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Displaying 1-17 out of 17 total
A Genomic Analysis Pipeline and Its Application to Pediatric Cancers
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Michael Zeller,Christophe N. Magnan,Vishal R. Patel,Paul Rigor,Leonard Sender,Pierre Baldi
Issue Date:September 2014
pp. 1-1
We present a cancer genomic analysis pipeline which takes as input sequencing reads for both germline and tumor genomes and outputs filtered lists of all genetic mutations in the form of short ranked list of the most affected genes in the tumor, using eith...
 
Exploring Java software vocabulary: A search and mining perspective
Found in: Search-Driven Development-Users, Infrastructure, Tools and Evaluation, ICSE Workshop on
By Erik Linstead, Lindsey Hughes, Cristina Lopes, Pierre Baldi
Issue Date:May 2009
pp. 29-32
We conduct a large-scale analysis of Java source code vocabulary for 12,151 open source projects from Source-Forge and Apache, a corpus substantially larger than considered previously. Simple statistical analysis demonstrates robust power-law behavior for ...
 
SourcererDB: An aggregated repository of statically analyzed and cross-linked open source Java projects
Found in: Mining Software Repositories, International Workshop on
By Joel Ossher, Sushil Bajracharya, Erik Linstead, Pierre Baldi, Cristina Lopes
Issue Date:May 2009
pp. 183-186
Abstract The open source movement has made vast quantities of source code available online for free, providing an extremely large dataset for empirical study and potential resuse. A major difficulty in exploiting this potential fully is that the data are c...
 
Mining the coherence of GNOME bug reports with statistical topic models
Found in: Mining Software Repositories, International Workshop on
By Erik Linstead, Pierre Baldi
Issue Date:May 2009
pp. 99-102
We adapt Latent Dirichlet Allocation to the problem of mining bug reports in order to define a new information-theoretic measure of coherence. We then apply our technique to a snapshot of the GNOME Bugzilla database consisting of 431,863 bug reports for mu...
 
An Application of Latent Dirichlet Allocation to Analyzing Software Evolution
Found in: Machine Learning and Applications, Fourth International Conference on
By Erik Linstead, Cristina Lopes, Pierre Baldi
Issue Date:December 2008
pp. 813-818
We develop and apply unsupervised statistical topic models, in particular Latent Dirichlet Allocation, to identify functional components of source code and study their evolution over multiple project versions. We present results for two large, open source ...
 
Effective Compression of Monotone and Quasi-Monotone Sequences of Integers
Found in: Data Compression Conference
By Daniel S. Hirschberg, Pierre Baldi
Issue Date:March 2008
pp. 520
No summary available.
   
Machine Learning Challenges in Chemoinformatics and Drug Screening and Design
Found in: Machine Learning and Applications, Fourth International Conference on
By Professor Pierre Baldi
Issue Date:December 2007
pp. xviii
No summary available.
   
Adaptive Low Power Listening for Wireless Sensor Networks
Found in: IEEE Transactions on Mobile Computing
By Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
Issue Date:August 2007
pp. 988-1004
Most sensor networks require application-specific network-wide performance guarantees, suggesting the need for global and flexible network optimization. The dynamic and nonuniform local states of individual nodes in sensor networks complicate global optimi...
 
Mining Eclipse Developer Contributions via Author-Topic Models
Found in: Mining Software Repositories, International Workshop on
By Erik Linstead, Paul Rigor, Sushil Bajracharya, Cristina Lopes, Pierre Baldi
Issue Date:May 2007
pp. 30
We present the results of applying statistical author-topic models to a subset of the Eclipse 3.0 source code consisting of 2,119 source files and 700,000 lines of code from 59 developers. This technique provides an intuitive and automated framework with w...
 
A Comparative Analysis and Experimental Study on Wireless Aerial and Underwater Acoustic Communications
Found in: Digital Telecommunications, International Conference on
By Raja Jurdak, Cristina Videira Lopes, Pedro M. Q. Aguiar, Pierre Baldi
Issue Date:August 2006
pp. 31
Widely available speakers and microphones in electronic devices motivate the use of generic audio hardware to establish acoustic communication links. Acoustic communication with generic hardware requires software modems for data modulation and demodulation...
 
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Samuel A. Danziger, S. 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
Issue Date:April 2006
pp. 114-125
Many biomedical problems relate to mutant functional properties across a sequence space of interest, e.g., flu, cancer, and HIV. Detailed knowledge of mutant properties and function improves medical treatment and prevention. A functional census of p53 canc...
 
State-Driven Energy Optimization in Wireless Sensor Networks
Found in: Wireless Technologies/High Speed Networks/Multimedia Communications Systems/Sensor Networks, International Conference on
By Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
Issue Date:August 2005
pp. 356-363
Most sensor network applications require quality of service guarantees on a network-wide basis, suggesting the need for global network cost optimization. The dynamic and nonuniform local states of individual nodes in sensor networks complicate global cost ...
 
A Principled Approach to Detecting Surprising Events in Video
Found in: Computer Vision and Pattern Recognition, IEEE Computer Society Conference on
By Laurent Itti, Pierre Baldi
Issue Date:June 2005
pp. 631-637
Primates demonstrate unparalleled ability at rapidly orienting towards important events in complex dynamic environments. During rapid guidance of attention and gaze towards potential objects of interest or threats, often there is no time for detailed visua...
 
Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology
Found in: IEEE Intelligent Systems
By Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness
Issue Date:May 2005
pp. 68-75
Sigmoid is a generative, scalable software infrastructure for pathway bioinformatics and systems biology. The Sigmoid modeling system is a three-tier architecture comprising distributed modules that implement pathway and cell model generation and simulatio...
 
An Acoustic Identification Scheme for Location Systems
Found in: Pervasive Services, IEEE/ACS International Conference on
By Raja Jurdak, Cristina Videira Lopes, Pierre Baldi
Issue Date:July 2004
pp. 61-70
Many pervasive computing applications require location awareness in order to successfully integrate technology into our daily lives. A location system consists of a group of sensors that determine the position of a mobile user and provide the user with use...
 
A Machine-Learning Strategy for Protein Analysis
Found in: IEEE Intelligent Systems
By Pierre Baldi, Gianluca Pollastri
Issue Date:March 2002
pp. 28-35
<p>The authors provide a brief overview of the application of machine-learning methods to proteomic problems. They outline a novel strategy for the complete prediction of protein 3D coordinates. The strategy relies on three main successive stages: pr...
 
Sourcerer: a search engine for open source code supporting structure-based search
Found in: Companion to the 21st ACM SIGPLAN conference on Object-oriented programming languages, systems, and applications (OOPSLA '06)
By Cristina Lopes, Erik Linstead, Paul Rigor, Pierre Baldi, Sushil Bajracharya, Trung Ngo, Yimeng Dou
Issue Date:October 2006
pp. 681-682
We present Sourcerer, a search engine for open-source code. Sourcerer extracts fine-grained structural information from the code and stores it in a relational model. This information is used to implement a basic notion of CodeRank and to enable search form...
     
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