Akira Funahashi

45 papers A 1B 9Misc 2Journal 23Unranked 10

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Cell Segmentation Without Annotation by Unsupervised Domain Adaptation Based on Cooperative Self-Learning. IEEE Access Shintaro Miyaki, Takashi Morikura, Shori Nishimoto, Yuta Tokuoka, Takahiro G. Yamada, Akira Funahashi
2026	J	`jnl`	Inference of Gene Regulatory Networks for Overcoming Low Performance in Real-World Data. IEEE Access Yusuke Hiki, Yuta Tokuoka, Takahiro G. Yamada, Akira Funahashi
2025	J	`jnl`	A Cross-Modal Tactile Reproduction Utilizing Tactile and Visual Information Generated by Conditional Generative Adversarial Networks. IEEE Access Koki Hatori, Takashi Morikura, Akira Funahashi, Kenjiro Takemura
2025	J	`jnl`	Nuclear segmentation in four-dimensional label-free microscopy images for predicting live birth potential of mouse embryos. Comput. Biol. Medicine Taichi Kanazawa, Tatsuma Yao, Sora Takeshita, Tatsuki Hirai, Ryo Suenaga, Takahiro G. Yamada, Yuta Tokuoka, Kazuo Yamagata, Akira Funahashi
2024	J	`jnl`	Asynchronous Batch Bayesian Optimization with Pipelining Evaluations for Experimental Resource-constrained Conditions. CoRR Yujin Taguchi, Yusuke Shibuya, Yusuke Hiki, Takashi Morikura, Takahiro G. Yamada, Akira Funahashi
2023	J	`jnl`	Mol-PECO: a deep learning model to predict human olfactory perception from molecular structures. CoRR Mengji Zhang, Yusuke Hiki, Akira Funahashi, Tetsuya J. Kobayashi
2023	J	`jnl`	SBML level 3 package: spatial processes, version 1, release 1. J. Integr. Bioinform. James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith
2022	J	`jnl`	An explainable deep learning-based algorithm with an attention mechanism for predicting the live birth potential of mouse embryos. Artif. Intell. Medicine Yuta Tokuoka, Takahiro G. Yamada, Daisuke Mashiko, Zenki Ikeda, Tetsuya J. Kobayashi, Kazuo Yamagata, Akira Funahashi
2022	J	`jnl`	BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022	J	`jnl`	BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022	J	`jnl`	Symbolic Integration by Integrating Learning Models With Different Strengths and Weaknesses. IEEE Access Hazumi Kubota, Yuta Tokuoka, Takahiro G. Yamada, Akira Funahashi
2021	J	`jnl`	Symbolic integration by integrating learning models with different strengths and weaknesses. CoRR Hazumi Kubota, Yuta Tokuoka, Takahiro G. Yamada, Akira Funahashi
2020	J	`jnl`	Direct Cell Counting Using Macro-Scale Smartphone Images of Cell Aggregates. IEEE Access Chikahiro Imashiro, Yuta Tokuoka, Kaito Kikuhara, Takahiro G. Yamada, Kenjiro Takemura, Akira Funahashi
2013	—	`conf`	In vivo oriented modeling with consideration of intracellular crowding. EMBC Noriko Hiroi, Keisuke Iba, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Takumi Hiraiwa, Tetsuya J. Kobayashi, Kotaro Oka, Akira Funahashi
2013	J	`jnl`	LibSBMLSim: a reference implementation of fully functional SBML simulator. Bioinform. Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi, Akira Funahashi
2013	J	`jnl`	The systems biology simulation core algorithm. BMC Syst. Biol. Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard R. Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger
2012	J	`jnl`	From Microscopy Data to in silico Environments for in vivo Oriented Simulations. EURASIP J. Bioinform. Syst. Biol. Noriko Hiroi, Michael Klann, Keisuke Iba, Pablo de Heras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi, Heinz Koeppl
2012	J	`jnl`	Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinform. Martijn P. van Iersel, Alice Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly A. Sorokin, Ugur Dogrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber
2011	J	`jnl`	BioPAX support in CellDesigner. Bioinform. Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas
2010	—	`conf`	A datapath classification method for FPGA-based scientific application accelerator systems. FPT Yui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri
2010	J	`jnl`	Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator. IPSJ Trans. Syst. LSI Des. Methodol. Hideki Yamada, Yui Ogawa, Tomonori Ooya, Tomoya Ishimori, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri
2010	J	`jnl`	The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi
2009	—	`conf`	A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA. ReConFig Hideki Yamada, Yasunori Osana, Tomoya Ishimori, Tomonori Ooya, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata, Kiyoshi Oguri
2009	B	`conf`	Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator. FPL Tomonori Ooya, Hideki Yamada, Tomoya Ishimori, Yuichiro Shibata, Yasunori Osana, Kiyoshi Oguri, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano
2009	—	`conf`	Pipeline Scheduling with Input Port Constraints for an FPGA-Based Biochemical Simulator. ARC Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Kiyoshi Oguri
2008	J	`jnl`	CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks. Proc. IEEE Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Mineo Morohashi, Norihiro Kikuchi, Hiroaki Kitano
2008	B	`conf`	Practical implementation of a network-based stochastic biochemical simulation system on an FPGA. FPL Masato Yoshimi, Yuri Nishikawa, Yasunori Osana, Akira Funahashi, Yuichiro Shibata, Hideki Yamada, Noriko Hiroi, Hiroaki Kitano, Hideharu Amano
2007	B	`conf`	A Combining technique of rate law functions for a cost-effective reconfigurable biological simulator. FPL Hideki Yamada, Naoki Iwanaga, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Kiyoshi Oguri
2007	—	`conf`	A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA. FPT Masato Yoshimi, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hideki Yamada, Hiroaki Kitano, Hideharu Amano
2007	B	`conf`	FPGA Implementation of a Data-Driven Stochastic Biochemical Simulator with the Next Reaction Method. FPL Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Yamada, Hiroaki Kitano, Hideharu Amano
2007	J	`jnl`	Integration of CellDesigner and SABIO-RK. Silico Biol. Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka, Hiroaki Kitano
2006	B	`conf`	An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems. FPL Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano
2006	Misc	`conf`	CellDesigner: a modeling tool for biochemical networks. WSC Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano, Norihiro Kikuchi
2006	B	`conf`	Performance Evaluation of an Fpga-Based Biochemical Simulator ReCSip. FPL Yasunori Osana, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano
2005	B	`conf`	A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA. FPL Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano
2005	A	`conf`	An FPGA-Based, Multi-model Simulation Method for Biochemical Systems. IPDPS Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Yuichiro Shibata, Hiroaki Kitano, Akira Funahashi, Noriko Hiroi, Hideharu Amano
2005	B	`conf`	Efficient Scheduling of Rate Law Functions for ODE-Based Multimodel Biochemical Simulation on an FPGA. FPL Naoki Iwanaga, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, Kiyoshi Oguri
2005	—	`conf`	The Design of Scalable Stochastic Biochemical Simulator on FPGA. FPT Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano
2002	—	`conf`	Routing Algorithms Based on 2D Turn Model for Irregular Networks. ISPAN Akiya Jouraku, Michihiro Koibuchi, Hideharu Amano, Akira Funahashi
2001	B	`conf`	L-Turn Routing: An Adaptive Routing in Irregular Networks. ICPP Michihiro Koibuchi, Akira Funahashi, Akiya Jouraku, Hideharu Amano
2001	—	`conf`	MMLRU Selection Function: An Output Selection Function on Adaptive Routing. PDCS Michihiro Koibuchi, Akiya Jouraku, Akira Funahashi, Hideharu Amano
2001	J	`jnl`	Recursive Diagonal Torus: An Interconnection Network for Massively Parallel Computers. IEEE Trans. Parallel Distributed Syst. Yulu Yang, Akira Funahashi, Akiya Jouraku, Hiroaki Nishi, Hideharu Amano, Toshinori Sueyoshi
2001	Misc	`conf`	The impact of output selection function on adaptive routing. CATA Akira Funahashi, Michihiro Koibuchi, Akiya Jouraku, Hideharu Amano
1999	—	`conf`	A Torus Assignment for an Interconnection Network Recursive Diagonal Torus. ISPAN Qin Fan, Yulu Yang, Akira Funahashi, Hideharu Amano
1997	—	`conf`	Adaptive Routing on the Recursive Diagonal Torus. ISHPC Akira Funahashi, Toshihiro Hanawa, Hideharu Amano, Tomohiro Kudoh