Selected Books, Book Chapters
[RT16] Sohel Rahman, Etsuji Tomita (Eds.), "Special issue on WALCOM 2015," Journal of Discrete Algorithms, Elsevier (2016) [RT16] Sohel Rahman, Etsuji Tomita (Eds.), "Special issue on WALCOM 2015," Journal of Graph Algorithms and Applications (2016) [RT15] Sohel Rahman, Etsuji Tomita (Eds.), "WALCOM: Algorithms and Computation," The 9th International Workshop, WALCOM 2015, Lecture Notes in Computer Science, 8973, Springer (2015) [TY13a] Etsuji Tomita, Takashi Yokomori, " Automata and Formal Languages (2nd Edition)," Morikita Publishing Co. Ltd. (In Japanese) (2013) [TY13b] Etsuji Tomita, Takashi Yokomori, "Automata and Formal Languages," Morikita Publishing Co. Ltd. (In Japanese, The 24th printing) (2013) [TAM11] Etsuji Tomita, Tatsuya Akutsu, Tsutomu Matsunaga,"Efficient algorithms for finding maximum and maximal cliques: Effective tools for bioinformatics" in "Biomedical Engineering, Trends in Electronics, Communications and Software," A. N. Laskovski (Ed.), ISBN: 978-953-307-475-7, InTech, pp.625-640 (2011). (Comparison of the running time of MCQ, MCR, MCS algorithms, and Correction in [TSHW10] is shown at page 631.) [PDF] intechopen.com [ST07] Hans U. Simon, Etsuji Tomita (Eds.), "Algorithmic Learning Theory," Theoretical Computer Science, Vol.387, Elsevier (2007) [SKSNT06] Yasubumi Sakakibara, Satoshi Kobayashi, Kengo Sato, Tetsuro Nishino, Etsuji Tomita (Eds.), " Grammaical Inference: Algorithms and Applications," The 8th International Colloquium on Grammatical Inference, ICGI 2006, Lecture Notes in Artificial Intelligence, 4201,Springer (2006) [PDF] tiera.ru [JST05] Sanjay Jain, Hans. U. Simon, Etsuji Tomita (Eds.), "Algorithmic Learning Theory," The 16th International Conference on Algorithmic Learning Theory, ALT 2005, Lecture Notes in Artificial Intelligence, 3734, Springer (2005) [PDF] tiera.ru [JKTY93] Klaus P. Jantke, Shigenobu Kobayashi, Etsuji Tomita, Takashi Yokomori (Eds.), "Algorithmic Learning Theory," The 4th International Workshop, ALT '93, Lecture Notes in Computer Science, 744, Springer (1993) Recent Publications and Others
[KKFT20] Kazuho Kanahara, Kengo Katayama, Nobuo Funabiki, Etsuji Tomita, " The Performance of a metaheuristic algorithm for finding a maximal weight clique in the fill-in-blank problem, " Proc. ICIET 2020, pp.257-261 (2020) [To19] Etsuji Tomita, " Enumeration of maximum cliques and its application to coding theory, " Dagstuhl Seminar on Enumeration in Data Management, Dagstuhl, Germany (2019) (joint work with Akira Mitsutake and Takayuki Nozaki) [To17] Etsuji Tomita, " Efficient algorithms for finding maximum and maximal cliques and their applications - Keynote - , "  WALCOM 2017, Hsinchu, Taiwan, Lecture Notes in Computer Science, 10167, pp.3-15 (2017) [PDF] nii.ac.jp [TYHNIW16] Etsuji Tomita, Kohei Yoshida, Takuro Hatta, Atsuki Nagao, Hiro Ito, Mitsuo Wakatsuki " A much faster branch-and-bound algorithm for finding a maximum clique, "  FAW 2016, Qingdao, China, Lecture Notes in Computer Science, 9711, pp.215-226 (2016) [ZHOT16a] Hongjie Zhai, Makoto Haraguchi, Yoshiaki Okubo, Etsuji Tomita, " A fast and complete algorithm for enumerating pseudo-cliques in large graphs, "  International Journal of Data Science and Analytics, Springer, pp.145-158 (2016) [OHT16] Yoshiaki Okubo, Makoto Haraguchi, Etsuji Tomita, " Enumerating maximal isolated cliques based on vertex-dependent connection lower bound, "  MLDM 2016, New York, USA, Lecture Notes in Artificial Intelligence, 9727, pp.569-583 (2016) [ZHOT16b] Hongjie Zhai, Makoto Haraguchi, Yoshiaki Okubo, Etsuji Tomita, " A fast and complete enumeration of pseudo-cliques for large graphs , " PAKDD 2016, Auckland, New Zealand, Lecture Notes in Artificial Intelligence, 9651, pp.423-435 (2016) [ZHOT15] Hongjie Zhai, Makoto Haraguchi, Yoshiaki Okubo, Etsuji Tomita, " Enumerating maximal clique sets with pseudo-clique constraint, " DS 2015, Banff, Canada, Lecture Notes in Artificial Intelligence, 9356, pp.324-339 (2015) [WTN15a] Mitsuo Wakatsuki, Etsuji Tomita, Tetsuro Nishino, "A polynomial-time algorithm for checking the inclusion of deterministic restricted one-counter transducers which accept by final state," CATA 2015, Honolulu, USA, Proc. 30th International Conference on Computers and Their Applications, pp.11-17 (2015) [WTN15b] Mitsuo Wakatsuki, Etsuji Tomita, Tetsuro Nishino, "A polynomial-time algorithm for checking the equivalence for deterministic restricted one-counter transducers which accept by final state," Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing Studies in Computational Intelligence, vol. 569, pp 131-144, Springer (2015) [OHT13] Yoshiaki Okubo, Makoto Haraguchi, Etsuji Tomita, "Relational change pattern mining based on modularity difference," MIWAI 2013, Krabi, Thailand, Lecture Notes in Artificial Intelligence, 8271, pp.187-198 (2013) ( The Second Best Paper in MIWAI 2013) [TSHW13] Etsuji Tomita, Yoichi Sutani, Takanori Higashi, Mitsuo Wakatsuki, " A simple and faster branch-and-bound algorithm for finding a maximum clique with computational experiments," IEICE Trans. on Information and Systems, Volume E96-D, pp.1286-1298 (2013) (Contains Correction in [TSHW10] (at page 1297), and Comparison of individual contributions in part of MCS algorithm [TSHW10] (at pages1291-11293.) [WTN13] Mitsuo Wakatsuki, Etsuji Tomita, Tetsuro Nishino, "A polynomial-time algorithm for checking the equivalence for real-time deterministic restricted one-counter transducers which accept by final state," International Journal of Computer and Information Sciences, vol. 14, pp. 45-53 (2013) [PDF] lsfk.org [OHT12] Yoshiaki Okubo, Makoto Haraguchi, Etsuji Tomita, "Structural change pattern mining based on constrained maximal k-plex search," Discovery Science 2012, Lyon, France, Lecture Notes in Artificial Intelligence, 7569, pp.284-298 (2012) [LHOT12] Aixiang Li, Makoto Haraguchi, Yoshiaki Okubo, Etsuji Tomita, "Finding what changes for two graphs constructed from different time intervals," Proc. 2012 IIAI International Conference on Advanced Applied Informatics, pp.48-53, Fukuoka, Japan (2012) [MTFTTA12] Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu, " A clique-based method using dynamic programming for computing edit distance between unordered trees," Journal of Computational Biology, 19, pp.1089-1104 (2012) [PDF] nih.gov [MTT11] Akinobu Miyata, Jun Tarui, Etsuji Tomita, "Learning Boolean functions in AC0 on attribute and classification noise - Estimating an upper bound on attribute and classification noise," Theoretical Computer Science, Volume 412, pp.4650-4660 (2011) [AMFTTT11] Tatsuya Akutsu, Tomoya Mori, Daiji Fukagawa, Atsuhiro Takasu, Takeyuki Tamura, Etsuji Tomita, " An improved clique-based method for the edit distance between unordered trees with application to similar glycan structures," The 4th International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2011), A Part of Proc. the 5th International Conference on Complex, Intelligent and Software Intensive Systems, pp.536-540, Seoul, Korea (2011) [FTTTA11] Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu, "A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures," BMC Boinformatics 2011, 12 (Suppl. 1):S13 (2011) [PDF] biomedcentral.com [WT10] Mitsuo Wakatsuki, Etsuji Tomita, "Polynomial time identification of strict prefix deterministic finite state transducers," International Colloquium on Grammatical Inference (ICGI 2010), Valencia, Spain, Lecture Notes in Artificial Intelligence, 6339, pp.313-316 (2010) [To10] Etsuji Tomita, "Plenary Lecture: The Maximum Clique Problem, " Proc. 14th WSEAS International Conference on Computers (Vol. I), p.19, Corfu, Greece (2010) [TSHW10] Etsuji Tomita, Yoichi Sutani, Takanori Higashi, Shinya Takahashi, Mitsuo Wakatsuki, "A simple and faster branch-and-bound algorithm for finding a maximum clique," International Workshop on Algorithms and Computation (WALCOM 2010), Dhaka, Bangladesh, Lecture Notes in Computer Science, 5942, pp.191-203 (2010) [PDF] googlecode.com (Proposes MCS algorithm. For Corrections and further details, see page 631 of [TAM11] (Book Chapter), [TSHW13] .) [MYTM09] Tsutomu Matsunaga, Chikara Yonemori, Etsuji Tomita, Masaaki Matsumura, " Clique-based data mining for related genes in a biomedical database," BMC Bioinformatics 10 (2009) (3rd of Most viewed articles in past 30 days: BMC Bioinformatics in July 2009). [PDF] biomedcentral.com [YMST09] Chikara Yonemori, Tsutomu Matsunaga, Jun Sekine, Etsuji Tomita, " A structural analysis of enterprise relationship using cliques," DBSJ Journal, Vol.7, pp.55-60 (2009) [WT08] Mitsuo Wakatsuki, Etsuji Tomita, " Polynomial time identification of strict deterministic restricted one-counter automata in some class from positive data," IEICE Trans. on Information and Systems, E91-D, pp.1704-1718 (2008) [To07a] Etsuji Tomita, "The Maximum Clique Problem and Its Applications - Invited Lecture - ," IPSJ SIG Technical Report, 2007-MPS-67/2007-BIO-11, pp.21-24 (2007) [To07b] Etsuji Tomita, "Advanced algorithms and their applications," Proc. Advanced ICT (AICT 2007), Beijing, China, pp.1-6 (2007) [WT07] Mitsuo Wakatsuki, Etsuji Tomita, " Polynomial time identification of finite state transducers in some class," Proc. Advanced ICT (AICT 2007), Beijing, China, pp.7-12 (2007) [TK07] Etsuji Tomita, Toshikatsu Kameda, "An efficient branch-and-bound algorithm for finding a maximum clique with computational experiments, " Journal of Global Optimization, Vol. 37, pp.95-111 (2007), Vol.44, p.311 (2009) (Proposes MCR algorithm. Example run can be seen at pages 628-630 of [TAM11]. ) [PDF] gla.ac.uk [KTW07] Kazushi Seino, Etsuji Tomita, Mitsuo Wakatsuki, " A direct branching algorithm for checking the equivalence of a pair of non-real-time deterministic pushdown transducers," IEICE Trans. D, Vol.J90-D, pp.2675-2690 (2007) [TTT06] Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi, "The worst-case time complexity for generating all maximal cliques and computational experiments," Theoretical Computer Science, Vol. 363 (Special Issue on COCOON 2004), pp.28-42 (2006) (Computational experiments are added to [TTT04]. Theoretical Computer Science Top Cited Article 2005-2010, 16th of TOP25 Hottest Articles within the journal: Theoretical Computer Science in Oct. 2009 - Sept. 2010). [PDF] sciencedirect.com [WTY06] Mitsuo Wakatsuki, Etsuji Tomita, Go Yamada: "A unified algorithm for extending classes of languages identifiable in the limit from positive data," International Colloquium on Grammatical Inference (ICGI 2006), Tokyo, Japan, Lecture Notes in Artificial Intelligence, 4201, pp.161-174 (2006). [PDF] tiera.ru [BBTA06] J.B. Brown, Dukka Bahadur K. C, Etsuji Tomita, Tatsuya Akutsu, " Multiple methods for protein side chain packing using maximum weight cliques ," Genome Informatics, Vol.17, pp.3-12 (2006) [PDF] jsbi.org [BTSHA06] Dukka Bahadur K. C, Etsuji Tomita, Jun'ichi Suzuki, Katsushi Horimoto, Tatsuya Akutsu, "Protein threading with profiles and distance constraints using clique based algorithms , " Journal of Bioinformatics and Computational Biology, Vol.4, pp.19-42 (2006). The preliminary version was presented in: Dukka Bahadur K. C, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu, "Clique based algorithms for protein threading with profiles and constraints," Proc. Asia-Pacific Bioinformatics Conference (APBC 2005), pp.51-64 (2005) [PDF] nus.edu.sg [AHBTS06] Tatsuya Akutsu, Morihiro Hayashida, Dukka Bahadur K. C, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, "Dynamic programming and clique based approaches for protein threading with profiles and constraints", IEICE Trans. on Fundamentals of Electronics, Communications and Computer Sciences, E89-A, pp.1215-1222 (2006). The preliminary version was presented in: Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, "Protein threading with profiles and constraints", Proc. IEEE Symp. on Bioinformatics and Bioengineering (BIBE 2004), pp.537-544 (2004) [PDF] psu.edu [BTSA05] Dukka Bahadur K. C, Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu, "Protein side-chain packing problem: A maximum edge-weight clique algorithmic approach," Journal of Bioinformatics and Computational Biology, Vol.3, pp. 103-126 (2005) The preliminary version was presented in: Dukka Bahadur K.C., Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki, "Protein side-chain packing: A maximum edge weight clique algorithmic approach, "Proc. Asia-Pacific Bioinformatics Conference (APBC 2004), pp.191-200 (2004) [PDF] crpit.com [BBTSA05] Dukka Bahadur K. C, J. B. Brown, Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu, "Large scale protein side-chain packing based on maximum edge-weight clique finding algorithm," Proc. 2005 International Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005), pp.228-233 (2005) [PDF] evansville.edu [TTT04] " Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi, "The worst-case time complexity for generating all maximal cliques," International Computing and Combinatorics Conference (COCOON 2004), Jeju, Korea, Lecture Notes in Computer Science, 3106, pp.161- 170 (2004) (Invited to [TTT06]) [TTWT04] Yasuhiro Tajima, Etsuji Tomita, Mitsuo Wakatsuki, Matsuaki Terada, "Polynomial time learning of simple deterministic languages via queries and a representative sample," Theoretical Computer Science, Vol.329, pp.203-221(2004). (4th of TOP25 Hottest Articles within the journal: Theoretical Computer Science in Oct.-Dec., 2004, and 14th in Apr.-June, 2005). The preliminary version was presented in: Yasuhoro Tajima, Etsuji Tomita, "A polynomial time learning algorithm via membership queries and a representative sample," International Colloquium on Grammatical Inference, Lisbon, Portugal (ICGI 2000), Lecture Notes in Artificial Intelligence, 1891, pp.284-297 (2000) [MTT04] Akinobu Miyata, Jun Tarui, Etsuji Tomita, "Learning Boolean functions in AC0 on attribute and classification noise," International Conference on Algorithmic Learning Theory (ALT 2004), Padova, Italy, Lecture Notes in Artificial Intelligence, 3244, pp.142-155 (2004). [PDF] tiera.ru [WTT04] Mitsuo Wakatsuki, Kiyoshi Teraguchi, Etsuji Tomita, "Polynomial time identification of strict deterministic restricted one-counter automata in some class from positive data," International Colloquium on Grammatical Inference (ICGI 2004), Athens, Greece, Lecture Notes in Artificial Intelligence, 3264, pp.260-272 (2004) [AHTS03] Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, " Algorithms for computing an optimal protein threading with profiles and distance restraints," Genome Informatics, 14, pp.480-481 (2003). [PDF] sakura.ne.jp [TS03] Etsuji Tomita, Tomokazu Seki, "An efficient branch-and bound algorithm for finding a maximum clique," Discrete Mathematics and Theoretical Computer Science (DMTCS 2003), Dijon, France, Lecture Notes in Computer Science, 2731, pp.278-289 (2003) (Proposes MCQ algorithm.) [PDF] tiera.ru [KKOT03] Satoshi Kobayashi, Tomohiro Kondo, Kohei Okuda, Etsuji Tomita, " Extracting globally structure free sequences by local structure freeness," Proc. International Meeting on DNA Based Computers 9, p.206 (2003) [HTT03] Kazuhiro Hotta, Etsuji Tomita, Haruhisa Takahashi, " A view-invariant object detection method based on maximum cliques," IPSJ Trans. on Mathematical Modeling and Its Applications, 44, pp.57-70 (2003) [To03] Etsuji Tomita, " IEICE Fellow Memorial Invited Talk: Studies and education on automata, formal languages, learning theory and combinatorial optimization," Technical Report of IEICE, COMP2003-60, pp.45-12 (2003) [BATS02] Dukka Bahadur K. C. , Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki, Asao Fujiyama, " Point matching under non-uniform distortions and protein side chain packing based on an efficient maximum clique algorithm," Genome Informatics, 13, pp.143-152 (2002) [PDF] jsbi.org [TTW00] Yasuhiro Tajima, Etsuji Tomita, Mitsuo Wakatsuki, "Polynomial time learnability of simple deterministic languages from MAT and a representative sample," IEICE Trans. on Information and Systems , E83-D, pp.757-765 (2000) [PDF] psu.edu Other Selected Publications
Basic Technical Reports
[TKT88] Etsuji Tomita, Yasuhiro Kohata, Haruhisa Takahashi, " A simple algorithm for finding a maximum clique," Technical Report of the University of Electro-Communications, UEC-TR-C5(1) (1988) (Earlier version of MCQ [TS03]: Reference [16] in [TS03] ) [PDF] nii.ac.jp [TMT88] Etsuji Tomita, Shinsuke Mitsuma, Haruhisa Takahashi, " Two algorithms for finding a near-maximum clique," Technical Report of the University of Electro-Communications, UEC-TR-C1 (1988) ( Reference [44] in [TSHW13] ) [PDF] nii.ac.jp (The above three Technical Reports were reviewed by the following well-known papers: P.M. Pardalos and J. Xue, "The maximum clique problem," J. Global Optimization, vol.4, pp.301-328 (1994), References 238, 239, 240. [HTML]spriner.com I.M. Bomze, M. Budinich, P.M. Pardalos, and M. Pelillo, "The maximum clique problem." In: D.-Z. Du and P.M. Pardalos (Eds.), Handbook of Combinatorial Optimization, Supplement vol.A, Kluwer Academic Publishers, pp.1-74 (1999), References 308, 309,310. [PDF]psu.edu ) |