PUBLICATIONS |
Presentations
| Presentations of 2003 | Author | Date |
| Kernel PLS Feature Selection with Sensitivity Analysis
for In-Silico Drug Design (Presented at Artificial Neural Networks in Engineering, November 2-5, 2003) |
Nov. 2003 | |
| The Direct-Kernel Self-Organizing Map (DK-SOM) (Presented at Artificial Neural Networks in Engineering, November 2-5, 2003) |
Nov. 2003 | |
| Use of Machine Learning for Classification of Magnetocardiograms (Presented at the 2003 IEEE Conference on Systems, Man, and Cybernetics, SMC 2003, October 5-8, Washington D.C.) |
Oct. 2003 | |
| Fuzzy
Bar-code Representations of DNA-Protein Interactions (Presented at the ACS National Meeting, New York City, September 2003) |
Nagamani
Sukumar Curt M. Breneman Kristin P. Bennett |
Sep. 2003 |
| Predicting 8-Aminocyclazocine Analogues using TAE,
PEST, PAD Descriptors and Machine Learning Methods (Presented at ACS NYC, Sept 2003 – CCG Award Winner) |
Lingling Shen, Curt M. Breneman, Mark J. Embrechts | Sep. 2003 |
| Outlier Detection (Presented at Concurrent Pharmaceuticals, Fort Washington, PA, September 17, 2003) |
Mark J. Embrechts | Sep. 2003 |
| Molecular Property Descriptors with High Information
Content for Producing Models with Chemistry-In/Chemistry-Out: From Virtual
Library Screening to Bioinformatics (Plenary Presentation - Computer Aided Drug Design Gordon Conference, Tilton School, NH, July 2003) |
Curt M. Breneman | Jul. 2003 |
| Partial Least Squares Support Vector Machines for
Molecular Drug Design: Feature Selection and Regularization (Presented at Gordon Conference on Drug Design, Tilton, NH., July 20-25, 2003) |
Mark J. Embrechts Curt M. Breneman Kristin P. Bennett |
Jul. 2003 |
| Introduction to Scientific data Mining with Direct
Kernels: Methods and Applications (Presented at 2003 Summer Course on Neural Networks, NN2003, Porto, Portugal, July 9, 2003 (invited)) |
Mark J. Embrechts | Jul. 2003 |
| Direct Kernel Methods: Methods and Applications (Presented at 2003 International IEEE Workshop on Soft Computing in Industrial Applications, SMCia/03, pp. 109-114, Binghamton, New York, June 23-25, 2003 (invited)) |
Mark J. Embrechts | Jun. 2003 |
| Feature Selection for In-Silico Drug Design using
Genetic Algorithms with Implicit Nonlinear Latent Variable Regression (Presented at the Joint 13th International Conference on Neural Networks and the 10th International Conference on Neuroinformation Processing, ICANN/IONIP 2003, Istanbul, Turkey, June 26-29, 2003) |
Jun. 2003 | |
| Direct Kernel Methods: Support Vector Machines for
the Rest of Us (Presented at GE R&D Center, Niskayuna, NY, May 9, 2003) |
Mark J. Embrechts | May 2003 |
| Least Squares Support Vector Machines for Molecular
Design: Feature Selection and Regularization (Presented at the 2003 Learning Workshop, Snowbird, Utah, April 1-4, 2003) |
Apr. 2003 | |
| Predicting Protein-Ligand Binding Affinities using
Transferable Atom Equivalent Techniques and Machine-Learning Methods,”
Paper #COMP297 (Presented at the 225th ACS National Meeting, New Orleans, LA, March 23-27, 2003) |
Curt M.
Breneman Nagamani Sukumar Mark J. Embrechts |
Mar. 2003 |
| Optimization of Molecular Properties through Structural
Mutation and Virtual Screening,” Paper #COMP376 (Presented at the 225th ACS National Meeting, New Orleans, LA, March 23-27, 2003) |
Mar. 2003 | |
| K-PLS for QSAR: A Nonlinear SVM-Like Approach to
PLS, Paper #COMP293 (Presented at the 225th ACS National Meeting, New Orleans, LA, March 23-27, 2003) |
Mar. 2003 | |
| Presentations of 2002 | Author | Date |
| Selecting Regressors with Partial Least Squares
Sensitivity Analysis: An Application to Currency Crises’ Real Effects (Presented as Paper C45 and F41 in Proceedings of the Latin American and Caribbean Economic Conference, pp. 898 – 943, Madrid, Spain, October 11-13, 2002) |
Mark J. Embrechts | Oct. 2002 |
| Exploiting Unlabeled Data in Ensemble Methods (Presented at the Knowledge Discovery and Data Mining Conference, Edmonton, Canada, August 2002) |
Kristin P. Bennett | Aug. 2002 |
| MARK: A Boosting Algorithm for Heterogeneous Kernel
Models (Presented at the Knowledge Discovery and Data Mining Conference, Edmonton, Canada, August 2002) |
Kristin P. Bennett | Aug. 2002 |
| Pharmacophore Identification and Bioactivity Prediction
Based on the TAE-Electronic Conformation Method (Presented at ACS Boston, August 2002) |
Curt M.
Breneman Nagamani Sukumar |
Aug. 2002 |
| Prediction Of Protein Retention Times In Anion Exchange
Chromatography Systems Using Support Vector Machine Regression (Presented at ACS Boston, August 2002 – CCG Award Winner) |
Curt M.
Breneman Nagamani Sukumar Kristin P. Bennett |
Aug. 2002 |
| Prediction of Glass Transition Temperatures for
Polymers using the TAE/RECON Method (Poster presentation at the Boston ACS Meeting, August 2002– CCG Award Winner) |
Qiong Luo, Nagamani
Sukumar, Curt M.
Breneman,
Kristin P. Bennett Mark J. Embrechts |
Aug. 2002 |
| Novel QSAR/QSPR Methods for Predicting the Acute
Toxicity of Organic Compounds (Poster presentation at the Boston ACS Meeting, August 2002) |
Curt M.
Breneman Nagamani Sukumar Mark J. Embrechts |
Aug. 2002 |
| New
Developments in PEST Shape/Property Hybrid Descriptors (Presented at ACS Boston, August 2002) |
Nagamani
Sukumar Curt M. Breneman Mark J. Embrechts |
Aug. 2002 |
| Kernel Regression with applications in drug design (Invited Speaker, NATO Advanced Study Institute on Learning Theory and Practice (LTP 2002), Leuven, Belgium, July 2002) |
Kristin P. Bennett | Jul. 2002 |
| Visual Explorations
in Clustering and Data Mining Bioinformatics Workshop, July 24-26, 2002, Rensselaer, Troy, NY |
Mark J. Embrechts | Jul. 2002 |
| K-PLS Experiments &
Practice NATO Advanced Study Institut, Learning Theory & Practice LTP 2002, Leuven, July 8-19, 2002 |
Mark J. Embrechts | Jul. 2002 |
| Mining for Molecules via Support Vector Machines (Invited Speaker, Mathematical Diagnostics Workshop, Erice, Italy, June 2002) |
Kristin P. Bennett | Jun. 2002 |
| StripMining for Molecules (Presented at the IEEE International Joint Conference on Neural Networks, IJCNN’02, Honolulu, Hawaii, May 12-15, 2002) |
Mark J. Embrechts Curt M. Breneman Kristin P. Bennett |
May 2002 |
| A-priori prediction of protein retention and displacer
efficacy in ion-exchange systems (ABSTR PAP AM CHEM S 223: 130-IEC Part 1 APR 7 2002) |
Curt M. Breneman | Apr. 2002 |
| Model Mining to Support Prediction of Molecule Activities (Presented at the Learning Workshop, Snowbird, Utah, April 2002) |
Kristin P. Bennett | Apr. 2002 |
| Protein-Ligand Interaction Scoring using TAE Knowledge-Based
Potential (ABSTR PAP AM CHEM S 223: 178-COMP Part 1, April 7, 2002) |
Curt M. Breneman | Apr. 2002 |
| Feature Selection and QSPR Modeling: Non-linear
PLS versus SVM (Poster presentation at the Orlando ACS Meeting, April 2002) |
Curt M.
Breneman Mark J. Embrechts |
Apr. 2002 |
| New
Developments in Molecular Property Descriptors, Machine Learning and Computational
ADME (Presented at the Mid-Atlantic Computational Chemistry meeting at Princeton University, April 17, 2002) |
Curt M. Breneman | Apr. 2002 |
| New
Electron Density-Derived Descriptors and Machine Learning Techniques for
Computational ADME and Molecular Design (Presented at 3D Pharmaceuticals, April 17, 2002) |
Curt M. Breneman | Apr. 2002 |
| The
use of RECON/PEST Software and Electron Density-derived Descriptors for
Virtual High Throughput Database Screening and Refinement (Presented at the symposium on : "Near-Neighbor Searching for Lead Follow-Up: Algorithms and Descriptors" at the Orlando ACS meeting, April 2002) |
Nagamani Sukumar | Apr. 2002 |
| Caco-2
Permeability Modeling: Feature Selection via Sparse Support Vector Machines
(Presented at the ADME/Tox symposium at the Orlando ACS meeting, April 2002) |
Curt M. Breneman | Apr. 2002 |
Presentations are best viewed with a resolution of 800x600 or higher.
Papers
Title |
Authors |
| “Molecular Modeling”, in “Yearbook of Science and Technology - 2004", pp 208-211. McGraw-Hill, New York (2004). | Curt M. Breneman and Nagamani Sukumar |
| Parallel screening of selective and high-affinity displacers for proteins in ion-exchange systems, JOURNAL OF CHROMATOGRAPHY A, 1033 (1): 19-28 APR 9 2004. | Rege K, Ladiwala A, Tugcu N, Breneman CM, Cramer SM |
| Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 44 (2): 699-703 MAR-APR 2004. | Deng W, Breneman C, Embrechts MJ |
| Three-dimensional quantitative structure-activity relationship analyses of piperidine-based CCR5 receptor antagonists, BIOORGANIC & MEDICINAL CHEMISTRY, 12 (2): 489-499 JAN 15 2004. | Song MS, Breneman CM, Sukumar N |
| Electronic van der Waals surface property descriptors and genetic algorithms for developing structure-activity correlations in olfactory databases, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 43 (6): 1890-1905 NOV-DEC 2003. | Lavine BK, Davidson CE, Breneman C, Katt W |
| “Identification of chemically selective displacers using parallel batch screening experiments and quantitative structure efficacy relationship models.” Analytical Chemistry, 2003. 75(21): p. 5806-5816. | Tugcu, N., Ladiwala, A., Breneman C.M., and Cramer, S.M. |
| “Prediction of the effect of mobile-phase salt type on protein retention and selectivity in anion exchange systems.” Analytical Chemistry, 2003. 75(14): p. 3563-3572. | Tugcu, N., Song, M.H., Breneman C.M., Sukumar, N., Bennett, K.P. and Cramer, S.M. |
| “Electronic van der Waals surface property descriptors and genetic algorithms for developing structure-activity correlations in olfactory databases.” Journal of Chemical Information and Computer Sciences, 2003. 43(6): p. 1890-1905. | Lavine, B.K., Davidson, C.E., Breneman, C. and Katt, W. |
| “Investigation of mobile phase salt type effects on protein retention and selectivity in cation-exchange systems using quantitative structure retention relationship models.” Langmuir, 2003. 19(20): p. 8443-8454. | Ladiwala, A., Rege, K., Breneman C.M. and Cramer, S.M. |
| “New Developments in PEST shape/property Hybrid Descriptors”, Journal of Computer-Aided Molecular Design, 17, 231-240, 2003. | C.M. Breneman, C.M. Sundling, N. Sukumar, L. Shen, W.P. Katt, and M.J. Embrechts |
| "Dimensionality Reduction via Sparse Support Vector Machines” Journal of Machine Learning Research, 3(Mar):1229-1243, 2003. | Jinbo Bi, Kristin Bennett, Mark Embrechts, Curt Breneman, Minghu Song; |
| “Transferable Atom Equivalent Multi-Centered Multipole Expansion Method”, J. Comp. Chem. (Special Issue on electron densities and electrostatic potentials) – S. R. Gadre, Ed.24(4), 512-529 MAR 2003. | C. E. Whitehead, C.M. Breneman, N. Sukumar and M.D. Ryan |
| "Descriptor Generation, Selection and Model Building in Quantitative Structure-Property Analysis" in "Experimental Design for Combinatorial and High Throughput Materials Development", James N. Cawse, ed. (John Wiley, New York, 2002), pp.203-238 | Curt M. Breneman, Kristin P. Bennett, Mark Embrechts, Steven Cramer, Minghu Song, Jinbo Bi and N. Sukumar |
| “Prediction of Protein Retention Times in Anion-exchange Chromatography Systems using Support Vector Machine Regression”, JCICS (Journal of Chemical Information and Computer Science), 42(6), 1347-1357 NOV-DEC 2002. See: http://dx.doi.org/10.1021/ci025580t | M. Song, C.M. Breneman, J. Bi, N. Sukumar, K.P. Bennett, S. Cramer, and N. Tugcu, |
| “Predictive Quantitative Structure-Retention Relationship Models for Ion-Exchange Chromatography”, Chromatographia, 56(3-4), 147-152, 2002. | C. B. Mazza, C. E. Whitehead, C. M. Breneman and Steven M. Cramer |
| “High Throughput Screening and Quantitative Structure-Efficacy Relationship Models for Designing Displacers for Anti-sense Oligonucleotide Purification in Anion-Exchange Systems”, Separation Science and Technology. 37(7) 1667-1681, 2002. | N. Tugcu, C. Mazza, C. Breneman, Y. Sanghvi, J. Moore and S. M. Cramer |
| “High Throughput Screening and Quantitative-Structure Efficacy Relationship Models of Potential Displacer Molecules for Ion Exchange Systems”. Biotechnology and Bioengineering 80(1), 60-72, 2002. | C. B. Mazza, K. Rege, C. M. Breneman, J. S. Dordick and S. M. Cramer |
| “Prediction of Protein Retention in Ion-Exchange Systems Using Molecular Descriptors Obtained from Crystal Structure”, Analytical Chemistry, 73(22) 5457-5461, 2001. | Mazza, C.B., Sukumar, N., Breneman C.M. and Cramer, S.M. |
| "Data Mining using 2-D Neural Network Sensitivity Analysis for Molecules", to be presented at the 2001 Intelligent Engineering Systems Through Artificial Neural Networks (ANNIE) Conference in Cooperation with the IEEE Neural Network Council, St. Louis - Missouri, November 4-7, 2001. | Mark J. Embrechts, Fabio A. Arciniegas, Muhsin Ozdemir, Curt M. Breneman, and Kristin P. Bennett |
| "Bagging Neural Network Sensitivity Analysis for Feature Reduction in QSAR Problems," in Proceedings, 2001 INNS - IEEE International Joint Conference on Neural Networks, IEEE Press, Washington D.C., vol. 4, pp. 2478 - 2482, July 14-19 2001. | Mark J. Embrechts, Fabio A. Arciniegas, Muhsin Ozdemir, Curt M. Breneman, Kristin P. Bennett, and Larry Lockwood. |
| "Scientific Data Mining with StripMinerTM," in Proceedings, 2001 SMCia Mountain Workshop on Soft Computing in Industrial Applications, M.J. Embrechts, H.F. VanLandingham, and S. Ovaska, ed., IEEE Press, Blacksburg - Virginia, pp. 13-16, June 25-27 2001. | Mark J. Embrechts, Fabio Arciniegas, Muhsin Ozdemir, and Michinari Momma |
| "Feature Selection for In-silico Drug design Using Genetic Algorithms and Neural Networks," in Proceedings, 2001 SMCia Mountain Workshop on Soft Computing in Industrial Applications, M.J. Embrechts, H.F. VanLandingham, and S. Ovaska, ed., IEEE Press, Blacksburg - Virginia, pp. 53-57, June 25-27 2001 | Muhsin Ozdemir, Mark J. Embrechts, Fabio Arciniegas, Curt Breneman, Larry Lockwood, and Kristin Bennett |
| "Support Vector Machine Regression in Chemometrics," to be presented at Interface '01 | Kristin Bennett, A. Demiriz, C. Breneman, M. Embrechts |
| “Data Strip Mining for the Virtual Design of Pharmaceuticals with Neural Networks,” IEEE Transactions on Neural Networks, Vol.11, No 3, pp. 668 – 679, May 2000. | Robert H. Kewley, Mark J. Embrechts and Curt Breneman |
| “Molecular Database Mining using Self-Organizing Maps for the Design of Novel Pharmaceuticals,” in Intelligent Engineering Systems through Artificial Neural Networks: Smart Engineering System Design: Vol. 10, C. H. Dagli et al., Eds, ASME Press, pp. 477 – 482 (2000). | Fabio Arciniegas, Kristin Bennett, Curt Breneman, and Mark J. Embrechts |
| "Molecular Database Mining using Self-Organizing Maps for the Design of Novel Pharmaceuticals," in Intelligent Engineering Systems through Artificial Neural Networks: Smart Engineering System Design: Vol. 10, C. H. Dagli et al., Eds, ASME Press, pp. 477 – 482 (2000). | Fabio Arciniegas, Kristin Bennett, Curt Breneman, and Mark J. Embrechts. |
| "Support Vector Machines: Hype or Hallelujah" SIGKDD Explorations, 2,2, 2000, 1-13. | Kristin Bennett and Colin Campbell |
| "Sparse regression ensembles in infinite and finite hypothesis spaces," NeuroCOLT2 technical report, Royal Holloway College, London, September 2000, to appear in Machine Learning. | Gunnar Raetsch, Ayhan Demiriz, and Kristin Bennett |
| "A Column Generation Algorithm for Boosting," Proceedings of the Seventeenth International Conference on Machine Learning, Pat Langley Editor, Morgan Kaufmann, San Francisco, 2000, pp. 65-72. | Ayhan Demiriz, Kristin Bennett, and John Shawe-Taylor. |
| "Duality and Geometry in SVM Classifiers," Proceedings of the Seventeenth International Conference on Machine Learning, Pat Langley Editor, Morgan Kaufmann, San Francisco, 2000, pp. 57-64. | Kristin Bennett and Erin Bredensteiner. |
| "Linear Programming Boosting via Column Generation," to appear in Machine Learning, 2000. | Kristin Bennett and Ayhan Demiriz and John Shawe-Taylor |
| "Optimization Approaches to Semi-Supervised Learning," to appear in Applications and Algorithms of Complementarity, M. C. Ferris, O. L. Mangasarian, and J. S. Pang, editors. Kluwer Academic Publishers. Boston 2000. | Kristin Bennett and Ayhan Demiriz. |
| "Semi-Supervised Clustering Using Genetic Algorithms," ANNIE'99 (Artificial Neural Networks in Engineering), November 1999. | Kristin Bennett, Ayhan Demiriz and Mark Embrechts |
| "Neural Network Analysis for data Strip Mining Problems," in Intelligent Engineering Systems through Artificial Neural Networks, Vol. 8, Cihan Dagli et al., Eds., pp. 391-396, ASME Press (1998). | Robert Kewley, Mark Embrechts, and Curt Breneman |