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Pierre Baldi: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Pierre Baldi
    Machine Learning Methods for Computational Proteomics and Beyond. [Citation Graph (0, 0)][DBLP]
    Canadian Conference on AI, 2003, pp:8- [Conf]
  2. Laurent Itti, Pierre Baldi
    A Principled Approach to Detecting Surprising Events in Video. [Citation Graph (0, 0)][DBLP]
    CVPR (1), 2005, pp:631-637 [Conf]
  3. Liva Ralaivola, Lin Wu, Pierre Baldi
    SVM and pattern-enriched common fate graphs for the game of go. [Citation Graph (0, 0)][DBLP]
    ESANN, 2005, pp:485-490 [Conf]
  4. Raja Jurdak, Cristina Videira Lopes, Pierre Baldi
    An Acoustic Identification Scheme for Location Systems. [Citation Graph (0, 0)][DBLP]
    ICPS, 2004, pp:61-70 [Conf]
  5. Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
    State-Driven Energy Optimization in Wireless Sensor Networks. [Citation Graph (0, 0)][DBLP]
    ICW/ICHSN/ICMCS/SENET, 2005, pp:356-363 [Conf]
  6. Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh
    Periodic Sequence Patterns in Human Exons. [Citation Graph (0, 0)][DBLP]
    ISMB, 1995, pp:30-38 [Conf]
  7. Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
    Computational Applications of DNA Structural Scales. [Citation Graph (0, 0)][DBLP]
    ISMB, 1998, pp:35-42 [Conf]
  8. Pierre Baldi, Yves Chauvin
    Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures. [Citation Graph (0, 0)][DBLP]
    ISMB, 1995, pp:39-47 [Conf]
  9. Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak
    Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. [Citation Graph (0, 0)][DBLP]
    ISMB, 2000, pp:25-36 [Conf]
  10. Jianlin Cheng, Pierre Baldi
    Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2005, pp:75-84 [Conf]
  11. Steven Hampson, Pierre Baldi, Dennis F. Kibler, Suzanne B. Sandmeyer
    Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods. [Citation Graph (0, 0)][DBLP]
    ISMB, 2000, pp:190-201 [Conf]
  12. Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin
    Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. [Citation Graph (0, 0)][DBLP]
    ISMB, 1996, pp:182-191 [Conf]
  13. Gianluca Pollastri, Pierre Baldi
    Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. [Citation Graph (0, 0)][DBLP]
    ISMB, 2002, pp:62-70 [Conf]
  14. Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio
    Improved prediction of the number of residue contacts in proteins by recurrent neural networks. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2001, pp:234-242 [Conf]
  15. Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi
    Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. [Citation Graph (0, 0)][DBLP]
    ISMB (Supplement of Bioinformatics), 2005, pp:359-368 [Conf]
  16. Pierre Baldi
    Linear Learning: Landscapes and Algorithms. [Citation Graph (0, 0)][DBLP]
    NIPS, 1988, pp:65-72 [Conf]
  17. Pierre Baldi
    Computing with Arrays of Bell-Shaped and Sigmoid Functions. [Citation Graph (0, 0)][DBLP]
    NIPS, 1990, pp:735-742 [Conf]
  18. Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh
    Hidden Markov Models for Human Genes. [Citation Graph (0, 0)][DBLP]
    NIPS, 1993, pp:761-768 [Conf]
  19. Pierre Baldi, Yves Chauvin, Tim Hunkapiller, Marcella A. McClure
    Hidden Markov Models in Molecular Biology: New Algorithms and Applications. [Citation Graph (0, 0)][DBLP]
    NIPS, 1992, pp:747-754 [Conf]
  20. Pierre Baldi, Jianlin Cheng, Alessandro Vullo
    Large-Scale Prediction of Disulphide Bond Connectivity. [Citation Graph (0, 0)][DBLP]
    NIPS, 2004, pp:- [Conf]
  21. Pierre Baldi, Kurt Hornik
    Universal Approximnation and Learning of Trajectories Using Oscillators. [Citation Graph (0, 0)][DBLP]
    NIPS, 1995, pp:451-457 [Conf]
  22. Pierre Baldi, Yosef Rinott, Charles Stein
    On the Distribution of the Number of Local Minima of a Random Function on a Graph. [Citation Graph (0, 0)][DBLP]
    NIPS, 1989, pp:727-732 [Conf]
  23. Pierre Baldi, Santosh S. Venkatesh
    On Properties of Networks of Neuron-Like Elements. [Citation Graph (0, 0)][DBLP]
    NIPS, 1987, pp:41-51 [Conf]
  24. Laurent Itti, Pierre Baldi
    Bayesian Surprise Attracts Human Attention. [Citation Graph (0, 0)][DBLP]
    NIPS, 2005, pp:- [Conf]
  25. Gianluca Pollastri, Pierre Baldi, Alessandro Vullo, Paolo Frasconi
    Prediction of Protein Topologies Using Generalized IOHMMS and RNNs. [Citation Graph (0, 0)][DBLP]
    NIPS, 2002, pp:1449-1456 [Conf]
  26. Padhraic Smyth, Usama M. Fayyad, Michael C. Burl, Pietro Perona, Pierre Baldi
    Inferring Ground Truth from Subjective Labelling of Venus Images. [Citation Graph (0, 0)][DBLP]
    NIPS, 1994, pp:1085-1092 [Conf]
  27. Pierre Baldi
    Probabilistic Models of Neuronal Spike Trains. [Citation Graph (0, 0)][DBLP]
    Summer School on Neural Networks, 1997, pp:198-228 [Conf]
  28. Sushil Bajracharya, Trung Ngo, Erik Linstead, Yimeng Dou, Paul Rigor, Pierre Baldi, Cristina Videira Lopes
    Sourcerer: a search engine for open source code supporting structure-based search. [Citation Graph (0, 0)][DBLP]
    OOPSLA Companion, 2006, pp:681-682 [Conf]
  29. Pierre Baldi, Søren Brunak
    Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. [Citation Graph (0, 0)][DBLP]
    Pacific Symposium on Biocomputing, 2001, pp:- [Conf]
  30. Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda
    Bidirectional Dynamics for Protein Secondary Structure Prediction. [Citation Graph (0, 0)][DBLP]
    Sequence Learning, 2001, pp:80-104 [Conf]
  31. Sanjay Joshua Swamidass, Pierre Baldi
    Statistical Distribution of Chemical Fingerprints. [Citation Graph (0, 0)][DBLP]
    WILF, 2005, pp:11-18 [Conf]
  32. Arlo Z. Randall, Pierre Baldi, Luis P. Villarreal
    Structural proteomics of the poxvirus family. [Citation Graph (0, 0)][DBLP]
    Artificial Intelligence in Medicine, 2004, v:31, n:2, pp:105-115 [Journal]
  33. Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen
    Flexibility of the genetic code with respect to DNA structure. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:3, pp:237-248 [Journal]
  34. Pierre-François Baisnée, Steven Hampson, Pierre Baldi
    Why are complementary DNA strands symmetric? [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:8, pp:1021-1033 [Journal]
  35. Pierre Baldi
    On the convergence of a clustering algorithm for protein-coding regions in microbial genomes. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2000, v:16, n:4, pp:367-371 [Journal]
  36. Pierre Baldi, Pierre-François Baisnée
    Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2000, v:16, n:10, pp:865-889 [Journal]
  37. Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen
    Assessing the accuracy of prediction algorithms for classification: an overview. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2000, v:16, n:5, pp:412-424 [Journal]
  38. Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
    Structural basis for triplet repeat disorders: a computational analysis. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1999, v:15, n:11, pp:918-929 [Journal]
  39. Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri
    Exploiting the past and the future in protein secondary structure prediction. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1999, v:15, n:11, pp:937-946 [Journal]
  40. Pierre Baldi, Anthony D. Long
    A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:6, pp:509-519 [Journal]
  41. Jonathan H. Chen, Sanjay Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi
    ChemDB: a public database of small molecules and related chemoinformatics resources. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:22, pp:4133-4139 [Journal]
  42. Jianlin Cheng, Pierre Baldi
    A machine learning information retrieval approach to protein fold recognition. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:12, pp:1456-1463 [Journal]
  43. Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi
    ICBS: a database of interactions between protein chains mediated by ?-sheet formation. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:16, pp:2767-2777 [Journal]
  44. Steven E. Hampson, B. S. Gaut, Pierre Baldi
    Statistical detection of chromosomal homology using shared-gene density alone. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:8, pp:1339-1348 [Journal]
  45. Steven Hampson, Dennis F. Kibler, Pierre Baldi
    Distribution patterns of over-represented k-mers in non-coding yeast DNA. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2002, v:18, n:4, pp:513-528 [Journal]
  46. Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Philip L. Felgner, Pierre Baldi
    Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2006, v:22, n:14, pp:1760-1766 [Journal]
  47. Anders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak
    The Biology of Eukaryotic Promoter Prediction - A Review. [Citation Graph (0, 0)][DBLP]
    Computers & Chemistry, 1999, v:23, n:3-4, pp:191-207 [Journal]
  48. Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
    Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. [Citation Graph (0, 0)][DBLP]
    Data Min. Knowl. Discov., 2005, v:11, n:3, pp:213-222 [Journal]
  49. Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
    DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. [Citation Graph (0, 0)][DBLP]
    Data Min. Knowl. Discov., 2006, v:13, n:1, pp:1-10 [Journal]
  50. Pierre Baldi, Gianluca Pollastri
    A Machine-Learning Strategy for Protein Analysis. [Citation Graph (0, 0)][DBLP]
    IEEE Intelligent Systems, 2002, v:17, n:2, pp:28-35 [Journal]
  51. Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness
    Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology. [Citation Graph (0, 0)][DBLP]
    IEEE Intelligent Systems, 2005, v:20, n:3, pp:68-75 [Journal]
  52. Amir F. Atiya, Pierre Baldi
    Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis. [Citation Graph (0, 0)][DBLP]
    Int. J. Neural Syst., 1989, v:1, n:2, pp:103-124 [Journal]
  53. Yann Guermeur, Gianluca Pollastri, André Elisseeff, Dominique Zelus, Hélène Paugam-Moisy, Pierre Baldi
    Combining protein secondary structure prediction models with ensemble methods of optimal complexity. [Citation Graph (0, 0)][DBLP]
    Neurocomputing, 2004, v:56, n:, pp:305-327 [Journal]
  54. Santosh S. Venkatesh, Pierre Baldi
    Programmed interactions in higher-order neural networks: Maximal capacity. [Citation Graph (0, 0)][DBLP]
    J. Complexity, 1991, v:7, n:3, pp:316-337 [Journal]
  55. Santosh S. Venkatesh, Pierre Baldi
    Programmed interactions in higher-order neural networks: The outer-product algorithm. [Citation Graph (0, 0)][DBLP]
    J. Complexity, 1991, v:7, n:4, pp:443-479 [Journal]
  56. Pierre Baldi
    Substitution Matrices and Hidden Markov Models. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1995, v:2, n:3, pp:487-491 [Journal]
  57. Pierre Baldi, Yves Chauvin
    Hidden Markov Models of the G-Protein-Coupled Receptor Family. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 1994, v:1, n:4, pp:311-336 [Journal]
  58. Pierre Baldi, Michael C. Vanier, James M. Bower
    On the Use of Bayesian Methods for Evaluating Compartmental Neural Models. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Neuroscience, 1998, v:5, n:3, pp:285-314 [Journal]
  59. Pierre Baldi
    Group Actions and Learning for a Family of Automata. [Citation Graph (0, 0)][DBLP]
    J. Comput. Syst. Sci., 1988, v:36, n:1, pp:1-15 [Journal]
  60. Pierre Baldi, Gianluca Pollastri
    The Principled Design of Large-Scale Recursive Neural Network Architectures--DAG-RNNs and the Protein Structure Prediction Problem. [Citation Graph (0, 0)][DBLP]
    Journal of Machine Learning Research, 2003, v:4, n:, pp:575-602 [Journal]
  61. Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, Douglas C. Wallace
    MITOMAP: a human mitochondrial genome database - 2004 update. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:611-613 [Journal]
  62. Jianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi
    SCRATCH: a protein structure and structural feature prediction server. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:72-76 [Journal]
  63. Eduardo Ruiz-Pesini, Marie T. Lott, Vincent Procaccio, Jason C. Poole, Marty C. Brandon, Dan Mishmar, Christina Yi, James Kreuziger, Pierre Baldi, Douglas C. Wallace
    An enhanced MITOMAP with a global mtDNA mutational phylogeny. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2007, v:35, n:Database-Issue, pp:823-828 [Journal]
  64. Pierre Baldi, Kurt Hornik
    Neural networks and principal component analysis: Learning from examples without local minima. [Citation Graph (0, 0)][DBLP]
    Neural Networks, 1989, v:2, n:1, pp:53-58 [Journal]
  65. Pierre Baldi, Michal Rosen-Zvi
    On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks. [Citation Graph (0, 0)][DBLP]
    Neural Networks, 2005, v:18, n:8, pp:1080-1086 [Journal]
  66. Liva Ralaivola, Sanjay Joshua Swamidass, Hiroto Saigo, Pierre Baldi
    Graph kernels for chemical informatics. [Citation Graph (0, 0)][DBLP]
    Neural Networks, 2005, v:18, n:8, pp:1093-1110 [Journal]
  67. Pierre Baldi
    Neural Networks, Acyclic Orientations of the Hypercube, and Sets of Orthogonal Vectors. [Citation Graph (0, 0)][DBLP]
    SIAM J. Discrete Math., 1988, v:1, n:1, pp:1-13 [Journal]
  68. Cristina Videira Lopes, Amir Haghighat, Atri Mandal, Tony Givargis, Pierre Baldi
    Localization of off-the-shelf mobile devices using audible sound: architectures, protocols and performance assessment. [Citation Graph (0, 0)][DBLP]
    Mobile Computing and Communications Review, 2006, v:10, n:2, pp:38-50 [Journal]
  69. Samuel A. Danziger, Sanjay Joshua Swamidass, Jue Zeng, Lawrence R. Dearth, Qiang Lu, Jonathan H. Chen, Jianlin Cheng, Vinh P. Hoang, Hiroto Saigo, Ray Luo, Pierre Baldi, Rainer K. Brachmann, Richard H. Lathrop
    Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. [Citation Graph (0, 0)][DBLP]
    IEEE/ACM Trans. Comput. Biology Bioinform., 2006, v:3, n:2, pp:114-125 [Journal]
  70. Pierre Baldi
    Neural networks, orientations of the hypercube, and algebraic threshold functions. [Citation Graph (0, 0)][DBLP]
    IEEE Transactions on Information Theory, 1988, v:34, n:3, pp:523-530 [Journal]
  71. Pierre Baldi, Santosh S. Venkatesh
    Random interactions in higher order neural networks. [Citation Graph (0, 0)][DBLP]
    IEEE Transactions on Information Theory, 1993, v:39, n:1, pp:274-0 [Journal]
  72. Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
    U-MAC: a proactive and adaptive UWB medium access control protocol. [Citation Graph (0, 0)][DBLP]
    Wireless Communications and Mobile Computing, 2005, v:5, n:5, pp:551-566 [Journal]
  73. Erik Linstead, Paul Rigor, Sushil Bajracharya, Cristina Videira Lopes, Pierre Baldi
    Mining Eclipse Developer Contributions via Author-Topic Models. [Citation Graph (0, 0)][DBLP]
    MSR, 2007, pp:30- [Conf]
  74. Lin Wu, Pierre Baldi
    A Scalable Machine Learning Approach to Go. [Citation Graph (0, 0)][DBLP]
    NIPS, 2006, pp:1521-1528 [Conf]
  75. Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
    Adaptive Low Power Listening for Wireless Sensor Networks. [Citation Graph (0, 0)][DBLP]
    IEEE Trans. Mob. Comput., 2007, v:6, n:8, pp:988-1004 [Journal]

  76. Effective Compression of Monotone and Quasi-Monotone Sequences of Integers. [Citation Graph (, )][DBLP]


  77. An Application of Latent Dirichlet Allocation to Analyzing Software Evolution. [Citation Graph (, )][DBLP]


  78. Machine Learning Challenges in Chemoinformatics and Drug Screening and Design. [Citation Graph (, )][DBLP]


  79. From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. [Citation Graph (, )][DBLP]


  80. BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. [Citation Graph (, )][DBLP]


  81. Capturing Java naming conventions with first-order Markov models. [Citation Graph (, )][DBLP]


  82. CodeGenie: using test-cases to search and reuse source code. [Citation Graph (, )][DBLP]


  83. Mining concepts from code with probabilistic topic models. [Citation Graph (, )][DBLP]


  84. SourcererDB: An aggregated repository of statically analyzed and cross-linked open source Java projects. [Citation Graph (, )][DBLP]


  85. Mining the coherence of GNOME bug reports with statistical topic models. [Citation Graph (, )][DBLP]


  86. Mining Internet-Scale Software Repositories. [Citation Graph (, )][DBLP]


  87. A theory of aspects as latent topics. [Citation Graph (, )][DBLP]


  88. User contribution and trust in Wikipedia. [Citation Graph (, )][DBLP]


  89. Learning and Charting Chemical Space with Strings and Graphs: Challenges and Opportunities for AI and Machine Learning. [Citation Graph (, )][DBLP]


  90. Software-driven sensor networks for short-range shallow water applications. [Citation Graph (, )][DBLP]


  91. Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. [Citation Graph (, )][DBLP]


  92. ChemDB update - full-text search and virtual chemical space. [Citation Graph (, )][DBLP]


  93. TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. [Citation Graph (, )][DBLP]


  94. PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. [Citation Graph (, )][DBLP]


  95. MotifMap: a human genome-wide map of candidate regulatory motif sites. [Citation Graph (, )][DBLP]


  96. SOLpro: accurate sequence-based prediction of protein solubility. [Citation Graph (, )][DBLP]


  97. Data structures and compression algorithms for genomic sequence data. [Citation Graph (, )][DBLP]


  98. A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. [Citation Graph (, )][DBLP]


  99. Improved residue contact prediction using support vector machines and a large feature set. [Citation Graph (, )][DBLP]


  100. A survey, classification and comparative analysis of medium access control protocols for ad hoc networks. [Citation Graph (, )][DBLP]


  101. Sourcerer: mining and searching internet-scale software repositories. [Citation Graph (, )][DBLP]


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