Pierre Baldi - RankMe

321 papers A* 18A 13B 6C 6Misc 3Journal 219Unranked 50

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A theory of synaptic neural balance: From local to global order. Artif. Intell. Pierre Baldi, Antonios Alexos, Ian Domingo, Alireza Rahmansetayesh
2025	J	`jnl`	Adapting Vision-Language Models for Neutrino Event Classification in High-Energy Physics. CoRR Dikshant Sagar, Kaiwen Yu, Alejandro Yankelevich, Jianming Bian, Pierre Baldi
2025	J	`jnl`	Antenna Near-Field Reconstruction from Far-Field Data Using Convolutional Neural Networks. CoRR Sahar Bagherkhani, Jackson Christopher Earls, Franco De Flaviis, Pierre Baldi
2025	J	`jnl`	Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction. J. Chem. Inf. Model. Mohammadamin Tavakoli, Yin Ting T. Chiu, Ann Marie Carlton, David Van Vranken, Pierre Baldi
2025	J	`jnl`	ClimSim-Online: A Large Multi-Scale Dataset and Framework for Hybrid Physics-ML Climate Emulation. J. Mach. Learn. Res. Sungduk Yu, Zeyuan Hu, Akshay Subramaniam, Walter M. Hannah, Liran Peng, Jerry Lin, Mohamed Aziz Bhouri, Ritwik Gupta, Björn Lütjens, Justus C. Will, Gunnar Behrens, Julius J. M. Busecke, Nora Loose, Charles Stern, Tom Beucler, Bryce E. Harrop, Helge Heuer, Benjamin R. Hillman, Andrea M. Jenney, Nana Liu, Alistair White, Tian Zheng, Zhiming Kuang, Fiaz Ahmed, Elizabeth A. Barnes, Noah D. Brenowitz, Christopher S. Bretherton, Veronika Eyring, Savannah L. Ferretti, Nicholas J. Lutsko, Pierre Gentine, Stephan Mandt, J. David Neelin, Rose Yu, Laure Zanna, Nathan M. Urban, Janni Yuval, Ryan Abernathey, Pierre Baldi, Wayne Chuang, Yu Huang, Fernando Iglesias-Suarez, Sanket R. Jantre, Po-Lun Ma, Sara Shamekh, Guang Zhang, Michael S. Pritchard
2025	J	`jnl`	Evaluating the Intelligence of large language models: A comparative study using verbal and visual IQ tests. Comput. Hum. Behav. Artif. Humans Sherif Abdelkarim, David Lu, Dora-Luz Flores, Susanne M. Jaeggi, Pierre Baldi
2025	J	`jnl`	Fine-Tuning Vision-Language Models for Neutrino Event Analysis in High-Energy Physics Experiments. CoRR Dikshant Sagar, Kaiwen Yu, Alejandro Yankelevich, Jianming Bian, Pierre Baldi
2025	J	`jnl`	Heterogeneous Point Set Transformers for Segmentation of Multiple View Particle Detectors. CoRR Edgar E. Robles, Dikshant Sagar, Alejandro Yankelevich, Jianming Bian, Pierre Baldi, NOvA Collaboration
2025	A*	`conf`	Improving Deep Learning Speed and Performance Through Synaptic Neural Balance. AAAI Antonios Alexos, Ian Domingo, Pierre Baldi
2025	J	`jnl`	Interpretable Deep Learning for Polar Mechanistic Reaction Prediction. CoRR Ryan J. Miller, Alexander E. Dashuta, Brayden Rudisill, David Van Vranken, Pierre Baldi
2025	J	`jnl`	Memorization: A Close Look at Books. CoRR Iris Ma, Ian Domingo, Alberto Krone-Martins, Pierre Baldi, Cristina V. Lopes
2025	B	`conf`	Optimization of Sparse Phased Arrays Using Deep Learning. IJCNN Jackson Earls, Lior Maman, David Lin Yi Lu, Amir Boag, Pierre Baldi
2025	J	`jnl`	Particle Hit Clustering and Identification Using Point Set Transformers in Liquid Argon Time Projection Chambers. CoRR Edgar E. Robles, Alejandro Yankelevich, Wenjie Wu, Jianming Bian, Pierre Baldi
2025	—	`conf`	Realizable Continuous-Space Shields for Safe Reinforcement Learning. L4DC Kyungmin Kim, Davide Corsi, Andoni Rodríguez, JB Lanier, Benjami Parellada, Pierre Baldi, César Sánchez, Roy Fox
2025	J	`jnl`	Sparse Phased Array Optimization Using Deep Learning. CoRR David Lu, Lior Maman, Jackson Earls, Amir Boag, Pierre Baldi
2024	J	`jnl`	AttentionStitch: How Attention Solves the Speech Editing Problem. CoRR Antonios Alexos, Pierre Baldi
2024	—	`conf`	Deep Learning Over-Parameterization: the Shallow Fallacy. NLDL Pierre Baldi
2024	—	`conf`	FastStitch: Speech editing by hitch-hiking a pre-trained FastSpeech2 model. NLDL Antonios Alexos, Pierre Baldi
2024	J	`jnl`	From Local to Global Order: A Theory of Neural Synaptic Balance. CoRR Pierre Baldi, Alireza Rahmansetayesh
2024	J	`jnl`	Full Event Particle-Level Unfolding with Variable-Length Latent Variational Diffusion. CoRR Alexander Shmakov, Kevin Greif, Michael James Fenton, Aishik Ghosh, Pierre Baldi, Daniel Whiteson
2024	J	`jnl`	Make the Pertinent Salient: Task-Relevant Reconstruction for Visual Control with Distractions. CoRR Kyungmin Kim, JB Lanier, Pierre Baldi, Charless C. Fowlkes, Roy Fox
2024	J	`jnl`	Neural Erosion: Emulating Controlled Neurodegeneration and Aging in AI Systems. CoRR Antonios Alexos, Yu-Dai Tsai, Ian Domingo, Maryam Pishgar, Pierre Baldi
2024	A*	`conf`	Nuclear Fusion Diamond Polishing Dataset. NeurIPS Antonios Alexos, Junze Liu, Shashank Galla, Sean Hayes, Kshitij Bhardwaj, Alexander Schwartz, Monika Biener, Pierre Baldi, Satish T. S. Bukkapatnam, Suhas Bhandarkar
2024	J	`jnl`	PMechDB: A Public Database of Elementary Polar Reaction Steps. J. Chem. Inf. Model. Mohammadamin Tavakoli, Ryan J. Miller, Mirana Angel, Michael A. Pfeiffer, Eugene S. Gutman, Aaron Mood, David Van Vranken, Pierre Baldi
2024	J	`jnl`	Realizable Continuous-Space Shields for Safe Reinforcement Learning. CoRR Kyungmin Kim, Davide Corsi, Andoni Rodríguez, JB Lanier, Benjami Parellada, Pierre Baldi, César Sánchez, Roy Fox
2024	J	`jnl`	Reconstruction of boosted and resolved multi-Higgs-boson events with symmetry-preserving attention networks. CoRR Haoyang Li, Marko Stamenkovic, Alexander Shmakov, Michael Fenton, Darius Shih-Chieh Chao, Kaitlyn Maiya White, Caden Mikkelsen, Jovan Mitic, Cristina Mantilla Suarez, Melissa Quinnan, Greg Landsberg, Harvey B. Newman, Pierre Baldi, Daniel Whiteson, Javier M. Duarte
2024	—	`conf`	Selective Perception: Learning Concise State Descriptions for Language Model Actors. NAACL (Short Papers) Kolby Nottingham, Yasaman Razeghi, Kyungmin Kim, JB Lanier, Pierre Baldi, Roy Fox, Sameer Singh
2024	A*	`conf`	Toward Optimal Policy Population Growth in Two-Player Zero-Sum Games. ICLR Stephen Marcus McAleer, JB Lanier, Kevin A. Wang, Pierre Baldi, Tuomas Sandholm, Roy Fox
2024	J	`jnl`	Unraveling the Molecular Magic: AI Insights on the Formation of Extraordinarily Stretchable Hydrogels. CoRR Shahriar Hojjati Emmami, Ali Pilehvar Meibody, Lobat Tayebi, Mohammadamin Tavakoli, Pierre Baldi
2023	—	`conf`	AI and Veterinary Medicine: Performance of Large Language Models on the North American Licensing Examination. SNAMS Mirana Angel, Anuj Patel, Haiyi Xing, Dylan Balsz, Cody L. Arbuckle, David Bruyette, Pierre Baldi
2023	A*	`conf`	AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning. NeurIPS Mohammadamin Tavakoli, Pierre Baldi, Ann Marie Carlton, Yin Ting T. Chiu, Alexander Shmakov, David Van Vranken
2023	J	`jnl`	AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning. CoRR Mohammadamin Tavakoli, Yin Ting T. Chiu, Alexander Shmakov, Ann Marie Carlton, David Van Vranken, Pierre Baldi
2023	A*	`conf`	ClimSim: A large multi-scale dataset for hybrid physics-ML climate emulation. NeurIPS Sungduk Yu, Walter M. Hannah, Liran Peng, Jerry Lin, Mohamed Aziz Bhouri, Ritwik Gupta, Björn Lütjens, Justus C. Will, Gunnar Behrens, Julius Busecke, Nora Loose, Charles Stern, Tom Beucler, Bryce E. Harrop, Benjamin R. Hillman, Andrea M. Jenney, Savannah L. Ferretti, Nana Liu, Animashree Anandkumar, Noah D. Brenowitz, Veronika Eyring, Nicholas Geneva, Pierre Gentine, Stephan Mandt, Jaideep Pathak, Akshay Subramaniam, Carl Vondrick, Rose Yu, Laure Zanna, Tian Zheng, Ryan Abernathey, Fiaz Ahmed, David C. Bader, Pierre Baldi, Elizabeth A. Barnes, Christopher S. Bretherton, Peter M. Caldwell, Wayne Chuang, Yilun Han, Yu Huang, Fernando Iglesias-Suarez, Sanket R. Jantre, Karthik Kashinath, Marat Khairoutdinov, Thorsten Kurth, Nicholas J. Lutsko, Po-Lun Ma, Griffin Mooers, J. David Neelin, David A. Randall, Sara Shamekh, Mark Taylor, Nathan M. Urban, Janni Yuval, Guang Zhang, Mike Pritchard
2023	J	`jnl`	ClimSim: An open large-scale dataset for training high-resolution physics emulators in hybrid multi-scale climate simulators. CoRR Sungduk Yu, Walter M. Hannah, Liran Peng, Mohamed Aziz Bhouri, Ritwik Gupta, Jerry Lin, Björn Lütjens, Justus C. Will, Tom Beucler, Bryce E. Harrop, Benjamin R. Hillman, Andrea M. Jenney, Savannah L. Ferretti, Nana Liu, Anima Anandkumar, Noah D. Brenowitz, Veronika Eyring, Pierre Gentine, Stephan Mandt, Jaideep Pathak, Carl Vondrick, Rose Yu, Laure Zanna, Ryan P. Abernathey, Fiaz Ahmed, David C. Bader, Pierre Baldi, Elizabeth A. Barnes, Gunnar Behrens, Christopher S. Bretherton, Julius J. M. Busecke, Peter M. Caldwell, Wayne Chuang, Yilun Han, Yu Huang, Fernando Iglesias-Suarez, Sanket R. Jantre, Karthik Kashinath, Marat Khairoutdinov, Thorsten Kurth, Nicholas J. Lutsko, Po-Lun Ma, Griffin Mooers, J. David Neelin, David A. Randall, Sara Shamekh, Akshay Subramaniam, Mark A. Taylor, et al.
2023	—	`conf`	Clinical Knowledge and Reasoning Abilities of Large Language Models in Pharmacy: A Comparative Study on the NAPLEX Exam. SNAMS Mirana Angel, Anuj Patel, Amal Alachkar, Pierre Baldi
2023	A*	`conf`	End-To-End Latent Variational Diffusion Models for Inverse Problems in High Energy Physics. NeurIPS Alexander Shmakov, Kevin Greif, Michael James Fenton, Aishik Ghosh, Pierre Baldi, Daniel Whiteson
2023	J	`jnl`	End-To-End Latent Variational Diffusion Models for Inverse Problems in High Energy Physics. CoRR Alexander Shmakov, Kevin Greif, Michael James Fenton, Aishik Ghosh, Pierre Baldi, Daniel Whiteson
2023	J	`jnl`	Evaluating the Performance of Large Language Models for Spanish Language in Undergraduate Admissions Exams. CoRR Sabino Miranda, Obdulia Pichardo-Lagunas, Bella Martínez-Seis, Pierre Baldi
2023	J	`jnl`	Evaluating the Performance of Large Language Models for Spanish Language in Undergraduate Admissions Exams. Computación y Sistemas (CyS) Sabino Miranda, Obdulia Pichardo-Lagunas, Bella Martínez-Seis, Pierre Baldi
2023	J	`jnl`	Extended Symmetry Preserving Attention Networks for LHC Analysis. CoRR Michael James Fenton, Alexander Shmakov, Hideki Okawa, Yuji Li, Ko-Yang Hsiao, Shih-Chieh Hsu, Daniel Whiteson, Pierre Baldi
2023	J	`jnl`	Generalizing to new calorimeter geometries with Geometry-Aware Autoregressive Models (GAAMs) for fast calorimeter simulation. CoRR Junze Liu, Aishik Ghosh, Dylan Smith, Pierre Baldi, Daniel Whiteson
2023	J	`jnl`	Interpretable Joint Event-Particle Reconstruction for Neutrino Physics at NOvA with Sparse CNNs and Transformers. CoRR Alexander Shmakov, Alejandro Yankelevich, Jianming Bian, Pierre Baldi
2023	A*	`conf`	Language Models can Solve Computer Tasks. NeurIPS Geunwoo Kim, Pierre Baldi, Stephen McAleer
2023	J	`jnl`	Language Models can Solve Computer Tasks. CoRR Geunwoo Kim, Pierre Baldi, Stephen McAleer
2023	J	`jnl`	Machine Learning-Enhanced Prediction of Surface Smoothness for Inertial Confinement Fusion Target Polishing Using Limited Data. CoRR Antonios Alexos, Junze Liu, Akash Tiwari, Kshitij Bhardwaj, Sean Hayes, Pierre Baldi, Satish T. S. Bukkapatnam, Suhas Bhandarkar
2023	J	`jnl`	RMechDB: A Public Database of Elementary Radical Reaction Steps. J. Chem. Inf. Model. Mohammadamin Tavakoli, Yin Ting T. Chiu, Pierre Baldi, Ann Marie Carlton, David Van Vranken
2023	J	`jnl`	Selective Perception: Optimizing State Descriptions with Reinforcement Learning for Language Model Actors. CoRR Kolby Nottingham, Yasaman Razeghi, Kyungmin Kim, JB Lanier, Pierre Baldi, Roy Fox, Sameer Singh
2023	J	`jnl`	The quarks of attention: Structure and capacity of neural attention building blocks. Artif. Intell. Pierre Baldi, Roman Vershynin
2022	J	`jnl`	Anytime PSRO for Two-Player Zero-Sum Games. CoRR Stephen McAleer, Kevin Wang, John B. Lanier, Marc Lanctot, Pierre Baldi, Tuomas Sandholm, Roy Fox
2022	J	`jnl`	Call for a Public Open Database of All Chemical Reactions. J. Chem. Inf. Model. Pierre Baldi
2022	J	`jnl`	CircadiOmics: circadian omic web portal. Nucleic Acids Res. Muntaha Samad, Forest Agostinelli, Tomoki Sato, Kohei Shimaji, Pierre Baldi
2022	J	`jnl`	Deep Learning Models of the Discrete Component of the Galactic Interstellar Gamma-Ray Emission. CoRR Alexander Shmakov, Mohammadamin Tavakoli, Pierre Baldi, Christopher M. Karwin, Alex Broughton, Simona Murgia
2022	J	`jnl`	Feasible Adversarial Robust Reinforcement Learning for Underspecified Environments. CoRR John B. Lanier, Stephen McAleer, Pierre Baldi, Roy Fox
2022	J	`jnl`	Geometry-aware Autoregressive Models for Calorimeter Shower Simulations. CoRR Junze Liu, Aishik Ghosh, Dylan Smith, Pierre Baldi, Daniel Whiteson
2022	J	`jnl`	Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity. J. Chem. Inf. Model. Mohammadamin Tavakoli, Aaron Mood, David Van Vranken, Pierre Baldi
2022	J	`jnl`	Reproducible Hyperparameter Optimization. J. Comput. Graph. Stat. Lars Hertel, Pierre Baldi, Daniel L. Gillen
2022	J	`jnl`	Rxn Hypergraph: a Hypergraph Attention Model for Chemical Reaction Representation. CoRR Mohammadamin Tavakoli, Alexander Shmakov, Francesco Ceccarelli, Pierre Baldi
2022	J	`jnl`	SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity. Bioinform. Gregor Urban, Christophe N. Magnan, Pierre Baldi
2022	J	`jnl`	Self-Play PSRO: Toward Optimal Populations in Two-Player Zero-Sum Games. CoRR Stephen McAleer, John B. Lanier, Kevin A. Wang, Pierre Baldi, Roy Fox, Tuomas Sandholm
2022	J	`jnl`	The Quarks of Attention. CoRR Pierre Baldi, Roman Vershynin
2022	J	`jnl`	Weakly Supervised Polyp Segmentation in Colonoscopy Images Using Deep Neural Networks. J. Imaging Siwei Chen, Gregor Urban, Pierre Baldi
2021	J	`jnl`	A theory of capacity and sparse neural encoding. CoRR Pierre Baldi, Roman Vershynin
2021	J	`jnl`	A theory of capacity and sparse neural encoding. Neural Networks Pierre Baldi, Roman Vershynin
2021	J	`jnl`	A* Search Without Expansions: Learning Heuristic Functions with Deep Q-Networks. CoRR Forest Agostinelli, Alexander Shmakov, Stephen McAleer, Roy Fox, Pierre Baldi
2021	C	`conf`	D-REX: Static Detection of Relevant Runtime Exceptions with Location Aware Transformer. SCAM Farima Farmahinifarahani, Yadong Lu, Vaibhav Saini, Pierre Baldi, Cristina V. Lopes
2021	A*	`conf`	Deep Bucket Elimination. IJCAI Yasaman Razeghi, Kalev Kask, Yadong Lu, Pierre Baldi, Sakshi Agarwal, Rina Dechter
2021	J	`jnl`	Detecting Pulmonary Coccidioidomycosis (Valley fever) with Deep Convolutional Neural Networks. CoRR Jordan Ott, David Bruyette, Cody L. Arbuckle, Dylan Balsz, Silke Hecht, Lisa Shubitz, Pierre Baldi
2021	J	`jnl`	Development and validation of an interpretable neural network for prediction of postoperative in-hospital mortality. npj Digit. Medicine Christine K. Lee, Muntaha Samad, Ira Hofer, Maxime Cannesson, Pierre Baldi
2021	J	`jnl`	Fold recognition by scoring protein maps using the congruence coefficient. Bioinform. Pietro di Lena, Pierre Baldi
2021	J	`jnl`	Improving Social Welfare While Preserving Autonomy via a Pareto Mediator. CoRR Stephen McAleer, John B. Lanier, Michael Dennis, Pierre Baldi, Roy Fox
2021	J	`jnl`	Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity. CoRR Mohammadamin Tavakoli, Aaron Mood, David Van Vranken, Pierre Baldi
2021	J	`jnl`	SPANet: Generalized Permutationless Set Assignment for Particle Physics using Symmetry Preserving Attention. CoRR Alexander Shmakov, Michael James Fenton, Ta-Wei Ho, Shih-Chieh Hsu, Daniel Whiteson, Pierre Baldi
2021	J	`jnl`	SPLASH: Learnable activation functions for improving accuracy and adversarial robustness. Neural Networks Mohammadamin Tavakoli, Forest Agostinelli, Pierre Baldi
2021	J	`jnl`	Tourbillon: a Physically Plausible Neural Architecture. CoRR Mohammadamin Tavakoli, Peter J. Sadowski, Pierre Baldi
2021	A*	`conf`	XDO: A Double Oracle Algorithm for Extensive-Form Games. NeurIPS Stephen McAleer, John B. Lanier, Kevin A. Wang, Pierre Baldi, Roy Fox
2021	J	`jnl`	XDO: A Double Oracle Algorithm for Extensive-Form Games. CoRR Stephen McAleer, John B. Lanier, Pierre Baldi, Roy Fox
2020	J	`jnl`	A Fortran-Keras Deep Learning Bridge for Scientific Computing. CoRR Jordan Ott, Mike Pritchard, Natalie Best, Erik Linstead, Milan Curcic, Pierre Baldi
2020	J	`jnl`	A Fortran-Keras Deep Learning Bridge for Scientific Computing. Sci. Program. Jordan Ott, Mike Pritchard, Natalie Best, Erik Linstead, Milan Curcic, Pierre Baldi
2020	J	`jnl`	Continuous Representation of Molecules Using Graph Variational Autoencoder. CoRR Mohammadamin Tavakoli, Pierre Baldi
2020	—	`conf`	Continuous Representation of Molecules using Graph Variational Autoencoder. AAAI Spring Symposium: MLPS Mohammadamin Tavakoli, Pierre Baldi
2020	J	`jnl`	Deep machine learning-assisted multiphoton microscopy to reduce light exposure and expedite imaging. CoRR Stephen McAleer, Alex Fast, Yuntian Xue, Magdalene Seiler, William Tang, Mihaela Balu, Pierre Baldi, Andrew W. Browne
2020	J	`jnl`	Deep-Learning-Based Kinematic Reconstruction for DUNE. CoRR Junze Liu, Jordan Ott, Julian Collado, Benjamin Jargowsky, Wenjie Wu, Jianming Bian, Pierre Baldi
2020	J	`jnl`	Development and validation of a deep neural network model to predict postoperative mortality, acute kidney injury, and reintubation using a single feature set. npj Digit. Medicine Ira Hofer, Christine K. Lee, Eilon Gabel, Pierre Baldi, Maxime Cannesson
2020	J	`jnl`	Learning in the machine: To share or not to share? Neural Networks Jordan Ott, Erik Linstead, Nicholas LaHaye, Pierre Baldi
2020	J	`jnl`	Permutationless Many-Jet Event Reconstruction with Symmetry Preserving Attention Networks. CoRR Michael James Fenton, Alexander Shmakov, Ta-Wei Ho, Shih-Chieh Hsu, Daniel Whiteson, Pierre Baldi
2020	A*	`conf`	Pipeline PSRO: A Scalable Approach for Finding Approximate Nash Equilibria in Large Games. NeurIPS Stephen McAleer, John B. Lanier, Roy Fox, Pierre Baldi
2020	J	`jnl`	Pipeline PSRO: A Scalable Approach for Finding Approximate Nash Equilibria in Large Games. CoRR Stephen McAleer, John B. Lanier, Roy Fox, Pierre Baldi
2020	J	`jnl`	Quantity vs. Quality: On Hyperparameter Optimization for Deep Reinforcement Learning. CoRR Lars Hertel, Pierre Baldi, Daniel L. Gillen
2020	J	`jnl`	SPLASH: Learnable Activation Functions for Improving Accuracy and Adversarial Robustness. CoRR Mohammadamin Tavakoli, Forest Agostinelli, Pierre Baldi
2020	J	`jnl`	Sherpa: Robust Hyperparameter Optimization for Machine Learning. CoRR Lars Hertel, Julian Collado, Peter J. Sadowski, Jordan Ott, Pierre Baldi
2020	J	`jnl`	Sherpa: Robust hyperparameter optimization for machine learning. SoftwareX Lars Hertel, Julian Collado, Peter J. Sadowski, Jordan Ott, Pierre Baldi
2019	J	`jnl`	ColosseumRL: A Framework for Multiagent Reinforcement Learning in N-Player Games. CoRR Alexander Shmakov, John B. Lanier, Stephen McAleer, Rohan Achar, Cristina V. Lopes, Pierre Baldi
2019	J	`jnl`	Curiosity-Driven Multi-Criteria Hindsight Experience Replay. CoRR John B. Lanier, Stephen McAleer, Pierre Baldi
2019	J	`jnl`	Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images. IEEE ACM Trans. Comput. Biol. Bioinform. Gregor Urban, Kevin Bache, Duc T. T. Phan, Agua Sobrino, Alexander Shmakov, Stephanie J. Hachey, Christopher C. W. Hughes, Pierre Baldi
2019	A*	`conf`	Efficient Neutrino Oscillation Parameter Inference with Gaussian Process. AAAI Lingge Li, Nitish Nayak, Jianming Bian, Pierre Baldi
2019	J	`jnl`	Highly Accurate Machine Fault Diagnosis Using Deep Transfer Learning. IEEE Trans. Ind. Informatics Siyu Shao, Stephen McAleer, Ruqiang Yan, Pierre Baldi
2019	A*	`conf`	Learning in the Machine: Random Backpropagation and the Deep Learning Channel (Extended Abstract). IJCAI Pierre Baldi, Peter J. Sadowski, Zhiqin Lu
2019	J	`jnl`	Learning in the Machine: To Share or Not to Share? CoRR Jordan Ott, Erik Linstead, Nicholas LaHaye, Pierre Baldi
2019	A*	`conf`	Modeling Dynamic Functional Connectivity with Latent Factor Gaussian Processes. NeurIPS Lingge Li, Dustin S. Pluta, Babak Shahbaba, Norbert Fortin, Hernando Ombao, Pierre Baldi
2019	J	`jnl`	Neural network gradient Hamiltonian Monte Carlo. Comput. Stat. Lingge Li, Andrew Holbrook, Babak Shahbaba, Pierre Baldi
2019	J	`jnl`	Polynomial Threshold Functions, Hyperplane Arrangements, and Random Tensors. SIAM J. Math. Data Sci. Pierre Baldi, Roman Vershynin
2019	—	`conf`	Solving the Rubik's Cube with Approximate Policy Iteration. ICLR (Poster) Stephen McAleer, Forest Agostinelli, Alexander Shmakov, Pierre Baldi
2019	J	`jnl`	Solving the Rubik's cube with deep reinforcement learning and search. Nat. Mach. Intell. Forest Agostinelli, Stephen McAleer, Alexander Shmakov, Pierre Baldi
2019	J	`jnl`	The capacity of feedforward neural networks. CoRR Pierre Baldi, Roman Vershynin
2019	J	`jnl`	The capacity of feedforward neural networks. Neural Networks Pierre Baldi, Roman Vershynin
2019	A*	`conf`	Towards automating precision studies of clone detectors. ICSE Vaibhav Saini, Farima Farmahinifarahani, Yadong Lu, Di Yang, Pedro Martins, Hitesh Sajnani, Pierre Baldi, Cristina V. Lopes
2018	J	`jnl`	CircadiOmics: circadian omic web portal. Nucleic Acids Res. Nicholas Ceglia, Yu Liu, Siwei Chen, Forest Agostinelli, Kristin Eckel-Mahan, Paolo Sassone-Corsi, Pierre Baldi
2018	J	`jnl`	ClusterCAD: a computational platform for type I modular polyketide synthase design. Nucleic Acids Res. Clara H. Eng, Tyler W. H. Backman, Constance B. Bailey, Christophe N. Magnan, Héctor García Martín, Leonard Katz, Pierre Baldi, Jay D. Keasling
2018	J	`jnl`	Inner and Outer Recursive Neural Networks for Chemoinformatics Applications. J. Chem. Inf. Model. Gregor Urban, Niranjan Subrahmanya, Pierre Baldi
2018	J	`jnl`	Learning in the machine: Random backpropagation and the deep learning channel. Artif. Intell. Pierre Baldi, Peter J. Sadowski, Zhiqin Lu
2018	J	`jnl`	Learning in the machine: Recirculation is random backpropagation. Neural Networks Pierre Baldi, Peter J. Sadowski
2018	A*	`conf`	On Neuronal Capacity. NeurIPS Pierre Baldi, Roman Vershynin
2018	J	`jnl`	Oreo: Detection of Clones in the Twilight Zone. CoRR Vaibhav Saini, Farima Farmahinifarahani, Yadong Lu, Pierre Baldi, Cristina V. Lopes
2018	—	`conf`	Oreo: detection of clones in the twilight zone. ESEC/SIGSOFT FSE Vaibhav Saini, Farima Farmahinifarahani, Yadong Lu, Pierre Baldi, Cristina V. Lopes
2018	J	`jnl`	Solving the Rubik's Cube Without Human Knowledge. CoRR Stephen McAleer, Forest Agostinelli, Alexander Shmakov, Pierre Baldi
2018	J	`jnl`	The inner and outer approaches to the design of recursive neural architectures. Data Min. Knowl. Discov. Pierre Baldi
2018	J	`jnl`	Towards Automating Precision Studies of Clone Detectors. CoRR Vaibhav Saini, Farima Farmahinifarahani, Yadong Lu, Di Yang, Pedro Martins, Hitesh Sajnani, Pierre Baldi, Cristina V. Lopes
2017	J	`jnl`	A multi-resolution approach for spinal metastasis detection using deep Siamese neural networks. Comput. Biol. Medicine Juan Wang, Zhiyuan Fang, Ning Lang, Huishu Yuan, Min-Ying Su, Pierre Baldi
2017	—	`conf`	Deep Learning in the Natural Sciences: Applications to Physics. Braverman Readings in Machine Learning Peter J. Sadowski, Pierre Baldi
2017	J	`jnl`	Detecting Cardiovascular Disease from Mammograms With Deep Learning. IEEE Trans. Medical Imaging Juan Wang, Huanjun Ding, Fatemeh Azamian Bidgoli, Brian Zhou, Carlos Iribarren, Sabee Molloi, Pierre Baldi
2017	J	`jnl`	Efficient Antihydrogen Detection in Antimatter Physics by Deep Learning. CoRR Peter J. Sadowski, Balint Radics, Ananya, Yasunori Yamazaki, Pierre Baldi
2017	—	`conf`	From Reinforcement Learning to Deep Reinforcement Learning: An Overview. Braverman Readings in Machine Learning Forest Agostinelli, Guillaume Hocquet, Sameer Singh, Pierre Baldi
2017	J	`jnl`	Learning in the Machine: the Symmetries of the Deep Learning Channel. CoRR Pierre Baldi, Peter J. Sadowski, Zhiqin Lu
2017	J	`jnl`	Learning in the machine: The symmetries of the deep learning channel. Neural Networks Pierre Baldi, Peter J. Sadowski, Zhiqin Lu
2017	J	`jnl`	MotifMap-RNA: a genome-wide map of RBP binding sites. Bioinform. Yu Liu, Sha Sun, Timothy Bredy, Marcelo A. Wood, Robert C. Spitale, Pierre Baldi
2016	J	`jnl`	A theory of local learning, the learning channel, and the optimality of backpropagation. Neural Networks Pierre Baldi, Peter J. Sadowski
2016	J	`jnl`	ISMB 2016 Proceedings. Bioinform. Pierre Baldi, Teresa M. Przytycka
2016	J	`jnl`	Learning in the Machine: Random Backpropagation and the Learning Channel. CoRR Pierre Baldi, Peter J. Sadowski, Zhiqin Lu
2016	J	`jnl`	Parameterized Machine Learning for High-Energy Physics. CoRR Pierre Baldi, Kyle Cranmer, Taylor Faucett, Peter J. Sadowski, Daniel Whiteson
2016	C	`conf`	Revealing Fundamental Physics from the Daya Bay Neutrino Experiment Using Deep Neural Networks. ICMLA Evan Racah, Seyoon Ko, Peter J. Sadowski, Wahid Bhimji, Craig Tull, Sang-Yun Oh, Pierre Baldi, Prabhat
2016	J	`jnl`	Revealing Fundamental Physics from the Daya Bay Neutrino Experiment using Deep Neural Networks. CoRR Evan Racah, Seyoon Ko, Peter J. Sadowski, Wahid Bhimji, Craig Tull, Sang-Yun Oh, Pierre Baldi, Prabhat
2016	J	`jnl`	Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction. J. Chem. Inf. Model. Peter J. Sadowski, David Fooshee, Niranjan Subrahmanya, Pierre Baldi
2016	J	`jnl`	VIRALpro: a tool to identify viral capsid and tail sequences. Bioinform. Clovis Galiez, Christophe N. Magnan, François Coste, Pierre Baldi
2016	J	`jnl`	What time is it? Deep learning approaches for circadian rhythms. Bioinform. Forest Agostinelli, Nicholas Ceglia, Babak Shahbaba, Paolo Sassone-Corsi, Pierre Baldi
2016	J	`jnl`	What time is it? Deep learning approaches for circadian rhythms. Bioinform. Forest Agostinelli, Nicholas Ceglia, Babak Shahbaba, Paolo Sassone-Corsi, Pierre Baldi
2015	J	`jnl`	Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. J. Cheminformatics Alessandro Lusci, Michael R. Browning, David Fooshee, S. Joshua Swamidass, Pierre Baldi
2015	—	`conf`	Learning Activation Functions to Improve Deep Neural Networks. ICLR (Workshop) Forest Agostinelli, Matthew D. Hoffman, Peter J. Sadowski, Pierre Baldi
2015	J	`jnl`	The Ebb and Flow of Deep Learning: a Theory of Local Learning. CoRR Pierre Baldi, Peter J. Sadowski
2015	J	`jnl`	The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework. Bioinform. Vishal R. Patel, Nicholas Ceglia, Michael Zeller, Kristin Eckel-Mahan, Paolo Sassone-Corsi, Pierre Baldi
2014	J	`jnl`	A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. IEEE ACM Trans. Comput. Biol. Bioinform. Michael Zeller, Christophe N. Magnan, Vishal R. Patel, Paul Rigor, Leonard Sender, Pierre Baldi
2014	—	`conf`	Deep Learning, Dark Knowledge, and Dark Matter. HEPML@NIPS Peter J. Sadowski, Julian Collado, Daniel Whiteson, Pierre Baldi
2014	J	`jnl`	Deep Learning: Theory, Algorithms, and Applications (NII Shonan Meeting 2014-5). NII Shonan Meet. Rep. Pierre Baldi, Kenji Fukumizu, Tomaso A. Poggio
2014	—	`conf`	Deep autoencoder neural networks for gene ontology annotation predictions. BCB Davide Chicco, Peter J. Sadowski, Pierre Baldi
2014	J	`jnl`	Enhanced Higgs to $τ^+τ^-$ Searches with Deep Learning. CoRR Pierre Baldi, Peter J. Sadowski, Daniel Whiteson
2014	J	`jnl`	Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. Bioinform. Ken Nagata, Arlo Z. Randall, Pierre Baldi
2014	—	`conf`	Parallel Multicut Segmentation via Dual Decomposition. NFMCP Julian Yarkony, Thorsten Beier, Pierre Baldi, Fred A. Hamprecht
2014	—	`ed.`	Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB '14, Newport Beach, California, USA, September 20-23, 2014 BCB Pierre Baldi, Wei Wang
2014	J	`jnl`	SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. Bioinform. Christophe N. Magnan, Pierre Baldi
2014	—	`conf`	Searching for Higgs Boson Decay Modes with Deep Learning. NIPS Peter J. Sadowski, Daniel Whiteson, Pierre Baldi
2014	J	`jnl`	The dropout learning algorithm. Artif. Intell. Pierre Baldi, Peter J. Sadowski
2013	J	`jnl`	A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions. Bioinform. Ivan Chang, Pierre Baldi
2013	—	`conf`	An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases. WIRN Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi
2013	J	`jnl`	Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules. J. Chem. Inf. Model. Alessandro Lusci, Gianluca Pollastri, Pierre Baldi
2013	J	`jnl`	ReactionMap: An Efficient Atom-Mapping Algorithm for Chemical Reactions. J. Chem. Inf. Model. David Fooshee, Alessio Andronico, Pierre Baldi
2013	J	`jnl`	Small-Molecule 3D Structure Prediction Using Open Crystallography Data. J. Chem. Inf. Model. Peter J. Sadowski, Pierre Baldi
2013	—	`conf`	Understanding Dropout. NIPS Pierre Baldi, Peter J. Sadowski
2012	—	`conf`	Autoencoders, Unsupervised Learning, and Deep Architectures. ICML Unsupervised and Transfer Learning Pierre Baldi
2012	J	`jnl`	Boolean autoencoders and hypercube clustering complexity. Des. Codes Cryptogr. Pierre Baldi
2012	J	`jnl`	Complex-valued autoencoders. Neural Networks Pierre Baldi, Zhiqin Lu
2012	J	`jnl`	Cyber-T web server: differential analysis of high-throughput data. Nucleic Acids Res. Matthew A. Kayala, Pierre Baldi
2012	—	`conf`	Deep Spatio-Temporal Architectures and Learning for Protein Structure Prediction. NIPS Pietro di Lena, Pierre Baldi, Ken Nagata
2012	J	`jnl`	Deep architectures for protein contact map prediction. Bioinform. Pietro di Lena, Ken Nagata, Pierre Baldi
2012	J	`jnl`	ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning. J. Chem. Inf. Model. Matthew A. Kayala, Pierre Baldi
2012	J	`jnl`	Speeding Up Chemical Searches Using the Inverted Index: The Convergence of Chemoinformatics and Text Search Methods. J. Chem. Inf. Model. Ramzi Nasr, Rares Vernica, Chen Li, Pierre Baldi
2012	J	`jnl`	The Universal Campus: An open virtual 3-D world infrastructure for research and education. eLearn Mag. Pierre Baldi, Cristina Videira Lopes
2011	—	`conf`	A Machine Learning Approach to Predict Chemical Reactions. NIPS Matthew A. Kayala, Pierre Baldi
2011	J	`jnl`	Complex-Valued Autoencoders CoRR Pierre Baldi, Sholeh Forouzan, Zhiqin Lu
2011	A*	`conf`	Countering GATTACA: efficient and secure testing of fully-sequenced human genomes. CCS Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, Gene Tsudik
2011	J	`jnl`	Countering Gattaca: Efficient and Secure Testing of Fully-Sequenced Human Genomes CoRR Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, Gene Tsudik
2011	—	`book`	DNA Microarrays and Gene Expression - From Experiments to Data Analysis and Modeling. Pierre Baldi, G. Wesley Hatfield
2011	J	`jnl`	Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. J. Chem. Inf. Model. Alessio Andronico, Arlo Z. Randall, Ryan W. Benz, Pierre Baldi
2011	J	`jnl`	Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response to the Letter by the Cambridge Crystallographic Data Centre. J. Chem. Inf. Model. Pierre Baldi
2011	J	`jnl`	Learning to Predict Chemical Reactions. J. Chem. Inf. Model. Matthew A. Kayala, Chloé-Agathe Azencott, Jonathan H. Chen, Pierre Baldi
2011	J	`jnl`	MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinform. Kenneth Daily, Vishal R. Patel, Paul Rigor, Xiaohui Xie, Pierre Baldi
2011	J	`jnl`	Privacy-Enhanced Methods for Comparing Compressed DNA Sequences CoRR David Eppstein, Michael T. Goodrich, Pierre Baldi
2010	J	`jnl`	A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinform. Sanjay Joshua Swamidass, Chloé-Agathe Azencott, Kenny Daily, Pierre Baldi
2010	B	`conf`	A scalable reference-point based algorithm to efficiently search large chemical databases. IJCNN Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi
2010	—	`conf`	Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery. WIRN Pierre Baldi, Chloé-Agathe Azencott, Sanjay Joshua Swamidass
2010	J	`jnl`	Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors. PLoS Comput. Biol. Thomas C. Whisenant, David T. Ho, Ryan W. Benz, Jeffrey S. Rogers, Robyn M. Kaake, Elizabeth A. Gordon, Lan Huang, Pierre Baldi, Lee Bardwell
2010	J	`jnl`	Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinform. Kenny Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi
2010	J	`jnl`	Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors. J. Chem. Inf. Model. Ramzi Nasr, Daniel S. Hirschberg, Pierre Baldi
2010	J	`jnl`	High-throughput prediction of protein antigenicity using protein microarray data. Bioinform. Christophe N. Magnan, Michael Zeller, Matthew A. Kayala, Adam Vigil, Arlo Z. Randall, Philip L. Felgner, Pierre Baldi
2010	C	`conf`	Information-Theoretic Metrics for Project-Level Scattering and Tangling. SEKE Erik Linstead, Lindsey Hughes, Cristina Videira Lopes, Pierre Baldi
2010	J	`jnl`	Modeling user reputation in wikis. Stat. Anal. Data Min. Sara Javanmardi, Cristina Videira Lopes, Pierre Baldi
2010	J	`jnl`	Of bits and wows: A Bayesian theory of surprise with applications to attention. Neural Networks Pierre Baldi, Laurent Itti
2010	J	`jnl`	When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values. J. Chem. Inf. Model. Pierre Baldi, Ramzi Nasr
2009	J	`jnl`	An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases. J. Chem. Inf. Model. Pierre Baldi, Daniel S. Hirschberg
2009	A	`conf`	Capturing Java naming conventions with first-order Markov models. ICPC Erik Linstead, Lindsey Hughes, Cristina Videira Lopes, Pierre Baldi
2009	J	`jnl`	Data structures and compression algorithms for genomic sequence data. Bioinform. Marty C. Brandon, Douglas C. Wallace, Pierre Baldi
2009	J	`jnl`	Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. J. Chem. Inf. Model. S. Joshua Swamidass, Chloé-Agathe Azencott, Ting-Wan Lin, Hugo Gramajo, Shiou-Chuan Tsai, Pierre Baldi
2009	J	`jnl`	Large scale study of multiple-molecule queries. J. Cheminformatics Ramzi Nasr, Sanjay Joshua Swamidass, Pierre Baldi
2009	A	`conf`	Mining the coherence of GNOME bug reports with statistical topic models. MSR Erik Linstead, Pierre Baldi
2009	J	`jnl`	MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinform. Xiaohui Xie, Paul Rigor, Pierre Baldi
2009	J	`jnl`	No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms. J. Chem. Inf. Model. Jonathan H. Chen, Pierre Baldi
2009	J	`jnl`	SOLpro: accurate sequence-based prediction of protein solubility. Bioinform. Christophe N. Magnan, Arlo Z. Randall, Pierre Baldi
2009	J	`jnl`	Software-driven sensor networks for short-range shallow water applications. Ad Hoc Networks Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
2009	J	`jnl`	Sourcerer: mining and searching internet-scale software repositories. Data Min. Knowl. Discov. Erik Linstead, Sushil Krishna Bajracharya, Trung Chi Ngo, Paul Rigor, Cristina Videira Lopes, Pierre Baldi
2009	A	`conf`	SourcererDB: An aggregated repository of statically analyzed and cross-linked open source Java projects. MSR Joel Ossher, Sushil Krishna Bajracharya, Erik Linstead, Pierre Baldi, Cristina Videira Lopes
2009	C	`conf`	User contribution and trust in Wikipedia. CollaborateCom Sara Javanmardi, Yasser Ganjisaffar, Cristina Videira Lopes, Pierre Baldi
2008	A	`conf`	A theory of aspects as latent topics. OOPSLA Pierre Baldi, Cristina Videira Lopes, Erik Linstead, Sushil Krishna Bajracharya
2008	C	`conf`	An Application of Latent Dirichlet Allocation to Analyzing Software Evolution. ICMLA Erik Linstead, Cristina Videira Lopes, Pierre Baldi
2008	A	`conf`	BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. ISMB Pierre Baldi, Ryan W. Benz
2008	J	`jnl`	Discovery of Power-Laws in Chemical Space. J. Chem. Inf. Model. Ryan W. Benz, S. Joshua Swamidass, Pierre Baldi
2008	B	`conf`	Effective Compression of Monotone and Quasi-Monotone Sequences of Integers. DCC Daniel S. Hirschberg, Pierre Baldi
2008	J	`jnl`	Learning to play Go using recursive neural networks. Neural Networks Lin Wu, Pierre Baldi
2008	J	`jnl`	PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinform. Michael J. Sweredoski, Pierre Baldi
2008	J	`jnl`	Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive OR. J. Chem. Inf. Model. Pierre Baldi, Daniel S. Hirschberg, Ramzi Nasr
2008	J	`jnl`	TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinform. Arlo Z. Randall, Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
2007	J	`jnl`	Adaptive Low Power Listening for Wireless Sensor Networks. IEEE Trans. Mob. Comput. Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
2007	J	`jnl`	An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res. 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
2007	J	`jnl`	Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. J. Chem. Inf. Model. S. Joshua Swamidass, Pierre Baldi
2007	J	`jnl`	ChemDB update - full-text search and virtual chemical space. Bioinform. Jonathan H. Chen, Erik Linstead, Sanjay Joshua Swamidass, Dennis Wang, Pierre Baldi
2007	A*	`conf`	CodeGenie: using test-cases to search and reuse source code. ASE Otávio Augusto Lazzarini Lemos, Sushil Krishna Bajracharya, Joel Ossher, Ricardo Santos Morla, Paulo César Masiero, Pierre Baldi, Cristina Videira Lopes
2007	—	`conf`	From protein microarrays to diagnostic antigen discovery: a study of the pathogen ISMB/ECCB (Supplement of Bioinformatics) Suman 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
2007	J	`jnl`	Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinform. Jianlin Cheng, Pierre Baldi
2007	—	`conf`	Learning and Charting Chemical Space with Strings and Graphs: Challenges and Opportunities for AI and Machine Learning. MLG Pierre Baldi
2007	J	`jnl`	Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval. J. Chem. Inf. Model. Pierre Baldi, Ryan W. Benz, Daniel S. Hirschberg, S. Joshua Swamidass
2007	C	`conf`	Machine Learning Challenges in Chemoinformatics and Drug Screening and Design. ICMLA Pierre Baldi
2007	J	`jnl`	Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. J. Chem. Inf. Model. S. Joshua Swamidass, Pierre Baldi
2007	J	`jnl`	Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. Bioinform. Michael J. Sweredoski, Kevin J. Donovan, Bao D. Nguyen, A. J. Shaka, Pierre Baldi
2007	A	`conf`	Mining Eclipse Developer Contributions via Author-Topic Models. MSR Erik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi
2007	—	`conf`	Mining Internet-Scale Software Repositories. NIPS Erik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi
2007	A*	`conf`	Mining concepts from code with probabilistic topic models. ASE Erik Linstead, Paul Rigor, Sushil Krishna Bajracharya, Cristina Videira Lopes, Pierre Baldi
2007	J	`jnl`	One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. J. Chem. Inf. Model. Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan H. Chen, Liva Ralaivola, Pierre Baldi
2006	—	`conf`	A Scalable Machine Learning Approach to Go. NIPS Lin Wu, Pierre Baldi
2006	J	`jnl`	A machine learning information retrieval approach to protein fold recognition. Bioinform. Jianlin Cheng, Pierre Baldi
2006	J	`jnl`	DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. Data Min. Knowl. Discov. Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
2006	J	`jnl`	Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. IEEE ACM Trans. Comput. Biol. Bioinform. 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
2006	J	`jnl`	Global landscape of recent inferred Darwinian selection for Proc. Natl. Acad. Sci. USA Eric T. Wang, Greg Kodama, Pierre Baldi, Robert K. Moyzis
2006	J	`jnl`	Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinform. Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Philip L. Felgner, Pierre Baldi
2006	J	`jnl`	Localization of off-the-shelf mobile devices using audible sound: architectures, protocols and performance assessment. ACM SIGMOBILE Mob. Comput. Commun. Rev. Cristina Videira Lopes, Amir Haghighat, Atri Mandal, Tony Givargis, Pierre Baldi
2006	J	`jnl`	Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. J. Comput. Biol. Gianluca Pollastri, Alessandro Vullo, Paolo Frasconi, Pierre Baldi
2006	—	`conf`	Sourcerer: a search engine for open source code supporting structure-based search. OOPSLA Companion Sushil Krishna Bajracharya, Trung Chi Ngo, Erik Linstead, Yimeng Dou, Paul Rigor, Pierre Baldi, Cristina Videira Lopes
2005	—	`conf`	A Principled Approach to Detecting Surprising Events in Video. CVPR (1) Laurent Itti, Pierre Baldi
2005	J	`jnl`	Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. Data Min. Knowl. Discov. Jianlin Cheng, Michael J. Sweredoski, Pierre Baldi
2005	—	`conf`	Bayesian Surprise Attracts Human Attention. NIPS Laurent Itti, Pierre Baldi
2005	—	`conf`	Beep: 3D indoor positioning using audible sound. CCNC Atri Mandal, Cristina V. Lopes, Tony Givargis, Amir Haghighat, Raja Jurdak, Pierre Baldi
2005	J	`jnl`	ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinform. Jonathan H. Chen, Sanjay Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi
2005	B	`conf`	Exploring chemical space with computers: challenges and opportunities. IJCNN Pierre Baldi
2005	J	`jnl`	Graph kernels for chemical informatics. Neural Networks Liva Ralaivola, Sanjay Joshua Swamidass, Hiroto Saigo, Pierre Baldi
2005	J	`jnl`	How noisy and replicable are DNA microarray data? Int. J. Bioinform. Res. Appl. Suman Sundaresh, She-pin Hung, G. Wesley Hatfield, Pierre Baldi
2005	—	`conf`	Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. ISMB (Supplement of Bioinformatics) Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi
2005	J	`jnl`	MITOMAP: a human mitochondrial genome database - 2004 update. Nucleic Acids Res. Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, Douglas C. Wallace
2005	J	`jnl`	On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks. Neural Networks Pierre Baldi, Michal Rosen-Zvi
2005	J	`jnl`	SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. Jianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi
2005	B	`conf`	SVM and pattern-enriched common fate graphs for the game of go. ESANN Liva Ralaivola, Lin Wu, Pierre Baldi
2005	J	`jnl`	Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology. IEEE Intell. Syst. Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness
2005	—	`conf`	State-Driven Energy Optimization in Wireless Sensor Networks. Systems Communications Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
2005	—	`conf`	Statistical Distribution of Chemical Fingerprints. WILF Sanjay Joshua Swamidass, Pierre Baldi
2005	J	`jnl`	Statistical detection of chromosomal homology using shared-gene density alone. Bioinform. Steven E. Hampson, Brandon S. Gaut, Pierre Baldi
2005	—	`conf`	Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. ISMB (Supplement of Bioinformatics) Jianlin Cheng, Pierre Baldi
2005	J	`jnl`	U-MAC: a proactive and adaptive UWB medium access control protocol. Wirel. Commun. Mob. Comput. Raja Jurdak, Pierre Baldi, Cristina Videira Lopes
2004	J	`jnl`	A survey, classification and comparative analysis of medium access control protocols for ad hoc networks. IEEE Commun. Surv. Tutorials Raja Jurdak, Cristina Videira Lopes, Pierre Baldi
2004	—	`conf`	An Acoustic Identification Scheme for Location Systems. ICPS Raja Jurdak, Cristina Videira Lopes, Pierre Baldi
2004	J	`jnl`	Combining protein secondary structure prediction models with ensemble methods of optimal complexity. Neurocomputing Yann Guermeur, Gianluca Pollastri, André Elisseeff, Dominique Zelus, Hélène Paugam-Moisy, Pierre Baldi
2004	J	`jnl`	ICBS: a database of interactions between protein chains mediated by ?-sheet formation. Bioinform. Yimeng Dou, Pierre-François Baisnée, Gianluca Pollastri, Yann Pécout, James Nowick, Pierre Baldi
2004	—	`conf`	Large-Scale Prediction of Disulphide Bond Connectivity. NIPS Pierre Baldi, Jianlin Cheng, Alessandro Vullo
2004	J	`jnl`	Structural proteomics of the poxvirus family. Artif. Intell. Medicine Arlo Z. Randall, Pierre Baldi, Luis P. Villarreal
2003	Misc	`conf`	Machine Learning Methods for Computational Proteomics and Beyond. AI Pierre Baldi
2003	—	`book`	Modeling the Internet and the Web: Probabilistic Method and Algorithms Pierre Baldi, Paolo Frasconi, Padhraic Smyth
2003	J	`jnl`	The Principled Design of Large-Scale Recursive Neural Network Architectures--DAG-RNNs and the Protein Structure Prediction Problem. J. Mach. Learn. Res. Pierre Baldi, Gianluca Pollastri
2002	J	`jnl`	A Machine-Learning Strategy for Protein Analysis. IEEE Intell. Syst. Pierre Baldi, Gianluca Pollastri
2002	J	`jnl`	Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinform. Steven Hampson, Dennis F. Kibler, Pierre Baldi
2002	J	`jnl`	Modeling and optimization of UWB communication networks through a flexible cost function. IEEE J. Sel. Areas Commun. Pierre Baldi, Luca De Nardis, Maria-Gabriella Di Benedetto
2002	—	`conf`	Prediction of Protein Topologies Using Generalized IOHMMS and RNNs. NIPS Gianluca Pollastri, Pierre Baldi, Alessandro Vullo, Paolo Frasconi
2002	A	`conf`	Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. ISMB Gianluca Pollastri, Pierre Baldi
2002	—	`book`	The Shattered Self - The End of Natural Evolution. Pierre Baldi
2002	J	`jnl`	Why are complementary DNA strands symmetric? Bioinform. Pierre-François Baisnée, Steven Hampson, Pierre Baldi
2001	J	`jnl`	A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. Bioinform. Pierre Baldi, Anthony D. Long
2001	—	`conf`	Bidirectional Dynamics for Protein Secondary Structure Prediction. Sequence Learning Pierre Baldi, Søren Brunak, Paolo Frasconi, Gianluca Pollastri, Giovanni Soda
2001	Misc	`conf`	Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. Pacific Symposium on Biocomputing Pierre Baldi, Søren Brunak
2001	—	`book`	Bioinformatics - the machine learning approach (2. ed.). Pierre Baldi, Søren Brunak
2001	Misc	`conf`	DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction. Pacific Symposium on Biocomputing Pierre Baldi, Richard H. Lathrop
2001	J	`jnl`	Flexibility of the genetic code with respect to DNA structure. Bioinform. Pierre-François Baisnée, Pierre Baldi, Søren Brunak, Anders Gorm Pedersen
2001	—	`conf`	Improved prediction of the number of residue contacts in proteins by recurrent neural networks. ISMB (Supplement of Bioinformatics) Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio
2000	A	`conf`	Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods. ISMB Steven Hampson, Pierre Baldi, Dennis F. Kibler, Suzanne B. Sandmeyer
2000	J	`jnl`	Assessing the accuracy of prediction algorithms for classification: an overview. Bioinform. Pierre Baldi, Søren Brunak, Yves Chauvin, Claus A. F. Andersen, Henrik Nielsen
2000	—	`book`	Bioinformatics - the machine learning approach. Pierre Baldi, Søren Brunak
2000	A	`conf`	Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. ISMB Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak
2000	J	`jnl`	On the convergence of a clustering algorithm for protein-coding regions in microbial genomes. Bioinform. Pierre Baldi
2000	—	`conf`	Protein β-Sheet Partner Prediction by Neural Networks. ANNIMAB Pierre Baldi, Gianluca Pollastri, Claus A. F. Andersen, Søren Brunak
2000	J	`jnl`	Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinform. Pierre Baldi, Pierre-François Baisnée
1999	J	`jnl`	Exploiting the past and the future in protein secondary structure prediction. Bioinform. Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri
1999	J	`jnl`	Structural basis for triplet repeat disorders: a computational analysis. Bioinform. Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
1999	J	`jnl`	The Biology of Eukaryotic Promoter Prediction - A Review. Comput. Chem. Anders Gorm Pedersen, Pierre Baldi, Yves Chauvin, Søren Brunak
1998	A	`conf`	Computational Applications of DNA Structural Scales. ISMB Pierre Baldi, Søren Brunak, Yves Chauvin, Anders Gorm Pedersen
1998	J	`jnl`	On the Use of Bayesian Methods for Evaluating Compartmental Neural Models. J. Comput. Neurosci. Pierre Baldi, Michael C. Vanier, James M. Bower
1997	—	`conf`	Probabilistic Models of Neuronal Spike Trains. Summer School on Neural Networks Pierre Baldi
1996	A	`conf`	Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. ISMB Anders Gorm Pedersen, Pierre Baldi, Søren Brunak, Yves Chauvin
1996	J	`jnl`	Hybrid Modeling, HMM/NN Architectures, and Protein Applications. Neural Comput. Pierre Baldi, Yves Chauvin
1995	J	`jnl`	Gradient descent learning algorithm overview: a general dynamical systems perspective. IEEE Trans. Neural Networks Pierre Baldi
1995	J	`jnl`	Learning in linear neural networks: a survey. IEEE Trans. Neural Networks Pierre Baldi, Kurt Hornik
1995	A	`conf`	Periodic Sequence Patterns in Human Exons. ISMB Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh
1995	A	`conf`	Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures. ISMB Pierre Baldi, Yves Chauvin
1995	J	`jnl`	Substitution Matrices and Hidden Markov Models. J. Comput. Biol. Pierre Baldi
1995	—	`conf`	Universal Approximnation and Learning of Trajectories Using Oscillators. NIPS Pierre Baldi, Kurt Hornik
1994	J	`jnl`	Hidden Markov Models of the G-Protein-Coupled Receptor Family. J. Comput. Biol. Pierre Baldi, Yves Chauvin
1994	J	`jnl`	How delays affect neural dynamics and learning. IEEE Trans. Neural Networks Pierre Baldi, Amir F. Atiya
1994	—	`conf`	Inferring Ground Truth from Subjective Labelling of Venus Images. NIPS Padhraic Smyth, Usama M. Fayyad, Michael C. Burl, Pietro Perona, Pierre Baldi
1994	J	`jnl`	Smooth On-Line Learning Algorithms for Hidden Markov Models. Neural Comput. Pierre Baldi, Yves Chauvin
1993	—	`conf`	Hidden Markov Models for Human Genes. NIPS Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh
1993	—	`conf`	Learning trajectories with a hierarchy of oscillatory modules. ICNN Pierre Baldi, Nikzad Benny Toomarian
1993	J	`jnl`	Neural Networks for Fingerprint Recognition. Neural Comput. Pierre Baldi, Yves Chauvin
1993	J	`jnl`	Random interactions in higher order neural networks. IEEE Trans. Inf. Theory Pierre Baldi, Santosh S. Venkatesh
1993	B	`conf`	Trajectory learning using hierarchy of oscillatory modules. ESANN Nikzad Benny Toomarian, Pierre Baldi
1992	—	`conf`	Hidden Markov Models in Molecular Biology: New Algorithms and Applications. NIPS Pierre Baldi, Yves Chauvin, Tim Hunkapiller, Marcella A. McClure
1991	J	`jnl`	Contrastive Learning and Neural Oscillations. Neural Comput. Pierre Baldi, Fernando J. Pineda
1991	J	`jnl`	Programmed interactions in higher-order neural networks: Maximal capacity. J. Complex. Santosh S. Venkatesh, Pierre Baldi
1991	J	`jnl`	Programmed interactions in higher-order neural networks: The outer-product algorithm. J. Complex. Santosh S. Venkatesh, Pierre Baldi
1991	J	`jnl`	Temporal Evolution of Generalization during Learning in Linear Networks. Neural Comput. Pierre Baldi, Yves Chauvin
1990	—	`conf`	Computing with Arrays of Bell-Shaped and Sigmoid Functions. NIPS Pierre Baldi
1990	J	`jnl`	Computing with Arrays of Coupled Oscillators: An Application to Preattentive Texture Discrimination. Neural Comput. Pierre Baldi, Ronny Meir
1990	J	`jnl`	On a generalized family of colorings. Graphs Comb. Pierre Baldi
1989	J	`jnl`	Neural networks and principal component analysis: Learning from examples without local minima. Neural Networks Pierre Baldi, Kurt Hornik
1989	—	`conf`	On the Distribution of the Number of Local Minima of a Random Function on a Graph. NIPS Pierre Baldi, Yosef Rinott, Charles Stein
1989	J	`jnl`	Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis. Int. J. Neural Syst. Amir F. Atiya, Pierre Baldi
1988	J	`jnl`	Group Actions and Learning for a Family of Automata. J. Comput. Syst. Sci. Pierre Baldi
1988	—	`conf`	Linear Learning: Landscapes and Algorithms. NIPS Pierre Baldi
1988	J	`jnl`	Neural Networks, Acyclic Orientations of the Hypercube, and Sets of Orthogonal Vectors. SIAM J. Discret. Math. Pierre Baldi
1988	J	`jnl`	Neural networks, orientations of the hypercube, and algebraic threshold functions. IEEE Trans. Inf. Theory Pierre Baldi
1987	—	`conf`	On Properties of Networks of Neuron-Like Elements. NIPS Pierre Baldi, Santosh S. Venkatesh