| Articles and Presentations |
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Speeding Up Chemical Database Searches Using the Inverted Index: the Convergence of Cheminformatics and Text Search Methods
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R. J. Nasr, R. Vernica, C. Li, and P. Baldi.
Speeding Up Chemical Database Searches Using a the Inverted Index: the Convergence of Cheminformatics and Text Search Methods.
Journal of Chemical Information and Modeling in submission, (2011).
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Learning to Predict Chemical Reactions
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M. A. Kayala, C. A. Azencott, J. Chen, and P. Baldi
Journal of Chemical Information and Modeling 51, 9, 2209-2222 (2011).
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| Machine Learning Data (300M tar.gz) |
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When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values
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P. Baldi and R. Nasr
Journal of Chemical Information and Modeling Submitted (2010).
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| Supplementary Data |
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No Electron Left-Behind: a Rule-Based Expert System to Predict Chemical Reactions and Reaction Mechanisms
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J. Chen and P. Baldi. No Electron Left-Behind: a Rule-Based Expert System to Predict Chemical Reactions and Reaction Mechanisms.
Journal of Chemical Information and Modeling, 49, 9, 2034-2043, (2009).
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An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases
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P. Baldi and D. Hirschberg. An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases.
Journal of Chemical Information and Modeling, in press, (2009).
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Large Scale Study of Multiple-molecule Queries
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R. Nasr*, S. Joshua Swamidass*, and P. Baldi.
Large scale study of multiple-molecule queries.
Journal of Cheminformatics 1, 7, (2009).
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| Supplementary Data |
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Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR
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P. Baldi, D. S. Hirschberg and R. J. Nasr.
Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR.
Journal of Chemical Information and Modeling 48 (7), 1367-1378, (2008).
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| 100K random chemical data set |
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Discovery of Power-Laws in Chemical Space
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R. W. Benz, S. Joshua Swamidass, and P. Baldi.
"Discovery of Power-Laws in Chemical Space."
Journal of Chemical Information and Modeling 48(6), 1138-1151, (2008).
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Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction
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J. H. Chen and P. Baldi.
Synthesis Explorer: A Chemical Reaction Tutorial System for Organic Synthesis Design and Mechanism Prediction.
Journal of Chemical Education 2008(85):1699, (2008).
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Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval
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P. Baldi, R. W. Benz, D. S. Hircshberg, and S. Joshua Swamidass.
Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval.
Journal of Chemical Information and Modeling, 47, 6, 2098-2109, (2007).
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A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval
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S. Joshua Swamidass and P. Baldi.
A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval.
Journal of Chemical Information and Modeling, 47, 3, 952-964, (2007).
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Bounds and Algorithms for Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time
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S. Joshua Swamidass and P. Baldi.
Bounds and Algorithms for Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time.
Journal of Chemical Information and Modeling, 47, 2, 302-317, (2007).
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Virtual High-Throughput Screening with Two-Dimensional Kernels
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C. A. Azencott and P. Baldi.
Virtual High-Throughput Screening with Two-Dimensional Kernels.
In: Hands-On Pattern Recognition. Challenges in Data Representation, Model Selection, and Performance Prediction,
I. Guyon, G. Cawley, G. Droor, and A. Saffari Editors, Lulu Press, (2007).
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Effective Compression of Monotone and Quasi-Monotone Sequences of Integers
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D. S. Hirschberg and P. Baldi.
Effective Compression of Monotone and Quasi-Monotone Sequences of Integers.
Proceedings of the 2008 Data Compression Conference (DCC 08), Snowbird, UTA, IEEE Computer Society Press, (2008).
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ChemDB Update - Full-Text Search and Virtual Chemical Space
(Supplementary Materials)
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J. H. Chen, E. Linstead, S. Joshua Swamidass, D. Wang, P. Baldi.
Bioinformatics Advance Access 2007; doi: 10.1093/bioinformatics/btm341.
Bioinformatics 23: 2348-2351.
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| Chemoinformatics Tutorial, ISMB 2006 |
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P. Baldi presents a tutorial on chemoinformatics at the
2006 ISMB Conference
in Fortaleza, Brazil.
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One-to-Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties
(Supplementary Materials)
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C. Azencott, A. Ksikes, S. Joshua Swamidass, J. H Chen, L. Ralaivola and P. Baldi.
One-to-Four-Dimensional Kernels for Small Molecules and Predictive Regression of Physical, Chemical, and Biological Properties.
Journal of Chemical Informatics and Modeling, 47(3):965-974, (2007).
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ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources
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J. Chen*, S. Joshua Swamidass*, Y. Dou, J. Bruand, P. Baldi.
ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources.
Bioinformatics, 21 (22): 4133-4139, (2005).
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Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity
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S. Joshua Swamidass*, J. Chen*, P. Phung, J. Bruand, L. Ralaivola, and P. Baldi.
Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.
Proceedings of the 2005 Conference on Intelligent Systems for Molecular Biology, ISMB 05.
Bioinformatics, 21 (Supplement 1), i359-368, (2005).
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Graph Kernels for Chemical Informatics
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L. Ralaivola, S. Joshua Swamidass, H. Saigo, and P. Baldi.
Graph Kernels for Chemical Informatics.
Neural Networks, special issue on Neural Networks and Kernel Methods for Structured Domains,
18 (8): 1093-1110, (2005).
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* These authors contributed equally