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NEMO Publications (Dumped from old portal)

Here we list relevant peer-reviewed publications by NEMO co-Investigators (Dou, Frishkoff, Malony, & Tucker) covering EEG/ERP component analysis and classification methods, head modeling and source localization, and development of ERP and related ontologies.

NEMO Pattern Analysis

  • Dien, J., Frishkoff, G. A., Cerbone, A., & Tucker, D. M. (2003). Parametric analysis of event-related potentials in semantic comprehension: evidence for parallel brain mechanisms.Cognitive Brain Research, 15(2), 137-153.
  • Dien, J. & Frishkoff, G. A. (2005). Principal components analysis of event-related potential datasets. In T. Handy (Ed.), Event-Related Potentials: A Methods Handbook. Cambridge, MA: MIT Press.
  • Frank, R.M & Frishkoff, G.A. (2007). Automated protocol for evaluation of electromagnetic component separation (APECS) : Application of a framework for evaluating statistical methods of blink extraction from multichannel EEG. Clinical Neurophysiology, 118(1), pp. 80-97.
  • Frishkoff, G., Frank, R., Rong, J., Dou, D., Dien, J., & Halderman, L. (2007). A framework to support automated ERP pattern classification and labeling. Computational Intelligence and Neuroscience, vol. 2007, Article ID 14567, 13 pages.
  • Frishkoff, G. A. (2007, under review). Fractionating the N400 Effect: Separation of frontal and posterolateral responses in semantic priming. Clinical Neurophysiology.
  • Glass, K., Frishkoff, G., et al. (2004). A Framework for Evaluating ICA Methods of Artifact Removal from Multichannel EEG. Independent Component Analysis Conference (ICA 2004), Granada, Spain.
  • Junghofer, M., Elbert, T., Tucker, D. M., & Rockstroh, B. (2000). Statistical control of artifacts in dense array EEG/MEG studies. Psychophysiology, 37(4), 523-532.
  • Luu, P., Tucker, D. M., & Makeig, S. (2004). Frontal midline theta and the error-related negativity: neurophysiological mechanisms of action regulation. Clinical Neurophysiology, 115(8), 1821-1835.
  • Makeig, S., Luu, P., Briggman, K., Visser, E., Sejnowski, T. J., & Tucker, D. M. (2008, in preparation). Error-related dynamics in distributed brain networks.
  • Nunez, P. L., Silberstein, R. B., Shi, Z., Carpenter, M. R., Srinivasan, R., Tucker, D. M., et al. (1999). EEG coherency II: experimental comparisons of multiple measures. Clinical Neurophysiology, 110(3), 469-486.
  • Nunez, P. L., Srinivasan, R., Westdorp, A. F., Wijesinghe, R. S., Tucker, D. M., Silberstein, R. B., et al. (1997). EEG coherency. I: Statistics, reference electrode, volume conduction, Laplacians, cortical imaging, and interpretation at multiple scales. Electroencephalography and Clinical Neurophysiology, 103(5), 499-515.
  • Potts, G. F., Dien, J., Hartry-Speiser, A. L., McDougal, L. M., & Tucker, D. M. (1998). Dense sensor array topography of the event-related potential to task-relevant auditory stimuli. Electroencephalography and Clinical Neurophysiology, 106(5), 444-456.
  • Russell, G. S., Jeffrey Eriksen, K., Poolman, P., Luu, P., & Tucker, D. M. (2005). Geodesic photogrammetry for localizing sensor positions in dense-array EEG. Clinical Neurophysiology, 116(5), 1130-1140.
  • Srinivasan, R., Nunez, P. L., Tucker, D. M., Silberstein, R. B., & Cadusch, P. J. (1996). Spatial sampling and filtering of EEG with spline laplacians to estimate cortical potentials. Brain Topography, 8(4), 355-366.
  • Srinivasan, R., & Tucker, D. M. (1995). Joint time frequency analysis of event related EEG perturbations. Paper presented at the Annual Meeting of the American EEG Society, Washigton, D.C.
  • Srinivasan, R., Tucker, D. M., & Murias, M. (1998). Estimating the spatial Nyquist of the human EEG. Behavioral Research Methods, Instruments, & Computers, 30, 8-19.
  • Tucker, D. M., Dawson, S. L., Roth, D. L., & Penland, J. G. (1985). Regional changes in EEG power and coherence during cognition: intensive study of two individuals. Behavioral Neuroscience, 99(3), 564-577.
  • Tucker, D. M., Liotti, M., Potts, G. F., Russell, G. S., & Posner, M. I. (1994). Spatiotemporal analysis of brain electrical fields. Human Brain Mapping, 1, 134-152.
  • Tucker, D. M., & Roth, D. L. (1984). Factoring the coherence matrix: patterning of the frequency-specific covariance in a multichannel EEG. Psychophysiology, 21(2), 228-236.
  • Tucker, D. M., Roth, D. L., & Bair, T. B. (1986). Functional connections among cortical regions: topography of EEG coherence. Electroencephalography and Clinical Neurophysiology, 63(3), 242-250.

NEMO Ontology Development

  • LePendu, P., Dou, D., Howe, D. (2009, to appear). Detecting Inconsistencies in the Gene Ontology using Ontology Databases with Not-gadgets. Proceedings of the International Conference on Ontologies, Databases and Application of SEmantics (ODBASE2009).
  • Frishkoff, G., LePendu, P., Frank, R., Liu, H., & Dou, D. (2009). Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials. Proceedings of the International Conference on Biomedical Ontology (ICBO2009).
  • Dou, D., Frishkoff, G., Rong, J., Frank, R., Malony, A., and Tucker, D. (2007). Development of NeuroElectroMagnetic Ontologies (NEMO): A framework for mining brain wave ontologies, Proceedings of the Thirteenth International Conference on Knowledge Discovery and Data Mining (KDD2007), pp. 270-279, San Jose, CA. (nominated for Best research paper award)
  • LePendu, P., Dou, D., Frishkoff, G., & Rong, J. (2008). Ontology Database: a New Method for Semantic Modeling and an Application to Brainwave Data. 20th International Conference on Scientific and Statistical Database Management (SSDBM2008). Hong Kong, China
  • Qin, H., Dou, D., & LePendu, P. (2007). Discovering Executable Semantic Mappings Between Ontologies. International Conference on Ontologies, Databases and Applications of SEmantics (ODBASE 2007), Springer Lecture Notes in Computer Science, LNCS 4803, pp. 832-849.
  • Rong, J., Dou, D., Frishkoff, G., Frank, R., Malony, A., & Tucker, D. (2007). A semi-automatic framework for mining ERP patterns. IEEE International Symposium on Data Mining and Information Retrieval (DMIR-07), pp. 329-334, Ontario, Canada.

High-Performance Software and Portals

  • Hansen-Smith, V., Malony, A., Frishkoff, G., (2007). Towards Automated Portal Design: Using AJAX and portlets to engineer a neuroscience collaboratory. Technical report. Dept. Computer and Information Science, University of Oregon, Eugene, OR.
  • Hansen-Smith, V. (2007). The APECS portal: A collaborative neuroscience repository. Unpublished M.S. Thesis. Dept. Computer and Information Science, University of Oregon, Eugene, OR.
  • Hoge, C., Keith, D., & Malony, A (2006). Client-side task support in Matlab for concurrent distributed execution. Austrian-Hungarian Workshop on Distributed and Parallel Systems (DAPSYS), September.
  • Keith, D., Hoge, C., Malony, A., & Frank, R. (2006). Parallel ICA methods for EEG neuroimaging, International Parallel and Distributed Processing Symposium (IPDPS), May.

Computational Head Modeling and EEG/ERP Source Localization

  • Ferree, T. C., Eriksen, K. J., & Tucker, D. M. (2000). Regional head tissue conductivity estimation for improved EEG analysis. IEEE Transactions on Biomedical Engineering, 47(12), 1584-1592.
  • Frishkoff, G. A., Tucker, D. M., Davey, C., & Scherg, M. (2004). Frontal and posterior sources of event-related potentials in semantic comprehension. Cognitive Brain Research, 20(3), 329-354.
  • Frishkoff, G. A. (2007). Hemispheric differences in strong versus weak semantic priming: Evidence from event-related brain potentials. Brain and Language, 100(1), 23-43.
  • Holmes, M. D., Brown, M., & Tucker, D. M. (2004). Are "generalized" seizures truly generalized? Evidence of localized mesial frontal and frontopolar discharges in absence. Epilepsia, 45(12), 1568-1579.
  • Li, Kai (2007). Neuroanatomical segmentation in MRI exploiting a priori knowledge. Ph.D thesis, Department of Computer and Information Science, University of Oregon, March 2007.
  • Li, K., Malony, A. & Tucker, D. (2006). Automatic brain MR image segmentation with relative thresholding and morphological image analysis. First International Conference on Computer Vision Theory and Applications (VISAPP), pp. 354-364, Portugal, February.
  • Li, K., Malony, A. & Tucker, D. (2006). A multiscale morphological approach to topology correction of cortical surfaces. Medical Imaging and Augmented Reality - MIAR 2006, G.-Z. Yang et al (eds.), Springer Lecture Notes in Computer Science, LNCS 4091, pp. 52-59.
  • Russell, G. S., Srinivasan, R., & Tucker, D. M. (1998). Bayesian estimates of error bounds for EEG source imaging [letter]. IEEE Transactions on Medical Imaging, 17(6), 1084-1089.
  • Salman, A., Malony, A., Turovets, S. (2008, in submission). On the role of skull parcellation in the computational modeling of human head conductivity. IEEE 11th International Conference on Computational Science and Engineering.
  • Salman, A., Malony, A., Turovets, S., & Tucker, D. (2007). Use of parallel simulated annealing for computational modeling of human head conductivity. International Conferences on Computational Science (ICCS 2007), Y. Shi et al. (eds.), Part I, Springer Lecture Notes in Computer Science, LNCS 4487, pp. 86-93. (Best paper award)
  • Salman, A., Turovets, S. & Malony, A. (2005). Computational modeling of human head conductivity. International Conference on Computational Science (ICCS 2005), V.S. Sundrem et al. (eds.), Springer Lecture Notes in Computer Science, LNCS 3514, pp. 631-638. (Best paper award)
  • Salman, A. Turovets, S., Malony, A., & Volkov, V. (2008). Multi-cluster, Mixed-Mode Computational Modeling of Human Head Conductivity. International Workshop on OpenMP (IWOMP 2005/2006), Springer Lecture Notes in Computer Science 4315, pp. 119-130.
  • Salman, A., Turovets, S., Malony, A., Poolman, P., Davey, C., Eriksen, J., & Tucker, D.(2006). Noninvasive conductivity extraction for high-resolution EEG source localization. Advances in Clinical Neuroscience and Rehabilitation, 6(1), 27-28 (invited paper).
  • Tucker, D. M., Brown, M., Luu, P., & Holmes, M. D. (2007). Discharges in ventromedial frontal cortex during absence spells. Epilepsy and Behavior, 11, 546-557.
  • Turovets, S., Salman, A., Malony, A., Poolman, P., Davey, C., & Tucker, D. (2006). Anatomically constrained conductivity estimation of the human head tissues in vivo: computational procedure and preliminary experiments. 7th Conference on Biomedical Applications of Electrical Impedance Tomography, pp. 23-26, Seoul, Korea.
  • Turovets, S.I., Lovely, P.S., & Tucker, D.M. (2006). Intracranial hematoma detection using near infrared light and local reference method. Biomedical Optics 2006 Technical Digest (Optical Society of America), Washington, DC), paper ME26.


References motivating need for Neurocognitive Ontologies

  • Bilder, R. M., Sabb, F. W., Parker, D. S., Kalar, D., Chu, W. W., Fox, J., et al. (2009). Cognitive ontologies for neuropsychiatric phenomics research. Cogn Neuropsychiatry, 14(4-5), 419-450.
  • Decety, J., & Lamm, C. (2007). The role of the right temporoparietal junction in social interaction: how low-level computational processes contribute to meta-cognition. Neuroscientist, 13(6), 580-593.
  • Fox, P. T., Laird, A. R., Fox, S. P., Fox, P. M., Uecker, A. M., Crank, M., et al. (2005). BrainMap taxonomy of experimental design: description and evaluation. Hum Brain Mapp, 25(1), 185-198.
  • Henson, R. (2005). What can functional neuroimaging tell the experimental psychologist? Q J Exp Psychol A, 58(2), 193-233.
  • Laird, A. R., Eickhoff, S. B., Kurth, F., Fox, P. M., Uecker, A. M., Turner, J. A., et al. (2009). ALE Meta-Analysis Workflows Via the Brainmap Database: Progress Towards A Probabilistic Functional Brain Atlas. Front Neuroinformatics, 3, 23.
  • Laird, A. R., Lancaster, J. L., & Fox, P. T. (2009). Lost in localization? The focus is meta-analysis. Neuroimage, 48(1), 18-20.
  • Laird, A. R., Lancaster, J. L., & Fox, P. T. (2005). BrainMap: the social evolution of a human brain mapping database. Neuroinformatics, 3(1), 65-78.
  • Laird, A. R., McMillan, K. M., Lancaster, J. L., Kochunov, P., Turkeltaub, P. E., Pardo, J. V., et al. (2005). A comparison of label-based review and ALE meta-analysis in the Stroop task. Hum Brain Mapp, 25(1), 6-21.
  • Poldrack, R. A. (2006). Can cognitive processes be inferred from neuroimaging data? Trends Cogn Sci, 10(2), 59-63.
  • Poldrack, R. A. (2008). The role of fMRI in Cognitive Neuroscience: where do we stand? Curr Opin Neurobiol.
  • Van Horn, J. D., & Toga, A. W. (2009). Multisite neuroimaging trials. Curr Opin Neurol, 22(4), 370-378.

References for Upper Ontologies and Ontology Development Methods

  • Arp, R., and Smith, B., (2008). Function, Role, and Disposition in Basic Formal Ontology. In Nature Precedings : hdl:10101/npre.2008.1941.1. Paper on function, role, and disposition in BFO and two proposed sub-categories of artifactual function and biological function.
  • Bittner, T. (2009). Logical properties of foundational mereogeometrical relations in bio-ontologies. In Applied Ontology, Vol. 4, Issue 2 (April 2009) pp. 109-138. Paper providing axiomatic specifications for logical properties of relations such as part_of, located_in, connected_to, adjacent_to, attached_to, etc. which are currently only loosely specified in OBO.
  • Bittner, T. and Smith, B. (2003). A Theory of Granular Partitions. In Ducham, M., Goodchild, M. F., Worboys, M., (Eds.) Foundations of Geographical Information Science, Chapter 7. pp. 117-150. Taylor and Francis, New York, NY. An alternative to set theory both as a tool of formal ontology and as a framework for the representation of human cognition.
  • Bug, W. J., Giorgio A. Ascoli, G. A., Grethe, J. S., Gupta, A., Fennema-Notestine C., Laird, A. R., Stephen D. Larson, S. D., Rubin, D., Shepherd, G. M., Jessica A. Turner, J. A., Martone, M. E. (2008). The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. In Neuroinformatics, Vol. 6, Num. 3, September, 2008, pp.175-94. About the structure of the NIFSTD and BIRNLex vocabularies.
  • Castro, A. G., Rocca-Sera, P., Stevens, R., Taylor, C., Nashar, K., Ragan, M. A., Sansone, S. (2006). The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case. In BMC Bioinformatics 2006, 7:267. Recommendations for processes and tools (inc CMAP) for use in knowledge elicitation (informal ontologies, conceptualization).
  • Cook, D. L., Mejino, J. L. V., Rosse, C. Evolution of a Foundational Model of Physiology: Symbolic Representation for Functional Bioinformatics. In Fiesci, M., Coiera, E., Yu-Chan J. L. (Eds.). In Medinfo 2004: Proceedings Of THe 11th World Congress On Medical Informatics (Studies in Health Technology and Formatics). IOS Press, Fairfax, VA, pp. 336-340. Foundational Model of Physiology (FMP), a reference ontology for “functional bioinformatics” able to support support symbolic lookup, logical inference and mathematical analysis by integrating descriptive, qualitative and quantitative functional knowledge.
  • Cook, D., Mejino, J. L., Maxwell, N. L., Gennari, J. H. Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. (2008). In Proceedings, American Medical Informatics Association Fall Symposium 2008, Washington, D.C., pp. 136-140. Defining the Ontology of Physics for Biology (OPB), a reference ontology of physical principles, linking the semantics of biosimulation mathematics to structural bio-ontologies.
  • Courtot, M., Bug, W., Gibson, F., Lister, A. L., Malone, J., Schoeber, D., Brinkman, R. R., Ruttenberg, A. (2008). The OWL of Biomedical Investigations. In OWLED 2008 (October 2008). Paper about developing an ontology for the description of biological and clinical investigations written in OWL DL.
  • Drumond, N., Rector, A., Stevens, R., Moulton, G., Horridge, M., Wang, H. H., Seidenberg, J. (2006). Putting OWL in Order: Patterns for Sequences in OWL. In OWL Experiences and Directions. Proceedings from OWLEd 2006, Athens, GA. A paper on design pattern for modeling order within OWL-DL. How to use standard DL reasoning to perform pattern matching similar to regular expression matching.
  • Grenon, P. (2003). BFO in a Nutshell: A Bi-categorial Axiomatization for BFO and Comparison with DOLCE. In Institute for Formal Ontology and Medical Information Science (IFOMIS) Reports, 06/2003, December 2003, Leipzig, Germany. Bi-categorial axiomatization of BFO; Characterization of SNAP-SPAN; comparison between BFO and DOLCE and formal characterization of BFO.
  • Grenon, P. (2003). Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization for BFO. In Institute for Formal Ontology and Medical Information Science (IFOMIS) Reports, 07/2003, Dedcember 2003, Leipzig, Germany. The amended version of section 4 of the above listed Grenon, P. (2003) BFO in a Nutshell (IFOMIS Report, 06/03).
  • Grenon, P. (2003). Spatio-temporality in Basic Formal Ontology. SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization. Part I. Technical report. Institute for Formal Ontology and Medical Information Science University of Leipzig, Leipzig, Germany. Pierre Grenon's description of BFO's SNAP and SPAN ontologies.
  • Grenon, P., and Smith, B. (2004). SPAN and SNAP: Towards Dynamic Spatial Ontology. In Spatial Cognition & Computation: An Interdisciplinary Journal, Vol. 4, No. 1. (2004), pp. 69-104. Methodological and philosophical foundations of dynamic spatial ontology.
  • Grenon, P., Smith, B., Goldberg, L., (2004). Biodynamic Ontology:Applying BFO in the Biomedical Domain. In From D. M. Pisanelli (Ed.), In Ontologies in Medicine, Amsterdam: IOS Press, 2004, pp. 20–38. Proposal for a modular formal ontology of the biomedical domain with two components, one for biological objects (anatomical entities) and the other for biological processes (physiological processes).
  • Gruber, T. (1993). A translation approach to portable ontology specifications. In Knowledge Acquisition Journal, Vol 5 , Issue 2 (June 1993) pp. 199-199. Discussion about how the translation approach to portability addresses several technical problems: how to accommodate the stylistic and organizational differences among representations while preserving declarative content, how to translate from a very expressive language into restricted languages etc.
  • Gruber, T. (1995). Toward Principles for the Design of Ontologies Used for Knowledge Sharing. In International Journal Human-Computer Studies, Vol. 43, Issues 5-6, Novemer 1995, pp. 907-928. Description of the role of ontologies; setting of criteria to guide the development of ontologies; application of the criteria in design of ontologies for engineering mathematics and bibliographic data.
  • Guarino, N. (1995). Formal ontology, conceptual analysis and knowledge representation. In International Journal of Human-Computer Studies, Special issue: Guarino, N. and Poli, R., (Eds.) (1995). The role of formal ontology in the information technology, Vol. 43, Issue 5-6 (Nov./Dec. 1995) pp. 625-640. Systematic introduction of formal ontologies principles in current engineering practice; exploration in relationship between ontology and knowledge representation.
  • Handschuh, S., Staab, S., Volz, R. (2003). On Deep Annotation. In The Proceedings of the 12th International Conference on World Wide Web, Budapest, Hungary (May 2003). pp. 431-438. Presentation of the framework of metadata creation when web pages are generated from a database and the database owner, The framework combines the presentation layer with the data description layer, such annotation is referred as deep annotation
  • Horridge, M., Knublauch, H., Rector, A., Stevens, R., Wroe, C. (2004). A Practical Guide To Building OWL Ontologies Using The Protege-OWL Plugin and CO-ODE Tools. The University of Manchester, Manchester UK. Protege tutorial guidelines for development of OWL ontologies.
  • Montecchi-Palazzi, L., Gibson, F., Schoeber, D., Sansone, S. (2007). Guidelines for the development of Controlled Vocabularies. Proteomics Standards Initiative / Metabolomics Standards Initiative 2007. PSI best practices and design principles for the systematic development of "controlled vocabularies".
  • Munn, K. and Smith, B. (2008). Applied Ontology, An Introduction. Ontos Verlag, Frankfurt; Transaction Books, Rutgers University Piscataway, NJ. An e-book on "Applied Ontologies" (Downloadable from http://tinyurl.com/4d37jt5)
  • Rector, A. (2003). Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL. In Proceedings of the 2nd International Conference on Knowledge capture, Sanibel Island, FL, USA, Session: Technical papers, pp. 121-128. Proposal for initial criteria for a two-step normalisation of ontologies implemented using OWL or related DL based formalisms.
  • Rosse, C., Kumar, A., Mejino, J. L. V., Cook, D. L., Detwiler, L. T., Smith, B. (2005). A Strategy for Improving and Integrating Biomedical Ontologies. In Proceedings of AMIA Symposium 2005, Washington D.C., pp. 639–643. Presenting the framework of OBR (Ontology of Biomedical Reality) designed to facilitate inference across the boundaries of domain ontologies in anatomy, physiology and pathology, by using SNAP and SPAN ontologies.
  • Schoeber, D., Kunierczyk, Lewis, S., Lomax, J., Members of the MSI, PSI Ontology Working Groups, Mungall, C., Rocca-Serra, P., Smith, B., Sansone, S. (2007). Proposed conventions for terminology/naming of concepts.
  • Schoeber, D., MSI Ontology Working Group, PSI Ontology Working Groups, OBI Ontology Working Group. (2006). Naming Conventions for Controlled Vocabularies (CVs) and Ontologies. Draft v12. OBI & MSI, PSI) proposed guidelines for terminology/naming of concepts.
  • Schoeber, D., MSI Ontology Working Group, PSI Ontology Working Groups, OBI Ontology Working Group. (2006). Metadata Annotations for Representational Units and Representational Artifacts. Draft v2. OBI (& MSI, PSI) proposed guidelines for annotation of concepts/metadata.
  • Sharma, J., Flewelling, D. M., Egenhofer, M. J. (1994). A qualitative spatial reasoner. Sixth International Symposium on Spatial Data Handling, Edinburgh, Scotland (1994) pp. 665-681. Paper describing efforts to build a prototype of a qualitative spatial reasoner about spatial relations such as topological relations, cardinal directions, and approximate distances.
  • Smith, B., (1996). Mereotopology: A Theory of Parts and Boundaries. From Mereotopology: A Theory of Parts and Boundaries, Data and Knowledge Engineering, 20 (1996), 287–303. Good source of many definitions and formulae regarding parts, boundaries and topology in general.
  • Smith, B., (1997). Boundaries: An Essay in Mereotopology. From L. Hahn, ed., The Philosophy of Roderick Chisholm (Library of Living Philosophers), LaSalle: Open Court, 1997, 534–561. A very useful paper on boundaries and related issues.
  • Smith, B. (2004). Beyond concepts: Ontology as reality representation. In Varzi, A. and Vieu, L. (Eds.), Proceedings of FOIS 2004. International Conference on Formal Ontology and Information Systems, Turin, 4-6 November 2004 Formal Ontology and Information Systems 2004, (2004) pp. 73-84. A paper about the application of ontology in support of research in the natural sciences, emphasizing that ontologies developed for natural sciences should have as their subject the universals and particulars which exist in reality (and are captured in scientific laws).
  • Smith, B.(2005). Against Fantology. In Reicher, M. E. and Marek, J. C. (Eds.), Experience and Analysis: Proceedings of the 27th International Witgenstein Symposium Vienna 2005, pp. 153-170. Arguments against predicate logic.
  • Smith, B., Ashburner, M., Rosse, C., Bard J., Bug, W., Ceusters, W., Goldberg, L. J.,Eilbeck, K., Ireland, A., Mungall, C. J., The OBI Consortium11, Leontis, N., Rocca-Serra, P., Ruttenberg1, A., Sansone, S-A., Scheuermann, R. H., Shah, N., Whetzel, P. L. and Lewis, S. (2007).The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. In Nature Biotechnology, vol. 25, (2007), pp. 1251-1255. Description of OBO Foundry initiative for coordinated reform of existing biomedical ontologies, also providing guidelines for design of interoperable and well formed ontologies, and integration of ontologies.
  • Smith, B., Ceusters, W., Klagges, B., Koehler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A. L., Rosse, C. (2005). Relations in biomedical ontologies. In Genome Biology 2005, Volume 6, Issue 5, Article R46. Paper introducing OBO relational ontology.
  • Smith, B., Grenon, P. (2004). The cornucopia of formal-ontological relations. In Dialectica, Vol. 58, Number 3, pp. 279-296. A method for generating typologies of formal-ontological relations with examples of ontologies.
  • Smith, B., Koehler, J. and Kumar, A. (2004). On the application of formal principles to life science data: A case study in the Gene Ontology. In Rahim, E. (Ed.) (2004). Data Integration in the Life Sciences: First International Workshop, DILS 2004, Leipzig, Germany, March 25-26, 2004, proceedings (Lecture Notes in Computer Science / Lecture Notes in Bioinformatics), pp. 79-94. Arguments for the use of formal principles governing best practices in classification and definition, in ontology construction and development.
  • Smith, B., Kumar, A. (2004). Controlled vocabularies in bioinformatics: A case study in the gene ontology. In Drug Discovery Today: BIOSILICO (2004) vol. 2 (6) pp. 246-252. A survey some of problematic features of controlled vocabularies, focusing especially on issues of compositionality and syntactic regimentation.
  • Smith, B., Kusnierczyk, W., Schober, D., Ceusters, W. (2006). Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. In Proceedings of KR-MED 2006, pp. 57–66. Paper on what ontologies are for and what they are intended to model.
  • Smith, B., Varzi, A. (1999). The niche. In Nous, 33:2, (1999) pp. 198-222. Formal theory of niches, a theory of the relations between objects and their niches, built upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology.
  • Smith, B., Welty, C. (2001). Ontology: Towards a New Synthesis. In FOIS '02: Proceedings of the international conference on Formal Ontology in Information Systems (2001), Introduction. Brief history of ontology; growth of ontology; use of the term ontology: ontology and information sciences.
  • Spear, A. (2006). Ontology for the Twenty First Century: An Introduction with Recommendations. (Book in progress) with Robert Arp and Barry Smith. Andrew Spear's description of BFO Classes and Relations (Properties).

See also http://www.bioontology.org/top-10-errors

References for Microstate Analysis

References related to microstate analysis (more generally, automated "windowing" or segmentation of ERP patterns or "components") are found below.

  • Brandeis, D., Lehmann, D., Michel, C. M., & Mingrone, W. (1995). Mapping event-related brain potential microstates to sentence endings. Brain Topogr, 8(2), 145-159.
  • Koenig, T., Kochi, K., & Lehmann, D. (1998). Event-related electric microstates of the brain differ between words with visual and abstract meaning. Electroencephalogr Clin Neurophysiol, 106(6), 535-546.
  • Koenig, T., & Lehmann, D. (1996). Microstates in language-related brain potential maps show noun-verb differences. Brain Lang, 53(2), 169-182.
  • Lehmann, D., & Skrandies, W. (1984). Spatial analysis of evoked potentials in man--a review. Prog Neurobiol, 23(3), 227-250.
  • Maurer, U., Brandeis, D., & McCandliss, B. D. (2005). Fast, visual specialization for reading in English revealed by the topography of the N170 ERP response. Behav Brain Funct, 1, 13.
  • Michel, C. M., Thut, G., Morand, S., Khateb, A., Pegna, A. J., Grave de Peralta, R., et al. (2001). Electric source imaging of human brain functions. Brain Res Brain Res Rev, 36(2-3), 108-118.
  • Murray, M. M., Brunet, D., & Michel, C. M. (2008). Topographic ERP analyses: a step-by-step tutorial review. Brain Topogr, 20(4), 249-264.
  • Skrandies, W., & Lehmann, D. (1982). Spatial principal components of multichannel maps evoked by lateral visual half-field stimuli. Electroencepholography and Clinical Neurophysiology, 54, 662-667.
  • Vitacco, D., Brandeis, D., Pascual-Marqui, R., & Martin, E. (2002). Correspondence of event-related potential tomography and functional magnetic resonance imaging during language processing. Hum Brain Mapp, 17(1), 4-12.

References for Principal Components Analysis

References related to PCA are found below. This collection is curated by Robert Frank.

PCA Rotations (General)

  • Browne. An overview of analytic rotation in exploratory factor analysis. Multivariate Behavioral Research (2001) vol. 36 (1) pp. 111-150
  • Cureton and Mulaik. The weighted varimax rotation and the promax rotation. Psychometrika (1975) vol. 40 (2) pp. 183-195
  • Darton. Rotation in factor analysis. The Statistician (1980) pp. 167-194

PCA for ERPs

  • Dien. Addressing misallocation of variance in principal components analysis of event-related potentials. Brain Topography (1998) vol. 11 (1) pp. 43-55
  • Dien et al. Evaluation of PCA and ICA of simulated ERPs: Promax vs. infomax rotations. Human Brain Mapping (2007) vol. 28 (8)
  • Dien et al. Optimizing principal components analysis of event-related potentials: Matrix type, factor loading weighting, extraction, and rotations. Clinical Neurophysiology (2005) vol. 116 (8) pp. 1808-1825
  • Dien et al. Parametric analysis of event-related potentials in semantic comprehension: evidence for parallel brain mechanisms. Cognitive Brain Research (2003) vol. 15 (2) pp. 137-153
  • Dien & Frishkoff. Introduction to Principal Components Analysis of Event-Related Potentials. In Handy (Ed.), In T. Handy (Ed.), Event-Related Potentials: A Methods Handbook (2005). Cambridge, MA: MIT Press. pp. 137-153
  • Dien. Progressing towards a consensus on PCA of ERPs. Clinical Neurophysiology (2006) vol. 117 (3) pp. 699-702
  • Kayser and Tenke. Consensus on PCA for ERP data, and sensibility of unrestricted solutions. Clinical Neurophysiology (2006) vol. 117 (3) pp. 703-707
  • Kayser and Tenke. Optimizing PCA methodology for ERP component identification and measurement: theoretical rationale and empirical evaluation. Clinical Neurophysiology (2003) vol. 114 (12) pp. 2307-2325
  • Kayser and Tenke. Trusting in or breaking with convention: towards a renaissance of principal components analysis in electrophysiology. Clinical Neurophysiology (2005) vol. 116 (8) pp. 1747-1753
  • Pourtois et al. Beyond conventional event-related brain potential (ERP): Exploring the time-course of visual emotion processing using topographic and principal component analyses. Brain Topography (2008) vol. 20 (4) pp. 265-277

Rotation Criteria

Oblimin  
  • Carroll, J.B. (1960). IBM 704 program for generalized analytic rotation solution in factor analysis. Harvard University, unpublished.
  • Harman, H.H. (1976). Modern factor analysis (3rd. ed.). Chicago: The University of Chicago Press. Page 322.
  • Jennrich, R.I. (1979). Admissible values of γ in direct oblimin rotation. Psychometrika, 44, 173–177.
Orthomax
  • Harman, H.H. (1976). Modern factor analysis (3rd. ed.). Chicago: The University of Chicago Press. Page 299.
Varimax  
  • Kaiser, H.F. (1958). The varimax criterion for analytic rotation in factor analysis. Psychometrika, 23, 187–200.
  • Harman, H.H. (1976). Modern factor analysis (3rd. ed.). Chicago: The University of Chicago Press. Page 290.
Quartimax
  • Carroll, J.B. (1953). An analytic solution for approximating simple structure in factor analysis. Psychometrika, 18, 23–38.
  • Ferguson, G.A. (1954). The concept of parsimony in factor analysis. Psychometrika, 19, 281–290.
  • Neuhaus, J.O. & Wrigley, C. (1954). The quartimax method: An analytical approach to orthogonal simple structure. British Journal of Statistical Psychology, 7, 81–91.
Quartimin 
  • Carroll, J.B. (1960). IBM 704 program for generalized analytic rotation solution in factor analysis. Harvard University, unpublished.
Crawford-Ferguson family
  • Crawford, C.B. and Ferguson, G.A. (1970). A general rotation criterion and its use in orthogonal rotation. Psychometrika, 35, 321–332.
  • Browne. An overview of analytic rotation in exploratory factor analysis. Multivariate Behavioral Research (2001) vol. 36 (1) pp. 111-150
Infomax
  • McKeon, J.J. (1968). Rotation for maximum association between factors and tests. Unpublished manuscript, Biometric Laboratory, George Washington University.
  • Browne. An overview of analytic rotation in exploratory factor analysis. Multivariate Behavioral Research (2001) vol. 36 (1) pp. 111-150
Minimum entropy
  • Jennrich, R.I. (2004). Rotation to simple loadings using component loss functions: the orthogonal case. Psychometrika, 69, 257–274.
McCammon minimum entropy ratio
  • McCammon, R.B. (1966). Principal components analysis and its application in large-scale correlation studies. Journal of Geology, 74, 721–733.
  • Browne. An overview of analytic rotation in exploratory factor analysis. Multivariate Behavioral Research (2001) vol. 36 (1) pp. 111-150
Oblimax
  • Pinzka, C. and Saunders, D.R. (1954). Analytic rotation to simple structure: II. Extension to an oblique solution. Research Bulletin 54–31 Princeton, N.J.: Educational Testing Service. Saunders, D.R. (1961). The rationale for an “oblimax” method of transformation in factor analysis. Psychometrika, 26, 317–324.
  • Harman, H.H. (1976). Modern factor analysis (3rd. ed.). Chicago: The University of Chicago Press. Page 302.
Bentler’s invariant pattern simplicity
  • Bentler, P.M. (1977). Factor simplicity index and transformations. Psychometrika, 42, 277–295.
The tandem criteria
  • Comrey, A.L. (1967). Tandem criteria for analytic rotation in factor analysis. Psychometrika, 32, 277–295.
Geomin
  • Yates, A. (1984) Multivariate Exploratory Data Analysis: A perspective on Exploratory Factor analysis. Albany: State University of New York Press.
  • Browne. An overview of analytic rotation in exploratory factor analysis. Multivariate Behavioral Research (2001) vol. 36 (1) pp. 111-150
Target rotation
  • Harman, H.H. (1976). Modern factor analysis (3rd. ed.). Chicago: The University of Chicago Press.
Partially specified target rotation
  • Browne, M.W. (1972a). Orthogonal rotation to a partially specified target. British Journal of Mathematical and Statistical Psychology, 25, 115–120.
  • Browne, M.W. (1972b). Oblique rotation to a partially specified target. British Journal of Mathematical and Statistical Psychology, 25, 207–212.
Simplimax
  • Kiers, H.A.L. (1994). SIMPLIMAX: Oblique rotation to an optimal target with simple structure. Psychometrika, 59, 567–579.
Procrustes
  • Hurley, J.R. and Cattell, R.B. (1962). The Procrustes program: Producing direct rotation to test a hypothesized factor structure. Behavioral Science, 7, 258–262.
  • Luk. Orthogonal rotation to a partially specified target. Department of Computer Science: Cornell (1981)
  • Schönemann. A generalized solution of the orthogonal Procrustes problem. Psychometrika (1966) vol. 31 (1) pp. 1-10
Promax
  • Hendrickson, A.E. and White, P.O. (1964). Promax: A quick method for rotation to oblique simple structure. The British Journal of Statistical Psychology, 17, 65–70
  • Cureton, E.E. (1976). Studies of the promax and optres rotations. Multivariate Behavioral Research, 11, 449–460.

References for Cluster Analysis

References related to cluster analysis are found below. (PDF files are available in Scholar Google)

  • Anil K. Jain, M. Narasimha Murty and Patrick J. Flynn: Data Clustering: A Review. ACM Comput. Surv. 31(3): 264-323 (1999)
  • Richard C. Dubes: How many clusters are best? - An experiment. Pattern Recognition 20(6): 645-663 (1987)
  • Glenn W. Milligan and Martha C. Cooper: An examination of procedures for determining the number of clusters in a data set. Psychometrika 50(2): 159-179 (1985)
  • M. Narasimha Murty and Anil K. Jain: Knowledge-based clustering scheme for collection management and retrieval of library books. Pattern Recognition 28(7): 949-963 (1995)
  • Chris Fraley and Adrian E. Raftery: How Many Clusters? Which Clustering Method? Answers Via Model-Based Cluster Analysis. Computer Journal 41(8): 578-588 (1998)
  • Catherine A. Sugar and Gareth M. James: Finding the Number of Clusters in a Dataset: An Information-Theoretic Approach. Journal of the American Statistical Association, Vol. 98 (2003)
  • Robert Tibshirani, Guenther Walther and Trevor Hastie: Estimating the Number of Clusters in a Data Set via the Gap Statistic. Journal of the Royal Statistical Society. Series B (Statistical Methodology), Vol. 63, No. 2: 411-423 (2001)
  • Stan Salvador and Philip Chan: Determining the Number of Clusters/Segments in Hierarchical Clustering/Segmentation Algorithms. ICTAI 2004: 576-584 (2004)
  • Tibshirani and Walther. Cluster validation by prediction strength. Journal of Computational and Graphical Statistics (2005)
  • TMurray, M. M., Brunet, D., & Michel, C. M. (2008). Topographic ERP analyses: a step-by-step tutorial review. Brain Topogr, 20(4), 249-264.
  • Pascual-Marqui et al. Segmentation of brain electrical activity into microstates: model estimation and validation. IEEE transactions on bio-medical engineering (1995) vol. 42 (7) pp. 658-65
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