papers

• Takenouchi,T.,Ishii,S.(2017)
  Binary classifiers ensemble based on Bregman divergence for multi-class classification.
  Neurocomputing, 273(17), 424-434
• Murakami, Y., Koyama, M., Oba, S., Kuroda, S. and Ishii, S. (2017)
  Model-based control of the temporal patterns of intracellular signaling in silico.
  Biophysics and Physicobiology, 14: 29-40.
• Meshgi, K., Maeda, S., Oba, S. and Ishii, S. (2017)
  Constructing a Meta-Tracker using Dropout to Imitate the Behavior of an Arbitrary Black-box Tracker Learning Systems.
  Neural Networks, 87: 132-138

Conference papers

• Uchida, S.Oba, S., Ishii,S. (2017)
  Estimation of the change of agents behavioral strategy using state-action history.
  International Conference on Artificial Neural Networks. ICANN proceeding Part2,100-107
• Nishimoto, T., Morioka, H., Ishii, S. (2017)
  Individual identification by resting-state EEG using common dictionary learning.
  International Conference on Artificial Neural Networks. ICANN proceeding Part1,199-207

Publications 2016

Journal papers

• Kondo, Y., Hayashi, K., and Maeda, S. (2016)
  Sparse Bayesian linear regression with latent masking variables.
  Neurocomputing, 258(4), pp. 3-12
• Shikauchi, Y. and Ishii, S. (2016)
  Robust encoding of scene anticipation during human spatial navigation.
  Scientific Reports, 6, 37599.
• Naoki, H., Nishiyama, M., Togashi, K., Igarashi, Y., Hong, K. and Ishii, S. (2016)
  Multi-phasic bi-directional chemotactic responses of the growth cone.
  Scientific Reports, 6, 36256
• Yamao, M., Aoki, K., Yukinawa, N., Ishii, S., Matsuda, M. and Naoki, H. (2016)
  Two new FRET imaging measures: linearly proportional to and highly contrasting the fraction of active molecules.
  PLoS ONE, 11(10): e0164254
• Li, Y., Nakae, K., Ishii, S. and Naoki, H. (2016)
  Uncertainty-dependent Extinction of Fear Memory in an Amygdala-mPFC Neural Circuit Model.
  PLoS Computational Biology 12(9): e1005099.
• Tsukada, Y., Yamao, M., Naoki, H., Shimowada, T., Ohnishi, N., Kuhara, A., Ishii, S. and Mori, I. (2016)
  Reconstruction of spatial thermal gradient encoded in thermosensory neuron AFD in Caenorhabditis elegans.
  Journal of Neuroscience 36(9), 2571-2581.
• Kato, K., Uchida, J., Kukita, Y., Kumagai, T., Nishino, K., Inoue, T., Kimura, M., Oba, S., Imamura, F. (2016)
  Numerical indices based on circulating tumor DNA for the evaluation of therapeutic response and disease progression in lung cancer patients.
  Scientific Reports. 6:29093.
• Kamino, K. and Kondo, Y. (2016)
  Rescaling of spatio-temporal sensing in eukaryotic chemotaxis.
  PLoS ONE 11(10): e0164674.
• Oba, S., Nakae, K., Ikegaya, Y., Aki, S., Yoshimoto, J., and Ishii, S. (2016)
  Empirical Bayesian significance measure of neuronal spike response.
  BMC neuroscience 17 (1).
• Meshgi, K., Maeda, S.i., Oba, S., Skibbe, H., Li, Y.z. , and Ishii. S. (2016)
  Occlusion Aware Particle Filter Tracker to Handle Complex and Persistent Occlusions using Multiple Feature Fusion.
  Journal of Computer Vision and Image Understanding 150(C): 81-94
• Imamura, F., Uchida, J., Kukita, Y., Kumagai, K., Nishino, K., Inoue, T., Kumura, M., Oba, S., and Kato, K. (2016)
  Monitoring of treatment responses and clonal evolution of tumor cells by circulating tumor DNA of heterogeneous mutant EGFR genes in lung cancer.
  Lung Cancer, 94, pp. 68-73

Conference papers

• Urakubo, H., Aoki, K., Yagishita, S., Kasai, H., Ishii, S. (2016)
  The role of adenylate cyclase 1 in reinforcement synaptic plasticity: a modeling and experimental study.
  SfN annual meeting (126.03), San Diego, USA
• Baek, J., Oba, S., Yoshimoto, J., Doya, K. and Ishii, S. (2016)
  Descriptive, generative, and hybrid approaches for neural connectivity inference from neural activity data.
  CNS2016, Jeju island, South Korea
• Fuchigami, T., Shikauchi, Y., Nakae, K., Shikauchi, M. and Ishii, S. (2016)
  Brain decoding can be improved by diffusion imaging based registration.
  4th AINI 2016 and 14th INCF Nodes Workshop, RIKEN Wako, Japan
• Meshgi, K., Maeda, S., Oba, S. and Ishii, S. (2016)
  Data-driven Probabilistic Occlusion Mask to Promote Visual Tracking.
  CRV2016, Victoria, Canada.
• Miyato, T., Maeda, S., Koyama, M., Nakae, K. and Ishii, S. (2016)
  Distributional Smoothing with Virtual Adversarial Training.
  ICLR2016, San Juan, Puerto Rico.

Publications 2015

Journal papers

• Meshgi, K. and Ishii, S. (2015).
  Occlusion Handling in Visual Object Tracking: A Survey
  IEICE Information and Systems Transaction, vol. E98-D, no.7.
• Uchida, J., Kato, K., Kukita, Y., Kumagai, T., Nishio, K., Daga, H., Nagatomo, I., Inoue, T., Kimura, M., Oba, S., Ito, Y., Takeda, K., and Imamura, F. (2015)
  Diagnostic accuracy of noninvasive genotyping of EGFR in lung cancer patients using deep sequencing of plasma cell-free DNA
  Clinical Chemistry, 61:9, 1191-1196
• Asada, A., Ujita, S., Nakayama, R., Oba, S., Ishii, S., Matsuki, N., and Ikegaya, Y. (2015)
  Subtle Modulation of Ongoing Calcium Dynamics in Astrocytic Microdomains by Sensory Inputs.
  Physiological Reports 3:e12454.
• Shikauchi, Y., and Ishii, S. (2015).
  Decoding the view expectation during learned maze navigation from human fronto-parietal network
  Scientific Reports, 5, 17648.
• Yamao, M., Naoki, H., Kunida, K., Aoki, K., Matsuda, M., and Ishii, S. (2015)
  Distinct predictive performance of Rac1 and Cdc42 in cell migration
  Scientific Reports, 5, 17527.
• Uchida, J., Imamura, F., Kukita, Y., Oba, S., Kumagai, T., Nishino, K., Inoue, T., Kimura, M., Kato, K.
  Dynamics of circulating tumor DNA represented by the activating and resistant mutations in the EGFR-TKI treatment
  Cancer Science, 107(3), pp. 353–358
• Morioka, H., Kanemura, A., Hirayama, J., Shikauchi, M., Ogawa, T., Ikeda, S., Kawanabe, M., Ishii, S. (2015)
  Learning a common dictionary for subject-transfer decoding with resting calibration
  NeuroImage, 111(1), pp 167-178

Conference papers

• Kondo Y., Aoki K., and Ishii S. (2015).
  A data assimilation approach for estimating rheological properties of moving cell sheets
  The Third Annual Winter Q-bio Meeting, USA.
• Koyama M. (2015).
  Inference of stochastic dynamical system from snapshot data
  The Third Annual Winter Q-bio Meeting, USA.
• Shikauchi, Y. & Ishii, S. (2015).
  Detecting representation of the view expectation in mPFC and posterior parietal cortex
  Computational and Systems Neuroscience (Cosyne), USA.
• Oba, S. (2015)
  How to handle rich dynamical intention with co-adaptive BCI?
  German-Japanese Adaptive BCI Workshop, Speaker 2-8, Kyoto, Japan.
• Azuma, Y., Shikauchi, Y., and Ishii, S. (2015)
  Reconstruction of three-dimensional multi-finger movements from MEG signals
  German-Japanese Adaptive BCI Workshop, Poster No.9, Kyoto, Japan.
• Shikauchi, Y., and Ishii, S. (2015)
  Robust anticipation of future scene views during goal-directed navigation in frontoparietal network
  German-Japanese Adaptive BCI Workshop, Poster No.8, Kyoto, Japan
• K. Meshgi, S. Maeda, S. Oba, and S. Ishii. (2015)
  Imitation Game: How a Imitate any Visual Tracker using a few Videos
  International Meeting on High-Dimensional Data Driven Science (HD3-2015), Poster No. 12, Kyoto, Japan, 2015.12.16.
• Shikauchi, Y., and Ishii, S. (2015).
  Robust anticipation of future scene views during goal-directed navigation in frontoparietal network
  International Symposium on Prediction and Decision Making 2015, Poster No.37, Tokyo, Japan, 2015.10.31-11.1
• Kondo, Y., Hayashi, K., and Maeda, S. (2015).
  Bayesian Masking: Sparse Bayesian Estimation with Weaker Shrinkage Bias.
  ACML2015, JMLR Workshop and Conference Proceedings, vol.45, pp.49-64.
• Hayashi, K., Maeda, S & Fujimaki, R. (2015).
  Rebuilding Factorized Information Criterion: Asymptotically Accurate Marginal Likelihood.
  ICML2015, JMLR Workshop and Conference Proceedings, vol.37, pp.1358–1366.
• Meshgi, K. and Ishii, S. (2015).
  Expanding Histogram of Colors with Gridding to Improve Tracking Accuracy
  Proc. of MVA'15, pp. 475-479, Tokyo, Japan
• Koyamada, S., Koyama, M., Nakae, K., and Ishii, S. (2015).
  Principal Sensitivity Analysis.
  PAKDD 2015, Part I, LNAI 9077, pp. 621-632, Vietnam
• Sakurai, S., Oba, S., and Ishii, S.
  Inverse Reinforcement Learning Based on Behaviors of a Learning Agent.
  International Conference on Neural Information Processing(ICONIP), Lecture Notes in Computer Science, 9489, pp. 724-732, Istanbul, Turkey, 2015.11.9-12.
• Baek, J., Oba, S., Yoshimoto, J., Doya, K., and Ishii, S.
  Computational Complexity Reduction for Functional Connectivity Estimation in Large Scale Neural Network
  International Conference on Neural Information Processing(ICONIP), Lecture Notes in Computer Science, 9491, pp. 583–591, Istanbul, Turkey, 2015.11.9-12.

Publications 2014

Journal papers

• Urakubo, H., Sato, M., Ishii, S., & Kuroda, S. (2014).
  In vitro reconstitution of a memory switch of CaMKII.
  Biophysical Journal, 106(6), 1414-1420.
  New and Notable: "First Demonstration of Bistability in CaMKII, a Memory-Related Kinase." Michalski PJ. (2014). Biophys J 106(6): pp. 1233-1235.
• Hayashi, Y., Ishii, S., & Urakubo, H. (2014).
  A computational model of afterimage rotation in the peripheral drift illusion based on retinal ON/OFF response.
  PLoS ONE, 9(12): e115464.
• Ahamed, T., Kawanabe, M., Ishii, S., & Callan, D. (2014).
  Structural differences in gray matter between glider pilots and non-pilots. A voxel based morphometry study.
  Frontiers in Neurology 5:248.
• Skibbe, H., Reisert, M., Maeda, S., Koyama, M., Oba, S., Ito, K., & Ishii, S. (2014).
  Efficient Monte Carlo image analysis for the location of vascular entity.
  IEEE Transactions on Medical Imaging, 34(2), pp. 628-643
• Nakae, K., Ikegaya, Y., Ishikawa, T., Oba, S., Urakubo, H., Koyama, M. & Ishii, S. (2014).
  A statistical method of identifying interactions in neuron-glia systems based on functional multicell Ca2+ imaging.
  PLoS Computational Biology, 10(11), e1003949.
• Yagishita, S., Hayashi-Takagi, A., Ellis-Davies, G.C.R., Urakubo, H., Ishii, S., & Kasai, H. (2014).
  A critical time window for dopamine actions on the structural plasticity of dendritic spines.
  Science, 345(6204), 1616-1620.
• Kunkel, S., Schmidt, M., Eppler, J.M., Plesser, H.E., Masumoto, G., Igarashi, J., Ishii, S., Fukai, T., Morrison, A., Diesmann, M., & Helias, M. (2014).
  Spiking network simulation code for petascale computers.
  Frontiers in Neuroinfomatics 8:78.
• Murakami, Y. (2014).
  Bayesian Parameter Inference and Model Selection by Population Annealing in Systems Biology.
  PLoS ONE, 9(8): e104057.
• Naoki, H., & Ishii, S. (2014).
  Mathematical modeling of neuronal polarization during development.
  Progress in Molecular Biology and Translational Science, 41, 123-127.
• Morioka, H., Kanemura, A., Morimoto, S., Yoshioka, T., Oba, S., Kawanabe, M., & Ishii, S. (2014).
  Decoding spatial attention by using cortical currents estimated from electroencephalography with near-infrared spectroscopy prior information. 
  NeuroImage 90:128-39.

Conference papers

• Koyamada, S., Shikauchi, Y., Nakae, K., & Ishii, S. (2014).
  Construction of subject-independent brain decoders for human fMRI with deep learning.
  Proceedings of the International Conference on Data Mining, Internet Computing, and Big Data, 60-68.
• Skibbe, H., Reisert, M., & Ishii, S. (2014).
  Efficient Metropolis-Hasting image analysis for the location of vascular entity.
  Proceedings of the 36th German Conference on Pattern Recognition (GCPR), Lecture Notes in Computer.
• Naoki, H., Yamao, M., and Ishii, S. (2014).
  Reconstruction of cellular migrating behavior based on molecular activity.
  ESF-EMBO Symposium, Flies, worms and robots: combining perspectives on minibrains and behaviour, Spain
• Yamao, M., Tsukada, Y., Naoki, H., Mori, I., and Ishii, S. (2014).
  Functional identification of thermotactic neural system in C. elegans.
  ESF-EMBO Symposium, Flies, worms and robots: combining perspectives on minibrains and behaviour, Spain

Publications 2013

Journal papers

• Kukita, Y., Uchida, J., Oba, S., Nishino, K., Kumagai, T., Taniguchi, K., Okuyama, T., Imamura, F., and Kato K. (2013)
  Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data. 
  PLoS ONE 8(11): e81468. doi:10.1371/journal.pone.0081468.

Conference papers

• Urakubo, H., Ishii, S., and Kuroda, S. (2013.11)
  In vitro Reconstitution of an Erasable Memory Switch of CaMKII.
  SfN annual meeting , No. 233.17.
• Shikauchi, Y., and Ishii, S. (2013.7)
  Prediction is predictable from human brain activity in frontal-parietal cortex. 
  Computational neuroscience meeting (CNS2013), P181
• Shikauchi, Y., and Ishii, S. (2013)
  Decoding scene prediction associated with decision making
  Neuro2013, P1-2-184.
• Hirayama, J., Shikauchi, Y., Nakamura, Y., Maeda, S., Takenouchi, T., Kanemura, A., Kawanabe, M., and Ishii, S. (2013.6)
  Decoding hand movements in everyday activities from magnetoencephalography. 
  Neuro2013, P1-1-242.
• Okadome, Y., Nakamura, Y., Shikauchi, Y., Ishii, S., and Ishiguro, H. (2013)
  Fast approximation method for gaussian process regression using hash function for non-uniformly distributed data.
  23rd International Conference on Artificial Neural Networks (ICANN 2013), Lecture Notes in Computer Science, 8131, pp. 17-25.

Invited Lecture

• Ishii, S. (2013.3.7)
  Network-based BMI: toward brain machine interface in real envionments.
  IPAM Workshop on Multimodal Neuroimaging, University of California, Los Angeles

Publications 2012

Journal papers

• Ihara, M., Maeda, S., Ikeda, K., and Ishii, S. (2012)
  Low-dimensional Feature Representation for Instrument Identification.
  SICE Jounal of Control,Measument,and System Integration, 5(4), pp.249-258.
• Ueno, T. Maeda, S. and Ishii,S. (2012)
  Asymptotic analysis of value prediction by well-specified and misspecified models. 
  Neural Networks, 31, pp.88-92.
• Kouno, M., Nakae, K., Oba, S., and Ishii, S. (2012)
  Microscopic image restoration based on tensor factorization of rotated patches.
  Artificial Life and Robotics, 17, pp.417-425.

Conference papers

• Nakano, D., Maeda, S., & Ishii, S. (2012)
  Control of a Free-Falling Cat by Policy-Based Reinforcement Learning. 
  The International Conference on Artificial Neural Networks (ICANN), Lecture Notes in Artificial Intelligence , 7553, pp.116-123

Invited Lecture

• Ishii, S. (2012.6.13) Modeling and simulation of neuronal morphology.
  Okinawa Computational Neuroscience Course, Okinawa Institute of Science and Technology

Publications 2011

Journal papers

• Kim, W., Matsui, T., Yamao, M., Ishibashi, M., Tamada, K., Takumi, T., Kohno, K., Oba, S., Ishii, S., Sakumura, Y., Bessho, Y. (2011). 
  The period of the somite segmentation clock is sensitive to Notch activity.
  Molecular Biology of Cell, 22(18), 3541-3549.
• Naoki, H., Nakamuta, S., Kaibuchi, K., and Ishii, S. (2011)
  Flexible Search for Single-Axon Morphology during Neuronal Spontaneous Polarization.
  PLoS one, 6(4), e19034. doi:10.1371/journal.pone.0019034.
• Nishiyama, M., Togashi, K., von Schimmelmann, M. J., Lim, C.-J., Maeda, S., Yamashita, N., Goshima, Y., Ishii, S. and Hong, K. (2011)
  Semaphorin 3A induces Ca_v2.3 channel-dependent conversion of axons to dendrites.
  Nature Cell Biology, 13(6), pp.676-685, doi:10.1038/ncb2255.
• Ueno, T., Maeda, S., Kawanabe, M. and Ishii, S. (2011)
  Generalized TD Learning.
  Journal of Machine Learning Research, 12, pp.1977-2020.
• Takahashi, N., Oba, S., Yukinawa, N., Ujita, S., Mizunuma, M., Matsuki, N., Ishii, S. and Ikegaya, Y. (2011)
  High-speed multineuron calcium imaging using Nipkow-type confocal microscopy . Curr. Protoc. Neurosci., 57:2.14.1-2.14.10. doi:10.1002/0471142301.ns0214s57.
• Nonaka, S., Naoki, H. and Ishii, S. (2011)
  A multiphysical model of cell migration integrating reaction–diffusion, membrane and cytoskeleton.
  Neural Networks, 24, pp.979-989.
• Yoshimoto, J., Sato, M., and Ishii, S. (2011)
  Bayesian normalized Gaussian network and hierarchical model selection method.
  Intelligent Automation and Soft Computing, 17(1), 71-94.
• Yamao, M., Naoki, H. and Ishii, S. (2011)
  Multi-Cellular Logistics of Collective Cell Migration.
  PLoS ONE, 6(12), e27950. doi:10.1371/journal.pone.0027950.
• Takenouchi, T., & Ishii, S. (2011)
  Ternary Bradley-Terry model-based decoding for multiclass classfication.
  Machine Learning, 1-24, doi:10.1007/s10994-011-5240-0. 
• Mori, T., & Ishii, S. (2011).
  Incremental State Aggregation for Value Function Estimation in Reinforcement Learning.
  IEEE Transactions on Systems, Man and Cybernetics, 41(5), 1407-1416.

Conference papers

• Naito, S., Yukinawa N., and Ishii, S.(2011.1)
  A simulation study of visualperceptual learning with attetional signals.
  International Symposium on Artificial Life and Robotics (AROB 16th '11), GS11-103.
• Hikaru, H. Oba, S., and Ishii, S. (2011)
  Multiple Granger causality tests for network structure estimation from time-series data. 
  International Symposium on Artificial Life and Robotics (AROB), GS14-4.
• Tanaka, T., Maeda, S., & Ishii, S. (2011)
  Motion compensated X-ray CT algorithm for moving objects.
  The Tenth International Conference on Machine Learning and Applications, doi:10.1109/icmla.2011.97
• Aki, S., Oba, S.,  Nakae, K., & Ishii, S. (2011)
  A sparse regression method to estimate neuronal structure from spike sequence.
  The Seventeenth International Symposium on Artificial Life and Robotics 2012, 718-721.
• Kambara, S., Oba, S. (2011)
  Density map of attentional capacity allocation.
  The Seventeenth International Symposium on Artificial Life and Robotics 2012, 710-713.
• Kouno, M., Nakae, K., Oba, S., & Ishii, S. (2011)
  Microscopic image restoration based on tensor factorization of rotated patches.
  The Seventeenth International Symposium on Artificial Life and Robotics 2012, 902-905.

Publications 2010

Journal papers

• Kanemura, A., Maeda, S., Fukuda, W. and Ishii, S. (2010)
  Bayesian Image Superresolution and Hidden Variable Modeling.
  Journal of Systems Science and Complexity, 23(1), pp. 116-136.
• Yoshida, W., Funakoshi, H., and Ishii, S. (2010)
  Hierarchical rule switching in prefrontal cortex.
  NeuroImage, 50(1), 314-322.
• Kanemura, A., Maeda, S., and Ishii, S. (2010)
  Sparse Bayesian learning of filters for efficient image expansion.
  IEEE Transactions on Image Processing, 19(6), pp.1480-1490.
• Kanemura, A., Maeda, S., Fukuda, W., and Ishii, S. (2010)
  Bayesian image superresolution and hidden variable modeling.
  Journal of Systems Science and Complexity,23(1), 116-136.
• Maeda, S., Fukuda, W., Kanemura, A. and Ishii, S. (2010)
  Maximum a Posteriori X-ray Computed tomography using graph cuts.
  Journal of Physics: Conference Series, 233 012023.
• Toriyama, M., Sakumura, Y., Shimada, T., Ishii, S. and Inagaki, N. (2010)
  A diffusion-based neurite length sensing mechanism involved in neuronal symmetry-breaking. 
  Molecular Systems Biology, 6 364.
• Shinji Hotta, Shigeyuki Oba and Shin Ishii. (2010)
  Visual attention model involving feature-based inhibition of return.
  ARTIFICIAL LIFE AND ROBOTICS, 15(2), pp. 129-132. 

Conference papers

• W. Fukuda, S. Maeda, A. Kanemura, and S. Ishii. (2010.3)
  Bayesian X-ray computed tomography using material class knowledge.
  International Conference on Acoustics, Speech, and Signal Processing (ICASSP), pp. 2126-2129, Dallas, TX, USA.
• Fukuda, W., Maeda, S., Kanemura, A., and Ishii, S. (2010)
  X-ray computed tomography using material-class modeling by Markov random field minimization.
  International Symposium on Artificial Life and Robotics (AROB), pp. 662-665.
• Hotta, S., Oba, S., and Ishii, S. (2010)
  Visual attention model involving feature-based inhibition of return.
  International Symposium on Artificial Life and Robotics (AROB), pp. 533-536.
• Nishioka, S. Maeda, S., and Ishii, S. (2010)
  Machine learning approach to 9-dof arm robot control.
  International Symposium on Artificial Life and Robotics (AROB), pp. 282-285.
• Yamao, M., Naoki, H., and Ishii, S. (2010.9)
  Noise-Induced Collective Migration for Neural Crest Cells.
  International Conference on Artificial Neural Networks (ICANN), Lecture Notes in Computer Science , 6352, pp. 155-163.
• Adomi, M., Shikauchi, Y., and Ishii, S. (2010.9)
  Hidden Markov model for human decision process in a partially observable environment.
  International Conference on Artificial Neural Networks (ICANN), Lecture Notes in Computer Science , 6353 , pp. 94-103.
• Shikauchi, Y., Adomi, M., and Ishii, S. (2010.9)
  Separation of exploration and exploitation in maze navigation task.
  Neuro2010, O2-9-1-4.
• Shigeyuki Oba, Shin Ishii. (2010.9)
  Restoration of 3d microscopic image stack by hierarchical estimation of diffusion tensor field.
  Neuro2010, P1-r18.
• Kevin C.Y. Chien, Shigeyuki Oba, Shin Ishii. (2010.9)
  Human brain image registration for diffusion MRI data and neuro-fiber categorization.
  Neuro2010, P2-r17.
• Hikaru Harima, Shigeyuki Oba, Shin Ishii. (2010.9)
  Neuronal network structure estimation by a modification of Granger causality.
  Neuro2010, P3-r06.
• Satoshi Naito, Naoto Yukinawa, and Shin Ishii. (2010.9)
  A spiking neural network model of primary visual cortex for perceptual learning.
  Neuro2010, P1-q21.
• Naoto Yukinawa and Shin Ishii. (2010.9)
  Learning spatio-temporal visual features by a large scale neural network model.
  Neuro2010, P3-q13.
• Tomohiro Noda , Shin Ishii, and Shin-ichi Maeda. (2010.9)
  A statistical method for defining two-point resolution in optical microscopy.
  Neuro2010, P1-r17.
• Seigo Nonaka, Naoki Honda, and Shin Ishii. (2010.9)
  Multi-physical full-scale simulation for neuronal morphogenesis.
  Neuro2010, O2-10-1-2.
• Naoto Yukinawa and Shin Ishii. (2010.8)
  Learning spatio-temporal visual features by a large-scale neural network model.
  Frontiers in Neuroscience. Conference Abstract: Neuroinformatics 2010, DOI: 10.3389/conf.fnins.2010.13.0009.
• Seigo Nonaka, Honda Naoki, and Shin Ishii. (2010.8)
  Large Scale Neuronal Simulation.
  Frontiers in Neuroscience. Conference Abstract: Neuroinformatics 2010, DOI: 10.3389/conf.fnins.2010.13.0009. 

Publications 2009

Journal papers

• Ihara, M., Maeda, S., and Ishii, S. (2009)
  Solo instrumental music analysis using the source-filter model as a sound production model considering temporal dynamics.
  Neural Computing and Applications, 18(1), pp. 3-14.
• Shibata, K., Yamagishi, N., Ishii, S., and Kawato, M. (2009)
  Boosting perceptual learning by fake feedback.
  Vision Research, 49(21), pp.2574-2585.
• Oba, S. and Ishii,S. (2009)  
  Differential gene detection incorporating common expression patterns.
  Journal of Physics: Conference Series, 197 012007.
• Kanemura, A., Maeda, S., and Ishii, S. (2009)
  Superresolution with compound Markov random fields via the variational EM algorithm.
  Neural Networks, 22(7), pp. 1025-1034.
  2010年度日本神経回路学会論文賞受賞
• Maeda, S. and Ishii, S. (2009)
  Learning a multidimensional companding function for lossy source coding.
  Neural Networks, 22(7), pp. 998-1010.
• 兼村 厚範，前田 新一，石井信．(2009)
  複層マルコフ確率場を事前分布とする超解像法におけるハイパーパラメータ推定．
  電子情報通信学会論文誌(D)，J92-D(10), pp. 1802-1811．
• Takenouchi, T., and Ishii, S. (2009)
  A multi-class classification method based on decoding of binary classifiers.
  Neural Computation, 21(7), pp.2049-2081.
• Suzuki, I., Takenouchi, T., Ohira, M., Oba, S., and Ishii, S. (2009)
  Robust model selection for classification of microarrays.
  Cancer Informatics, 7, pp. 141-157.
• Oba, S., and Ishii, S. (2009)
  Optimal sufficient statistics for parametric and non-parametric multiple simultaneous hypothesis testing.
  International Journal of Biostatistics, 5(1), 20.
• Yukinawa, N., Yoshioka, T., Kobayashi, K., Ogasawara, N., and Ishii, S. (2009)
  A constrained Gaussian mixture model forcorrelation-based cluster analysis of gene expression data.
  IPSJ Transactions on Bioinformatics, 2, pp. 47-62.
• Yu, M., Ohira, M., Li, M., Niizuma, H., Oo, M., Zhu, Y., Ozaki, Y., Isogai, E., Nakamura, Y., Koda, T., Oba, S., Yu, B. and Nakagawara, A. (2009)
  High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma.
  International Journal of Oncology, 34, pp. 931-938.
• Shirahata, M., Oba, S., Iwao-Koizumi, K., Saito, S., Ueno, N., Oda, M., Hashimoto, M., Ishii, S, Takahashi, J. A. and Kato, K. (2009)
  Using gene expression profiling to identify a prognostic molecular spectrum in gliomas.
  Cancer Science, 100(1), pp. 165-172.
• Yukinawa, N., Oba, S., Kato, K., and Ishii, S.  (2009)
  Optimal aggregation of binary classifiers for multi-class cancer diagnosis using gene expression profiles.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(2), pp. 333-343.

Conference papers

• Fukuda, W., Kanemura, A., Maeda, S., and Ishii, S. (2009)
  Superresolution from occluded scenes.
  International Conference on Neural Information Processing (ICONIP), Lecture Notes in Computer Science, 5864, pp. 19-27.
• Tomizawa, H., Maeda, S., and Ishii, S. (2009)
  Learning of Go board state evaluation function by artificial neural network.
  International Conference on Neural Information Processing (ICONIP), Lecture Notes in Computer Science, 5863, pp. 598-605.
• Mori, T. and Ishii, S. (2009)
  Robust approximation in decomposed reinforcement learning.
  International Conference on Neural Information Processing (ICONIP), Lecture Notes in Computer Science, 5863, pp. 590-597.
• Kanemura, A., Maeda, S., and Ishii, S. (2009)
  Learning color image expansion filters.
  IEEE International Conference on Image Processing (ICIP), pp. 357-360.
• Oba, S. and Ishii, S. (2009)
  Differential gene detection incorporating common expression patterns.
  International Workshop on Statistical-Mechanical Informatics (IW-SMI).
• Ueno T, Maeda, S., Kawanabe, M., and Ishii, S.(2009)
  Optimal online learning procedures for model-free policy evaluation.
  European Conference on Machine Learning and Knowledge Discovery in Databases (ECML-PKDD), Lecture Notes in Artificial Intelligence, 5782, pp. 473-488.
• Mori, T. and Ishii, S.(2009)
  An additive reinforcement learning.
  International Conference on Artificial Neural Networks (ICANN), Lecture Notes in Computer Science, 5768, pp. 608-617.
• Hayashi, K., Hirayama, J., and Ishii, S. (2009)
  Dynamic exponential family matrix factorization.
  The 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Lecture Notes in Computer Science, 5476, pp.452-462.

Publications 2008

Journal papers

• Osaga, S., Hirayama, J., Takenouchi, T., and Ishii, S. (2008)
  A probabilistic modeling of MOSAIC learning. 
  Artificial Life and Robotics, 12(1-2) , 167-171 
• Makino, K., Nakamura, Y., Shibata, T., Ishii, S. (2008)
  Adaptive Control of a Looper-like Robot based on the CPG-Actor-Critic Method. 
  Artificial Life and Robotics, 12(1-2) ,pp.129-132.
• Tomioka, N., Oba, S., Ohira, M., Misra, A., Fridlyland, J., Ishii, S., Nakamura, Y., Isogai, E., Hirata, T., Yoshida, Y., Todo, S., Kaneko, Y., Albertson, D. G., Pinkel, D., Feurstein, B. G., and Nakagawara, A. (2008) 
  Novel Risk Stratification of Patients with Neuroblastoma by Genomic Signature which is Independent of Molecular Signature.
  Oncogene, 27(4), pp.441-449.
• Yukinawa, N., Takenouchi, T., Oba, S. and Ishii, S. (2008)
  Combining multiple decisions: applications to bioinformatics.
  Journal of Physics: Conference Series, 95, pp.12-18.
• Honda, N., Sakumura, Y., and Ishii, S. (2008)
  Stochastic control of spontaneous signal generation for gradient sensing in chemotaxis.
  Journal of Theoretical Biology, 255, 259-266.
• Hirayama, J., Nakatomi, M., Takenouchi, T., and Ishii, S. (2008)
  Collaborative prediction by multiple Bayesian networks and its application to printer usage modeling.
  Behaviormetrika, 35(2), pp. 99-114.
• Tamei, T., Ishii, S., and Shibata, T. (2008)
  Virtual force/tactile sensors for interactive machines using user's biological signals.
  Advanced Robotics, 22(8), pp. 893-911.
• Hirayama, J., Nakatomi, M., Takenouchi, T., and Ishii, S. (2008)
  α-Bayesian collaboration of multiple predictors and its applications to hybrid recommendation and user modeling. 
  Neural Information Processing - Letters and Reviews, 12(1-3), pp. 11-20.
• Shikauchi, M., Ishii, S., and Shibata, T. (2008)
  Prediction of aperiodic target sequences by saccades.
  Behavioural Brain Research, 189(2), pp.325-31.

Conference papers

• Maeda, C., Oba, S., Yukinawa, N., and Ishii, S.(2008)
  Detection of multiple overlapping string-shaped objects using special clustering.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS18-5.
• Taniguchi, Y., Mori, T., and Ishii, S. (2008)
  Continuous Internal-State Controller for a Partially Observable Linear Dynamical System.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS1-1.
• Sodebayashi, K., Oba, S., and Ishii, S. (2008)
  Two-Way Factor Analysis for Missing Value Estimation of Matrix Data.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS5-6.
• Ishihara, A., Hirayama, J., Takenouchi, T., and Ishii, S. (2008)
  A Unified Approach to Collaborative and Feature-based Recommendation based on Probabilistic Latant Semantic Models.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS17-2.
• Nomura, H., Oba, S., and Ishii, S. (2008)
  Re-weighted ODP for differential gene expression analysis.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS5-2.
• Furuya, M., Oba, S., and Ishii, S. (2008)
  Collaborative filtering based on a Weighted Maximum Margin Matrix Factorization.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS14-5.
• Nanjoh, N., Mori, T., and Ishii, S. (2008)
  An effective reinforcement learning with automatic construction of basis function and sequential approximation.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS2-3.
• Kazuhiro, T., Mori, T., and Ishii, S. (2008)
  Active Sampling based on Gaussian Process for Reinforcement Learning.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS1-2.
• Yano, N., Shibata, T., and Ishii, S. (2008)
  Adaptive Particle Allocation for Multifocal Visual Attention based on Particle Filtering.
  International Symposium on Artificial Life and Robotics (AROB 13th '08), GS16-4.
• Asahina, A., Hirayama, J., and Ishii, S. (2008)
  Interpreting dopamine activities in stochastic reward tasks.*
  The 15th International Conference on Neural Information Processing (ICONIP), Auckland, New Zealand.
  * Received Best APNNA Student Paper Award.
• Hirayama, J. and Ishii, S. (2008)
  A closed-form estimator of fully visible Boltzmann machines.
  The 15th International Conference on Neural Information Processing (ICONIP), Auckland, New Zealand.
• Takenouchi, T. and Ishii, S. (2008)
  Ternary Bradley-Terry model-based decoding for multi-class classification.
  IEEE International Workshop on Machine Learning for Signal Processing (MLSP).
• Hiei, Y., Mori, T., and Ishii, S. (2008) 
  Self-organized reinforcement learning based on policy gradient in nonstationary environment. 
  International Conference on Artificial Neural Networks (ICANN).
• Taniguchi, Y., Mori, T., and Ishii, S. (2008) 
  A continuous internal-state controller for partially observable Markov decision processes. 
  International Conference on Artificial Neural Networks (ICANN).
• Ueno, T., Kawanabe, M., Mori, T., Maeda, S., and Ishii, S. (2008)
  A semiparametric statistical approach to model-free policy evaluation.
  The 25th International Conference on Machine Learning (ICML 2008), pp. 1072-1079, Helsinki, Finland.

Publications 2007

Journal papers

• Hirayama, J., Maeda, S., and Ishii, S. (2007)
  Markov and Semi-Markov Switching of Source Appearances for Non-Stationary Independent Component Analysis. 
  IEEE Transactions on Neural Networks, 18(5), pp.1326-1342.
• Fujita, H., and Ishii, S. (2007)
  Model-based reinforcement learning for partially observable games with sampling-based state estimation.
  Neural Computation, 19(11), pp.3051-3087.
• Nakamura, Y., Mori, T., Sato, M., and Ishii, S. (2007)
  Reinforcement Learning for a Biped Robot Based on a CPG-Actor-Critic Method. 
  Neural Networks, 20(6), pp.723-735.
• Tanabe, A., Fukumizu, K., Oba, S., Takenouchi, T., and Ishii, S. (2007)
  Parameter Estimation for von Mises-Fisher Distributions.
  Computational Statistics, 22(1), pp. 145-157.

Book chapter

• Shibata, T., Hitomi, K., Nakamura, Y., and Ishii, S. (2007)
  Reinforcement Learning of Stable Trajectory for Quasi-Passive Dynamic Walking of an Unstable Biped Robot.
  In Mackel, M. Eds., Humanoid Robots: Human-like Machines, pp. 211-226, I-Tech Education and Publishing.

Conference papers

• Ihara, M., Maeda, S. and Ishii, S. (2007)
  Instrument Identification in Monophonic Music Using Spectral Information.
  IEEE International Symposium on Signal Processing and Information Technology (ISSPIT), pp.607-611.
• Kanemura, A., Maeda, S. and Ishii, S. (2007)
  Image Superresolution under Spatially Structured Noise.
  IEEE International Symposium on Signal Processing and Information Technology (ISSPIT), pp.279-284.
• Takenouchi, T., Ishii, S. (2007)
  A multi-class classification with a probabilistic localized decoder.
  IEEE International Symposium on Signal Processing and Information Technology (ISSPIT), pp.861-865.
• Oba, S., Kawanabe, M., Mueller, K-R., and Ishii, S. (2007)
  Heterogeneous Component Analysis.
  Advances in Neural Information Processing Systems (NIPS 20),  Platt, J. C. et al. eds., MIT Press, Cambridge, MA, pp. 1097--1104.
• Hirayama, J., Nakatomi, M., Takenouchi, T., and Ishii, S. (2007) 
  Bayesian collaborative predictors for general user modeling tasks.
  International Conference on Neural Information Processing (ICONIP), LNCS 4984, pp.742–751.
• Maeda, S. and Ishii, S. (2007)
  Optimization of parametric companding function for an efficient coding.
  International Conference on Neural Information Processing (ICONIP), LNCS 4984, pp.713-722.
• T.Shibata, T.Bando and S.Ishii (2007)
  Visual tracking achieved by adaptive sampling from hierarchical and parallel predictions.
  International Conference on Neural Information Processing (ICONIP), LNCS 4984, pp.604-613.
• Y.Tsukada, Y.Sakumura and S.Ishii (2007) 
  Quantitative morphodynamic analysis of time-lapse imaging by edge evolution tracking.
  International Conference on Neural Information Processing (ICONIP), LNCS 4985 pp.817-826.
• Ishii, S., Yukinawa, N., Takenouchi, T., and Oba, S. (2007)
  Combining multiple decisions: applications to bioinformatics.
  The International Workshop on Statistical-Mechanical Informatics, pp. 151-161.
• Kanemura, A., Maeda, S., and Ishii, S. (2007) 
  Edge-Preserving Bayesian Image Superresolution Based on Compound Markov Random Fields. 
  International Conference on Artificial Neural Networks (ICANN), LNCS 4669, pp. 611-620.
• Taniguchi, Y., Mori, T., and Ishii, S. (2007) 
  Reinforcement Learning for Cooperative Actions in a Partially Observable Multi-Agent System. 
  International Conference on Artificial Neural Networks (ICANN), LNCS 4668, pp. 229-238.
• Maeda, S. and Ishii, S. (2007) 
  Convergence analysis of the EM algorithm and Joint minimization of free energy. 
  IEEE International Workshop on Machine Learning for Signal Processing (MLSP), pp.318-323.
• Kanemura, A., Maeda, S., and Ishii, S. (2007) 
  Hyperparameter Estimation in Bayesian Image Superresolution with a Compound Markov Random Field Prior. 
  IEEE International Workshop on Machine Learning for Signal Processing (MLSP), pp.181-186.
• Tamei, T., Ishii, S. and Shibata, T. (2007)
  Dynamic and Cooperative Interaction with a Robot that Possesses No Force/Tactile Sensors.
  International Conference on Advanced Robotics (ICAR 2007), pp.647-652.
• Takenouchi, T. and Ishii, S. (2007) 
  A Probabilistic Decoding Approach to Multi-Class Classification. 
  International Joint Conference on Neural Networks (IJCNN 2007) , p.1696.
• Ihara, M., Maeda, S., and Ishii, S. (2007) 
  Estimation of the Source-Filter Model Using Temporal Dynamics. 
  International Joint Conference on Neural Networks (IJCNN 2007) , p.1803.
• Takenouchi, T. and Ishii, S. (2007) 
  Multiclass Classification as a Decoding Problem. 
  The First IEEE Symposium on Foundations of Computational Intelligence (FOCI'07), pp. 470-475.
• Osaga, S., Hirayama, J., Takenouchi, T., and Ishii, S. (2007) 
  A Probabilistic Model of MOSAIC. 
  The First IEEE Symposium on Foundations of Computational Intelligence (FOCI'07), pp. 41-46