Abstract
This paper addresses the issue of analogical inference, and its potential role as the mediator of new therapeutic discoveries, by using disjunction operators based on quantum connectives to combine many potential reasoning pathways into a single search expression. In it, we extend our previous work in which we developed an approach to analogical retrieval using the Predication-based Semantic Indexing (PSI) model, which encodes both concepts and the relationships between them in high-dimensional vector space. As in our previous work, we leverage the ability of PSI to infer predicate pathways connecting two example concepts, in this case comprising of known therapeutic relationships. For example, given that drug x TREATS disease z, we might infer the predicate pathway drug x INTERACTS_WITH gene y ASSOCIATED_WITH disease z, and use this pathway to search for drugs related to another disease in similar ways. As biological systems tend to be characterized by networks of relationships, we evaluate the ability of quantum-inspired operators to mediate inference and retrieval across multiple relations, by testing the ability of different approaches to recover known therapeutic relationships. In addition, we introduce a novel complex vector based implementation of PSI, based on Plate’s Circular Holographic Reduced Representations, which we utilize for all experiments in addition to the binary vector based approach we have applied in our previous research.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bruza, P.: Semantic space: Bridging the divide between cognitive science, information processing technology and quantum mechanics. In: Proc. Inform. Symp. on Inform. Tech. (ITsim 2008), pp. 1–9 (2008)
Cohen, T., Widdows, D., Schvaneveldt, R., Rindflesch, T.C.: Finding Schizophrenia’s Prozac Emergent Relational Similarity in Predication Space. In: Song, D., Melucci, M., Frommholz, I., Zhang, P., Wang, L., Arafat, S. (eds.) QI 2011. LNCS, vol. 7052, pp. 48–59. Springer, Heidelberg (2011)
Dudley, J., Schadt, E., et al.: Drug discovery in a multidimensional world: systems, patterns, and networks. J. Cardiovasc Transl. Res. 3(5), 438–447 (2010)
Widdows, D., Cohen, T., De Vine, L.: Real, complex, and binary semantic vectors. In: Proc. Sixth Intl. Symp. on Quantum Interactions, Paris, France (2012)
Landauer, T., Dumais, S.: A solution to plato’s problem: The latent semantic analysis theory of acquisition, induction, and representation of knowledge. Psych. Review 104, 211–240 (1997)
Swanson, D.R.: Fish oil, raynaud’s syndrome, and undiscovered public knowledge. Perspect Biol. Med. 30(1), 7–18 (1986)
Gordon, M.D., Dumais, S.: Using latent semantic indexing for literature based discovery. Journal of the American Society for Information Science 49, 674–685 (1998)
Cole, R.J., Bruza, P.D.: A Bare Bones Approach to Literature-Based Discovery: An Analysis of the Raynaud’s/Fish-Oil and Migraine-Magnesium Discoveries in Semantic Space. In: Hoffmann, A., Motoda, H., Scheffer, T. (eds.) DS 2005. LNCS (LNAI), vol. 3735, pp. 84–98. Springer, Heidelberg (2005)
Cohen, T., Schvaneveldt, R., Widdows, D.: Reflective random indexing and indirect inference: A scalable method for discovery of implicit connections. Journal of Biomedical Informatics 43, 240–256 (2010)
Hristovski, D., Friedman, C., Rindflesch, T., Peterlin, B.: Literature-based knowledge discovery using natural language processing. In: Bruza, P., Weeber, M. (eds.) Literature Based Discovery, pp. 133–152. Springer, Heidelberg (2008)
Ahlers, C., Hristovski, D., Kilicoglu, H., Rindflesch, T.: Using the Literature-Based discovery paradigm to investigate drug mechanisms. In: AMIA Annu. Symp. Proc., pp. 6–10 (2007)
Wren, J.: The ‘open discovery’challenge. In: Literature-Based Discovery, pp. 39–55 (2008)
Swanson, D.R.: Medical literature as a potential source of new knowledge. Bulletin of the Medical Library Association 78 (1990)
Cohen, T., Schvaneveldt, R., Rindflesch, T.: Predication-based semantic indexing: Permutations as a means to encode predications in semantic space. In: AMIA Annu. Symp. Proc., pp. 114–118 (2009)
Cohen, T., Widdows, D., Schvaneveldt, R.W., Rindflesch, T.C.: Logical leaps and quantum connectives: Forging paths through predication space. In: Proc. AAAI Fall Symp. on Quantum Informatics for Cognitive, Social, and Semantic Processes, pp. 11–13 (2010)
Widdows, D., Peters, S.: Word vectors and quantum logic experiments with negation and disjunction. In: Proc. 8th Math. of Language Conference, Bloomington, Indiana (2003)
Gayler, R.W.: Vector symbolic architectures answer jackendoff’s challenges for cognitive neuroscience. In: Slezak, P. (ed.) ICCS/ASCS International Conference on Cognitive Science, pp. 133–138. University of New South Wales, Sydney (2004)
Smolensky, P.: Tensor product variable binding and the representation of symbolic structures in connectionist systems. Artificial Intelligence 46(1-2), 159–216 (1990)
Kanerva, P.: Binary Spatter-Coding of Ordered k-tuples. In: Vorbrüggen, J.C., von Seelen, W., Sendhoff, B. (eds.) ICANN 1996. LNCS, vol. 1112, Springer, Heidelberg (1996)
Plate, T.A.: Holographic Reduced Representation: Distributed Representation for Cognitive Structures. CSLI Publications, Stanfpord (2003)
De Vine, L., Bruza, P.: Semantic oscillations: Encoding context and structure in complex valued holographic vectors. In: Proc. AAAI Fall Symp. on Quantum Informatics for Cognitive, Social, and Semantic Processes (2010)
Rindflesch, T.C., Fiszman, M.: The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. Journal of Biomedical Informatics 36, 462–477 (2003)
Bodenreider, O.: The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Research 32, D267 (2004) (database Issue)
Kilicoglu, H., Fiszman, M., Rosemblat, G., Marimpietri, S., Rindflesch, T.C.: Arguments of nominals in semantic interpretation of biomedical text. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp. 46–54 (2010)
Eliasmith, C., Thagard, P.: Integrating structure and meaning: A distributed model of analogical mapping. Cognitive Science 25(2), 245–286 (2001)
Kanerva, P.: What we mean when we say “What’s the dollar of mexico?”: Prototypes and mapping in concept space. In: Proc. AAAI Fall Symp. on Quantum Informatics for Cognitive, Social, and Semantic Processes (2010)
Holyoak, K.J., Thagard, P.: Mental Leaps: Analogy in Creative Thought. MIT Press (1995)
Birkhoff, G., Neumann, J.V.: The logic of quantum mechanics. The Annals of Mathematics 37(4), 823–843 (1936)
Cohen, T., Widdows, D., Schvaneveldt, R., Davies, P., Rindflesch, T.: Discovering discovery patterns with predication-based semantic indexing. Journal of Biomedical Informatics (July 2012) [epub ahead of print]
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Cohen, T., Widdows, D., De Vine, L., Schvaneveldt, R., Rindflesch, T.C. (2012). Many Paths Lead to Discovery: Analogical Retrieval of Cancer Therapies. In: Busemeyer, J.R., Dubois, F., Lambert-Mogiliansky, A., Melucci, M. (eds) Quantum Interaction. QI 2012. Lecture Notes in Computer Science, vol 7620. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-35659-9_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-35659-9_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-35658-2
Online ISBN: 978-3-642-35659-9
eBook Packages: Computer ScienceComputer Science (R0)