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__Journal Papers:__

*Self-Organizing Map Convergence*, Robert Tatoian, Lutz Hamel,
the International Journal of Service Science, Management, Engineering, and Technology (IJSSMET),
IGI Global, to appear.

*Advanced Classification of Carbonate Sediments Based on Physical Properties,*
Tania Lado-Insua, Lutz Hamel, Kathryn Moran, Louise M. Anderson, and Jody M. Webster,
Sedimentology, Volume 62, Issue 2, pages 590-606, February 2015, DOI:10.1111/sed.12168

*Adverse moisture events predict seasonal abundance of Lyme disease vector ticks (Ixodes scapularis)*,
Kathryn A Berger, Howard S Ginsberg, Katherine D Dugas, Lutz H Hamel and Thomas N Mather, Parasites & Vectors 2014, 7:181 doi:10.1186/1756-3305-7-181

*Bayesian Probability Approach to Feature Significance for Infrared Spectra of Bacteria*,
Lutz Hamel, Chris W. Brown, Applied Spectroscopy, Volume 66, Number 1, 2012. (R code for map construction and
feature selection)

*Sensitivity of Raman Spectra to Chemical Functional Groups*,
Kevin Judge, Chris W. Brown, and Lutz Hamel. Appl Spectrosc. 2008 Nov;62(11):1221-5.

*Sensitivity of Infrared Spectra to Chemical Functional Groups*,
Kevin Judge, Chris W. Brown, and Lutz Hamel.
Anal. Chem., 80 (11), 4186-4192, 2008.

*Unsupervised Learning in Detection of Gene Transfer*,
Lutz Hamel, Neha Nahar, Maria S. Poptsova, Olga Zhaxybayeva, and J. Peter Gogarten.
Journal of Biomedicine and Biotechnology, vol. 2008, Article ID 472719, 7 pages, 2008. doi:10.1155/2008/472719

*PentaPlot: A Software Tool for the Illustration of Genome Mosaicism*,
Lutz Hamel, Olga Zhaxybayeva, and J. Peter Gogarten.
BMC Bioinformatics, 2005 6:139, http://www.biomedcentral.com/1471-2105/6/139

*The Error Engine, *
Judd Morrissey, Lori Talley and Lutz Hamel.
Performance Research, Vol 9 Issue 2, pp 63, December 2004.

*Visualization of the phylogenetic content of five genomes using dekapentagonal maps*,
Olga Zhaxybayeva, Lutz Hamel, Jason Raymond and J Peter Gogarten.
Genome Biology, 2004 5:R20, http://genomebiology.com/2004/5/3/R20

*Industrial Strength Compiler Construction with Equations*,
ACM SIGPLAN Notices, Vol 27(8), August 1992.

__Books and Book Chapters__

*Programming Language Implementation with Python*, Lutz Hamel, Franklin, Beedle & Assoc., to appear. (a draft of the book appears here

*Knowledge Discovery with Support Vector Machines*, Lutz Hamel, Wiley & Sons, 2009.

*Customer Relationship Management and Knowledge Discovery in Databases.* Dholakia, N., Joung Hae Bang, Lutz Hamel and Seung-Kyoon Shim, Encyclopedia of Information Science and Technology. 2d ed. 2009. II:902-907.

*Database Queries, Data Mining and OLAP*, Lutz Hamel, The Encyclopedia of Data Warehousing and Mining, 2nd Edition, Idea Group Publishers, 2008.

*Model Assessment with ROC Curves*, Lutz Hamel, The Encyclopedia of Data Warehousing and Mining, 2nd Edition, Idea Group Publishers, 2008. (R code and data used in this chapter.)

*A Brief Tutorial on Database Queries, Data Mining and OLAP*, Lutz Hamel, The Encyclopedia of Data Warehousing and Mining, Idea Group Publishers, 2005.

*The CRM-KDD Nexus,* Nikhilesh Dholakia, Jounghae Bang, Lutz Hamel and Seung-Kyoon Shin, Encyclopedia of Information Science and Technology, pp 2803-2808, Idea Group Publishers, 2005.

*An Optimizing C* Compiler for a Hypercube Multicomputer*, in Languages, Compilers, and Run-Time Environments for Distributed Memory Machines, pp. 285-298, Elsevier Science Publishers, 1992. J. Saltz and P. Mehrotra (eds.). Joint publication with Philip Hatcher and Michael Quinn.

__Conference and Workshop Proceedings:__

*Assortative Mixture of English Parts of Speech*, Leonard, T., Hamel, L., Daniels, N.M. and Katenka, N.V., Complex Networks & Their Applications VI,
Proceedings of Complex Networks 2017, pp 463- 476, Springer Verlag, 2017.

*SVM Constraint Discovery using KNN applied to the Identification of Cyberbullying*,
D. Ducharme, L. Costa, L. DiPippo, and L. Hamel.
Proceedings of the 2017 International Conference on Data Mining (DMIN'17), pp111-117, 2017, Las Vegas, Nevada, USA, ISBN: 1-60132-453-7, CSREA Press.

*Formal Methods: A First Introduction using Prolog to specify Programming Language Semantics*,
Lutz Hamel.
Proceedings of the 12th International Conference on Foundations of Computer Science (FCS'16), pp70-76, July 25-28, 2016, Las Vegas, Nevada, USA, ISBN: 1-60132-434-0, CSREA Press.
(proof scores)

*Protein Structure-Function Analysis with Self-Organizing Maps*,
Seojoo Lim, Stephen Jaegle, and Lutz Hamel.
Proceedings of the 17th International Conference on Bioinformatics & Computational Biology (BIOCOMP'16), pp10-16, July 25-28, 2016, Las Vegas, Nevada, USA, ISBN: 1-60132-428-6, CSREA Press.

*Self-Organizing Map Convergence*,
Robert Tatoian and Lutz Hamel.
Proceedings of the 2016 International Conference on Data Mining (DMIN'16), pp92-98, July 25-28, 2016, Las Vegas, Nevada, USA, ISBN: 1-60132-431-6, CSREA Press.

*SOM Quality Measures: An Efficient Statistical Approach*,
Lutz Hamel, Proceedings of the 11th International Workshop WSOM 2016, Houston, Texas USA,
E. Merenyi et al. (eds.), Advances in Self-Organizing Maps and Learning
Vector Quantization, Advances in Intelligent Systems and Computing 428, Springer, pp 49-59,
DOI 10.1007/978-3-319-28518-4_4, 2016.

*Cartogram Data Projection for Self-Organizing Maps*,
David H. Brown and Lutz Hamel.
Proceedings of the 2012 International Conference on Data Mining (DMIN'12), pp91-97, July 16-19, 2012, Las Vegas Nevada, USA.

*A Population Based Convergence Criterion for Self-Organizing Maps*,
Lutz Hamel and Benjamin Ott.
Proceedings of the 2012 International Conference on Data Mining (DMIN'12), pp98-104, July 16-19, 2012, Las Vegas Nevada, USA. (R code available here)

*Improved Interpretability of the Unified Distance Matrix with Connected Components*,
Lutz Hamel and Chris W. Brown.
Proceedings of the 7th International Conference on Data Mining (DMIN'11), July 18-21, 2011, Las Vegas Nevada, USA, ISBN: 1-60132-168-6, pp338-343,
CSREA Press, 2011. (R code available here)

*Experience Report: Erlang in Acoustic Ray Tracing*,
Christian Convey, Andrew Fredricks, Christopher Gagner, Douglas Maxwell, and Lutz Hamel.
Proceeding of the 13th ACM SIGPLAN International Conference on Functional programming, pp115-118,
Victoria, BC, Canada, 2008.
(C++ and Erlang source code)

*Unsupervised Learning in Spectral Genome Analysis*,
Lutz Hamel, Neha Nahar, Maria S. Poptsova, Olga Zhaxybayeva, and J. Peter Gogarten. Proceeding of the IEEE Conference Frontiers in the Convergence of
Bioscience and Information Technologies (FBIT 2007), October 2007, pp317 - 321, IEEE Press, ISBN 0-7695-2999-2.

*GPX: A Tool for the Exploration and Visualization of Genome Evolution*,
Neha Nahar, Maria S. Poptsova, Lutz Hamel, and J. Peter Gogarten.
Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07), Oct 14th-17th 2007, Boston, pp1338 - 1342, IEEE Press, ISBN 1-4244-1509-8.

*An Inductive Programming Approach to Algebraic Specification*,
Lutz Hamel and Chi Shen.
Proceedings of the ECML 2007 Workshop on Approaches and Applications of Inductive Programming (AAIP'07), September 2007, pp. 3-15.

*The Internet Democracy: A Predictive Model Based on Web Text Mining*,
Scott Pion and Lutz Hamel.
Proceedings of the 2007 International Conference on Data Mining. Robert Stahlbock, Sven F. Crone, Stefan Lessman, Hamid R. Arabnia; Editors. pp292-298, CSREA Press, U.S.A., 2007.

*Comparing the Results of Support Vector Machines with
Traditional Data Mining Algorithms*, Scott Pion and Lutz Hamel, Proceedings of the 2007 International Conference on Data Mining. Robert Stahlbock, Sven F. Crone, Stefan Lessman, Hamid R. Arabnia; Editors. pp79-83, CSREA Press, U.S.A., 2007.

*Visualizing Support Vector Machines with Unsupervised Learning, *Lutz Hamel, IEEE 2006 Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp148-155, Toronto, Canada, IEEE, 2006, ISBN 1-4244-0623-4.

*Toward Protein Structure Analysis with Self-Organizing Maps*, Lutz Hamel, Gongqin Sun, and Jing Zhang, IEEE 2005 Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp506-513, La Jolla, CA, IEEE, 2005, ISBN 0-7803-9387-2.

*A Genetic Algorithm for Energy Minimization in Bio-molecular Systems*, Xiaochun Weng, Lutz Hamel, Lenore Martin and Joan Peckham, IEEE 2005 Congress of Evolutionary Computation, pp49-56, Edinburgh, UK, IEEE, 2005, ISBN 0-7803-9363-5.

*Classification for Scaling Methods in Data Mining, *Eric Kyper, Lutz Hamel, and Scott Lloyd, Annual Meeting of Decision Sciences Institute (DSI 2005), San Francisco, 2005.

*Data Mining Of CRM Knowledge Bases For Effective Market Segmentation*, Jounghae Bang, Nikhilesh Dholakia, Lutz Hamel, and Ruby Roy Dholakia, Proceedings of the 6th International Conference on Enterprise Information Systems (ICEIS 2004), Porto, Portugal, 2004.

*Comparing CRM-based Data Mining and Collaborative Filtering as E-Commerce Strategic Tools, *Nikhilesh Dholakia, Jounghae Bang, Lutz Hamel, and Ruby Roy Dholakia, Proceedings of the 2004 IRMA International Conference, New Orleans, Information Resources Management Association, 2004.

*Evolutionary Search in Inductive Equational Logic Programming*, Lutz Hamel, Proceedings of the Congress on Evolutionary Computation, pp2426-2434, Canberra, Australia, IEEE, 2003, ISBN 0-7803-7805-9

*Breeding Algebraic Structures--An Evolutionary Approach To Inductive Equational Logic Programming*, GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference, 2002, pp 748-755, Morgan Kaufmann Publishers.

*Adding Equations to PCCTS*, Lutz Hamel, Proceedings of the Second Annual Workshop on PCCTS, 1995.

*Towards a Povably Correct Compiler for OBJ3*, Proceedings of the Programming Language Implementation and Logic Programming Symposium 1994, Lecture Notes in Computer Science 844, Springer-Verlag, 1994. Joint publication with Joseph Goguen.

*UCG-E: An Equational Logic Programming System*, Proceedings of the Programming Language Implementation and Logic Programming Symposium 1992, Lecture Notes in Computer Science 631, Springer-Verlag, 1992.

__Abstracts and Posters:__

*Self Organizing Maps and Locally Linear Embedding for Dimensionality Reduction*, Vishakh Gopu and Lutz Hamel,
Poster presented at the Sigma Xi Conference 2015, won best poster in the category of computer science, mathematics, and engineering.

*Population Based Convergence Criterion for Self-Organizing Maps*, Benjamin Ott, Gregory Breard, Lutz Hamel,
Poster presented at the NESS meeting at UCONN, 2013.

*Inductive Acquisition of Algebraic Specifications*, Lutz Hamel and Chi Shen, Abstract presented at Workshop for Algebraic Development Techniques (WADT 2006), La Roche, Belgium, June, 2006.

*Protein Structure Analysis with Self-Organizing Maps,* Jing Zhang, Gongqin Sun, and Lutz Hamel, Poster presented at the INBRE Summer meeting, Exeter, Rhode Island, June, 2005.

*High-Throughput Active Site Structure Analysis of Proteins Using Self-Organizing Map-Based Unsupervised Machine Learning,* Jing Zhang, Gongqin Sun, and Lutz Hamel. Poster presented at the INBRE winter meeting,

*Can we predict IVF outcomes?* Julie Goodside, Leah Passmore, Lutz Hamel, Liliana Gonzalez, Tali Silberstein, Richard Hackett, David L. Keefe and James R. Trimarchi, Abstract presented at the 2004 First Quarterly Meeting of The New England Fertility Society and The Annual Assembly of the New England Fertility Society (NEFS2004), March 12 – 14, 2004.

*Comparing Data Mining and Logistic Regression for Predicting IVF Outcome*, J. R. Trimarchi, J. Goodside, L. Passmore, T. Silberstein, L. Hamel, L. Gonzalez, Abstract presented at the 59th Annual meeting of the American Society for Reproductive Medicine (ASRM 2003), San Antonio, TX, October 11-15, 2003.

*An Improved Probability Mapping Approach*, Olga Zhaxybayeva, Lutz Hamel, and J. Peter Gogarten, Poster presented at the Annual Retreat of the Department of Molecular and Cell Biology,

*An Improved Probability Mapping Approach*, Olga Zhaxybayeva, Lutz Hamel, and J. Peter Gogarten, Poster presented at the Annual Meeting of the Canadian Institute for Advanced Research, Evolutionary Biology Program at

*An Improved Probability Mapping Approach*, Olga Zhaxybayeva, Lutz Hamel, and J. Peter Gogarten, Poster presented at Exobiology Principal Investigators' Seventh, Triennial Science Conference,

*Comparing Data Mining and Logistic Regression for Predicting IVF Outcome*, J. R. Trimarchi, J. Goodside, L. Passmore, T. Silberstein, L. Hamel, L. Gonzalez, Poster presented at the Annual BRIN meeting,

*Genetic Operators and Inductive Logic Programming: Fisher's Theorem of Natural Selection*, Lutz Hamel. Poster accepted at the Genetic and Evolutionary Computation Conference (GECCO 2003), Chicago, July 2003, retracted due to personal reasons.

__Theses:__

Plat: A Web Based Protein Local Alignment Tool, Stephen H. Jaegle, MS Thesis, 2017.

Evaluating Self-Organizing Map Quality Measures as Convergence Criteria, Gregory T. Breard, MS Thesis, 2017.

Deep Belief Networks in Clojure, J. Christopher Sims, MS Thesis, December 2015. **Best CS Thesis Award**

Protein Structure Analysis with SOM, Seonjoo Lim, MS Thesis, December 2015.

Training And Source Code Generation For Artificial Neural Networks, Brandon Winrich, MS Thesis, November 2015.

A Constructive Semantics For Rewriting Logic, Michael N. Kaplan, PhD Thesis, December 2014.

Use Of Reinforcement Learning (RL) For Plan Generation In Belief-Desire-Intention (BDI) Agent Systems, Jose L. Feliu, MS Thesis, December 2013.

Towards Efficient Stochastic Optimization of Functions of Convex Sets, Christian Convey, PhD Thesis, May 2013.

A Self-Interpreter for Prolog, Aseel Alkhelaiwi, MS Thesis, April 2012.

Cartogram Data Projection for Self-Organizing Maps , David Brown, MS Thesis, April 2012. **Best CS Thesis Award**

A Convergence Criterion for Self-Organizing Maps, Benjamin Ott, MS Thesis, April 2012.

Bipartition Visualization using Self-Organizing Maps, Neha Nahar, MS Thesis, July 2007.

The Internet Democracy: A Predictive Model Based On Web Text Mining, Scott Pion, MS Thesis, April 2007.

Automatic Narrative Evolution Web Crawler, Hyejin Yun, MS Thesis, April 2006.

Evolutionary Concept Learning in Equational Logic, Chi Shen, MS Thesis, April 2006.

Text Mining with Support Vector Machines and Non-Negative Matrix Factorization Algorithms, Neelima Guduru, MS Thesis, April 2006.

*Support Vector Machines as Pattern Classifier for In Vitro Fertilization Data*, Natalya Dymova, MS Thesis, April 2005.

*A Genetic Algorithm for Bio-Molecular Systems*, Wendy Weng, MS Thesis, April 2005.

*Prediction Analysis Using In Vitro Fertilization Data Based on Data Mining Techniques*, Julie Goodside, MS Thesis, May 2004.

__Technical Reports and White Papers__

*Inductive Acquisition of Algebraic Specifications*, Lutz Hamel, and Chi Shen, Technical Report TR06-317, Department of Computer Science and Statistics,

*Evaluating the SVM Component in Oracle 10g Beta*, Lutz Hamel, Angela Uvarov, and Susie Stephens, Technical Report TR04-299, Department of Computer Science and Statistics,

*Automatic Narrative Evolution: A White Paper*, Lutz Hamel, Judd Morrissey and Lori Talley, White Paper, errorengine.org, 2004.

*On the Use of Machine Learning in Formal Software Verification*, Lutz Hamel, Technical Report TR03-294, Dept. of Computer Science and Statistics,

*Assessing Decision Tree Models for Clinical In-Vitro Fertilization Data*, J. R. Trimarchi, J. Goodside, L. Passmore, T. Silberstein, L. Hamel, L. Gonzalez, Technical Report TR03-296, Dept. of Computer Science and Statistics,

*Introducing TRIM*, Lutz Hamel, Technical Report TR01-283, Dept. of Computer Science and Statistics,

*An Algebraic View of Inductive Equational Logic Programming*, Lutz Hamel, Technical Report TR00-278, Dept. of Computer Science and Statistics,

*The Object-Oriented Architecture of High-Performance Compilers*, Lutz Hamel, Diane Meirowitz and Spiro Michaylov, Technical Report, Thinking Machines Corporation, 1996.

*Towards a provable correct compiler for OBJ3,* Lutz Hamel,* *Programming Research Group Technical Report TR-1-94, *February 1994, 52pp.*

__Seminars, Talks, Panel Discussions, etc:__

*The Evolution of Programming Languages: A Personal Perspective*, Lutz Hamel, Talk, URI Programming Language Research Group, Spring '16.

*Automatic Theorem Proving: A Very Brief Introduction*, Lutz Hamel, Talk, URI Discrete Mathematics Group, Spring '15. (Prolog code)

*Big Data: The Science of Patterns*, Lutz Hamel, Talk, High-Performance Computing Class, Fall '14.

*Advances in Self-Organizing Maps*, Lutz Hamel, Invited Talk, Connecticut Data Mining Conference, April 2012.

*Practical Tools for Self-Organizing Maps*, Lutz Hamel and Chris Brown, Talk, Bioinformatics Class, Spring '09.

*New Tools for Visualizing Genome Evolution*, Lutz Hamel and Peter Gogarten, talk given at the NASA AISRP PI Meeting, University of Maryland, May 2008.

*An Inductive Programming Approach to Algebraic Specification*, Lutz Hamel, invited talk, ECML 2007 Workshop on Approaches and Applications of Inductive Programming, Warsaw, Poland, September 17th, 2007.

*Investigating Support Vector Machines with Unsupervised Learning*, Lutz Hamel, Invited Talk, DIMACS Workshop on Discrete Mathematical Problems in Computational Biomedicine
DIMACS Center, CoRE Building, Rutgers University, April 18 - 20, 2007.

*Expect the Unexpected: AI in Games and Narrative*, Lutz Hamel, E-Fest 2006, Brown University, Providence, March 22-24, 2006.

*A Genetic Algorithm for Energy Minimization in Bio-molecular Systems, *Lutz Hamel, Chemistry Department Seminar Series, University of Rhode Island, September 2005.

*Protein Structure Analysis with Self-Organizing Maps, *Lutz Hamel, INBRE Bioinformatics Seminar Series,

*Investigating Genome Mosaicism using the Oracle Data Miner,* Lutz Hamel, Oracle Life Sciences User Group Conference, Bio-IT World,

*New Tools for Visualizing Genome Evolution, *Lutz Hamel, given at NASA, NASA AISRP PI Meeting, NASA Ames Research Center, April 2005.

*Data Mining and Science Informatics, *Lutz Hamel, Chemical Engineering Seminar Series,

*Bioinformatics at the University of Rhode Island, *Lutz Hamel, given at Framingham State College, Bioinformatics Colloquium Series, February 2005.

*From The Error Engine: Experiments in Self-Evolving Narrative,* Lutz Hamel, Judd Morrissey, and Lori Talley, Exhibition, Fine Arts Gallery, University of Rhode Island, Kingston, RI, January 27^{th}-March 6^{th}, 2005.

*What Exactly is the Difference between Database Queries, Data Mining, and OLAP?,* Lutz Hamel, Data Mining Series Talk, October 2004.

*From The Error Engine,* Judd Morrissey, Lori Talley, Lutz Hamel, Exhibition, 1926 Gallery, Chicago, September 24^{th} – October 3^{rd}, 2004.

*The Error Engine: Creative Evolutionary Systems and Narrative*, Judd Morrissey, Lori Talley, Lutz Hamel, Panel discussion at the Computers and Writing Conference (CW2004), University of Hawaii, Honolulu, Hawaii, June 10-13, 2004.

*Beyond Attribute-Value Data Mining, *Lutz Hamel, invited talk at the

*Narrative Time and Machine Writing*, Judd Morrissey, Lori Talley, Lutz Hamel, Panel discussion at the 17th Annual meeting of the Society for Literature and Science (SLS2003), Austin, TX, October 23-26, 2003.

*Data Mining 101*, Data mining seminar for BRIN participants, Lutz Hamel and Julie Goodside, August 13, 2003.