Cliff Joslyn

Publications

Updated July, 2006

Long Publications

  • Heylighen, Francis; Joslyn, Cliff; and Turchin, Valentin, eds.: (1995) The Quantum of Evolution: Towards a Theory of Meta-System Transitions, Gordon and Breach, New York.
    • Special issue of World Futures: The Journal of General Evolution, v. 45:1
  • Joslyn, Cliff: (1994) Possibilistic Processes for Complex Systems Modeling, PhD Dissertation, SUNY-Binghamton, Systems Science

    • Journal Papers

  • KM Verspoor, JD Cohn, SM Mniszewski, and CA Joslyn: "A Categorization Approach to Automated Ontological Protein Function Annotation", Protein Science, v. 15, pp. 1544-1549, 2006
    • Categorization of GO neighborhoods induced by BLAST neighborhoods of unknown proteins; evaluation measures in hierarchical knowledge spaces
  • Joslyn, Cliff and Kreinovich, Vladik (2005): "Convergence Properties of an Interval Probabilistic Approach to System Reliabilility Estimation", Int. J. General Systems, v. 34:4, pp. 465-482, 2005
  • Verspoor, Karin, J Cohn, CA Joslyn, SM Mniszewski; A Rechtsteiner, LM Rocha, and T Simas: "Protein Annotation as Term Categorization in the Gene Ontology Using Word Proximity Networks", BMC Bioinformatics, v. 6:s1, 2005
    • LANL submission to BioCreAtive, use of Gene Ontology Categorizer.
    Joslyn, Cliff, SM Mniszewski, AW Fulmer, and GG Heaton: (2004) "The Gene Ontology Categorizer", Bioinformatics, v. 20:s1, pp. 169-177
  • Oberkampf WL, JC Helton, SF Wojtkiewicz, Cliff Joslyn, and Scott Ferson: (2004) "Uncertainty in System Response Given Uncertain Parameters", Reliabilty Engineering and Safety Systems, v. 85:1-3, pp. 11-20

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  • Ferson, Scott, CA Joslyn, JC Helton, WL Oberkampf, and K Sentz: (2004) "Summary of the Epistemic Uncertainty Workshop: Consensus Amid Diversity", Reliability Engineering and Systems Safety, v. 85:1-3, pp.355-370

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  • Joslyn, Cliff: (2001) "The Semiotics of Control and Modeling Relations in Complex Systems", Biosystems, v. 60:1-3, pp. 131-48, 2001
    • Modeling and control as canonical systems-environment relations; constraint descriptions; semiotics of selection constraint.
  • Joslyn, Cliff: (2000) "Levels of Control and Closure in Complex Semiotic Systems", Annals of the New York Academy of Sciences, special issue on "Closure", ed. J. Chandler, G. van de Vijver, v. 901, pp. 67-74, 2000.
    • Modeling and control relations as forms of semiotic closure in evolved systems.
  • Joslyn, Cliff, and Luis Rocha: (1998) "Towards a Formal Taxonomy of Hybrid Uncertainty Representations", Information Sciences, v. 110:3-4, pp. 255-277.
    • Fuzzy weighting and nonspecific collecting as atomic transformations to generate hybrid uncertainty representations; transitive and intransitive methods; probabilistic, possibilistic, and interval constraints.
  • Joslyn, Cliff: (1997) "Possibilistic Normalization of Inconsistent Random Intervals", Advances in Systems Science and Applications, special issue, ed. ed. Wansheng Tang, p. 44-51.
    • Specialization of focused consistent transformation possibilistic normalization to random intervals.
  • Joslyn, Cliff: (1997) "Measurement of Possibilistic Histograms from Interval Data", International Journal of General Systems, v. 26:1-2, pp. 9-33.
    • Possibilistic histograms as the plausibilistic traces of empirical random intervals. Relation to fuzzy intervals. Continuous approximations yield standard fuzzy interval forms.
  • Joslyn, Cliff: (1996) "Aggregation and Completion of Random Sets with Distributional Fuzzy Measures", Int. J. of Uncertainty, Fuzziness, and Knowledge-Based Systems, v. 4:4, pp. 307-329.
    • Conorm-distributional and -decomposable fuzzy measures; random set completion and structural and numerical aggregation functions; existing probabilistic and possibilistic cases; hypothetical Sugeno-conorm distributional and ring-aggregable cases.
  • Heylighen, Francis and Joslyn, Cliff: (1995) "Towards a Theory of Meta-System Transitions", World Futures, v. 45, pp. 1-4
    • Preface to the special issue on Meta-System Transition Theory
  • Joslyn, Cliff: (1995) "Semantic Control Systems", World Futures, v. 45, pp.87-123
    • Systems and metasystems in terms of dimensional and cardinal variety and constraint; control as dynamic equilibrium; semantic relations and control; relation to biosemiotics, Artificial Life, and the origins of life problem.
  • Joslyn, Cliff: (1994) "A Possibilistic Approach to Qualitative Model-Based Diagnosis", Telematics and Informatics, v. 11:4, pp.365-384
    • Consideration of the application of possibilistic systems theory to the model-based diagnosis of the faults of a spacecraft system: fault and behavior models as possibilistic automata; fault hypotheses and prediction errors with possibilistic weights; possibilistic distance of telemetry from predicted and nominal state. Consideration of sensor failure modeling and indirect and redundant measurements in evidence theory.
  • Heylighen, Francis, and Joslyn, Cliff: (1993) "Electronic Networking for Philosophical Development in the Principia Cybernetica Project", with Francis Heylighen. Informatica, v. 17:3, pp. 285-293

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  • Heylighen, Francis; Joslyn, Cliff; and Turchin, Valentin: (1991) "Short Introduction to the Principia Cybernetic Project", J. Ideas, v. 2:1, pp.26-29
    • Semantic analysis of entropy; syntactic vs. semantic definitions of entropy; type-specificity of entropy measures; the origin and identification of emergent levels in physical systems; and the ontological status of non-thermodynamic entropies.
  • Joslyn, Cliff: (1991) "On the Semantics of Entropy Measures of Emergent Phenomena", Cybernetics and Systems, v. 22:6, pp.631-640

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  • Turchin, Valentin and Joslyn, Cliff: (1990) "Cybernetic Manifesto", Kybernetes, v. 19:2-3, pp.63-64

    • Book Chapters

  • Joslyn, Cliff and Bruno, William J: (2005) "Weighted Pseudo-Distances for Categorization in Semantic Hierarchies", Conceptual Structures: Common Semantics for Sharing Knowledge, Lecture Notes in AI, v. 3596, eds. F Dau, M-L Mugnier, and G Stumme, pp.  381-395
    • Towards distance measures in quantified semantic hierarchies.
  • Joslyn, Cliff and Booker, Jane: (2004) "Generalized Information Theory for Engineering Modeling and Simulation", in: Engineering Design Reliability Handbook, ed. E Nikolaidis and D Ghiocel, CRC Press, pp. 9:1-40
    • Survey of some of the most prominent GIT formalisms in the context of classical approaches, including probability theory. Introduction of the formal specifications of a range of theories; interval analysis and probability theory; generalization to fuzzy systems theory; monotone or fuzzy measures; random sets and Dempster-Shafer structures; possibility theory.
  • Joslyn, Cliff: (2004) "Poset Ontologies and Concept Lattices as Semantic Hierarchies", in: Conceptual Structures at Work, Lecture Notes in Artificial Intelligence, v. 3127, ed. Wolff, Pfeiffer and Delugach, pp. 287-302, Springer-Verlag, Berlin
  • Heylighen, Francis and Cliff Joslyn: (2001) "Cybernetics and Second Order Cybernetics", Encyclopedia of Physical Science and Technology, ed. AJ Meyer, Academic Press, New York, v. 4, pp. 155-170.

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  • Joslyn, Cliff and Francis Heylighen: (1999) "Cybernetics", in: Encyclopedia of Computer Science, ed. J. Hemmendinger and A. Ralston, MacMillan Reference, pp. 372-375.

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  • Joslyn, Cliff: (1998) "Are Life and Meaning Coextensive?" , in: Evolutionary Systems, ed. G. van de Vijvers, pp. 413-422, Kluwer Academic Publishers.
    • Consideration of the possible relations between the classes of living and control systems in terms of extensional and ontological necessity and sufficiency.
  • Joslyn, Cliff: (1997) "Distributional Representations of Random Interval Measurements", in: Uncertainty Analysis in Engineering and the Sciences, ed. Bilal Ayyub and Madan Gupta, pp. 37-52, Kluwer.
    • Mathematics of random interval representations; strongly compatible and other frequency-based probabilistic transformations.
  • Joslyn, Cliff: (1996) "An Object-Oriented Architecture for Possibilistic Models", in: Computer-Aided Systems Technology, ed. T. Oren and G. Klir, pp. 80-94, Springer-Verlag, Berlin, in series: Lecture Notes in Computer Science # 1105
    • (Selected for publication in the select proceedings of the 1994 Computer-Aided Systems Theory Conference) Design for C++ classes for random sets, probability and possibility distributions, and possibilistic processes.
  • Joslyn, Cliff and Henderson, Scott: (1996) "CAST Extensions to DASME to Support Generalized Information Theory", in: Computer Aided Systems Theory---EUROCAST '95, ed. F. Pichler, pp. 237-252, in series: Lecture Notes in Computer Science # 1030, Springer-Verlag, Berlin.
    • (Selected for publication in the select proceedings of the 1995 Computer-Aided Systems Theory Conference) Design for generalization of the DASME modeling environment to support GIT qualitative modeling concepts: strong typing, link weighting, internal and external link types.
  • Heylighen, Francis and Joslyn, Cliff: (1995) "Systems Theory and Systems Analysis", in: Cambridge Dictionary of Philosophy, ed. R. Audi, pp. 784-785, Cambridge U. Press, Cambridge MA
    • Definition of systems theory and systems analysis.
  • Joslyn, Cliff: (1995) "In Support of an Independent Possibility Theory", in: Foundations and Applications of Possibility Theory, eds. G. de Cooman, D. Ruan, and E.E. Kerre, pp. 152-164, World Scientific, Singapore.
    • Arguments to support the position that possibility is related to, but distinct from, both fuzzy and probability theory: the role of normalization in articulation of a "regular" view of possibility; alpha cuts and focal elements; the role of the maximum operator.
  • Joslyn, Cliff: (1994) "On Possibilistic Automata", in: Computer Aided Systems Theory---EUROCAST '93, ed. F. Pichler and R. Moreno-Diaz, pp. 231-242, in series: Lecture Notes in Computer Science # 763, Springer-Verlag, Berlin
    • (Selected for publication in the select proceedings of the 1993 Computer-Aided Systems Theory Conference) Possibilistic automata as pessimistic fuzzy automata which are normal in the sense of general automata; properties of possibilistic automata;possibilistic automata are identical with strongly consistent stochastic automata.
  • Joslyn, Cliff: (1993) "Empirical Possibility and Minimal Information Distortion", in: Fuzzy Logic: State of the Art, ed. R Lowen and M Roubens, pp.143-152, Kluwer, Dordrecht
    • (Invited paper) Normal possibility distributions are available for consistent random sets, and a set of focused consistent transformations is available for inconsistent random sets. The Principle of Uncertainty Invariance is modified to provide a method which selects that consistent transformationwith Minimal Information Distortion from the measured random set.

    Peer-Reviewed Conference Proceedings

  • Joslyn, Cliff; Gessler, DDG; Schmidt, SE; and Verspoor, KM: (2006) "Distributed  Representations of Bio-Ontologies for Semantic Web Services'', Joint BioLINK and 9th Bio-Ontologies Meeting (JBB 06), ISMB 06
    • Distributed representation for taxonomic ontologies, lattice theoretical analysis to gaurantee validity and identify inconsistencies in the inheritance structure.
  • CA Joslyn, SM Mniszewski, SA Smith, and PM Weber: (2006) "SpindleViz: A Three Dimensional, Order Theoretical Visualization Environment for the Gene Ontology", Joint BioLINK and 9th Bio-Ontologies Meeting (JBB 06), ISMB 06
    • Lattice theoretical visualization approach for large taxonomies.
  • Verspoor, Karin; Judith Cohn; Susan Mniszewski;  and Cliff Joslyn: (2005) "Nearest Neighbor Categorization for Function Prediction", in: Proc. 5th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP 05)

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  • Verspoor, Karin; Judith Cohn; Susan Mniszewski;  and Cliff Joslyn: (2005) "POSOLE: Automated Ontological Annotation for Function Prediction", in: Proc. Automated Function Prediction SIG, ISMB 05

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  • Joslyn, Cliff: (2004) "Reports On Two Recent Bio-Ontology Workshops", in: Proc. 7th Annual Bio-Ontologies Meeting, ISMB 04

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  • Joslyn, Cliff and Ferson, Scott: (2004) "Approximate Representations of Random Intervals for Hybrid Uncertainty Quantification", in: Sensitivity Analysis of Model Output (SAMO04)}, ed. KM Hanson and FM

    • Hemez, pp. 453-469, LANL, Los Alamos
    Approximateion of random intervals by probability boxes and traces.
  • Joslyn, Cliff: (2003) "Multi-Interval Elicitation of Random Intervals for Engineering Reliability Analysis", in: 2003 Int. Symp. on Uncertainty Modeling and Analysis (ISUMA 03)
  • Verspoor, Karin; Joslyn, Cliff; and Papcun, George: (2003) "Gene Ontology as a Source of Lexical Semantic Knowledge for a Biological Natural Language Processing Application", in: Workshop on Text Analysis and Search for Bioinformatics (SIGIR 03)
  • Joslyn, Cliff: (2002) "Network Worlds: From Link Analysis to Virtual Places", in: Proc. 2002 Conf. on Virtual Worlds and Simulation (VWSim 02)
    • From network analytical to link analytic approaches, focusing on smaller graphs with heterogeneous link types; chaining of views of multidimensional databases; connections to virtual world architectures.
  • Joslyn, Cliff and Jon C Helton: (2002) "Bounds on Plausibility and Belief of Functionally Propagated Random Sets", in: Proc. Conf. Northe American Fuzzy Information Processing Society (NAFIPS 2002), pp.412-417
    • Introduction of Monte Carlo approach to smapling a functionally propagated general random sets; bounding and convergence properties.
  • Ross, T, Vladik Kreinovich and Cliff Joslyn (2001) "Assessing the Predictive Accuracy of Complex Simulation Models"', Proc. 2001 Joint Conf. of the North American Fuzzy Information Processing Society and the International Fuzzy Systems Association, Vancouver, July, 2001, pp. 2008-2012.
  • Joslyn, Cliff: (2000) "Measures of Distortion in Possibilistic Approximations of Consistent Random Sets and Intervals", Proc. 2001 Joint Conf. of the North American Fuzzy Information Processing Society and the International Fuzzy Systems Association, Vancouver, July, 2001, pp. 1735-1740.
    • Normal possibility distributions are available for consistent random sets, and a set of focused consistent transformations is available for inconsistent random sets. The Principle of Uncertainty Invariance is modified to provide a method which selects that consistent transformationwith Minimal Information Distortion from the measured random set.
  • Joslyn, Cliff: (2000) "Towards Measures of Intelligence Based on Semiotic Control'', 2000 Workshop on Performance Metrics in Intelligent Systems, ed. A. Meystel, NIST
    • Identification and measurement of degree of intelligence in systems; hierarchical and anticipatory control relations.
  • Joslyn, Cliff: (2000) "Virtual Environments as Constraints on Decision-Making in Agent Models of Socio-Technical Organizations", in: 2000 Workshop on Virtual Worlds in Simulation, ed. K. Bellman and C. Landauer
    • Constraints from virtual physics, common communication structures, and shared knowledge on the decision-making capabilities semiotic agents.
  • Joslyn, Cliff and Rocha, Luis: (2000) "Towards Semiotic Agent-Based Models of Socio-Technical Organizations", in: Proc. AI, Simulation and Planning in High Autonomy Systems, ed. HS Sarjoughian et al., pp. 70-79.
    • An approach to agent modeling of socio-technical organizations on semiotic principles; semiotic agents as decision-making entities embedded in artificial environments exchanging semiotic tokens.
  • Joslyn, Cliff: (1999) "Possibilistic Systems Theory Within a General Information Theory", Proc. 1999 Workshop on Imprecise Probabilities and Their Applications, ed. G. de Cooman et al., pp.206-215
    • Overview of possibilistic systems in an imprecise probabilities context.
  • Joslyn, Cliff: (1998) "Formal Designed and Informal Emergent Ontologies in Webs and Multi-User Virtual Environments (MUVEs)", in: 1998 Workshop on Emergent Semantic and Computational Processes in Distribtued Information Systems
  • Johnson, Norman; Steen Rasmussen; Cliff Joslyn; Luis Rocha; Steven Smith; and Marianna Kantor: (1998) "Symbiotic Intelligence: Self-Organizing Knowledge on Distributed Networks", Proc. 6th Conf. on Artificial Life, ed. C. Adami et al., MIT Press.
  • Joslyn, Cliff: (1998) "Models, Controls, and Levels of Semiotic Autonomy", in: Proc. 1998 Conference on Intelligent Systems, ed. J. Albus and A. Meystel, pp.747-752, IEEE, Gaithersburg MD,
  • Rocha, Luis, and Cliff Joslyn: (1998) "Simulations of Evolving Embodied Semiosis: Emergent Semantics in Artificial Environments", Proc. 1998 Conf. on Virtual Worlds in Simulation, ed. C. Landauer and K. Bellman, Society for Computer Simulation, San Diego, pp. 233-238
    • Evolutionary systems in the context of this community of interaction: 1) a coupled interaction between a system and its environment; 2) an environment with sufficient initial richness and structure to allow for; 3) embodied emergent classification of that environment-system coupling; 4) which is subject to pragmatic selection.
  • Joslyn, Cliff: (1997) "Towards General Information Theoretical Representations of Databases Problems", in: Proc. 1997 Conf. of the IEEE Society for Systems, Man and Cybernetics, Orlando, FL, v. 2, pp. 1662-1667.
    • Systems theoretical representation of relational databases, including fuzzy measure and set theoretical, possibilistic, and random set theoretical.
  • Joslyn, Cliff: (1996) "Hybrid Methods to Represent Incomplete and Uncertain Information", in: Proc. 1996 Interdisciplinary Conference on Intelligent Systems: A Semiotic Perspective, ed. James Albus and Alex Meystel, pp. 133-140, NIST, Gaithersburg, MD.
    • Mathematical issues in information representation from a semiotic perspective.
  • Joslyn, Cliff: (1996) "Semantic Webs: A Cyberspatial Representational Form for Cybernetics", in: Proc. 1996 European Conf. on Cybernetics and Systems Research, ed. R. Trappl, Vienna, v. 2, pp. 905-910.
    • Semantic webs as acyclic multirelations.
  • Joslyn, Cliff: (1996) "The Process Theoretical Approach to Qualitative DEVS", Proc. 1996 Conference on AI, Simulation, and Planning in High Autonomy Systems, pp. 235-242, San Diego CA.
    • Discrete EVent Systems (DEVS) extended to general processes: fuzzy, stochastic, possibilistic, nondeterministic.
  • Joslyn, Cliff: (1995) "Strong Probabilistic Compatibility of Possibilistic Histograms", in: Proc. 1995 Joint Int. Symposium on Uncertainty Modeling and Analysis and Conf. of the North American Fuzzy Information Processing Society, ed. Bilal Ayyub, pp. 383, A17-A22, IEEE Computer Society Press, Los Alamitos, CA.
    • Empirical random sets and possibilistic histograms considered in conjunction with strong probabilistic compatibility.
  • Joslyn, Cliff: (1994) "Aggregation and Completion in Probability and Possibility", in: Proc. 1994 Joint Conf. on Information Systems, ed. PP Wang, pp.333-336, Pinehurst NC
    • Extended abstract: fuzzy measures with distributions; random set completion and structural and numerical aggregation functions; probabilistic, possibilistic, and ring-structured cases.
  • Joslyn, Cliff: (1994) "Qualitative Model-Based Diagnosis Using Possibility Theory", in: Proc. 1994 Goddard Conf. on Space Applications of Artificial Intelligence, pp.269-283
    • Consideration of the application to the model-based diagnosis (MBD) of the faults of a spacecraft system: fault and behavior models as possibilistic automata; fault hypotheses and prediction errors with possibilistic weights; possibilistic distance of telemetry from predicted and nominal state. Consideration of sensor failure modeling and indirect and redundant measurements in evidence theory.
  • Joslyn, Cliff; Heylighen, Francis; and Turchin, Valentin: (1993) "Synopsis of the Principia Cybernetica Project", in: Proc. 13th Int. Congress on Cybernetics, ed. J. Ramaekers, pp.509-513, International Association of Cybernetics, Namur, Belgium
  • Joslyn, Cliff: (1993) "Some New Results on Possibilistic Measurement", in: Proc. NAFIPS 1993, pp.227-231, Allentown PA
    • Possibilistic histograms, their interpretation as fuzzy numbers, and their continuous approximations.
  • Joslyn, Cliff: (1993) "Possibilistic Semantics and Measurement Methods in Complex Systems", in: Proc. 2nd Int. Symposium on Uncertainty Modeling and Analysis, ed. Bilal Ayyub, pp.208-215, IEEE Computer Society
    • Towards development of a strictly possibilistic semantics of natural systems: the semantics of possibility statements in relation to modal logic, natural language, and mathematical possibility; strong consistency relation for probability and possibility; the application of possibility theory to complex systems.
  • Joslyn, Cliff: (1992) "Possibilistic Measurement and Set Statistics", in: Proc. NAFIPS 1992, v. 2, pp.458-467, Puerto Vallerta
    • Set-based statistics to generate possibility distributions from measured data; physical measurement methods to generate statistical data.
  • Joslyn, Cliff and Klir, George: (1992) "Minimal Information Loss Possibilistic Approximations of Random Sets", in: Proc. 1992 FUZZ-IEEE Conference, ed. Jim Bezdek, pp.1081-1088, IEEE, San Diego
    • An empirical measuring procedure which yields data governed by possibility theory. Set-based statistics are used to generate empirically derived random sets. Normal possibility distributions are available for all consistent random sets, and a set of ``consistent transformations'' are available for all inconsistent random sets. The Principle of Uncertainty Invariance is used in a modified form to select the consistent transformation with minimal information loss from the original random set.
  • Joslyn, Cliff: (1991) "Hierarchy, Strict Hierarchy, and Generalized Information Theory", in: Proc. ISSS 1991, v. 1, pp.123-132
    • (Winner, Vickers Memorial Award for Best Student Paper) Strict hierarchy as tree, loose hierarchy as DAG; loose structural hierarchies as class relations; proposed measure of looseness of random sets.
  • Joslyn, Cliff: (1991) "Software Support for Principia Cybernetica Development", in: Workbook of the First Principia Cybernetica Workshop, ed. F. Heylighen, pp.49, Principia Cybernetica, Brussels, NY
  • Joslyn, Cliff: (1991) "Control Theory and Metasystem Theory", in: Workbook of the First Principia Cybernetica Workshop, ed. F. Heylighen, pp.24-32, Principia Cybernetica, Brussels, NY
    • Comparison of Turchin's and Powers' cybernetic theories.
  • Joslyn, Cliff: (1991) "Towards an Empirical Semantics of Possibility Through Maximum Uncertainty", in: Proc. IFSA 1991, v. A, pp.86-89
    • Extended abstract: application of maximum nonspecificity as normalization method for possibilistic random sets.
  • Joslyn, Cliff: (1989) "Notes on the Semantics of Entropy", in: Proceedings of the 1989 Conference of the American Society for Cybernetics
    • (Winner, ASC Travel Scholarship Award)

    Peer Reviewed Posters and Presentations

  • CA Joslyn: (2006) "Semantic Hierarchies as Ordered Data Objects'', Extended MetaData Registry project (XMDR) project meeting, Lawrence Berkeley National Laboratory, Berkeley, California, July, 2006

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  • CA Joslyn: (2006) "Reconstructibility Analysis as an Order Theoretical Knowledge Discovery Technique'', special session on Reconstructibility Analysis, 2006 International Conference on Complex Systems, Boston, July, 2006

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  • KM Verspoor, JD Cohn, SM Mniszewski, and CA Joslyn: (2005) "Mathematical Techniques for Predicting and Analyzing Ontological Protein Function Annotations", 3rd Annual Rocky Mountain Regional Bioinformatics Conf. (Rocky 05)
  • Joslyn, CA; Cohn, JD; Verspoor, KM; and Mniszewski: (2005) "Automating Ontological Function Annotation: Towards a Common Methodological Framework", Bio-Ontologies SIG, ISMB 05
  • Joslyn, CA; Cohn, JD; Verspoor, KM; and Mniszewski: (2005) "Automating Ontological Function Annotation: Towards a Common Methodological Framework", Bio-Ontologies SIG, ISMB 05
  • Joslyn, CA; SM Mniszewski, KM Verspoor; and JD Cohn: (2005) "Improved Order Theoretical Techniques for GO Functional Annotation'', Intelligent Systems for Molecular Biology (ISMB 05)
  • KM Verspoor; JD Cohn; SM Mniszewski, and Joslyn, CA : (2005) "Nearest Neighbor Categorization for CASP Function Prediction'', Intelligent Systems for Molecular Biology (ISMB 05)
  • Cohn, Judith; Verspoor, K; Mniszewski, SM; and Joslyn, CA: (2004) "Predicting Protein Function Using Nearest Neighbor Categorization", Proc. 2nd Annual Rocky Mountain Regional Bioinformatics Conf. (Rocky 04)
  • Joslyn, Cliff and Mniszewski, Susan: (2004) "Combinatorial Approaches to Bio-Ontology Management with Large Partially Ordered Sets", in: SIAM Workshop on Combinatorial Scientific Computing (CSC 04)
  • Booker, JM, TM Ross, F Hemez, M Anderson, B Reardon, and CA Joslyn: (2003) "Quantifying Total Uncertainty in a Validation Assessment Using Different Mathematical Theories", Ninth ASCE Joint Specialty Conference on Probabilistic Mechanics and Structural Reliability
  • Joslyn, Cliff: (2003) "Multi-Poset-Based Approaches to Bio-Ontologies", in: First Rocky Mountain Regional Bioinformatics Meeting
  • Joslyn, Cliff; Verspoor, Karin; and Papcun, George: (2003) "Lexical Management of Domains: Towards Integration of Computational Linguistic and Ontological Resources", Poster at NAS Sackler Workshop on Mapping Knowledge Domains
  • Booker, JM, TM Ross, F Hemez, MC Anderson, CA Joslyn, and B Reardon: (2003) "Quantifying Total Uncertainty and Performance Margin in Assessing the Reliability of Manufactured Systems", Fifth Tri-Laboratory Engineering Conference
  • Joslyn, Cliff, SM Mniszewski, AW Fulmer, and GG Heaton: (2003) "Structural Classification in the Gene Ontology", in: Proc. 6th Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB 03)
  • Verspoor, Karin; Joslyn, Cliff; and Papcun, George: (2003) "Interactions Between the Gene Ontology and a Domain Corpus for a Biological Natural Language Processing Application", in: Proc. 6th Bio-Ontologies Workshop, Intelligent Systems for Molecular Biology (ISMB 03)
  • Joslyn, Cliff, Susan Mniszewski, Andy Fulmer, and Gary Heaton: (2003) "Measures on Ontological Spaces of Biological Function", poster at the 2003 Pacific Symposium on Biocomputing (PSB 03)
  • Joslyn, Cliff and Oberkampf, William: (2002) "Uncertainty Quantification of Simulation Codes Using Probability Intervals", presented at the 2002 Workshop on Quantification of Uncertainty in Physics Simulations, Los Alamos National Laboratory
  • Joslyn, Cliff: (2002) "The Bio-Ontological Challenge: Representations of, and Measures in, Lattice-Valued Spaces", presented at the 2002 Workshop on Enabling Concepts for Systems Biological Modeling, Santa Fe

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  • Joslyn, Cliff: (2002) "Link Anlaysis of Social Meta-Networks", presented at the 2002 Conf. on Computational Analysis of Social and Organizational Systems (CASOS 02)

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  • Joslyn, Cliff: (2001) "A Semiotic Critique of the Limits of Formal Models", 2001 Workshop on Virtual Worlds and Simulation (VWSim01)
  • Joslyn, Cliff: (2001) "Systems Concepts for the Simulation of Ultra-Large Networks", NSF Workshop on Modeling and Simulation of Ultra-Large, SCS, Tucson
  • Joslyn, Cliff: (2001) "What Could We Mean By `Global Brain': How Distributed Knowledge Systems Facilitate Social Control in Semiotic Agent-Based Architectures", in: Workshop on Intelligent Networks and Social Evolution
  • Joslyn, Cliff: (1995) "Network Dynamical Approach to Articial Life: Morowitz' Challenge", accepted for poster at 1995 European Conf. on Artificial Life
    • Consideration of the consequences of Morowitz's chemical network dynamical, cellular, approach ot the origins of life for Artificial Life research.

    Lecture Notes

  • Joslyn, Cliff: (2004) "A Formerly Breathless Introduction to Generalized Information Theory", LANL short course
  • Joslyn, Cliff: (2003) "Ontologies for Knowledge-Based Science: Building a Computational Semiotics", presented at the NASA Godrard Information Science and Technology Colloquium
  • Joslyn, Cliff: (2001) "Semiotic Approach to Knowledge Integration Technologies and Environments"
    • LAUR = 01-1577
  • Joslyn, Cliff: (2000) "A Semiotic Systems Approach to Distributed Knowledge Systems", Presented at SRI International
    • LAUR=003596

    Technical Reports and Electronic Publications

  • KM Verspoor, CA Joslyn, JA Ambrosiano, A Backer, O Bodenreider, L Hirschman, P Karp, H Kelly, S Loranger, M Musen. R Sriram, and C Wroe: (2005) "Knowledge Integration for Biothreat Response{}'', LAUR 05-0907
  • Joslyn, Cliff: (2004) "GIT Analysis of the Crushable Foam Experiment and Simulations", LANL Technical Report LAUR 04-6207

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  •  Joslyn, Cliff; W Buehring, PG Kaplan, and DR Powell: (2004) "Critical Infrastructure Protection Decision Support System (CIP/DSS): Addressing Uncertainty and Risk'', LAUR 04-6720
  • Joslyn, Cliff, Oliverira, Joseph, and Scherrer, Chad: (2004) "Order Theoretical Knowledge Discovery: A White Paper", LANL Technical Report LAUR 04-5812

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  • Verspoor, Karin; Joslyn, Cliff; and Papcun, George: (2004) "A Lexical Semantic Network Induced from the Gene Ontology", LANL Technical Report LAUR 04-3934
  • Joslyn, Cliff and Mniszeiski, Susan: (2002) "DEEP: Data Exploration through Extension and Projection", LANL Technical Report LAUR 02-1330
    • Guided discovery in relational databases using compression and entropy measures.
  • Voss, Susan and Cliff Joslyn: (2002) "Advanced Knowledge Integration in Assessing Terrorist Threats",  LANL Technical Report LAUR 02-7867
  • Joslyn, Cliff and Mniszewski, Susan: (2002) "Relational Analytical Tools: DataDelver and Formal Concept Analysis", LANL Technical Report 02-7697
    • VisTool provides a schema-speci.c visualizing front end to relational databases; user-guided knowledge discovery; Formal Concept Analysis (FCA) to provide an unbiased, visual display of the complex sub-relations present in database tables, and to support both manual inspsection and query of relational data, and automated hypothesis generation and analysis.
  • Joslyn, Cliff: (2000) "Hypergraph-Based Representations for Portable Knowledge Management Environments", LANL Technical Report LAUR 00-5660, 2000.
    • Semantic hyperwebs as labeled, weighted, directed hypergraph-theoretical structures, similar to weighted conceptual graphs, as a canonical framework. technologies to support implementation.
  • Joslyn, Cliff, Luis Rocha and Achla Marathe: (2000) "Development Environments and Systems Architectures for Hybrid Agent-Stochastic Event Models of Socio-Technical Organizations", LANL Technical Report LAUR 01-4693, 2000.
    • Proposed simulation environment for hybrid agent stochastic-event modeling; a proposed experimental paramaterization for agent models in general; and a consideration of various platforms for the development of agent models, with special attention on Swarm and DEVS/HLA.
  • Joslyn, Cliff: (1999) "Semiotic Agent Models for Simulating Socio-Technical Organizations", prepared for the Physical Science Laboratory, New Mexico State University, as part of the research project Decision Structures of Socio-Technical Organizations.
    • The semiotic approach to agent-based models of socio-technical organizations and command and control organizations.
  • Joslyn, Cliff; Hogden, John; Kantor, Marianna; and Johnson, Norman: (1997) "Semantic Representations for Collaborative, Distributed Scientific Information Systems", funding proposal for LDRD-IP grant, Los Alamos National Laboratory.
  • Joslyn, Cliff; Ames, Troy; Ziyad, Nigel; and Mueller, Karl: (1996) "TRENDS: Intelligent Model-Based Trend Analysis of Spacecraft Systems", Technical Report # DSTL-96-014, NASA Goddard Space Flight Center, Greenbelt MD
    • Model-based approach to trend analysis; qualitative approaches; architecture of DASME; implementation.
  • Kantrowitz, Mark; Horstkotte, Erik; and Joslyn, Cliff: (1994) Answers to Frequently Asked Questions about Fuzzy Logic and Fuzzy Expert Systems, for comp.ai.fuzzy
  • Joslyn, Cliff: (1994) "Possibilistic Qualitative Model-Based Diagnosis and Trend Analysis of Spacecraft Systems"
    • Succesful application for NRC postdoctoral research position with the NASA's Goddard Space Flight Center.
  • Joslyn, Cliff: (1994) "Possibilistic Representations of Measurement Combination Problems"
    • Succesful application for NRC postdoctoral research position with the National Institute of Standards and Technology's Statistical Engineering Laboratory in Boulder, CO: measurement as a random set problem; combination of consistent measurements through possibility theory.
  • Turchin, Valentin; Heylighen, Francis; and Joslyn, Cliff: (1992) 1992 Principia Cybernetica Nodes, Principia Cybernetica Technical Report
  • Joslyn, Cliff: (1991) "Control Theory and Cybernetic Ontology", PCP Technical Report
    • Comparison of William Powers' Control Theory and the Meta-System Transition Theory of Principia Cybernetica.
  • Joslyn, Cliff: (1991) "Errata of Life Itself by Robert Rosen"
    • Written in conjunction with book review.
  • Joslyn, Cliff: (1990) "Tools for Development of Consensually Based Philosophical Systems", PCP Technical Report
    • Early ideas about software technology to support Principia Cybernetica: hypertext, hypermedia, electronic mail, electronic publishing, HyTime, SGML.

    Book Reviews

  • Joslyn, Cliff: (1992) "Review: Self-Modifying Systems, by George Kampis", Int. J. of General Systems
  • Joslyn, Cliff: (1993) "Review: Life Itself, by Robert Rosen", Int. J. of General Systems, v. 21, pp.394-402


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