Pierre Baldi

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92EEErik Linstead, Sushil Krishna Bajracharya, Trung Chi Ngo, Paul Rigor, Cristina Videira Lopes, Pierre Baldi: Sourcerer: mining and searching internet-scale software repositories. Data Min. Knowl. Discov. 18(2): 300-336 (2009)
91EEDaniel S. Hirschberg, Pierre Baldi: Effective Compression of Monotone and Quasi-Monotone Sequences of Integers. DCC 2008: 520
90EEPierre Baldi, Ryan W. Benz: BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. ISMB 2008: 357-365
89EEPierre Baldi, Cristina Videira Lopes, Erik Linstead, Sushil Krishna Bajracharya: A theory of aspects as latent topics. OOPSLA 2008: 543-562
88EEMichael J. Sweredoski, Pierre Baldi: PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 24(12): 1459-1460 (2008)
87EEArlo Z. Randall, Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi: TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinformatics 24(4): 513-520 (2008)
86EELin Wu, Pierre Baldi: Learning to play Go using recursive neural networks. Neural Networks 21(9): 1392-1400 (2008)
85EEErik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi: Mining concepts from code with probabilistic topic models. ASE 2007: 461-464
84EEOtávio Augusto Lazzarini Lemos, Sushil Krishna Bajracharya, Joel Ossher, Ricardo Santos Morla, Paulo Cesar Masiero, Pierre Baldi, Cristina Videira Lopes: CodeGenie: using test-cases to search and reuse source code. ASE 2007: 525-526
83EESuman Sundaresh, Arlo Z. Randall, Berkay Unal, Jeannine M. Petersen, John T. Belisle, M. Gill Hartley, Melanie Duffield, Richard W. Titball, D. Huw Davies, Philip L. Felgner, Pierre Baldi: From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. ISMB/ECCB (Supplement of Bioinformatics) 2007: 508-518
82EEPierre Baldi: Learning and Charting Chemical Space with Strings and Graphs: Challenges and Opportunities for AI and Machine Learning. MLG 2007
81EEErik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi: Mining Eclipse Developer Contributions via Author-Topic Models. MSR 2007: 30
80EEErik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi: Mining Internet-Scale Software Repositories. NIPS 2007
79EEJonathan H. Chen, Erik Linstead, Sanjay Joshua Swamidass, Dennis Wang, Pierre Baldi: ChemDB update - full-text search and virtual chemical space. Bioinformatics 23(17): 2348-2351 (2007)
78EEMichael J. Sweredoski, Kevin J. Donovan, Bao D. Nguyen, A. J. Shaka, Pierre Baldi: Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. Bioinformatics 23(21): 2829-2835 (2007)
77EERaja Jurdak, Pierre Baldi, Cristina Videira Lopes: Adaptive Low Power Listening for Wireless Sensor Networks. IEEE Trans. Mob. Comput. 6(8): 988-1004 (2007)
76EEEduardo 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. Nucleic Acids Research 35(Database-Issue): 823-828 (2007)
75EELin Wu, Pierre Baldi: A Scalable Machine Learning Approach to Go. NIPS 2006: 1521-1528
74EESushil Krishna Bajracharya, Trung Chi Ngo, Erik Linstead, Yimeng Dou, Paul Rigor, Pierre Baldi, Cristina Videira Lopes: Sourcerer: a search engine for open source code supporting structure-based search. OOPSLA Companion 2006: 681-682
73EEJianlin Cheng, Pierre Baldi: A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22(12): 1456-1463 (2006)
72EESuman 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. Bioinformatics 22(14): 1760-1766 (2006)
71EEJianlin Cheng, Michael J. Sweredoski, Pierre Baldi: DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Data Min. Knowl. Discov. 13(1): 1-10 (2006)
70EESamuel 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. IEEE/ACM Trans. Comput. Biology Bioinform. 3(2): 114-125 (2006)
69EEGianluca Pollastri, Alessandro Vullo, Paolo Frasconi, Pierre Baldi: Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. Journal of Computational Biology 13(3): 631-650 (2006)
68EECristina 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. Mobile Computing and Communications Review 10(2): 38-50 (2006)
67EELaurent Itti, Pierre Baldi: A Principled Approach to Detecting Surprising Events in Video. CVPR (1) 2005: 631-637
66EELiva Ralaivola, Lin Wu, Pierre Baldi: SVM and pattern-enriched common fate graphs for the game of go. ESANN 2005: 485-490
65EERaja Jurdak, Pierre Baldi, Cristina Videira Lopes: State-Driven Energy Optimization in Wireless Sensor Networks. ICW/ICHSN/ICMCS/SENET 2005: 356-363
64EESanjay 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. ISMB (Supplement of Bioinformatics) 2005: 359-368
63EEJianlin Cheng, Pierre Baldi: Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. ISMB (Supplement of Bioinformatics) 2005: 75-84
62EELaurent Itti, Pierre Baldi: Bayesian Surprise Attracts Human Attention. NIPS 2005
61EESanjay Joshua Swamidass, Pierre Baldi: Statistical Distribution of Chemical Fingerprints. WILF 2005: 11-18
60EEJonathan H. Chen, Sanjay Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi: ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics 21(22): 4133-4139 (2005)
59EESteven E. Hampson, B. S. Gaut, Pierre Baldi: Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21(8): 1339-1348 (2005)
58EEJianlin Cheng, Michael J. Sweredoski, Pierre Baldi: Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. Data Min. Knowl. Discov. 11(3): 213-222 (2005)
57EEJianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness: Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology. IEEE Intelligent Systems 20(3): 68-75 (2005)
56EESuman Sundaresh, She-pin Hung, G. Wesley Hatfield, Pierre Baldi: How noisy and replicable are DNA microarray data? IJBRA 1(1): 31-50 (2005)
55EEPierre Baldi, Michal Rosen-Zvi: On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks. Neural Networks 18(8): 1080-1086 (2005)
54EELiva Ralaivola, Sanjay Joshua Swamidass, Hiroto Saigo, Pierre Baldi: Graph kernels for chemical informatics. Neural Networks 18(8): 1093-1110 (2005)
53EEMarty 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. Nucleic Acids Research 33(Database-Issue): 611-613 (2005)
52EEJianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi: SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research 33(Web-Server-Issue): 72-76 (2005)
51EERaja Jurdak, Pierre Baldi, Cristina Videira Lopes: U-MAC: a proactive and adaptive UWB medium access control protocol. Wireless Communications and Mobile Computing 5(5): 551-566 (2005)
50EERaja Jurdak, Cristina Videira Lopes, Pierre Baldi: An Acoustic Identification Scheme for Location Systems. ICPS 2004: 61-70
49EEPierre Baldi, Jianlin Cheng, Alessandro Vullo: Large-Scale Prediction of Disulphide Bond Connectivity. NIPS 2004
48EEArlo Z. Randall, Pierre Baldi, Luis P. Villarreal: Structural proteomics of the poxvirus family. Artificial Intelligence in Medicine 31(2): 105-115 (2004)
47EEYimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi: ICBS: a database of interactions between protein chains mediated by ?-sheet formation. Bioinformatics 20(16): 2767-2777 (2004)
46EEYann Guermeur, Gianluca Pollastri, André Elisseeff, Dominique Zelus, Hélène Paugam-Moisy, Pierre Baldi: Combining protein secondary structure prediction models with ensemble methods of optimal complexity. Neurocomputing 56: 305-327 (2004)
45 Pierre Baldi, Paolo Frasconi, Padhraic Smyth: Modeling the Internet and the Web: Probabilistic Method and Algorithms John Wiley 2003
44EEPierre Baldi: Machine Learning Methods for Computational Proteomics and Beyond. Canadian Conference on AI 2003: 8
43EEPierre Baldi, Gianluca Pollastri: The Principled Design of Large-Scale Recursive Neural Network Architectures--DAG-RNNs and the Protein Structure Prediction Problem. Journal of Machine Learning Research 4: 575-602 (2003)
42 Gianluca Pollastri, Pierre Baldi: Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. ISMB 2002: 62-70
41EEGianluca Pollastri, Pierre Baldi, Alessandro Vullo, Paolo Frasconi: Prediction of Protein Topologies Using Generalized IOHMMS and RNNs. NIPS 2002: 1449-1456
40 Steven Hampson, Dennis F. Kibler, Pierre Baldi: Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics 18(4): 513-528 (2002)
39 Pierre-François Baisnée, Steven Hampson, Pierre Baldi: Why are complementary DNA strands symmetric? Bioinformatics 18(8): 1021-1033 (2002)
38EEPierre Baldi, Gianluca Pollastri: A Machine-Learning Strategy for Protein Analysis. IEEE Intelligent Systems 17(2): 28-35 (2002)
37 Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio: Improved prediction of the number of residue contacts in proteins by recurrent neural networks. ISMB (Supplement of Bioinformatics) 2001: 234-242
36 Pierre Baldi, Søren Brunak: Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing 2001
35EEPierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda: Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning 2001: 80-104
34 Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen: Flexibility of the genetic code with respect to DNA structure. Bioinformatics 17(3): 237-248 (2001)
33 Pierre Baldi, Anthony D. Long: A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinformatics 17(6): 509-519 (2001)
32 Steven Hampson, Pierre Baldi, Dennis F. Kibler, Suzanne B. Sandmeyer: Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods. ISMB 2000: 190-201
31 Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak: Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. ISMB 2000: 25-36
30 Pierre Baldi, Pierre-François Baisnée: Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics 16(10): 865-889 (2000)
29 Pierre Baldi: On the convergence of a clustering algorithm for protein-coding regions in microbial genomes. Bioinformatics 16(4): 367-371 (2000)
28 Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16(5): 412-424 (2000)
27 Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen: Structural basis for triplet repeat disorders: a computational analysis. Bioinformatics 15(11): 918-929 (1999)
26 Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri: Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15(11): 937-946 (1999)
25EEAnders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak: The Biology of Eukaryotic Promoter Prediction - A Review. Computers & Chemistry 23(3-4): 191-207 (1999)
24 Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen: Computational Applications of DNA Structural Scales. ISMB 1998: 35-42
23 Pierre Baldi, Michael C. Vanier, James M. Bower: On the Use of Bayesian Methods for Evaluating Compartmental Neural Models. Journal of Computational Neuroscience 5(3): 285-314 (1998)
22EEPierre Baldi: Probabilistic Models of Neuronal Spike Trains. Summer School on Neural Networks 1997: 198-228
21 Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin: Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. ISMB 1996: 182-191
20 Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh: Periodic Sequence Patterns in Human Exons. ISMB 1995: 30-38
19 Pierre Baldi, Yves Chauvin: Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures. ISMB 1995: 39-47
18EEPierre Baldi, Kurt Hornik: Universal Approximnation and Learning of Trajectories Using Oscillators. NIPS 1995: 451-457
17 Pierre Baldi: Substitution Matrices and Hidden Markov Models. Journal of Computational Biology 2(3): 487-491 (1995)
16EEPadhraic Smyth, Usama M. Fayyad, Michael C. Burl, Pietro Perona, Pierre Baldi: Inferring Ground Truth from Subjective Labelling of Venus Images. NIPS 1994: 1085-1092
15 Pierre Baldi, Yves Chauvin: Hidden Markov Models of the G-Protein-Coupled Receptor Family. Journal of Computational Biology 1(4): 311-336 (1994)
14EEPierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh: Hidden Markov Models for Human Genes. NIPS 1993: 761-768
13 Pierre Baldi, Santosh S. Venkatesh: Random interactions in higher order neural networks. IEEE Transactions on Information Theory 39(1): 274- (1993)
12EEPierre Baldi, Yves Chauvin, Tim Hunkapiller, Marcella A. McClure: Hidden Markov Models in Molecular Biology: New Algorithms and Applications. NIPS 1992: 747-754
11EESantosh S. Venkatesh, Pierre Baldi: Programmed interactions in higher-order neural networks: Maximal capacity. J. Complexity 7(3): 316-337 (1991)
10EESantosh S. Venkatesh, Pierre Baldi: Programmed interactions in higher-order neural networks: The outer-product algorithm. J. Complexity 7(4): 443-479 (1991)
9EEPierre Baldi: Computing with Arrays of Bell-Shaped and Sigmoid Functions. NIPS 1990: 735-742
8EEPierre Baldi, Yosef Rinott, Charles Stein: On the Distribution of the Number of Local Minima of a Random Function on a Graph. NIPS 1989: 727-732
7EEAmir F. Atiya, Pierre Baldi: Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis. Int. J. Neural Syst. 1(2): 103-124 (1989)
6EEPierre Baldi, Kurt Hornik: Neural networks and principal component analysis: Learning from examples without local minima. Neural Networks 2(1): 53-58 (1989)
5EEPierre Baldi: Linear Learning: Landscapes and Algorithms. NIPS 1988: 65-72
4 Pierre Baldi: Neural networks, orientations of the hypercube, and algebraic threshold functions. IEEE Transactions on Information Theory 34(3): 523-530 (1988)
3 Pierre Baldi: Group Actions and Learning for a Family of Automata. J. Comput. Syst. Sci. 36(1): 1-15 (1988)
2 Pierre Baldi: Neural Networks, Acyclic Orientations of the Hypercube, and Sets of Orthogonal Vectors. SIAM J. Discrete Math. 1(1): 1-13 (1988)
1EEPierre Baldi, Santosh S. Venkatesh: On Properties of Networks of Neuron-Like Elements. NIPS 1987: 41-51

Coauthor Index

1Claus A. F. Andersen [28] [31]
2Amir F. Atiya [7]
3Pierre-François Baisnée [30] [34] [39] [47]
4Sushil Krishna Bajracharya [74] [80] [81] [84] [85] [89] [92]
5John T. Belisle [83]
6Ryan W. Benz [90]
7James M. Bower [23]
8Rainer K. Brachmann [70]
9Marty C. Brandon [53] [76]
10Jocelyne Bruand [60] [64]
11Søren Brunak [14] [20] [21] [24] [25] [26] [27] [28] [31] [34] [35] [36]
12Michael C. Burl [16]
13Rita Casadio [37]
14Yves Chauvin [12] [14] [15] [19] [20] [21] [24] [25] [27] [28]
15Jonathan H. Chen [60] [64] [70] [79]
16Jianlin Cheng [49] [52] [57] [58] [63] [70] [71] [73] [87]
17Samuel A. Danziger [70]
18D. Huw Davies [72] [83]
19Lawrence R. Dearth [70]
20Kevin J. Donovan [78]
21Denise L. Doolan [72]
22Yimeng Dou [47] [60] [74]
23Melanie Duffield [83]
24André Elisseeff [46]
25Jacob Engelbrecht [14] [20]
26Piero Fariselli [37]
27Usama M. Fayyad [16]
28Philip L. Felgner [72] [83]
29Paolo Frasconi [26] [35] [41] [45] [69]
30B. S. Gaut [59]
31Tony Givargis [68]
32Yann Guermeur [46]
33Amir Haghighat [68]
34Steven E. Hampson (Steven Hampson) [32] [39] [40] [59]
35M. Gill Hartley [83]
36G. Wesley Hatfield [56]
37Daniel S. Hirschberg [91]
38Siddiqua Hirst [72]
39Vinh P. Hoang [70]
40Kurt Hornik [6] [18]
41She-pin Hung [56]
42Tim Hunkapiller [12]
43Laurent Itti [62] [67]
44Raja Jurdak [50] [51] [65] [77]
45Dennis F. Kibler [32] [40]
46James Kreuziger [76]
47Anders Krogh [14] [20]
48Richard H. Lathrop [70]
49Otávio Augusto Lazzarini Lemos [84]
50Erik Linstead [74] [79] [80] [81] [85] [89] [92]
51Anthony D. Long [33]
52Cristina Videira Lopes [50] [51] [65] [68] [74] [77] [80] [81] [84] [85] [89] [92]
53Marie T. Lott [53] [76]
54Qiang Lu [70]
55Ray Luo [70]
56Atri Mandal [68]
57Paulo Cesar Masiero [84]
58Marcella A. McClure [12]
59Dan Mishmar [76]
60Eric Mjolsness [57]
61Ricardo Santos Morla [84]
62Yunxiang Mu [72]
63Shamkant B. Navathe [53]
64Trung Chi Ngo [74] [92]
65Bao D. Nguyen [78]
66Kevin Cuong Nguyen [53]
67Henrik Nielsen [28]
68James Nowick [47]
69Joel Ossher [84]
70Hélène Paugam-Moisy [46]
71Yann Pécout [47]
72Anders Gorm Pedersen [21] [24] [25] [27] [34]
73Pietro Perona [16]
74Jeannine M. Petersen [83]
75Peter Phung [64]
76Gianluca Pollastri [26] [31] [35] [37] [38] [41] [42] [43] [46] [47] [69]
77Jason C. Poole [76]
78Vincent Procaccio [76]
79Liva Ralaivola [54] [64] [66]
80Arlo Z. Randall [48] [52] [83] [87]
81Paul Rigor [74] [80] [81] [85] [92]
82Yosef Rinott [8]
83Michal Rosen-Zvi [55]
84Eduardo Ruiz-Pesini [76]
85Hiroto Saigo [54] [70]
86Suzanne B. Sandmeyer [32]
87Lucas Scharenbroich [57]
88A. J. Shaka [78]
89Padhraic Smyth [16] [45]
90Giovanni Soda [26] [35]
91Syawal Spolim [53]
92Charles Stein [8]
93Suman Sundaresh [56] [72] [83]
94Sanjay Joshua Swamidass [54] [60] [61] [64] [70] [79]
95Michael J. Sweredoski [52] [58] [71] [78] [87] [88]
96Richard W. Titball [83]
97Berkay Unal [72] [83]
98Michael C. Vanier [23]
99Santosh S. Venkatesh [1] [10] [11] [13]
100Luis P. Villarreal [48]
101Alessandro Vullo [41] [49] [69]
102Douglas C. Wallace [53] [76]
103Dennis Wang [79]
104Lin Wu [66] [75] [86]
105Christina Yi [76]
106Dominique Zelus [46]
107Jue Zeng [70]

Colors in the list of coauthors

Copyright © Sun May 17 03:24:02 2009 by Michael Ley (ley@uni-trier.de)