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Volumn 40, Issue 3, 2007, Pages 203-220

Applying hybrid reasoning to mine for associative features in biological data

Author keywords

Causal link; Deterministic machine learning; Phylogenetic profile analysis; Plausible reasoning; Protein secondary structure prediction

Indexed keywords

CORRELATION METHODS; DATA MINING; LEARNING SYSTEMS; LOGIC PROGRAMMING; MEDICAL COMPUTING; PROTEINS;

EID: 34248193809     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2006.07.002     Document Type: Article
Times cited : (11)

References (49)
  • 1
    • 2942734273 scopus 로고
    • On axiomatization of many-valued logics associated with formalization of plausible reasoning
    • Anshakov O.M., Finn V.K., and Skvortsov D.P. On axiomatization of many-valued logics associated with formalization of plausible reasoning. Studia Logica 42 4 (1989) 423-447
    • (1989) Studia Logica , vol.42 , Issue.4 , pp. 423-447
    • Anshakov, O.M.1    Finn, V.K.2    Skvortsov, D.P.3
  • 4
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequences
    • Dubchak I., Muchnik I., Holbrook S.R., and Kim S.-H. Prediction of protein folding class using global description of amino acid sequences. Proc Natl Acad Sci USA 92 (1995) 8700-8704
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.-H.4
  • 5
    • 34248231553 scopus 로고    scopus 로고
    • Finn VK. On the synthesis of cognitive procedures and the problem of induction. NTI Series 2, 1999;No. 1-2: p. 8-45.
  • 6
    • 34248225163 scopus 로고    scopus 로고
    • Furukawa K. From deduction to induction: logical perspective. In: Apt KR, Marek VW, Truszczynski M, Warren DS, editors. The logic programming paradigm. Springer: Berlin, Germany, Cambridge, MA, USA 1998.
  • 7
    • 0032574809 scopus 로고    scopus 로고
    • Predicting amino acid sequences of the antibody human VH chains from its first several residues
    • Galitsky B.A., Gelfand I.M., and Kister A.E. Predicting amino acid sequences of the antibody human VH chains from its first several residues. Proc Natl Acad Sci USA 95 (1998) 5193-5198
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 5193-5198
    • Galitsky, B.A.1    Gelfand, I.M.2    Kister, A.E.3
  • 8
    • 0032752718 scopus 로고    scopus 로고
    • Class-defining characteristics in the mouse heavy chains of variable domains
    • Galitsky B.A., Gelfand I.M., and Kister A.E. Class-defining characteristics in the mouse heavy chains of variable domains. Protein Eng 12 (1999) 919-925
    • (1999) Protein Eng , vol.12 , pp. 919-925
    • Galitsky, B.A.1    Gelfand, I.M.2    Kister, A.E.3
  • 9
    • 84898188855 scopus 로고    scopus 로고
    • Galitsky BA. Bioinformatics data management and data mining. In: Rivero LC, Doorn JH, Ferraggine VE, editors. Encyclopedia of database technologies and applications. Hershey, PA, USA: Idea Group Reference; 2005.
  • 10
    • 1842682603 scopus 로고    scopus 로고
    • Applying inductive logic programming to predicting gene function
    • King R.D. Applying inductive logic programming to predicting gene function. AI Mag 25 1 (2004) 57-68
    • (2004) AI Mag , vol.25 , Issue.1 , pp. 57-68
    • King, R.D.1
  • 12
    • 0034269305 scopus 로고    scopus 로고
    • The computational support of scientific discovery
    • Langley P. The computational support of scientific discovery. Int J Hum-Comput Stud 53 (2000) 393-410
    • (2000) Int J Hum-Comput Stud , vol.53 , pp. 393-410
    • Langley, P.1
  • 13
    • 0742287001 scopus 로고    scopus 로고
    • Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships
    • Liao L., and Noble W.S. Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships. J Comput Biol 10 (2003) 857-868
    • (2003) J Comput Biol , vol.10 , pp. 857-868
    • Liao, L.1    Noble, W.S.2
  • 14
    • 0034710981 scopus 로고    scopus 로고
    • Marcotte EM, Xenarios I, van der Bliek AM, Eisenberg D. Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci USA V97 2000 vol. 22. p. 12115-20.
  • 15
    • 0037661371 scopus 로고    scopus 로고
    • Benchmarking protein secondary structure prediction for protein fold recognition
    • McGuffin L.J., and Jones T.D. Benchmarking protein secondary structure prediction for protein fold recognition. Proteins 52 (2003) 166-175
    • (2003) Proteins , vol.52 , pp. 166-175
    • McGuffin, L.J.1    Jones, T.D.2
  • 16
    • 34248208902 scopus 로고    scopus 로고
    • Mill JS. A system of logic, racionative and inductive. London: Longmans, Green & Reader 1843.
  • 17
    • 2942622384 scopus 로고    scopus 로고
    • Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
    • Mirkin B., Fenner T., Galperin M., and Koonin E. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 3 (2003) 2
    • (2003) BMC Evol Biol , vol.3 , pp. 2
    • Mirkin, B.1    Fenner, T.2    Galperin, M.3    Koonin, E.4
  • 19
    • 4744344960 scopus 로고    scopus 로고
    • Research on machine learning issues in biomedical informatics modeling
    • (Editorial)
    • Ohno-Machado L. Research on machine learning issues in biomedical informatics modeling. J Biomed Inform 37 4 (2004) 221-303 (Editorial)
    • (2004) J Biomed Inform , vol.37 , Issue.4 , pp. 221-303
    • Ohno-Machado, L.1
  • 20
    • 34248230487 scopus 로고    scopus 로고
    • Muggleton S, Firth J. CProgol4.4: theory and use. In: Dzeroski S, Lavrac N., editors. Inductive logic programming and knowledge discovery in databases; 1999.
  • 21
    • 0001602577 scopus 로고
    • Edinburgh University Press
    • Plotkin G.D. A note on inductive generalization. Machine Intelligence vol. 5 (1970), Edinburgh University Press 153-163
    • (1970) Machine Intelligence , vol.5 , pp. 153-163
    • Plotkin, G.D.1
  • 23
    • 0032534020 scopus 로고    scopus 로고
    • Populations of hydrophobic amino acids within protein globular domains: identification of conserved "topohydrophobic" positions
    • Poupon A., and Mornon J.-P. Populations of hydrophobic amino acids within protein globular domains: identification of conserved "topohydrophobic" positions. Proteins 33 (1998) 329-342
    • (1998) Proteins , vol.33 , pp. 329-342
    • Poupon, A.1    Mornon, J.-P.2
  • 24
    • 34248208404 scopus 로고    scopus 로고
    • Scott C, Nowak R. Dyadic classification trees via structural risk minimization, Neural Information Processing Systems 2002.
  • 26
    • 34248192088 scopus 로고    scopus 로고
    • Vinogradov DV. Logic programs for quasi-axiomatic theories. NTI series vol. 2. N1-2 1999. p. 61-4.
  • 27
    • 14044266917 scopus 로고    scopus 로고
    • Ward JJ, Sodhi JS, Buxton BF, Jones DT. Predicting gene ontology annotations from sequence data using Kernel-based Machine Learning Algorithms. In: Proceedings of the 2004 IEEE computational systems bioinformatics conference (CSB 2004); 2004.
  • 28
    • 0345871261 scopus 로고    scopus 로고
    • Exploiting evolutionary relationships for predicting protein structures
    • Tramontano A., and Morea V. Exploiting evolutionary relationships for predicting protein structures. Biotechnology and Bioengineering 84 7 (2003) 756-762
    • (2003) Biotechnology and Bioengineering , vol.84 , Issue.7 , pp. 756-762
    • Tramontano, A.1    Morea, V.2
  • 29
    • 7044274801 scopus 로고    scopus 로고
    • Ganter B, Kuznetsov SO. Hypotheses and version spaces. In: de Moor A, Lex W, Ganter B, editors. Proceedings 10th international conference on conceptual structures ICCS'03. Lecture notes in artificial intelligence, vol. 2746; 2003. p. 83-95.
  • 32
    • 0036555973 scopus 로고    scopus 로고
    • Comparing performance of algorithms for generating concept lattices
    • Kuznetsov S.O., and Obiedkov S.A. Comparing performance of algorithms for generating concept lattices. J Exp Theor Artif Intell 14 2-3 (2002) 189-216
    • (2002) J Exp Theor Artif Intell , vol.14 , Issue.2-3 , pp. 189-216
    • Kuznetsov, S.O.1    Obiedkov, S.A.2
  • 33
    • 0022045348 scopus 로고
    • Horn clause queries and generalizations
    • Chandra A., and Harel D. Horn clause queries and generalizations. J Logic Programming 2 1 (1985) 1-15
    • (1985) J Logic Programming , vol.2 , Issue.1 , pp. 1-15
    • Chandra, A.1    Harel, D.2
  • 34
    • 0031565975 scopus 로고    scopus 로고
    • Sequence profiles of immunoglobulin and immunoglobulin-like domains
    • Smith D.K., and Xue H. Sequence profiles of immunoglobulin and immunoglobulin-like domains. J Mol Biol 274 (1997) 530-545
    • (1997) J Mol Biol , vol.274 , pp. 530-545
    • Smith, D.K.1    Xue, H.2
  • 36
    • 15944400052 scopus 로고    scopus 로고
    • Identifying reasoning strategies in medical decision making: A methodological guide
    • Arocha J.F., Wang D., and Patel V.L. Identifying reasoning strategies in medical decision making: A methodological guide. J Biomed Inform 38 2 (2005) 154-171
    • (2005) J Biomed Inform , vol.38 , Issue.2 , pp. 154-171
    • Arocha, J.F.1    Wang, D.2    Patel, V.L.3
  • 37
    • 34248163745 scopus 로고    scopus 로고
    • Mitchell TM. The need for biases in learning generalizations. Tech. Rep CBM-TR-117. New Brunswick, NJ: Dept of Computer Science, Rutgers Univ; 1980.
  • 38
    • 34248172721 scopus 로고
    • Classifying for Prediction: A Multistrategy Approach to Predicting Protein Structure
    • Michalski R.S., and Tecuci G. (Eds), Morgan Kaufman Publishers, San Mateo, CA
    • Hunter L. Classifying for Prediction: A Multistrategy Approach to Predicting Protein Structure. In: Michalski R.S., and Tecuci G. (Eds). Machine learning: a multi-strategy approach Vol. 4 (1993), Morgan Kaufman Publishers, San Mateo, CA
    • (1993) Machine learning: a multi-strategy approach , vol.4
    • Hunter, L.1
  • 39
    • 34248222947 scopus 로고    scopus 로고
    • Russell SJ. Preliminary steps toward the automation of induction. In: Proceedings of the 5th national conference on artificial intelligence. Los Altos, CA: Morgan Kaufmann; 1986. p. 477-84.
  • 41
    • 34248215973 scopus 로고    scopus 로고
    • Tan AC, Gilbert D. Machine learning and its application to bioinformatics: an overview. . Last accessed Sept 17, 2005.
  • 42
    • 2142657347 scopus 로고    scopus 로고
    • Defeasible logic programming: an argumentative approach
    • García A., and Simari G. Defeasible logic programming: an argumentative approach. Theory and Practice of Logic Programming 4 1 (2004) 95-138
    • (2004) Theory and Practice of Logic Programming , vol.4 , Issue.1 , pp. 95-138
    • García, A.1    Simari, G.2
  • 43
    • 34248140975 scopus 로고    scopus 로고
    • Smith RG, Winston HA, Mitchell TM, Buchanan BG. Representation and use of explicit justification for knowledge base refinement. In: Proceedings of the ninth IJCAI. Los Altos: Morgan Kaufmann; 1985. p. 673-80.
  • 44
    • 34248202896 scopus 로고    scopus 로고
    • [ref de;eted] Kedar-Cabelli ST. Formulating concepts according to purpose. In: sixth AAAI-87, Morgan Kaufmann, Los Altos; 1987. p. 182-6.
  • 45
    • 0020894549 scopus 로고    scopus 로고
    • Winston PH, Binford TO, Katz B, Lowry M. Learning physical descriptions from functional definitions, examples and precedents. In: second AAAI-83, Morgan Kaufmann, Los Altos; 1983. p. 433-9.
  • 46
    • 0036408311 scopus 로고    scopus 로고
    • Sequence variations within protein families are linearly related to structural variations
    • Koehl P., and Levitt M. Sequence variations within protein families are linearly related to structural variations. J Mol Biol 323 (2002) 551-562
    • (2002) J Mol Biol , vol.323 , pp. 551-562
    • Koehl, P.1    Levitt, M.2
  • 47
    • 0034963043 scopus 로고    scopus 로고
    • Anapproach to improving multiple alignments of protein sequences using predicted secondary structure
    • Jennings A.J., Edge C.M., and Sternberg M.J. Anapproach to improving multiple alignments of protein sequences using predicted secondary structure. Protein Eng 14 4 (2001) 227-231
    • (2001) Protein Eng , vol.14 , Issue.4 , pp. 227-231
    • Jennings, A.J.1    Edge, C.M.2    Sternberg, M.J.3
  • 48
    • 34248204907 scopus 로고    scopus 로고
    • Galitsky B. Biological Applications of Jasmine http://www.dcs.bbk.ac.uk/~galitsky/Jasmine/bio.html (Last downloaded March 2006).
  • 49
    • 0032946571 scopus 로고    scopus 로고
    • Gregory TR, Hebert PDN. The Modulation of DNA content: proximate causes and ultimate consequences genome research 1999;9(4):317-24.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.