University of California, Irvine (UCI)
School of Information and Computer Sciences (ICS)
Center for Machine Learning and Intelligent Systems (CML)
  AI in Science Institute (AI-Science)
  Institute for Genomics and Bioinformatics (IGB)
 
Publications

Publications

2025 2024 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1996 1995 1994 1993 1992 1991 1990 1989 1988 1987 1986

2025
Refereed Journals
Maternal Circadian Rhythms during Pregnancy Dictate Metabolic Plasticity in Offspring   Na Yao, Kenichiro Kinouchi, Manami Katoh, Kousha Changizi Ashtiani, Sherif Abdelkarim, Hiroyuki Morimoto, Takuto Torimitsu, Takahide Kozuma, Akihide Iwahara, Shotaro Kosugi, Jin Komuro, Kyosuke Kato, Shun Tonomura, Toshifumi Nakamura, Arata Itoh, et al. Cell Metabolism., 37, ( 2 ), 395-412, 2025.

Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction   M. Tavakoli, Y. T. Chiu, A. M. Carlton, D. Van Vranken, P. Baldi. Journal of Chemical Information and Modeling., 65, ( 3 ), 1228-1242, 2025.

On the imperative of including 24-h and longitudinal multidimensional physiological phenotyping in rodent models of sleep apnea   J. Gaucher, G. Vial, S. Bouyon, A. Briancon-Marjollet, G. Faury, C. Arnaud, S. Bailly, R. Tamisier, K. Kinouchi, P. Baldi, D. Gozal, J. L. Pepin. Sleep Medicine., ( 127 ), 133-137, 2025.

Cilia in the Brain Display Region-Dependent Oscillations of Length and Orientation   Roudabeh Vakil Monfared, Sherif Abdelkarim, Pieter Derdeyn, Kiki Chen, Hanting Wu, Kenneth Leong, Tiffany Chang, Justine Lee, Sara Versales, Surya M. Nauli, Kevin Beier, Pierre Baldi, Amal Alachkar. PLOS Biology., 23, ( 7 ), 2025.

A Theory of Synaptic Neural Balance: From Local to Global Order   P. Baldi, A. Alexos, I. Domingo, and A. Rahmansetayesh. Artificial Intelligence., 346, 2025.

Evaluating the Intelligence of Large Language Models: A Comparative Study Using Verbal and Visual IQ Tests   S. Abdelkarim, S. Jaeggi, and P. Baldi. Computers in Human Behavior: Artificial Humans., 5, 2025.

Optimization of Antenna Array Configurations Using Deep Learning   D. Lin, J. Earls, L. Ma, A. Boag, and P. Baldi. IEEE Open Journal of Antennas and Propagation., 1, ( 1 ), 99, 2025.

Particle hit clustering and identification using point set transformers in liquid argon time projection chambers   EE Robles, A Yankelevich, W Wu, J Bian, P Baldi. Journal of Instrumentation., 20, ( 7 ), 2025.

The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function   V Sica, T Sato, I Tsialtas, S Hernandez, S Chen, P Baldi, C. Munoz, P. Sassone-Corsi, K. Koronoski, and J. Smith. bioRxiv., 2025.

Domain Knowledge Inclusive Monotonic Neural Network Guides Patient-Specific Induction of General Anesthesia Dosing   Kathryn Sarulllo, Muntaha Samad, Samir Kendale, Pierre Baldi, and S. Joshua Swamidass. Anesthesia & Analgesia., 19, ( 8 ), 2025.

Precision Polishing of Ablator Capsules via in situ Process Monitoring and Machine Learning–Based Optimization   A. Tiwari, S. Jin, S. Galla, B. Botcha, S. Hayes, M. Biener, K. Bhardwaj, S. Bukkapatnam, Y. Ding, A. Antonios, P. Baldi, S. Bhandarkar. Fusion Science and Technology., 81, ( 3 ), 2025.

Full event particle-level unfolding with variable-length latent variational diffusion   A. Shmakov, K. Greif, M. Fenton, A. Ghosh, P. Baldi, D. Whiteson. SciPost Physics., 18, ( 4 ), 2025.

Monte Carlo method for constructing confidence intervals with unconstrained and constrained nuisance parameters in the NOvA experiment   MA Acero, B Acharya, P Adamson, N Anfimov, A Antoshkin, E Arrieta-Diaz, L Asquith, A Aurisano, A Back, N Balashov, P Baldi, et al. . Journal of Instrumentation., 20, ( 2 ), 2025.

Circadian reprogramming by timed sodium intake reveals transcriptional pathways of daily salt handling in the colon   Takuto Torimitsu; Kenichiro Kinouchi,; Kousha Changizi Ashtiani; Sherif Abdelkarim; Takahide Kozuma; Na Yao; Akihide Iwahara; Kyosuke Kato; Shun Tonomura; Toshifumi Nakamura; Kenichi Yokota; Isao Kurihara; Pierre Baldi; Hiroshi Itoh; Kaori Hayashi. Science Advances., 23, ( 6 ), 1019-26, 2025.

The liver clock tunes transcriptional rhythms in skeletal muscle to regulate mitochondrial function   Sica, Valentina; Sato, Tomoki; Tsialtas, Ioannis; Hernandez, Sophia; Chen, Siwei; Baldi, Pierre; Munoz-Canoves, Pura; Sassone-Corsi, Paolo; Koronowski, Kevin; Smith, Jacob. Journal of Biological Rhythms., 2025, 2025.

Reconstruction of boosted and resolved multi-Higgs-boson events with symmetry-preserving attention networks   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 Newman, Pierre Baldi, Daniel Whiteson, Javier Du. Journal of High Energy Physics., 2025.

ClimSim-Online: A Large Multi-Scale Dataset and Framework for Hybrid Physics-ML Climate Emulation   Sungduk Yu, Zeyuan Hu, Akshay Subramaniam, Walter Hannah, Liran Peng, Jerry Lin, Mohamed Aziz Bhouri, Ritwik Gupta, Bjorn Lutjens, Justus C. Will, Gunnar Behrens, Julius J. M. Busecke, Nora Loose, Charles I Stern, Tom Beucler, Bryce Harrop, Helge Heuer, B. Journal of Machine Learning Research., 142, ( 26 ), 1-85, 2025.

Refereed Conference Proceedings
Improving Deep Learning Speed and Performance through Synaptic Neural Balance. The Thirty-Ninth AAAI Conference on Artificial Intelligence   A. Alexos, I. Domingo, P. Baldi. Proceedings of the AAAI Conference on Artificial Intelligence., 2025.

Realizable Continuous-Space Shields for Safe Reinforcement Learning   K. Kim, D. Corsi, A. Rodriguez, J.B. Lanier, B. Parellada, P. Baldi, C. Sanchez, R. Fox. 7th Annual Learning for Dynamics & Control Conference ., 2025.

Memorization: A Close Look at Books   Iris Ma, Ian Domingo, Alberto Krone-Martins, Pierre Baldi, and Cristina Lopes. First Workshop on Large Language Model Memorization., 2025.

2024
Refereed Journals
Clinical Knowledge and Reasoning Abilities of AI Large Language Models in Anesthesiology: A Comparative Study on the American Board of Anesthesiology Examination   Mirana C Angel, Joseph Rinehart, Maxime Cannesson, and Pierre Baldi. Anesthesia & Analgesia., 139, ( 2 ), 349-356, 2024.

PMechDB: A Public Database of Elementary Polar Reaction Steps   Tavakoli, Mohammadamin; Miller, Ryan; Angel, Mirana; Pfeiffer, Michael ; Gutman, Eugene; Mood, Aaron; Van Vranken, David; Baldi, Pierre. . Journal of Chemical Information and Modeling., 64, ( 6 ), 2024.

Reconstruction of Unstable Heavy Particles Using Deep Symmetry-Preserving Attention Networks   M. Fenton, A. Schmakov, H. Okawa, Y. Li, K. Hsiao, S. Hsu, D. Whiteson, P. Baldi. Nature Communications Physics., 2024, ( 7 ), 2024.

Specific exercise patterns generate an epigenetic molecular memory window that drives long-term memory formation and identifies ACVR1C as a bidirectional regulator of memory   Marcelo Wood, Ashley Keiser, Tri Dong, Eniko Kramar, Christopher Butler, Siwei Chen, Dina Matheos, Jacob Rounds, Alyssa Rodriguez, Joy Beardwood, Agatha Augustynski, Ameer Al-Shammari, Yasaman Alaghband, Vanessa Alizo Vera, Nicole Berchtold, Sharmin Shanu. Nature Communications., 2024, ( 15 ), 3836, 2024.

Circadian Cilia Transcriptome in Mouse Brain Across Physiological and Pathological States.   Kiki Chen, Kousha Changizi Ashtiani, Roudabeh Vakil Monfared, Pierre Baldi, and Amal Alachkar. Molecular Brain., 17, ( 67 ), 2024.

Annotation of surgical tool depth in vitreoretinal surgical videos: Agreement and performance between vitreoretinal surgeons vs. non-surgeon graders   J. Dagoon, P.F. Baldi, S. Abdelkarim, J. Liu, M.E. Riazi, M. Andrade, A. Azzam, P.R. Esfahani, S. Chang, A. Browne. Investigative Ophthalmology & Visual Science., 65, ( 7 ), 3762-3762, 2024.

Build an international AI “telescope” to curb the power of big tech companies   P. Baldi, P. Fariselli, and G. Parisi. Nature., 8035, ( 634 ), 782-782, 2024.

Refereed Conference Proceedings
Nuclear fusion diamond polishing dataset   A. Alexos, J. Liu, S. Galla, S. Hayes, K. Bhardwaj, A. Schwartz, M. Biener, P. Baldi, S. Bukkapatnam, S. Bhandarkar. Advances in Neural Information Processing Systems., 2024.

Diamond Polishing Data Set   A Alexos, J Liu, S Galla, S Hayes, K Bhardwaj, A Schwartz, M Biener, P Baldi, S Bukkapatnam, S Bhandarkar. The Thirty-Eighth Annual Conference on Neural Information Processing Systems, NeurIPS 2024., 2024.

Consistent and intermittent exercise patterns that facilitate long-term memory formation identify ACVR1C as a bidirectional regulator of memory   A. Keiser, T. Dong, H. Shaikh, S. La Tour, D. Matheos, E. Kramar, C. Butler, S. Chen, J. Beardwood, A. Augustynski, A. Al-Shammari, Y. Alaghband, V. Alizo Vera, N. Berchtold, S. Shanur, P. Baldi, C. Cotman, M. Wood. Neuropshychopharmacology., 2024.

Sparse Convolution Transformers for DUNE FD Event and Particle Classification   A. Yankelevich, A. Shmakov, J. Bian, P. Baldi. American Physical Society, Session on Neutrino Analysis Techniques, Sacramento, CA, April 3, 2024., 2024.

Boosted and Resolved Jet Assignment using Symmetry-Preserving Attention Networks in Nonresonant Multi-Higgs-Boson Events   H. Li, M. Stamenkovic, A. Shmakov, M. Fenton, C. Mikkelsen, J. Mitic, C.M. Suarez, M. Quinnan, H. Newman, P. Baldi, D. Whiteson, J. Duarte. American Physical Society, Mini-Symposium: ML/AI/Computation on the Front End., 2024.

Q* search: Heuristic search with deep q-networks   F. Agostinelli, S. Shperberg, A. Shmakov, S. McAleer, R. Fox, P. Baldi. ICAPS Workshop on Bridging the Gap between AI Planning and Reinforcement Learning, Banff, Alberta, Canada., 2024.

Toward optimal policy population growth in two-player zero-sum games   SM. McAleer, JB. Lanier, K. Wang, P. Baldi, T. Sandholm, R.Fox. 12th International Conference on Learning Representations (ICLR)., 2024.

Fourier Guided Transformer for Diffusion   Haodong Zhang, Zhe Yuan, Antonios Alexos, Pierre Baldi. Conference on Computer Vision and Pattern Recognition 2024., 2024.

Deep Learning Overparameterization: the Shallow Fallacy   Pierre Baldi. Northern Lights Deep Learning Conference, Tromso, Norway., 2024.

Speech editing by hitch-hiking a pre-trained FastSpeech model   Antonios Alexos and Pierre Baldi. Northern Lights Deep Learning Conference, Tromso, Norway., 2024.

2023
Refereed Journals
Brain histone beta-hydroxy-butyrylation couples metabolism with gene expression   Sara Cornuti, Siwei Chen, Leonardo Lupori, Francesco Finamore, Fabrizia Carli, Muntaha Samad, Simona Fenizia, Matteo Caldarelli, Francesca Damiani, Francesco Raimondi, Raffaele Mazziotti, Christophe Magnan, Silvia Rocchiccioli, Amalia Gastaldelli, Pierre . Cellular and Molecular Life Sciences., 80, ( 28 ), 2023.

Deep learning models of the discrete component of the galactic interstellar gamma-ray emission   Alexander Shmakov, Mohammadamin Tavakoli, Pierre Baldi, Christopher M. Karwin, Alex Broughton, Simona Murgia. Physical Review D., 107, ( 6 ), 210, 2023.

Improved modeling of the discrete component of the galactic interstellar gamma-ray emission and implications for the Fermi—LAT galactic center excess   Christopher M. Karwin, Alex Broughton, Simona Murgia, Alex Shmakov, Mohammadamin Tavakoli, and Pierre Baldi. Physical Review D., 107, ( 6 ), 2023.

RMechDB: A Public Database of Elementary Radical Reaction Steps   Tavakoli, Mohammadamin; Chiu, Yin Ting; Baldi, Pierre; Carlton, Annmarie; Van Vranken, David. . Journal of Chemical Information and Modeling., 63, ( 4 ), 114-1123, 2023.

Vitreoretinal surgical instrument tracking in 3-Dimensions using Deep Learning   Pierre Baldi, Junze Liu, Sherif Abdelkarim, Josiah K To, Marialejandra Diaz Ibarra and Andrew W. Browne. Translational Vision Science and Technology., 12, ( 20 ), 2023.

Deducing Neutron Star Equation of State Parameters Directly From Telescope Spectra with Uncertainty-Aware Machine Learning   Delaney Farrell, Pierre Baldi, Jordan Ott, Aishik Ghosh, Andrew W. Steiner, Atharva Kavitkar, Lee Lindblom, Daniel Whiteson, and Fridolin Weber. Journal of Cosmology and Astroparticle Physics., 16, ( 2 ), 2023.

Deducing the EOS of Dense Neutron Star Matter with Machine Learning   Delaney Farrell, Pierre Baldi, Jordan Ott, Aishik Ghosh, Andrew W. Steiner, Atharva Kavitkar, Lee Lindblom, Daniel Whiteson, and Fridolin Weber. Astronomische Nachrichten., ( 344 ), 1-2, 2023.

The Quarks of Attention: Structure and Capacity of Neural Attention Building Blocks   P. Baldi and R. Vershynin. Artificial Intelligence., 319, 2023.

Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in Creatine Transporter Deficiency   Elsa Ghirardini, Giulia Sagona, Angel Marquez-Galera, Francesco Calugi, Carmen M. Navarron, Francesco Cacciante, Siwei Chen, Federica Di Vetta, Lorenzo Dada, Raffaele Mazziotti, Leonardo Lupori, Elena Putignano, Pierre Baldi, Jose P Lopez-Atala. Acta Neuropathologica Communications., 11, ( 34 ), 2023.

Generalizing to new geometries with Geometry-Aware autoregressive Models (GAAMs) for fast calorimeter simulation   Junze Liu, Aishik Ghosh, Dylan Smith, Pierre Baldi, and Daniel Whiteson. Journal of Instrumentation (JINST)., 18, 2023.

Deep Learning Assisted Imaging Methods to Facilitate Access to Ophthalmic Telepathology,   Andrew W. Browne, Geunwoo Kim, Anderson N. Vu, Josiah K. To, Don S. Minckler, Maria Del Valle Estopina, Narsing A. Rao, Christine A. Curcio, Pierre F. Baldi. Ophthalmology Science., 4, ( 3 ), 2023.

Liver and muscle circadian clocks cooperate to support glucose tolerance in mice   Jacob G Smith, Kevin B Koronowski, Thomas Mortimer, Tomoki Sato, Carolina M Greco, Paul Petrus, Amandine Verlande, Siwei Chen Muntaha Samad, Ekaterina Deyneka, Lavina Mathur, Ronnie Blazev, Jeffrey Molendijk, Arun Kumar, Oleg Deryagin, Mireia Vaca-Dempere. Cell Reports., 42, ( 6 ), 2023.

Evaluating the Performance of Large Language Models for Spanish Language in Undergraduate Admissions Exams   Sabino Miranda, Obdulia Pichardo-Lagunas, Bella Martinez-Seis, Pierre Baldi. Computacion y Sistemas., 2023.

Medical Informatics Operating Room Vitals and Events Repository (MOVER): a public-access operating room database   M Samad, M Angel, J Rinehart, Y Kanomata, P Baldi, M Cannesson. JAMIA open ., 6, ( 4 ), 2023.

Combining Allograft Adipose and Fascia Matrix as an Off-the-Shelf Scaffold for Adipose Tissue Engineering Stimulates Angiogenic Responses and Activates a Proregenerative Macrophage Profile in a Rodent Model   M. Ziegler, K. Khabaz, N. Khoshab, F. Halaseh, E. Chnari, S. Chen, P. Baldi, G. Evans, A. Widgerow. Annals of Plastic Surgery., 91, ( 2 ), 294-300, 2023.

Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations   J. Lee, S. Chen, R. Vakil Monfared, P. Derdeyn, K. Leong, T. Chang, K. Beier, P. Baldi, A. Alachkar. Iscience., 26, ( 10 ), 2023.

Developing new analysis tools for near surface radio-based neutrino detectors   A Anker, P Baldi, SW Barwick, Jakob Beise, et al. . Journal of Cosmology and Astroparticle Physics., 2023, ( 10 ), 2023.

Refereed Conference Proceedings
Recommending Anesthesia Dosages with Neural Networks   K. Sarullo, M.Samad, S. Kendale, S. Swamidass, P. Baldi. Conference Anesthesia and Analgesia., 2023.

A minimal circadian clock network for glucose tolerance in mice   KB Koronowski, JG Smith, A Verlande, S Chen, T Mortimer, O Deryagin, P Liu, Valerio Orlando, P. Baldi, C Jang, S Masri, SA Benitah, P Munoz-Canoves, P Sassone-Corsi. Conference Diabetologia., 2023.

Attentionstitch: How attention solves the speech editing problem   A. Alexos, P. Baldi. Thirty-seventh Conference on Neural Information Processing Systems Machine Learning for Audio Workshop, NeurIPS 2023., 2023.

Machine learning-enhanced prediction of surface smoothness for inertial confinement fusion target polishing using limited data   A. Alexos, J. Liu, A. Tiwari, K. Bhardwaj, S. Hayes, P. Baldi, S. Bukkapatnam, S. Bhandarkar. The 4th Workshop on Artificial Intelligence and Machine Learning for Scientific Applications., 2023.

Finding Reaction Mechanism Pathways with Deep Reinforcement Learning and Heuristic Search   R. Panta, M. Tavakoli, C. Geils, P. Baldi, F. Agostinelli. ICAPS Workshop on Bridging the Gap between AI Planning and Reinforcement Learning., 2023.

Interpretable Joint Event-Particle Reconstruction for Neutrino Physics at NOvA with Sparse CNNs and Transformers   A. Shmakov, A. Yankelevich, J. Bian, P. Baldi. Thirty-seventh Conference on Neural Information Processing Systems, NeurIPS ., 2023.

AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning   Mohammadamin Tavakoli, Pierre Baldi, Ann Marie Carlton, Yinting Chiu, Alexander Shmakov, David Van Vranken. Thirty-seventh Conference on Neural Information Processing Systems, NeurIPS., 2023.

ClimSim: A large multi-scale dataset for hybrid physics-ML climate emulation   Sungduk Yu, Walter Hannah, Liran Peng, Jerry Lin, Mohamed Aziz Bhouri, Ritwik Gupta, Bjorn Lutjens, Justus Christopher Will, Gunnar Behrens, Julius Busecke, Nora Loose, Charles I Stern, Tom Beucler, Bryce Harrop, Benjamin R Hillman, Andrea Jenney, Savanna. Thirty-seventh Conference on Neural Information Processing Systems Datasets and Benchmarks Track, NeurIPS., 2023.

End-To-End Latent Variational Diffusion Models for Inverse Problems in High Energy Physics   Alexander Shmakov, Kevin Greif, Michael James Fenton, Aishik Ghosh, Pierre Baldi, Daniel Whiteson. Thirty-seventh Conference on Neural Information Processing Systems Datasets and Benchmarks Track, NeurIPS., 2023.

Language ModelsCann Solve Computer Tasks   Geunwoo Kim, Pierre Baldi, Stephen Marcus McAleer. Thirty-seventh Conference on Neural Information Processing Systems Datasets and Benchmarks Track, NeurIPS., 2023.

Selective Perception: Learning Concise State Descriptions for Language Model Actors   Kolby Nottingham, Yasaman Razeghi, Kyungmin Kim, JB Lanier, Pierre Baldi, Roy Fox, Sameer Singh. Thirty-seventh Conference on Neural Information Processing Systems Datasets and Benchmarks Track, NeurIPS., 2023.

AI and Veterinary Medicine: Performance of Large Language Models on the North American Licensing Examination   Mirana Angel, Anuj Patel, Haiyi Xing, Dylan Balsz, Cody Arbuckle, David Bruyette and Pierre Baldi. IEEE International Symposium on Foundation and Large Language Models, FLLM 2023., 2023.

Clinical Knowledge and Reasoning Abilities of Large Language Models in Pharmacy: A Comparative Study on the NAPLEX Exam   Mirana Angel, Anuj Patel, Amal Alachkar and Pierre Baldi. IEEE International Symposium on Foundation and Large Language Models, FLLM 2023., 2023.

2022
Refereed Journals
Measuring the polarization reconstruction resolution of the ARIANNA neutrino detector with cosmic rays   A. Anker, P. Baldi, S. W. Barwick, J. Beise, et al. . Journal of Cosmology and Astroparticle Physics., 2022, ( 4 ), 022, 2022.

Automated detection of the spatial location of vitreoretinal instruments from retinal images using deep learning methods   M. Diaz Ibarra, J. K. To, J. Liu, S. Abdelkarim, A. Herekar, B. D. Kuppermann, P. Baldi, A. Browne. Investigative Ophthalmology & Visual Science., 63, ( 7 ), 2022.

Improved measurement of neutrino oscillation parameters by the NOvA experiment   MA Acero, P Adamson, L Aliaga, N Anfimov, A Antoshkin, E Arrieta-Diaz, Lily Asquith, A Aurisano, A Back, C Backhouse, M Baird, N Balashov, P Baldi, et al. . Physical Review D., 106, ( 3 ), 032004, 2022.

How to GAN higher jet resolution   P. Baldi, L. Blecher, A. Butter, J. Collado, J. N. Howard, F. Keilbach, T. Plehn, G. Kasieczka, D. Whiteson. SciPost Physics., 13, ( 3 ), 064, 2022.

Accurate Identification of the Trabecular Meshwork under Gonioscopic view in Real Time using Deep Learning   K. Lin, G. Urban, M. C. Yang, L.C Lee, D.W. Lu, W. L. M. Alwardand, and P. Baldi. Ophthalmology Glaucoma., 2022.

Permutationless many-jet event reconstruction with symmetry preserving attention networks   Michael James Fenton, Alexander Shmakov, Ta-Wei Ho, Shih-Chieh Hsu, Daniel Whiteson, and Pierre Baldi. Physical Review D., 105, ( 11 ), 2022.

Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis   S. Sato, K. A. Dyar, J. T. Treebak, S. L. Jepsen, A. M. Ehrlich, S. P. Ashcroft, K. Trost, T. Kunzke, V. M. Prade, L. Small, A. L. Basse, M. Schonke, S. Chen, M. Samad, P. Baldi, R. Barres, A. Walch, T. Moritz, J. J. Holst, D. Lutter, J. R. Zierath, P. Sa. Cell Metabolism., 34, ( 2 ), 2022.

Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity   A. Tavakoli, A. Mood, D. Van Vranken, and P. Baldi. Journal of Chemical Information and Modeling., 62, ( 9 ), 2022.

SSpro/ACCpro 6: Almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility Using Profiles, Deep Learning, and Structural Similarity   G. Urban, C. Magnan, and P. Baldi. Bioinformatics., ( 7 ), 2064-2065, 2022.

An Atlas of Posttranslational Modifications on RNA Binding Proteins   W. England, S. Chen, P. Baldi, and R. Spitale. Nucleic Acids Research., 50, ( 9 ), 4329-4339, 2022.

SPANet: Generalized Permutationless Set Assignment for Particle Physics using Symmetry Preserving Attention   Alexander Shmakov, Michael James Fenton, Ta-Wei Ho, Shih-Chieh Hsu, Daniel Whiteson, Pierre Baldi. SciPost Physics., 178, ( 12 ), 2022.

Real-time reconstruction of high energy, ultrafast laser pulses using deep learning   M. Stanfield, J. Ott, C. Gardner, N. F. Beier, D. Farinella, C. A. Mancuso, P. Baldi, and F. Dollar. Nature Scientific Reports,., 12, 5299, 2022.

Deep Learning to Enable Color Vision in the Dark   Andrew W. Browne, Ekaterina Deyneka, Francesco Ceccarelli, Siwei Chen, Josiah K. To, Jianing Tang, Anderson N. Vu, Pierre Baldi. PLOS ONE., 17, ( 4 ), 2022.

Resolving Extreme Jet Substructure   Yadong Lu, Alexis Romero, Michael James Fenton, Daniel Whiteson, and Pierre Baldi. Journal of High Energy Physics., 2022, ( 43 ), 2022.

The Hidden Link between Circadian Entropy and Mental Disorders   Amal Alachkar, Justine Lee, Kalyani Asthana, Roudabeh Vakil Monfared, Jiaqi Chen, Sammy Alhassen, Muntaha Samad, Marcelo Wood, Emeran Mayer, and Pierre Baldi. Translational Psychiatry., 12, ( 1 ), 1-12, 2022.

Weakly Supervised Polyp Segmentation in Colonoscopy Images using Deep Neural Networks   Siwei Chen, Gregor Urban, and Pierre Baldi. Journal of Imaging., 8, ( 5 ), 121, 2022.

CircadiOmics: Circadian Omic Web Portal   M. Samad, F. Agostinelli, T. Sato, K. Shimaji, and P. Baldi. Nucleic Acids Research., 50, 183-190, 2022.

Tryptophan Metabolism is a Physiological Integrator Regulating Circadian Rhythms   Paul Petrus; Marlene Cervantes; Muntaha Samad; Tomoki Sato; Alina Chao; Shogo Sato; Kevin B. Koronowski; Grace Park; Yasmine Alam; Niklas Mejhert; Marcus M. Seldin; Jose Manuel Monroy Kuhn; Kenneth A. Dyar; Dominik Lutter; Pierre Baldi; Peter Kaiser; Chol. Science Advances., 64, 101556, 2022.

Improving sensitivity of the ARIANNA detector by rejecting thermal noise with deep learning   A. Anker, P. Baldi, S. W. Barwick, J. Beise, et al. Journal of Instrumentation., 17, ( 3 ), 2022.

Refereed Conference Proceedings
Feasible Adversarial Robust Reinforcement Learning for Underspecified Environments   J, Lanier, S. McAleer, P. Baldi, and R. Fox. NeurIPS 2022 ., 2022.

Geometry-aware Autoregressive Models for Calorimeter Shower Simulations   J. Liu, A. Ghosh, D. Smith, P, Baldi, and D. Whiteson. NeurIPS 2022 ., 2022.

Development of an in-situ calibration device of firn properties for Askaryan neutrino detectors   J. Beise, C. Glaser, A. Anker, P. Baldi, et al. . 37th International Cosmic Ray Conference (ICRC2021), ., 2022.

Polarization Reconstruction of Cosmic Rays with the ARIANNA Neutrino Radio Detector   Zhao, A. Anker, P. Baldi, SW. Barwick, et al. . 37th International Cosmic Ray Conference (ICRC2021), ., 2022.

Capabilities of ARIANNA: Neutrino pointing resolution and implications for future ultra-high energy neutrino astronomy   SW. Barwick, G. Gaswint, A. Anker, P. Baldi, et al. . 37th International Cosmic Ray Conference (ICRC2021), ., 2022.

A novel trigger based on neural networks for radio neutrino detectors   A. Anker, MP. Paul, P. Baldi, SW. Barwick, et al. . 37th International Cosmic Ray Conference (ICRC2021), ., 2022.

Science Case and Detector Concept for the ARIANNA High Energy Neutrino Telescope at Moore’s Bay, Antarctica   SW. Barwick, A.. Anker, P Baldi, J. Beise, et al. . 37th International Cosmic Ray Conference (ICRC2021), ., 2022.

Snowmass neutrino frontier: Dune physics summary. 2021   DUNE Collaboration, A. Abud, B. Abi, R. Acciarri, MA. Acero, et al. Snowmass Summer Study., 2022.

A gaseous argon-based near detector to enhance the physics capabilities of DUNE   A. Abud, B. Abi, R. Acciarri, MA. Acero, et al. Snowmass Summer Study., 2022.

Anytime PSRO for two-player zero-sum gam   S. McAleer, K. Wang, J. Lanier, M. Lanctot, P. Baldi, T. Sandholm, R. Fox. The 36th AAAI Conference on Artificial Intelligence Reinforcement Learning in Games Workshop, Vancouver, BC, Canada., 2022.

Exercise Parameters That Open a 'Molecular Memory Window' for Cognitive Enhancement Shine Light on Key Memory Mechanism in the Adult, Aging, and Alzheimer's Disease Brain   A. Keiser, T. Dong, E. Kramar, C. Butler, S. Chen, D. Matheos, J. Beardwood, A. Al-Shammari, Y. Alaghband, V. Alizo Vera, N. Berchtold, S. Shanur, A. Augustynski, P. Baldi, C. Cotman, M. Wood. American College of Neuropsychopharmacology 61st Annual Meeting., 2022.

Low-energy physics in neutrino LArTPCs   D. Caratelli, W. Foreman, A. Friedland, S Gardiner, et al. . Snowmass Summer Study., 2022.

Deep-learning based event reconstruction for shallow in-ice UHE neutrino detectors   S. Stjarnholm, C. Glaser, P. Baldi, S. Barwick, O. Ericsson, A. Holmberg, S. McAleer, T. W. Choi. Proceedings of Science, 9th International Workshop on Acoustic and Radio EeV NeutrinoDetectionActivities-ARENA2022., 2022.

Foundations of Attention Mechanisms in Deep Neural Network Architectures.   P. Baldi and R. Vershynin. Attention Workshop, NeurIPS 2022., 2022.

Anytime Optimal PSRO for Two-Player Zero-Sum Games   Stephen McAleer, Kevin Wang, Marc Lanctot, John Lanier, Pierre Baldi, and Roy Fox. AAAI 2022 Workshop on Reinforcement Learning in Games., 2022.

Book Chapters
Deep Learning From Four-Vectors   P. Baldi, P. Sadowski, and D. Whiteson. Artificial Intelligence Applied to Particle Physics ., 2022.

2021
Refereed Journals
Development and Validation of an Interpretable Neural Network for Prediction of Postoperative In-hospital Mortality   C. Lee, M. Samad, I. Hofer, P. Baldi, and M. Cannesson. npj Digital Medicine., 4, ( 1 ), 109, 2021.

Fold recognition by scoring protein map similarities using the congruence coefficient   Pietro DiLena and Pierre Baldi. Bioinformatics., 17, ( 4 ), 2021.

Patterns of Cilia Gene Dysregulations in Major Psychiatric Disorders   Wedad Alhassen, Siwei Chen, Marquis Vawter, Brianna Kay Robbins, Henry Nguyen, Thant Nyi Myint, Yumiko Saito, Anton Schulmann, Surya M. Nauli, Olivier Civelli, Pierre Baldi, and Amal Alachkar. Progress in Neuropsychopharmacology & Biological Psychiatry., 110255, 2021.

SARM: Sparse Autoregressive Models for Scalable Generation of Sparse Images in Particle Physics   Y. Lu, J. Collado, D. Whiteson, and P. Baldi. Physical Review D., 103, ( 3 ), 2021.

Enforcing analytic constraints in neural networks emulating physical systems   Tom Beucler, Michael Pritchard, Stephan Rasp, Jordan Ott, Pierre Baldi, and Pierre Gentine. Physical Review Letters., 126, ( 9 ), 2021.

Methyl Cation Affinities of Canonical Organic Functional Groups   Kadish, Dora; Mood, Aaron; Tavakoli, Mohammadamin; Gutman, Eugene; Baldi, Pierre; Van Vranken, David. The Journal of Organic Chemistry., 86, ( 5 ), 2021.

SPLASH: Learnable Activation Functions for Improving Accuracy and Adversarial Robustness   A. Tavakoli, F. Agostinelli, and P. Baldi. Neural Networks., ( 140 ), 1-12, 2021.

Assessing the Potential of Deep Learning for Emulating Cloud Superparameterization in Climate Models with Real-Geography Boundary Conditions   Griffin Mooers, Michael Pritchard, Tom Beucler, Jordan Ott, Galen Yacalis, Pierre Baldi, Pierre Gentine. Journal of Advances in Modeling Earth Systems., 15, ( 3 ), 2021.

Intergenerational Stress Transmission is Associated with Brain Metabotranscriptome Remodeling and Mitochondrial Dysfunction   S. Chen, S. Alhassen, P. Baldi, G. Abott, A. Alachkar. Communications Biology., 4, ( 1 ), 1-15, 2021.

Cocaine induces paradigm-specific changes to the transcriptome within the Ventral Tegmental Area   Rianne Campbell, Siwei Chen, Joy Beardwood, Alberto Lopez, Lilyana Pham, Ashley Keiser, Jess Childs, Dina Matheos, Vivek Swarup, Pierre Baldi, and Marcelo Wood. Neuropsychopharmacology., 46, ( 10 ), 1768-1779, 2021.

Reproducible Hyperparameter Optimization   L. Hertel, and P. Baldi. Journal of Computational and Graphical Statistics., 2021.

A Theory of Capacity and Sparse Neural Encoding   P. Baldi and R. Vershynin. Neural Networks., ( 145 ), 12-27, 2021.

Detecting Pulmonary Coccidioidomycosis with Deep Convolutional Neural Networks   J. Ott, D. Bruyetter, C. Arbuckle, D. Balsz, S. Hecth, L. Shubitz, and P. Baldi. . Machine Learning with Applications., ( 5 ), 2021.

Learning to identify electrons   Julian Collado, Jessica N. Howard, Taylor Faucett, Tony Tong, Pierre Baldi, and Daniel Whiteson. Physical Review D., 103, ( 11 ), 2021.

Age-Related Neurometabolomic Signature of Mouse Brain   Chen, Siwei; Lee, Justine; Truong, Tri Minh; Alhassen, Sammy; Baldi, Pierre; Alachkar, Amal. ACS Chemical Neuroscience., 15, ( 12 ), 287-2902, 2021.

Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms   Carolina M. Greco, Kevin B. Koronowski, Jacob G. Smith, Jiejun Shi, Siwei Chen, Muntaha Samad, Patrick-Simon Welz, Valentina M. Zinna, Thomas Mortimer, Kohei Shimaji, Tomoki Sato, Paul Petrus, Arun Kumar, Mireia Vaca Dempere, Cassandra Van, Kenneth A. Dya. Science Advances., 39, ( 7 ), 2021.

Large-Scale Analysis Reveals Spatiotemporal Circadian Patterns of Cilia Transcriptomes in the Primate Brain   P. Baldi, W. Alhassen, S. Chen, H. Nguyen, M. Khoudari, A. Alachkar. Journal of Neuroscience Research., 99, ( 10 ), 2610-2624, 2021.

An End-to-End CNN with Attentional Mechanism Applied to Raw EEG in a BCI Classification Task   E. Lashgari, J. Ott, P. Baldi, and U. Maoz. Journal of Neural Engineering., 18, ( 4 ), 110255, 2021.

Deep Learning–Assisted Multiphoton Microscopy to Reduce Light Exposure and Expedite Imaging in Tissues With High and Low Light Sensitivity   Stephen McAleer; Alexander Fast; Yuntian Xue; Magdalene J. Seiler; William C. Tang; Mihaela Balu; Pierre Baldi; Andrew W. Browne. Translational Vision Science & Technology., 10, ( 30 ), 2021.

Dynamic Changes in Brain Cilia Transcriptomes across the Human Lifespan   Siwei Chen, Wedad Alhassen, Roudabeh Vakil Monfared, Benjamin Vachirakorntong, Surya Nauli, Pierre Baldi, and Amal Alachkar. International Journal of Molecular Sciences., 22, ( 19 ), 2021.

Learning to Isolate Muons   Julian Collado, Kevin Bauer, Edmund Witkowski, Taylor Faucett, Daniel Whiteson, and Pierre Baldi. Journal of High Energy Physics., 2021, ( 200 ), 2021.

Hippocampal Ensembles Represent Sequential Relationships Among Discrete Nonspatial Events   B. Shahbaba, L. Li, F. Agostinelli, M. Saraf, G. Elias, P. Baldi, and N. Fortin. Nature Communications., 13, ( 787 ), 2021.

Transcriptome Profiling of Dysregulated GPCRs Reveals Overlapping Patterns across Psychiatric Disorders and Age-Disease Interactions   Roudabeh Vakil Monfared, Wedad Alhassen, Tri Minh Truong, Michael Angelo Maglalang Gonzales, Vincent Vachirakorntong, Siwei Chen, Pierre Baldi, Olivier Civelli, and Amal Alachkar. Cells., 11, ( 10 ), 2021.

A Call for a Public Open Database of All Chemical Reactions   P. Baldi. . Journal of Chemical Information and Modeling., 62, ( 9 ), 2021.

Refereed Conference Proceedings
D-REX: static detection of relevant runtime exceptions with location aware transformer   F. Farmahinifarahani, Y. Lu, V. Saini, P. Baldi, C. Lopes. D-REX: static detection of relevant runtime exceptions with location aware transformer. IEEE 21st International Working Conference on Source Code Analysis and Manipulation (SCAM)., 2021.

Obtaining approximately admissible heuristic functions through deep reinforcement learning and A* search. Bridging the Gap between AI Planning and Reinforcement   F. Agostinelli, S. McAleer, A. Shmakov, R. Fox, M. Valtorta, B. Srivastava, P. Baldi. Learning workshop at International Conference on Automated Planning and Scheduling, Aug 2021., 2021.

Deep Bucket Elimination   R. Dechter, Y. Razeghi, Y. Lu, P. Baldi, K. Kask. Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence (IJCAI-21), ., 2021.

Rxn Hypergraph: a Hypergraph Attention Model for Chemical Reaction Representation   Mohammadamin Tavakoli, Alexander Shmakov, Francesco Ceccarelli and Pierre Baldi. The Seventh International Workshop on Deep Learning on Graphs: Methods and Applications (AAAI--DLG22)., 2021.

Exercise opens a ‘molecular memory window’ to facilitate changes in gene expression, synaptic plasticity, and memory   Keiser A, Dong T, Kramár E, Butler C, Matheos D, Tong L, Berchtold N, Chen S, Samad M, Magnan C, Beardwood J, Shanur S, Rodriguez A, Baldi, P, Cotman C, Wood M. Society for Neuroscience., 2021.

REX: Static Detection of Relevant Runtime Exceptions with Location Aware Transformer   Farima Farmahinifarahani, Yadong Lu Vaibhav Saini, Pierre Baldi, Cristina Lopes. IEEE SCAM 2021., 2021.

XDO: A Double Oracle Algorithm for Extensive-Form Games   S. McAleer, F. Agostinelli, A. Shmakov, R. Fox, and P. Baldi. Proceedings of the NeurIPS 2021 Conference., 2021.

CFR-DO: A double oracle algorithm for extensive-form games   S. McAleer, J. Lanier, P. Baldi, R. Fox. The Thirty-Fifth AAAI Conference on Artificial Intelligence (AAAI-21) Workshop on Reinforcement Learning in Games., 2021.

Books
Deep Learning in Science   P. Baldi. , Cambridge University Press , 2021.

Book Chapters
Bioinformatics and Systems Biology of Circadian Rhythms: BIO_CYCLE and CircadiOmics   M. Samad, F. Agostinelli, and P. Baldi. Methods in Molecular Biology, edition about "Circadian Regulation"., 2021.

2020
Refereed Journals
Training and Validation of Deep Neural Networks for the Prediction of 90-Day Post-Liver Transplant Mortality Using UNOS Registry Data   Lee C., Wray C., Agopian V., Urban G., Baldi P., Cannesson M., Ershoff B. Transplantation Proceedings., 52, ( 1 ), 246-258, 2020.

Efficient neutrino oscillation parameter inference using Gaussian processes   Li L., Nayak N., Bian J., Baldi P. Physical Review D., 12001, ( 101 ), 2020.

FKBP10 regulates protein translation to sustain lung cancer growth   Ramadori G., Ioris R.M., Villanyi Z., Firnkes R. Pannasenko O.O., Allen G., Konstantinidou G., Aras G., Brenachot X., Biscotti T., Charollais A., Luchetti M., Bezrukov F., Santinelli A., Samad M., Baldi P., Collart M.A., Coppari R. Cell Reports., 30, ( 11 ), 3851-3863, 2020.

Characterizing the skin and gut microbiome of alopecia areata patients   Juhasz M., Chen S., Khosrovi-Eghbal A., Ekelem C., Landaverde Y., Baldi P., Mesinkovska N.A. SKIN The Journal of Cutaneous Medicine., 4, ( 1 ), 2020.

Development and Validation of a Deep Neural Network Model to Predict Postoperative Mortality, Acute Kidney Injury, and Reintubation using a single feature set   Hofer I.S., Lee C., Gabel E., Baldi P., Cannesson M. npj Digital Medicine., 1, ( 58 ), 2020.

Learning in the Machine: To Share or Not to Share?   Ott J., Linstead E., LaHaye N. Baldi P. . Neural Networks., ( 126 ), 2020.

Methyl Anion Affinities of the Canonical Organic Functional Groups   Mood A., Tavakoli A., Gutman E., Kadish D., Baldi P., Van Vranken D. The Journal of Organic Chemistry., 85, ( 6 ), 235-249, 2020.

Classifying Shoulder Implants in X-ray Images using Deep Learning   G. Urban, S. Porhemmat, M. Stark, B. Feeley, K. Okada, and P. Baldi. Computational and Structural Biotechnology Journal., 18, 967-972, 2020.

Metabolomic and Transcriptomic Signatures of Prenatal Excessive Methionine in Mice Support Nature Rather than Nurture in the Pathogenesis of Schizophrenia   Siwei Chen, Wedad Alhassen, Ryan Yoshimura, Angele De Silva, Geoffrey W. Abbott, Pierre Baldi, Amal Alachkar. Communications Biology., 3, ( 1 ), 2020.

A non-pharmacological approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced metabolic dysfunction encmpasserd by metabolic syndrome   Carolina Magdalen Greco, Stefano Garretto, Emilie Montellier, Yu Liu, Siwei Chen, Pierre Baldi, Paolo Sassone-Corsi1 and Jacopo Lucci. Scientific Reports., 41, ( 6 ), 409-421, 2020.

Cocaine-mediated Circadian Reprogramming in the Striatum Through Dopamine-driven PPAR? Activation   Y. Liu, P. Baldi, P. Sassone-Corsi, E. Borrelli. Nature Communications., 11, ( 1 ), 1-14, 2020.

A Fortran-Keras Deep Learning Bridge for Scientific Computing   J. Ott, M. Pritchard, N. Best, E. Linstead, M. Curcic, and P. Baldi. Scientific Programming., 2020.

Protein Profiles: Biases and Protocols   G. Urban, M. Torrisi, C. Magnan, G. Pollastri, and P. Baldi. Computational and Structural Biotechnology Journal., ( 18 ), 2281-2289, 2020.

The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental epilepsy   K. J. Debski1, N. Ceglia, A. Ghestem, A. I. Ivanov, G. E. Brancati, S. Broer, A. M. Bot1, J. A. Muller, S. Schoch, A. Becker, W. Loscher, M. Guye, P. Sassone-Corsi, K. Lukasiuk, P. Baldi, C. Bernard. Science Advances., 41, ( 6 ), 2020.

MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex   Debora Napoli, Leonardo Lupori, Raffaele Mazziotti, Giulia Sagona, Sara Bagnoli, Muntaha Samad, Erika Kelmer Sacramento, Joanna Kirkpatrick, Elena Putignano, Siwei Chen, Eva Terzibasi Tozzini, Paola Tognini, Jessica Kwok, Pierre Baldi, Alessandro Cellerin. EMBO Reports., 21, ( 11 ), 1-19, 2020.

Combining Deep Learning with Optical Coherence Tomography Imaging to Determine Scalp Hair and Follicle Counts   Gregor Urban, Nate Feil, Ella Csuka, Kiana Hashemi, Chloe Ekelem, Franchesca Choi, Natasha Atanaskova Mesinkovska, and Pierre Baldi. Lasers in Surgery and Medicine., 52, ( 1 ), 171-178, 2020.

Sherpa: Robust Hyperparameter Optimization for Machine Learning   L. Hertel, Julian Collado, Peter Sadowski, Jordan Ott, Pierre Baldi. SoftwareX., ( 12 ), 2020.

Reshaping Circadian Metabolism in the Suprachiasmatic Nucleus and Prefrontal Cortex by Nutritional Challenge   Paola Tognini, Muntaha Samad, Kenichiro Kinouchi, Yu Liu, Jean-Christophe Helbling, Marie-Pierre Moisan, Kristin L. Eckel-Mahan, Pierre Baldi, and Paolo Sassone-Corsi. PNAS., 2020.

Structure, Self-Assembly, and Properties of a Truncated Reflectin Variant   Mehran J. Umerani, Preeta Pratakshya, Atrouli Chatterjee, Juana A. Cerna, Hoshin Kim, Gregor Ilc, Matic Kovacic, Christophe Magnan, Benedetta Marmiroli, Barbara Sartori, Andrew W. Bartlett, Erica M. Leung, Zhijing Feng, Kyle L. Naughton, Brenna Norton-Bak. Proceedings of the National Academy of Sciences., 117, ( 52 ), 2020.

Deep Learning Analysis of Vibrational Spectra of Bacterial Lysate for Rapid Antimicrobial Susceptibility Testing   William John Thrift, Sasha Ronaghi, Muntaha Samad, Hong Wei, Dean Gia Nguyen, Antony Superio Cabuslay, Chloe E Groome, Peter Joseph Santiago, Pierre Baldi, Allon I Hochbaum, Regina Ragan . ACS., 14, ( 11 ), 2020.

S-Adenosyl-L-Homocysteine Hydrolase Links Methionine Metabolism to the Circadian Clock and Chromatin Remodeling   C. Greco, M. Cervantes, J. Fustin, K. Ito, N. Ceglia, M. Samad, J. Shi, K. Koronowski, I. Forne, S. Ranjit, J. Gaucher, K. Kinouchi, R. Kojima, E. Gratton, W. Li, P. Baldi, A. Imhof, H. Okamura, P. Sassone-Corsi. Science Advances., 51, ( 6 ), 2020.

First results on ProtoDUNE-SP liquid argon time projection chamber performance from a beam test at the CERN Neutrino Platform   B. Abi, A. Abed Abud, R. Acciarri, M.A. Acero, G. Adamov, M. Adamowski, D. Adams, P. Adrien, M. Adinolfi, Z. Ahmad, et al. Journal of Instrumentation., 15, 2020.

Refereed Conference Proceedings
Deep-learning-based kinematic reconstruction for DUNE   Liu, J. Ott, J. Collado, B. Jargowsky, W. Wu, J. Bian, P. Baldi. Third Workshop on Machine Learning and the Physical Sciences (NeurIPS 2020)., 2020.

Postoperative In-Hospital Mortality Prediction Using Bayesian Neural Networks for Interpretability   M. Samad, C. Lee, I. Hofer, P. Baldi, M. Cannesson. Conference ANESTHESIA AND ANALGESIA., 2020.

An Interpretable Neural Network for Prediction of Postoperative In-hospital Mortality   C. Lee, M. Samad, I. Hofer, P. Baldi, M. Cannesson. Conference ANESTHESIA AND ANALGESIA., 2020.

Assessing the potential of deep neural networks for emulating cloud superparameterization in climate models under real geography boundary conditions   G. Mooers, M. S. Pritchard, T. Beucler, J. Ott, G. Yacalis, P. Baldi, P. Gentin. The American Geophysical Union (AGU) Fall Meeting 2020., 2020.

Gentin.Assessing the potential of deep neural networks for emulating cloud superparameterization in climate models under real geography boundary conditions   J. Ott, M. S. Pritchard, N. Best, E. Linstead, M. Curcic, P. Baldi. The American Geophysical Union (AGU) Fall Meeting 2020., 2020.

Hyperparameter Optimization and a Deep Learning Bridge to Fortran   M. S. Pritchard, T. Beucler, G. Mooers, J. Ott, P. Gentine, L. Peng, P. Baldi, S. K. Mukkavilli. The American Geophysical Union (AGU) Fall Meeting 2020., 2020.

Deep Bucket Elimination   Y. Razeghi, S. Kask, Y. Lu, P. Baldi, S. Agarwal, R. Dechter. 30th International Joint Conference on Artificial Intelligence., 2020.

Gaussian Process Accelerated Feldman-Cousins Approach for Physical Parameter Inference   . Nayak, L. Li, J. Bian, P. Baldi. American Physical Society April Meeting 2020., 2020.

Deep-Learning-Based Kinematic Reconstruction for DUNE   J. Liu, J. Ott, J. Collado, B. Jargowsky, W. Wu, J. Bian, P. Baldi. 34th Conference on Neural Information Processing Systems (NeurIPS), Machine Learning and the Physical Sciences Workshop, (2020)., 2020.

ColosseumRL: A Framework for Multiagent Reinforcement Learning in N-Player Games.   Shmakov, A., Lanier, J., McAleer, S., Achar, R., Lopes, C.V. and Baldi, P. Proceedings of Challenges and Opportunities for Multi-Agent Reinforcement Learning (COMARL AAAI)., 2020.

Pipeline PSRO: A Scalable Approach for Finding Approximate Nash Equilibria in Large Games   S. McAleer, J. B. Lanier, R. Fox, and P. Baldi. Proceedings of the NeurIPS 2020 Conference., 2020.

2019
Refereed Journals
Population-Wide Analysis of Differences in Disease Progression Patterns in Men and Women   Westergaard, D., Moseley, P., Sorup, F. K. H., Baldi, P., Brunak, S. Nature Communications., 10, ( 666 ), 2019.

Neural Network Gradient Hamiltonian Monte Carlo   Li, L., Holbrook, A.J., Shahbaba, B., Baldi, P. Computational Statistics., 34, 281-299, 2019.

Improved energy reconstruction in NOvA with regression convolutional neural network   Baldi, P., Bian, J., Hertel, L., et al. Physical Review D., 99, ( 12011 ), 2019.

The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction   Li, X., Zhou, Q., Wei, W., Lin, Q., Magnan, C., Emami, M., Wearick da Silva, L.E., Viola, T.W., Marshall, P., Edmunds, J., Nainar, S., Broberg Vagbo, C., Leighton, L., Zajackowski, E., Ke, K., Grassi-Oliveira, R., Bojoras, M., Balvdi, P., Spitale, C., Bre. Nature Neuroscience., 2019.

First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NOvA   Acero, M.A., et al. Physical Review Letters., 2019.

Solving the Rubik’s cube with deep reinforcement learning and search   Agostinelli, F., McAleer, S., Shmakov, A.K., Baldi, P. Nature Machine Intelligence., 1, 356-363, 2019.

Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons   Aras, E., Ramadori, G., Kinouchi, K., Liu, Y., Ioris, R.M., Brenachot, X., Ljubicic, S., Veyrat-Durebex, C., Mannucci, S., Galie, M., Baldi, P., Sassone-Corsi, P., Coppari, R. Cell Reports., 27, ( 8 ), 2385-2398, 2019.

Bayesian Causality   Baldi, P., Shahbaba, B. The American Statistician., 3, ( 74 ), 249-257, 2019.

Neuronal Capacity   Baldi, P., Vershynin, R. Journal of Statistical Mechanics, Theory and Experiment., 2019.

Polynomial threshold functions, hyperplane arrangements, and random tensors   Baldi, P., Vershynin, R. SIAM Journal of Mathematics of Data Science., 2019.

The capacity of feedforward neural networks   Baldi, P., Vershynin, R. Neural Networks., 116, 288-311, 2019.

Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells   Chen, Y-H., Su, C-C., Deng, W., Lock, L., Donovan, P., Kayala, M., Baldi, P., Lee, H-C., Chen, Y., Wang, P.H. Scientific Reports., 9, ( 9919 ), 2019.

Defining the Independence of the Liver Circadian Clock   Koronowski, K.B., Kinouchi, K., Welz,P-S., Zinna, V.M., Shi, J., Samad, M., Chen, S., Magnan, C., Kinchen, J., Li, W., Baldi, P., Benitah, S.A., Sassone-Corsi, P. Cell., 177, ( 6 ), 2019.

Functional conservation of lncRNA JPX despite sequence and structural divergence   Kraner, H., Webb, C-H., Carmona, S., Liu, Y., Lin, B., Erhard, M., Chen, D., Baldi, P., Spitale, R.C., Sun, S. Journal of Molecular Biology., 2019.

Gap Junction Channels of Innexins and Connexins: Relations and Computational Perspectives   Sanchez, A., Castro, C., Flores, D-L., Gutierrez, E., Baldi, P. International Journal of Molecular Science., 20, ( 10 ), 2019.

Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis   Sato, S., Linde, A., Schonke, M., Chen, S., Samad, M., Altintas, A., Laker, R.C., Dalbram, E., Barres, R., Baldi, P., Treebak, J.T., Zierath, J. R., Sassone-Corsi, P. Cell Metabolism., 30, ( 1 ), 2019.

First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NovA   Acero M.A., et al. Phys. Rev. Lett., ( 123 ), 2019.

Distinct Metabolic Adaptation of Liver Circadian Pathways to Acute and Chronic Patterns of Alcohol Intake   Gaucher j., Kinouchi K., Ceglia N., Montellier E., Peleg S., Greco C.M., Schmidt A., Forne I., Marsi S., Baldi P., Imhof A., Sassone-Corsi A. Proceedings of the National Academy of Sciences USA., 50, ( 116 ), 2019.

Refereed Conference Proceedings
Sparse Image Generation with Decoupled Generative Models   Y. Lu, J. Collado, K. Bauer, D. Whiteson, P. Baldi. NeurIPS 2019, Machine Learning and Physical Sciences Workshop., 2019.

Modeling Dynamic Functional Connectivity with Latent Factor Gaussian Processes   L. Li, D. Pluta, B. Shahbaba, P. Baldi, N. Fortin, H. Ombao. Proceedings of NIPS 2019., 2019.

Effects of exercise on memory performance and hippocampal gene expression   Keiser A, Butler C, Kramár E., Matheos D., Berchtold N., Chen S., Samad M, Magnan C, Baldi, Cotman C, Wood M. Society for Neuroscience., 2019.

Latent Factor Gaussian Process with Log-Euclidean Metric for Dynamic Covariance Modeling   Lingge Li, Dustin Pluta, Babak Shahbaba and Pierre Baldi. Latent Factor Gaussian Process with Log-Euclidean Metric for Dynamic Covariance Modeling. ICML19., 2019.

Towards Automating Precision Studies of Clone Detectors   Saini, V., Farahani, F.F., Lu, Y., Yand, D., Maritns, P., Sainani, H., Baldi, P., Lopes, C. ICSE 2019., 2019.

Solving the Rubik's Cube with Approximate Policy Iteration   McAleer, S., Agostinelli, F., Shmakov, A.K., Baldi, P. ICLR 2019., 2019.

2018
Refereed Journals
ClusterCAD: a computational platform for type I modular polyketide synthase design   Eng, C. H., Backman, W.H., Bailey, C. B., Magnan, C., Marin, H. G., Katz, L., Baldi, P., Keasling, J. D. Nucleic Acid Research., 46, D509-D515, 2018.

Deep Learning in Biomedical Data Science   Baldi, P. Annual Review of Biomedical Data Science., 1, 2018.

Development and Validation of a Deep Neural Network Model for Prediction of Postoperative In-Hospital Mortality   Lee, C. K., Hofer, I., Gabel, E., Baldi, P., Cannesson, M. Anestgesiology., 2018.

Inner and Outer Recursive Neural Networks for Chemoinformatics Applications   Urban, G., Subrahmanya, N., Baldi, P. Journal of Chemical Information and Modeling., 58, ( 2 ), 2018.

Deep learning convolutional neural networks accurately classify genetic mutation in gliomas   Chang, P., Su, L., Baldi, P., Choi, D. American Journal of Neuroradiolog., 2018.

Learning in the Machine: Random Backpropagation and the Learning Channel   Baldi, P., Sadowski, P., Lu, Z. Artifical Intelligence., 2018.

Longitudinal Monitoring of Biofilm Formation via Robust SERS Quantification of Pseudomonas aeruginosa-Produced Metabolite   Nguyen, C., Thrift, W. J., Bhattacharjee, A., Ranjbar, S., Gallagher, T., Darvishzadeh-Varcheie, M., Sandersion, R., Capolimo, F., Whiteson, K., Baldi, P., Hochbaum, A., Ragan, R. ACS, Applied Materilas and Interfaces., 2018.

Learning in the Machine: Random Backpropagation and the Deep Learning Channel   Baldi, P., Sadowski, P., Lu, Z. Artificial Intelligence., 260, 1-35, 2018.

CircadiOmics: Circadian Omic Data Web Portal   Ceglia, N., Liu, Y., Chen, S., Agostinelli, F., Eckel-Mahan, K, Sassone-Corsi, P., Baldi, P. Nuclei Acids Research., 2018.

Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images   Urban, G., Bache, K., Phan, D.T.T., Sorbrino, A., Shmakov, A.K., Hachey, S.J., Hughes, C.W., Baldi, P. IEEE/ACM Transactions on Computational Biology and Bioinformatics., 2018.

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas   Chang, P., Grinband, J., Winberg, B.D., Bardis, M., Khy, M., Cadena, G., Su, M.-Y., Cha, S., Filippi, C.G., Bota, D., Baldi, P., Poisson, L.M., Jain, R., Chow, D. American Journal of Neuroradiology., 2018.

Deep Learning Localizes and Identifies Polyps in Real Time with 96% Accuracy in Screening Colonoscopy   Urban, G., Tripathi, P., Alkayali, T., Mittal, M., Jalali, F., Karnes, W., Baldi, P. Gastroenterology,., 155, ( 4 ), 1069-1078, 2018.

A circadian metabolomics atlas reveals systems-wide coordination and communication between clocks   Dyar, K. A., Lutter, D., Artati, A., Ceglia, N., Liu, Y., Armenta, D., Jastroch, M., Schneider, S., de Maeo, S., Abbondante, S., Tognini, P., Orozco-Solis, R., Sahar, S., Wang, C., Swerdloff, R.S., Nadeef, S., Orlando, V., Uhlenhaut, N. H., Masri, S., Mai. Cell., 174, ( 6 ), P1571-1585.E11, 2018.

Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming   Liu, S., Chen, H., Ronquist, S., Seaman, L., Ceglia, N., Meixner, W., Muir, L.A., Chen, P., Higgins, G., Baldi, P., Smale, S., Hero, A., Rajapakse, I. ISCIENCE., 6, 232–246, 2018.

Epigenetic Regulation of the Circadian Gene Per1 in the Hippocampus Contributes to Age-Related Changes in Memory and Synaptic Plasticity   Kwapis, J.L., Alaghband, Y., Kramar, E., Lopez, A., Vogel-Ciernia, A., White, A., Shu, G., Rhee, D., Michael, C.M., Montellier, E., Liu, Y., Magnan, C., Chen, S., Sassone-Corsi, P., Baldi, P., Matheos, D. P., Wood, M. A. Nature Communicaitons., 9, 2018.

Highly-Accurate Machine Fault Diagnosis Using Deep Transfer Learning   Shao, S., McAleer, S., Yan, R., Baldi, P. IEEE Transactions on Industrial Informatics., 15, ( 4 ), 2018.

Learning in the machine: Recirculation is random backpropagation   Baldi, P., Sadowski, P. Neural Networks., 108, 479-494, 2018.

Fasting Imparts a Switch to Alternative Circadian Pathways in Liver and Muscle   Kinouchi, K., Magnan, C., Ceglia, N., Liu, Y., Cervantes, M., Baldi, P., Masri, S. Cell Reports., 12, ( 25 ), 2018.

Refereed Conference Proceedings
On the Capacity of Shallow and Deep Learning Architectures   Baldi, P., Vershynin, R. COLT., 2018.

The Asymptotic Number of Boolean Polynomial Threshold Functions   Baldi, P., Vershynin, R. FOCS., 2018.

Oreo: Detection of Clones in the Twilight Zone   Saini, V., Farahani, F.F., Lu, Y., Baldi, P., Lopes, C. ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering ESEC/FSE 2018., 2018.

On Neuronal Capacity. Advances in Neural Information Processing Systems   Baldi, P., Vershynin, R. NIPS 2018., 2018.

Book Chapters
Deep Learning in the Natural Sciences: Applications to Physics.   Sadowski, P., Baldi, P. Key Ideas in Learning Theory from Inception to Current State: Emmanuel Braverman's Legacy., 2018.

From Reinforcement Learning to Deep Reinforcement Learning: An Overview.   Agostinelli, F., Hocquet, G., Singh, S., Baldi, P. Key Ideas in Learning Theory from Inception to Current State: Emmanuel Braverman's Legacy., 2018.

2017
Refereed Journals
A Multi-Resolution Approach to Spinal Metastasis Detection using Dep Siamese Neural Networks   Wang, J., Fang, Z., Lang, N., Yuan, H., Su, M., Baldi, P. Computers in Biology and Medicine., 84, 137-146, 2017.

Detecting Cardiovascular Disease from Mammograms with Deep Learning   Wang, J., Ding, H., Azamian, F., Zhou, B., Iribarren, C., Molloi, S., Baldi, P. IEEE Transactions onBiomedical Imaging., 36, ( 5 ), 1172-1181, 2017.

Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet   Tognini, P., Murakami, M., Liu, Y., Eckel-Mahan, K, Newmand, J. C., Verdind, E., Baldi, P., Sassone-Corsi, P. Cell Metabolism., 2017.

Efficient Antihydrogen Detection in Antimater Physics by Deep Learning   Sadowski, P., Radics, B., Ananya, A., Yamazaki, Y., Baldi, P. Journal of Physics Communications., 2017.

Mir-132/212 is Required for Maturation of Binocular Matching Orientation Prference and Depth Perception   Mazziotti, R., Baroncelli, L., Ceglia, N., Chelini, G., Della Sala, G., Magnan, C., Napoli, D., Putugnano, E., Silingardi, D., Tola, J., Tognini, P., Baldi, P., Pizzorusso, T. Nature Communicaiton., 8, ( 23 ), 2017.

MotifMap-RNA: A Gnome-Wide Map of RBP Binding Sites   Liu, Y., Sun, S., Bredy, T., Wood, M. A., Spitale, R. C., Baldi, P. Bioinformatics., 33, ( 3 ), 2029-2031, 2017.

SIRT6 Hindrs Stemness of Tumors Bearing PI3K Activation   Irois, R. M., Galie, M., Ramadori, G., Anderson, J. G., Charollais, A., Konstantinidou, G., Brenachot, X., Aras, E., Goga, A., Ceglia, N., Sebastian, C., Martinvalet, D., Baldi, P., Coppari, R. Cell Reports., 18, ( 8 ), 1858-1868, 2017.

Mutation of neuron-specific chromatin remodeling subunit BAF53b: Rescue of plasticity and memory by manipulating actin remodeling   Ciernial, A. V., Kramar, E. A., Matheos, D. P., Havekes, R., Hemstedt, T. J., Magnan, C., Sakata, K., Tran, A., Azzawi, S., Lopez, A., Dang, R., Wang, W., Trieu, B., Tong, J., Barrett, R. M., Post, R.J., Baldi, P., Abel, T., Lynch, G., Wood, M. A. Learning and Memory., 24, 199-209, 2017.

Learning in the Machine: the Symmetries of the Deep Learning Channel   Baldi, P., Sadowski, P., Lu, Z. Neural Networks., 95, 110-133, 2017.

The Inner and Outer Approaches for the Design or Recursive Neural Networks Architctures   Baldi, P. Data Mining and Knowledg Discovery., 1-13, 2017.

Guidelines for Genome-Scale Analysis of Biological Rhythms   Hughes, M. E., Baldi, P., Hogenesh, J.B., et al. Journal of Biological Rhythms., 32, ( 5 ), 380-393, 2017.

Decorrelated Jet Substructure Tagging using Adversarial Neural Networks   Shimmin, C., Sadowski, P., Baldi, P., Weik, E., Whiteson, D., Goul, E., Sogaard, A. Physical Review D., 96, ( 74034 ), 2017.

Deep learning for chemical reaction prediction   Fooshee, D., Mood, A., Gutman, E., Tavakoli, A., Urban, G., Liu, F., Huynh, N., Van Vranken, D., Baldi, P. Molecular Systems Design & Engineering., 2018, ( 3 ), 2017.

Refereed Conference Proceedings
Deep Learning for Predicitng Postoperative Outcomes: AKI, Reintubation, and In-Hospital Mortality   Lee, C., Hofer, I., Baldi, P., Cannesson, M. American Society of Anesthesiologists Conference., 2017.

Deep Learning in Prediciting in Hospital Mortality   Lee, C., Hofer, I., Cannesson, M., Baldi, P. Society for Technology in Anesthesia., 2017.

2016
Refereed Journals
A Theory of Local Learning, the Learning Channel, and the Optimality of Backpropagation   Baldi, P., Sadowski, P. Neural Networks., 83, 51-74, 2016.

What Time is it? Deep Learning Approaches for Circadian Rhythms   Agostinelli, F., Ceglia, N., Shahbaba, B., Sassone-Corsi, P., Baldi, P. Bioinformatics., 32, ( 12 ), i8-i17, 2016.

Sequence assembly of Yarrowia lipolytica strain W29/CLIB89 shows transposonable element diversity   Magnan, C., Yu, J., Chang, I., Jahn, E., Kanomata, Y., Wu, J., Zeller, M., Oakes, M., Baldi, P., Sandmeyer, S. B. PLOS ONE., 2016.

Gut microbiota directs PPAR ? driven reprogramming of the liver circadian clock by nutritional challenge   Murakami, M., Tognini, P., Liu, Y., Eckel-Mahan, K, Baldi, P., Sassone-Corsi, P. EMBO Reports., 2016.

Jet Substructure Classification in High-Energy Physics with Deep Neural Networks   Baldi, P., Bauer, K., Eng, C., Sadowski, P., Whiteson, D. Physical Review D., 93, ( 94034 ), 2016.

Parameterized Neural Networks for High-Energy Physics   Baldi, P., Cranmer, K., Faucett, T., Sadowski, P., Whiteson, D. The European Physical Journal C., 76, ( 235 ), 1-7, 2016.

Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells   Borrego, S. L., Fahrmann, J., Datta, R., Stringari, C., Grapov, D., Zeller, M., Chen, Y., Wang, P., Baldi, P., Gratton, E., Fiehn, O., Kaiser, P. Cancer and Metabolism., 4, ( 9 ), 2016.

Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis   Masri, S., Papagiannakopoulos, T., Kinouchi, K., Liu, Y., Cervantes, M., Baldi, P., Jacks, T., Sassone-Corsi, P. Cell., 165, ( 4 ), 896-909, 2016.

Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver   Abbondante, S., Eckel-Mahan, K, Ceglia, N., Baldi, P., Sassone-Corsi, P. Journal of Biological Chemistry., 291, ( 6 ), 2812-28, 2016.

VIRALpro: a tool to identify viral capsid and tail sequences   Galiez, C., Magnan, C., Coste, F., Baldi, P. Bioinformatics., 32, ( 9 ), 1405-1407, 2016.

Jet Flavor Classification in High-Energy Physics with Deep Neural Networks   Guest, D., Collado, J., Baldi, P., Whiteson, D. Physical Review D., 94, ( 112002 ), 2016.

Gut microbiota directs PPAR ? driven reprogramming of the liver circadian clock by nutritional challenge   Murakami, M., Tognini, P., Liu, Y., Eckel-Mahan, K, Baldi, P., Sassone-Corsi, P. EMBO Reports., 2016.

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction   Sadowski, P., Fooshee, D., Subrahmanya, N., Baldi, P. Journal of Chemical Information and Modeling., 56, ( 11 ), 2125-2128, 2016.

2015
Enhanced Higgs to tau+tau- Search with Deep Learning   P. Baldi, P. Sadowski, D. Whiteson. Physical Review Letters., 114, 111801-1-111801-5, 2015.

Mitochondrial Mutations in Subjects with Psychiatric Disorders   Sequeira, A., Rollins, B., Magnan, C., van Oven, M., Baldi, P., Myers, R. M., Barchas, J. David, Schatzberg, A. F., Watson, S. J., Akil, H., Bunney, W. E., Vawter, M. P. PLOS ONE., 2015.

Deep Learning, Dark Knowledge, and Dark Matter   Sadowski, P., Collado, J., Whiteson, D., Baldi, P. Journal of Machine Learning Research., 42, 81-87, 2015.

The Pervasiveness and Plasticity of Circadian Oscillations: The Coupled Circadian-Oscillators Framework   Patel, V., Ceglia, N., Zeller, M., Eckel-Mahan, K., Sassone-Corsi, P., Baldi, P. Bioinformatics., 19, ( 31 ), 3181-3188, 2015.

Towards a Systems View of Irritable Bowel Syndrome   Mayer, E. A., Labus, J., Tillisch, K., Cole, S., Baldi, P. Nature Reviews Gastroenterolog yand Hepatology., 2015.

Function and regulation of Cph2 in Candida albicans   Lane, S., Di Lena, P., Tormanen, K., Baldi, P. Eukaryotic Cell., 11, ( 14 ), 1114-26, 2015.

Atmospheric Oxidation of Squalene: Molecular Study Using COBRA Modeling and High-Resolution Mass Spectrometry   Fooshee, D. R., Aiona, P. K., Laskin, A., Laskin J., Nizkorodov, S. A., Baldi, P. Environmental Sciences and Technology., 49, ( 22 ), 2015.

Accurate and Efficient Target Prediction Using a Potency-Sensitive Influence-Relevance Voter   Lusci, A., Browning, M., Fooshee, D., Swamidass, S. Josh, Baldi, P. Journal of Cheminformatics., 7, 63-79, 2015.

2014
The Dropout Learning Algorithm   P. Baldi, P. Sadowski. Artifical Intelligence., 210, 78-122, 2014.

A Genomic Analysis Pipeline and Its Application to Pediatric Cancers   M. Zeller, C. Magnan, V. R. Patel, P. Rigor, L. Sender, P. Baldi. IEEE/ACM Transactions on Computational Biology and Bioinformatics., 11, ( 5 ), 826-839, 2014.

Circadian Control of Fatty Acid Elongation by SIRT1-mediated Deacetylation of Acetyl-CoA Synthetase 1   S. Sahar, S. Masubuchi, K. Eckel-Mahan, S. Vollmer, L. Galla, N. Ceglia, S. Selma Masri, T. K. Barth, B. Grimaldi, O. Oluyemi, G. Astarita, W. C. Hallows, D. Piomelli, A. Imhof, P. Baldi, J. M. Denu, P. Sassone-Corsi. Journal of Biological Chemistry., 9, ( 289 ), 6091-7, 2014.

How Pervasive Are Circadian Oscillations?   V. R. Patel, K. Eckel-Mahan, P. Sassone-Corsi, P. Baldi. Trends in Cell Biology., 24, 329-331, 2014.

Incorporating Post-Translational Modifications and Unnatural Amino Acids into High-Throughput Modeling of Protein Structures   K. Nagata, A. Randall, P. Baldi. Bioinformatics., 30, ( 12 ), 1681-1689, 2014.

SIRT6 defines circadian transcription leading to control of lipid metabolism   S. Masri, P. Rigor, M. Cervantes, N. Ceglia, C. Sebastian, C. Xiao, M. Roqueta-Rivera, C. Deng, T. F. Osborne, R. Mostoslavsky, P. Baldi, P. Sassone-Corsi. Cell., 3, ( 158 ), 659-672, 2014.

Sspro/ACCpro 5.0: Almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility. Problem Solved?   C. Magnan, P. Baldi. Bioinformatics., 30, ( 18 ), 2592-2597, 2014.

Muscle Insulin Sensitivity and Glucose Metabolism are Controlled by the Intrinsic Muscle Clock   K. A. Dyar, S. Ciciliot, L. E. Wright, R. S. Bienso, G. Malagpli Tagliazucchi, V. R. Patel, M. Forcato, M. I. Pena Paz, A. Gudiksen, F. Solagna, M. Albiero, I. Moretti, K. L. Eckel-Mahan, P. Baldi, P. Sassone-Corsi, R. Rizzuto, S. Bicciato, H. Pilegaard, . Molecular Metabolism., 3, ( 1 ), 29-41, 2014.

Deep Learning in High-Energy Physics: Improving the Search for Exotic Particles   P. Baldi, P. Sadowski, D. Whiteson. Nature Communicaiton., 5, ( 4038 ), 2014.

A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia   W. Gordon, M. Zeller, R. Herndon, W. Swindell, H. Ho, F. Espetia, J.E. Gudjonsson, P. Baldi, B. Andersen. Journal of Clinical Inverstigation., 124, ( 12 ), 5205-5218, 2014.

The TCF C-clamp DNA Binding Domain Expands the Wnt Transcriptome via Alternative Target Recognition   N. P. Hoverter, M. Zeller, M. McQuade, A. Garibaldi, A. Busch, K. Hertel, P. Baldi, M. L. Waterman. Nucleic Acids Research., 42, ( 22 ), 13615-13632, 2014.

Enhanced Higgs to Tau-plus Tau-minus Search with Deep Learning   Baldi, P., Sadowski, P., Whiteson, D. Pyhsical Review letters., 2014.

Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions   Chicco, D., Sadowski, P., Baldi, P. IEEE/ACM Transactions on Computational Biology and Bioinformatics., 2014.

A Large-Scale Deep Learning Target-Prediction System for Diverse Molecules   Lusci, A., Browning, M., Swamidass, S. Josh, Baldi, P. Journal of Chemical Information and Modeling., 2014.

Towards a Systems View of Irritable Bowel Syndrome   Mayer, Emeran A., Labus, Jen, Cole, Steve, Baldi, P. Nature Reviews Gastroenterology., 2014.

The Pervasiveness and Plasticity of Circadian Oscillations   Patel, V., Ceglia, N., Zeller, M., Eckel-Mahan, K., Sassone-Corsi, P., Baldi, P. Bioinformatics., 2014.

Refereed Conference Proceedings
Massively Parallel Multicut Segmentation via Dual Decomposition   J. Yarkony, T. Beyer, B. Andres, B.S. Manjunath, P. Baldi, F. Hamprecht. ICML., 2014.

Deep Autoencoder Neural Networks for Gene Ontology Annotation Predictions   D. Chicco, P. Sadowski, P. Baldi. 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics., 2014.

Searching for Higgs Boson Decay Modes with Deep Learning   P. Sadowski, D. Whiteson, P. Baldi. NIPS., 2014.

2013
Refereed Journals
The Circadian Clock Regulates the Host Response to Salmonella   M. M. Bellet, E. Deriu, J. Liu, B. Grimaldi, C. Blaschitz, M. Zeller, R. A. Edwards, S. Sahar, S. Dandekar, P. Baldi, M. D. George, M. Raffatellu, P. Sassone-Corsi. Proceedings of the National Academy of Sciences USA., 110, ( 24 ), 9897-9902, 2013.

A Unifying Kinetic Framework for Modeling Oxidoreductase Catalyzed Reactions   I. Chang, P. Baldi. Bioinformatics., 29, ( 10 ), 1299-1307, 2013.

Cycles in Spatial and Temporal Chromosomal Organization Driven by the Circadian Clock   Lorena Aguilar-Arnal, Ofir Hakim, Vishal R. Patel, Pierre Baldi, Gordon L. Hager, Paolo Sassone-Corsi. Nature Structural and Molecular Biology., 2013.

An Efficient Atom-Mapping Algorithm   D. Fooshee, A. Andronico, P. Baldi. Journal of Chemical Information and Modeling., 2013.

Combining Docking Site and Phosphosite Predictions to Find New Substrates: Identification of Smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal Kinase (JNK) Substrate   E. A. Gordon, T. Whisenant, M. Zeller, R. Kaake, W. Gordon, P. Krotee, V. Patel, L. Huang, P. Baldi, L. Bardwell. Cellular Signalling., 2013.

Deep Architectures and Deep Learning in Chemoinformatics: the Prediction of Aqueous Solubility for Drug-Like Molecules   A. Lusci, G. Pollastri, P. Baldi. Journal of Chemical Information and Modeling., 53, ( 7 ), 1563-1575, 2013.

A 3-dimensional trimeric B-barrel model for Chlamydia MOMP contains conserved and novel elements of gram-negative bacterial porins   V. A. Feher, A. Randall, P. Baldi, R. M. Bush, L. M de la Maza, R. E. Amaro. PLOS One., 2013.

Leptin Engages a Hypothalamic Neurocircuitry to Permit Survival in the Absence of Insulin   Teppei Fujikawa, Eric D. Berglund, Vishal R. Patel, Giorgio Ramadori, Claudia R. Vianna, Linh Vong, Fabrizio Thorel, Simona Chera, Pedro L. Herrera, Bradford B. Lowell, Joel K. Elmquist, Pierre Baldi, Roberto Coppari. Cell Metabolism., 2013.

Small-molecule 3D Structure Prediction Using Open Crystallography Data   P. Sadowski, P. Baldi. Journal of Chemical Information and Modeling., 53, ( 12 ), 3127-3130, 2013.

Reprogramming of the Circadian Clock by Nutritional Challenge   K. L. Eckel-Mahan, V. R. Patel, S. de Mateo, N. J. Ceglia, S. Sahar, S. Dilag, K. A. Dyar, R. Orozco-Solis, P. Baldi, P. Sassone-Corsi. Cell., 155, ( 7 ), 1464-1478, 2013.

The Neuron-specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory   Vogel-Cierna, A.,Matheos, D.P., Barrett, R.M., Kramar, E, Azzaw, S. Chen, Y. Magnan, C. Zeller, M., Sylvain, A., Haettig, J., Jia, Y., Tran, A., Dang, R., Post, R. J., Chabrier, M. Babayan, A. Wu, J. I., Crabtree, G. R., Baldi, P., Baram, T. Z. Lynch, G. . Nature Neuroscience., 10, 552-561, 2013.

Neuron-Specific Nucleosome Remodeling Component BAF53b is Neccessary for Synaptic Plasticity and Memory   Vogel-Ciernia, A, Matheos, D. P., Barrett, R. M., Kramar, E., Chen, Y., Magnan, C., Zeller, M., Sylvain, A., Azzawi, S., Haettig, J., Tran, A., Post, R.J., Crabtree, G. R., Baram, T. Z., Baldi, P., Lynch, G., Wood, M. A. Nature Neuroscience., 16, 552-561, 2013.

Refereed Conference Proceedings
An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases   Francesco Napolitano, Roberto Tagliaferri, Pierre Baldi. WIRN., 2013.

Understanding Dropout   P. Sadowski, P. Baldi. NIPS., 26, 2814-2822, 2013.

Beyond Gradient Diffusion: New Algorithms for Training Deep Layers of Neural Networks   J. Yarkony, P. Sadowski, B.S. Manjunath, P. Baldi. NIPS., 2013.

Distributed training of very large networks   V. R. Patel,, N. Cegna, P. Sadowski, P. Baldi. NIPS., 2013.

2012
Refereed Journals
Rationally Selected Single-Site Mutants of the Thermoascus aurantiacus Endoglucanase Increase Hydrolytic Activity on Cellulosic Substrates.   S. Srikrishnan, A. Z. Randall, P. Baldi, N.A. Da Silva. Biotechnology and Bioengineering., 109, ( 6 ), 1595–1599, 2012.

Mitochondrial Mutations and Polymorphisms in Psychiatric Disorders.   A. Sequeira, M. V. Martin, B. Rollins, E. A. Moon, W. E. Bunney, F. Macciardi, S. Lupoli, E. Smith, J. Kelsoe, C. Magnan, M. van Oven, P. Baldi, D.C. Wallace, M. P. Vawter. Frontiers in Behavioral and Psychiatric Genetics., 3, 103, 2012.

Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport.   D. Ren, M. Dalmau, A. Randall, M. M. Shindel, P. Baldi, S. Wang. Advanced Functional Materials., 2012.

Retrotransposons Profiling of RNA Polymerase III Initiation Sites.   X. Qi, K. Daily, K. Nguyen, H. Wang, D. Mayhew, P. Rigor, S. Forouzan, M. Johnston, R. D. Mitra, P. Baldi, S. B. Sandmeyer. Genome Research., 681-692, 2012.

Speeding Up Chemical Searches Using the Inverted Index: the Convergence of Chemoinformatics and Text Search Methods.   R. Nasr, R. Vernica, C. Li, P. Baldi. Journal of Chemical Information and Modeling., 52, ( 4 ), 891-900, 2012.

SIDEpro: a Novel Machine Learning Approach for the Fast and Accurate Prediction of Side-Chain Conformations.   K. Nagata, A. Randall, P. Baldi. Protein: Structure, Function, and Bioinformaics., 80, ( 1 ), 142-153, 2012.

Cyber-T Webserver: Differential Analysis of High-Throughput Data.   M. Kayala, P. Baldi. Nucleic Acids Research., 1-7, 2012.

Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling.   Kao, Athit, Randall, Arlo, Yang, Yingying, Patel, Vishal R., Kandur, Wynne, Guan, Shenheng, Rychnovsky, Scott D., Baldi, Pierre, Huang, Lan. Molecular & Cellular Proteomics., 2012.

GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program.   Hopkin, Amelia Soto, Gordon, William, Klein, Rachel Herndon, Espitia, Francisco, Daily, Kenneth, Zeller, Michael, Baldi, Pierre, Andersen, Bogi. PLoS Genet., 8, ( 7 ), 2012.

COBRA: A Computational Brewing Application for Predicting the Molecular Composition of Organic Aerosols.   D. R. Fooshee, T. B. Nguyen, S. A. Nizkorodov, J. Laskin, A. Laskin, P. Baldi. Environmental Science & Technology., 46, ( 11 ), 6048-6055, 2012.

Mapping the Protein Interaction Network of the Human COP9 Signalosome (CSN) Complex Using a Label-Free QTAX Strategy.   L. Fang, R. M. Kaake, V. Patel, P. Baldi, L. Huang. Molecular and Cellular Proteomics., 2012.

Coordination of Metabolome and Transcriptome by the Circadian Clock.   K. L. Eckel-Mahan, V. R. Patel, K. S.Vignola, R. P. Mohney, P. Baldi, P. Sassone-Corsi. PNAS., 2012.

Complex-Valued Autoencoders.   P. Baldi, Z. Lu. Neural Networks., 33, 136-147, 2012.

The Universal Campus: An Open 3D Virtual World Infrastructure for Research and Education.   P. Baldi, C. Lopes. ACM eLearn Magazine., 2012, ( 4 ), 6, 2012.

Boolean autoencoders and hypercube clustering complexity   Baldi, P. Designs, Codes and Cryptography., 1-21, 2012.

Autoencoders, Unsupervised Learning, and Deep Architectures.   Baldi, P. Journal of Machine Learning Research., 2012.

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics.   Patel, Vishal R., Eckel-Mahan, Kristin, Sassone-Corsi, Paolo, Baldi, Pierre. Nature methods., 9, ( 8 ), 772-773, 2012.

Engineered Synthetic Polymer Nanoparticles as IgG Affinity Ligands.   Lee, Shih-Hui, Hoshino, Yu, Randall, Arlo, Zeng, Zhiyang, Baldi, Piere, Doong, Ruey-an, Shea, Kenneth J. Journal of the American Chemical Society., 134, ( 38 ), 15765-15772, 2012.

ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning   Kayala, Matthew A., Baldi, Pierre. Journal of Chemical Information and Modeling., 52, ( 10 ), 2526-2540, 2012.

A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs.   Hoverter, Nate P., Ting, Ju-Hui, Sundaresh, Suman, Baldi, Pierre, Waterman, Marian L. Molecular and cellular biology., 32, ( 18 ), 3648-3662, 2012.

Deep architectures for protein contact map prediction   Di Lena, Pietro, Nagata, Ken, Baldi, Pierre. Bioinformatics (Oxford, England)., 28, ( 19 ), 2449-2457, 2012.

Boolean autoencoders and hypercube clustering complexity.   Baldi, P. Designs, Codes and Cryptography., 1-21, 2012.

GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Pprogram.   A. S. Hopkin, W. Gordon, R. H. Klein, F. Espitia, K. Daily, M. Zeller, P. Baldi, B. Andersen. PLoS Genetics., 2012.

Refereed Conference Proceedings
Deep Architectures and Learning for Protein Structure Prediction   P. Di Lena, K. Nagata, P. Baldi. NIPS., 2012.

Deep Spatial-Temporal Architectures and Learning for Protein Structure Prediction   P. Di Lena, K. Nagata, P. Baldi. NIPS., 25, 512-520, 2012.

2011
Refereed Journals
Sterile Protective Immunity to Malaria is Associated with a Panel of Novel Plasmodium Falciparum Antigens.   Trieu, Angela, Kayala, Matthew A., Burk, Chad, Molina, Douglas M., Freilich, Daniel A., Richie, Thomas L., Baldi, Pierre, Felgner, Philip L., Doolan, Denise L. Molecular and Cellular Proteomics., 2011.

Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling.   B. Tang, P. Di Lena, L. Schaffer, S. R. Head, P. Baldi, E. A. Thomas. PLoS ONE., 6, ( 9 ), e23691, 2011.

Tree and Hashing Data Structures to Speedup Chemical Searches: Analysis and Experiments.   R. Nasr, T. Kristensen, P. Baldi. Molecular Informatics., 30, ( 9 ), 791-800, 2011.

SIDEpro: a Novel Machine Learning Approach for the Fast and Accurate Prediction of Side-Chain Conformations   K. Nagata, A. Randall, P. Baldi. Protein: Structure, Function, and Bioinformaics., 2011.

Learning to Predict Chemical Reactions   M. Kayala, C. Azencott, J. Chen, P. Baldi. Journal of Chemical Information and Modeling., 51, ( 9 ), 2209-2222, 2011.

Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes.   A. Kao, C. Chiu, D. Vellucci, Y. Yang, V. R. Patel, S. Guan, A. Randall, P. Baldi, S. Rychnowski, L. Huang. Molecular and Cellular Proteomics., 2011.

Identification of Immunodominant Antigens by Probing a Whole Chlamydia trachomatis Open Reading Frame Proteome Microarray Using Sera from Immunized Mice.   Cruz-Fisher, Maria I., Cheng, Chunmei, Sun, Guifeng, Pal, Sukumar, Teng, Andy, Molina, Douglas M., Kayala, Matthew A., Vigil, Adam, Baldi, Pierre, Felgner, Philip L., Liang, Xiaowu, de la Maza, Luis M. Infection and Immunity., 79, ( 1 ), 246-257, 2011.

The TY3 Gag3 Spacer Controls Intracellular Condensation and Uncoating.   Clemens, Kristina, Larsen, Liza, Zhang, Min, Kuznetsov, Yurii, Bilanchone, Virginia, Randall, Arlo, Harned, Adam, DaSilva, Rhonda, Nagashima, Kunio, McPherson, Alexander, Baldi, Pierre, Sandmeyer, Suzanne. Journal of Virology., 85, ( 7 ), 3055-3066, 2011.

Visual Adaptation and Novelty Responses in the Superior Colliculus.   S. Boehnke, D. Berg, R. Marino, P. Baldi, L. Itti, D. Munoz. European Journal of Neuroscience., 34, ( 5 ), 766-779, 2011.

The Stability and Complexity of Antibody Responses to the Major Surface Antigen of Plasmodium Falciparum are Associated with Age in a Malaria Endemic Area.   A. E. Barry, A. Trieu, F. J. I. Fowkes, J. Pablo, M. Kalantari-Dehaghi, A. Jasinskas, X. Tan, M.A. Kayala, L. Tavul, P.M. Siba, K. P. Day, P. Baldi, P. L. Felgner, D. L. Doolan. Molecular and Cellular Proteomics., 2011.

Autoencoders, Unsupervised Learning, and Deep Architectures.   Baldi, P. Journal of Machine Learning Research., 2011.

Data-driven High-throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.   Andronico, Alessio, Randall, Arlo, Benz, Ryan W., Baldi, Pierre. Journal of Chemical Information and Modeling., 51, ( 4 ), 760-776, 2011.

MotifMap: Integrative Genome-Wide Maps of Candidate Regulatory Motif Sites for Model Species.   K. Daily, V. Patel, P. Rigor, X. Xie, P. Baldi. BMC Bioinformatics., 12, ( 1 ), 495, 2011.

Data-driven High-throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.   Andronico, Alessio, Randall, Arlo, Benz, Ryan W., Baldi, Pierre. Journal of Chemical Information and Modeling., 51, ( 4 ), 760-776, 2011.

Data-driven High-throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.   Andronico, Alessio, Randall, Arlo, Benz, Ryan W., Baldi, Pierre. Journal of Chemical Information and Modeling., 51, ( 4 ), 760-776, 2011.

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 Center.   P. Baldi. Journal of Chemical Information and Modeling., 51, ( 12 ), 3029, 2011.

Refereed Conference Proceedings
Countering GATTACA: Efficient and Secure Testing of Fully-Sequenced Human Genomes.   P. Baldi, R. Baronio, E. De Cristofaro, P. Gasti, G. Tsudik. ACM Computer and Communication Security Conference (CCS 2011)., 2011.

Privacy-Enhanced Methods for Comparing Compressed DNA Sequences.   D. Eppstein, M. T. Goodrich, P. Baldi. Workshop on Privacy in the Electronic Society., 11, 2011.

A Machine Learning Approach to Predict Chemical Reactions.   M. Kayla, P. Baldi. Neural Information Processing Systems 2011 (NIPS 2011)., 2011.

2010
Refereed Journals
Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli transcription Factors.   T. C. Whisenant, D. T. Ho, R. Benz, J. Rogers, R. Kaake, E. A. Gordon, L. Huang, P. Baldi, L. Bardwell. PLoS Computational Biology., 2010.

High-throughput Prediction of Protein Antigenicity Using Protein Microarray Data.   Magnan, Christophe N., Zeller, Michael, Kayala, Matthew A., Vigil, Adam, Randall, Arlo, Felgner, Philip L., Baldi, Pierre. Bioinformatics (Oxford, England)., 26, ( 23 ), 2936-2943, 2010.

Data Structures and Compression Algorithms for High-throughput Sequencing Technologies   Daily, Kenny, Rigor, Paul, Christley, Scott, Xie, Xiaohui, Baldi, Pierre. BMC Bioinformatics., 11, 514-526, 2010.

Modeling of Mitochondrial Bioenergetics Based on a Composable Chemiosmotic Energy Transduction Rate Law: Theory and Experimental Validation.   I. Chang, M. Heiske, T. Letellier, D. C. Wallace, P. Baldi. PLoS ONE., 2010.

Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability.   D. Guzman, A. Randall, P. Baldi, Z. Guan. Proceedings of the National Academy of Sciences USA., 107, ( 5 ), 1989-1994, 2010.

An Antibody Signature Associated with Naturally-Acquired Malaria Immunity.   Peter D. Crompton, Matthew A. Kayala, Boubacar Traore, Kassoum Kayentao, Aissata Ongoiba, Greta Weiss, Douglas M. Molina, Chad R. Burk, Michael Waisberg, Algis Jasinskas, Safiatou Doumbo, Didier Doumtabe, Younoussou Kone, David L. Narum, Xiaowu Liang, Ogo. PNAS., 2010.

A CROC Stronger than ROC: Measuring, Visualizing, and Optimizing Early Retrieval.   S. J. Swamidass, C. Azencott, K. Daily, P. Baldi. Bioinformatics., 2010.

Modeling User Reputation in Wikis.   S. Javanmardi, C. Lopes, P. Baldi. Statistical Analysis and Data Mining., 3, ( 2 ), 126-139, 2010.

Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia.   A. B. Mochon1, J. Ye, M. A. Kayala, J. R. Wingard, C. J. Clancy, M. H. Nguyen, P. Felgner, P. Baldi, H. Liu. PLoS Pathogens., 6, ( 3 ), e1000827, 2010.

Of Bits and Wows: A Bayesian Theory of Surprise with Applications to Attention.   P. Baldi, L. Itti. Neural Networks., 23, 649-666, 2010.

Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors.   R. Nasr, D. Hirschberg, P. Baldi. Journal of Chemical Information and Modeling., 2010.

Large Scale Immune Profiling of Infected Humans and Goats Reveals Differential Recognition of Brucella melitensis Antigens.   Li Liang, Diana Leng, Chad Burk, Rie Nakajima-Sasaki, Matt Kayala, Vidya L. Atluri, Jozelyn Pablo, Berkay Unal, Thomas A. Ficht, Eduardo Gotuzzo, Mayuko Saito John Morrow, Xiaowu Liang, Pierre Baldi, Joseph M. Vinetz, Philip L. Felgner, Renee M. Tsolis. PLoS Neglected Tropical Diseases., 4, ( 5 ), 1-11, 2010.

A Prospective Analysis of the Antibody Response to Plasmodium falciparum Before and After a Malaria Season by Protein Microarray.   P. Crompton, M. Kayala, B. Traore, K. Kayentao, A. Ongoiba, G. Weiss, D. Molina, C. Burk, M. Waisberg, A. Jasinskas, X. Tan, S. Doumbo, D. Doumtabe, Y. Kone, D. Narum, X. Liang, O. Doumbo, L. Miller, D. Doolan, P. Baldi, P. Felgner, S. Pierce. PNAS., ( 15 ), 6958-6963, 2010.

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values.   P. Baldi, R. Nasr. Journal of Chemical Information and Modeling., 2010.

Refereed Conference Proceedings
Autoencoders, Unsupervised Learning, and Deep Architectures.   P. Baldi. Workshop on Deep Learning and Unsupervised Feature Learning., 2010.

A Scalable Reference-Point Based Algorithm to Efficiently Search Large Chemical Databases.   F. Napolitano, R. Tagliaferri, P. Baldi. IEEE Proceedings of the 2010 International Joint Conference on Neural Networks (IJCNN 2010)., 2010.

Information-Theoretic Metrics for Project-Level Scattering and Tangling.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. International Conference on Software Engineering and Knowledge Engineering (SEKE)., 2010.

Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery.   P. Baldi, C. Azencott, S. J. Swamidass. WIRN 2010., 2010.

Book Chapters
Transmembrane β-Barrel Protein Structure Prediction.   A. Randall, P. Baldi. Structural Bioinformatics of Membrane Proteins., 2010.

Reaction Explorer: Towards a Knowledge Map of Organic Chemistry to Support Dynamic Assessment and Personalized Instruction   J. Chen, M. A. Kayala, P. Baldi. Enhancing Learning with Online Resources, Social Networking and Digital Libraries., 191-209, 2010.

2009
Refereed Journals
Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia.   A. B. Mochon1, J. Ye, M. A. Kayala, J. R. Wingard, C. J. Clancy, M. H. Nguyen, P. Felgner, P. Baldi, H. Liu. PLoS Pathogens., 2009.

MotifMap: a human genome-wide map of candidate regulatory motif sites.   X. Xie, P. Rigor, P. Baldi. Bioinformatics., 25, ( 2 ), 167-174, 2009.

A Burkholderia pseudomallei protein array reveals serodiagnostic and cross-reative antigens.   P.Felgner, M. Kayala, A. Vigil, C. Burk, R. Nakajima-Sasaki, J. Pablo, D. Molina, S. Hirst, J. Chew, D. Wang, G. Tan, M. Duffield, R. Yang, J. Neel, N. Chantratita, G. Bancroft, G. Lertmemongkolchai, D. Davies, P. Baldi, S. Peacock, R. Titball. PNAS., 106, ( 32 ), 13499-13504, 2009.

COBEpro: A Novel System for Predicting Continuous B-cell Epitopes.   M. J. Sweredoski, P. Baldi. Protein Engineering Design and Selection., 22, ( 3 ), 113-120, 2009.

Sourcerer: Mining and Searching Internet-Scale Software Repositories.   E. Linstead, S. Bajracharya, T. Ngo, P. Rigor, C. Lopes, P. Baldi. Journal of Datamining and Knowledge Discovery., 18, ( 2 ), 300-336, 2009.

MITOMASTER: A Bioinformatics Tool For the Analysis of Mitochondrial DNA Sequences.   M. Brandon, E. Ruiz-pesini, D. Mishmar, V. Procaccio, M.T. Lott, K. C. Nguyen, S. Spolim, U. Patil, P. Baldi, D. Wallace. Human Mutation (Database Issue)., 30, ( 1 ), 16, 2009.

Software-Driven Sensor Networks for Short-Range Shallow Water Applications.   R. Jurdak, P. Baldi, C. Lopes. Ad Hoc Networks Journal., 7, ( 5 ), 837-848, 2009.

The Influence Relevance Voter: An Accurate and Interpretable Virtual High Throughput Screening Method.   S. J. Swamidass, C. Azencott, H. Gramajo, S. Tsai, P. Baldi. Journal of Chemical Information and Modeling., 49, ( 4 ), 756-766, 2009.

Data Structures and Compression Algorithms for Genomic Sequence Data.   M. C. Brandon, D. C. Wallace, P. Baldi. Bioinformatics., 25, ( 14 ), 1731-1738, 2009.

SOLpro: Accurate Sequence-Based Prediction of Protein Solubility.   C. N. Magnan, A. Randall, P. Baldi. Bioinformatics., 25, ( 17 ), 2200-2207, 2009.

Large Scale Study of Multiple-Molecule Queries.   R. J. Nasr, S. J. Swamidass, P. Baldi. Journal of Chemoinformatics., 1, 7, 2009.

An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases.   P. Baldi, D. Hirschberg. Journal of Chemical Information and Modeling., 49, ( 8 ), 1866-1870, 2009.

No Electron Left-Behind: a Rule-Based Expert System to Predict Chemical Reactions and Reaction Mechanisms.   J. Chen, P. Baldi. Journal of Chemical Information and Modeling., 49, ( 9 ), 2034-2043, 2009.

Identification of Immunodominant Antigens of Chlamydia Trachomatis Using Proteome Microarrays.   D. M. Molina, S. Pal, A. Teng, M. Kayala, P. Baldi, P. Felgner, X. Liang, L. M. de la Maza. Vaccine., 2009.

Bayesian Surprise Attracts Human Attention.   L. Itti, P. Baldi. Vision Research., 49, ( 10 ), 1295-1306, 2009.

Refereed Conference Proceedings
Exploring Java Software Vocabulary: A Search and Mining Perspective.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. SUITE 2009: Proceedings of the First International Workshop on Search-Driven Development - Users, Tools, and Applications., 2009.

Software Analysis with Unsupervised Topic Models.   E. Linstead, L. Hughes, C. Lopes, P. Baldi. Neural Information Processing Systems (NIPS) Conference., 2009.

Information-Theoretic Metrics for Project-Level Scattering and Tangling.   E. Linstead, L. Hughes, P. Baldi. Third International Symposium on Empirical Software Engineering and Measurement (ESEM)., 2009.

The Evolution of Concerns, Scattering, and Tangling in Eclipse and ArgoUML.   E. Linstead, L. Hughes, P. Baldi. Third International Symposium on Empirical Software Engineering and Measurement (ESEM)., 2009.

Mining the Coherence of GNOME Bug Reports with Statistical Topic Models.   E. Linstead, P. Baldi. MSR '09: Proceedings of the Sixth International Working Conference on Mining Software Repositories., 2009.

User Contribution and Trust in Wikipedia.   S. Javanmardi, C. Loes, P. Baldi. Proceedings of the 5th International Conference on Collaborative Computing: Networking, Applications and Worksharing., 2009.

An Empirical Analysis of User Contributions in Wikipedia.   S. Javanmardi, Y. Ganjisaffar, C. Lopes, P. Baldi. WikiSym., 2009.

2008
Refereed Journals
Profiling Humoral Immune Responses to P. falciparum Infection with Protein Microarrays.   D. L. Doolan, Y. Mu, B. Unal, S. Sundaresh, S. Hirst, C. Valdez, A. Randall, D. Molina, X. Liang, J. A. Oloo, P. L. Blair, J. C. Aguiar, P. Baldi, D. Huw Davies, P. L. Felgner. Proteomics., 8, 4680-4694, 2008.

SELECTpro: Effective Protein Model Selection Using a Structure-Based Energy Function Resistant to Blunders.   A. Randall, P. Baldi. BMC Structural Biology., 8, 52, 2008.

Machine Learning Methods for Protein Structure Prediction.   J. Cheng, A. N. Tegge, P. Baldi. IEEE Reviews in Biomedical Engineering., 1, 41-49, 2008.

Synthesis Explorer: Organic Chemistry Tutorial System for Multi-Step Synthesis Design and Reaction Prediction.   J. Chen, P. Baldi. Journal of Chemical Education., 85, ( 12 ), 1699-1703, 2008.

BLASTing Small Molecules—Statistics and Extreme Statistics of Chemical Similarity Scores.   P. Baldi, R. W. Benz. Bioinformatics., 24, ( 13 ), i357-i365, 2008.

PEPITO: Improved Discontinuous B-Cell Epitope Prediction Using Multiple Distance Thresholds and Half-Sphere Exposure.   M. J. Sweredoski, P. Baldi. Bioinformatics., 24, ( 12 ), 1459-1460, 2008.

Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR.   P. Baldi, D. S. Hirschberg, R. J. Nasr. Journal of Chemical Information and Modeling., 48, ( 7 ), 1367-1378, 2008.

Discovery of Power-Laws in Chemical Space.   R. W. Benz, S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling., 48, ( 6 ), 1138-1151, 2008.

Learning to Play Go Using Recursive Neural Networks.   L. Wu, P. Baldi. Neural Networks., ( 21 ), 1392-1400, 2008.

TMBpro: Secondary Structure, β-Contact, and Tertiary Structure Prediction of Transmembrane β-Barrel Proteins.   A. Randall, J. Cheng, M. Sweredoski, P. Baldi. Bioinformatics., 24, ( 4 ), 513-520, 2008.

A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia bugdorferi.   A. G. Barbour, A. Jasinskas, M. Kayala, D. Huw Davies, A. C. Steere, P. Baldi, P. Felgner. Infection and Immunity., 76, 3374-3389, 2008.

Dysregulation of the Hypothalamic-Pituitary-Adrenal (HPA) Axis in Irritable Bowel Syndrome.   L. Chang, S. Sundaresh, J. Elliott, P. A. Anton, P. Baldi, A. Licudine, M. Mayer, T. Vuong, M. Hirano, B. D. Naliboff, V. Z. Ameen, E. A. Mayer. Neurogastroenterology and Motility., 21, ( 2 ), 149-159, 2008.

Refereed Conference Proceedings
Effective Compression of Monotone and Quasi-Monotone Sequences of Integers.   D. S. Hirschberg, P. Baldi. Proceedings of the 2008 Data Compression Conference (DCC 08)., 520, 2008.

A Theory of Aspects as Latent Topics.   P. Baldi, C. Lopes, E. Linstead, S. Bajracharya. 2008 ACM SIGPLAN Conference on Object-Oriented Programming Systems, Languages, and Applications., 2008.

An Application of Latent Dirichlet Allocation to Analyzing Software Evolution.   E. Linstead, C. Lopes, P. Baldi. International Conference on Machine Learning and Applications (ICMLA)., 2008.

2007
Refereed Journals
An Enhanced MITOMAP with a Global mtDNA Mutational Philogeny.   E. Ruiz-Pesini, M. T. Lott, V. Procaccio, J. Poole, M. C. Brandon, D. Mishmar, C. Yi, J. Kreuziger, P. Baldi, D. C. Wallace. Nucleic Acids Research., 35, D823-D828, 2007.

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.   C. Azencott, A. Ksikes, S. Joshua Swamidass, J. Chen, L. Ralaivola, P. Baldi. Journal of Chemical Information and Modeling., 47, ( 3 ), 965-974, 2007.

Phylogenetic Analysis, Genome Evolution and the Rate of Gene Gain in the Herpesviridae.   N. Wang, P. Baldi, B. Gaut. Molecular Phylogenetics and Evolution., 43, ( 3 ), 1066-1075, 2007.

Ty3 Capsid Mutations Reveal Early and Late Functions of the Amino-Terminal Domain.   L. Zicker-Larsen, M. Zhang, N. Beliakova-Bethell, V. Bilanchone, A. Lamsa, K. Nagashima, R. Najdi, K. Kosaka, V. Kovacevic, J. Cheng, P. Baldi, G. Wesley Hatfield, S. Sandmeyer. The Journal of Virology., 81, ( 13 ), 6957-6972, 2007.

Adaptive Low Power Listening for Wireless Sensor Network.   R. Jurdak, P. Baldi, C. Lopes. IEEE Transactions on Mobile Computing., 6, ( 8 ), 988-1004, 2007.

A Theoretical Study of the In Vivo Mechanical Properties of Angiosperm Roots: Constitutive Theories and Methods of Parameter Estimation.   A. Sadovsky, P. Baldi, F. Wan. Journal of Engineering Materials and Technology., 129, ( 3 ), 483-487, 2007.

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time.   S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling., 47, ( 2 ), 302-317, 2007.

A Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval.   S. J. Swamidass, P. Baldi. Journal of Chemical Information and Modeling., 47, ( 3 ), 952-964, 2007.

A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition.   W. Einhäuser, T. N. Mundhenk, P. Baldi, C. Koch, L. Itti. Journal of Vision., 7, ( 10 ), 1-13, 2007.

Immunodominant Francisella tularensis antigens identified using proteome microarray.   J. E. Eyles, B. Unal, M. Gill Hartley, S. L. Newstead, H. Flick-Smith, J. L. Prior, P. C. F. Oyston, A. Randal, Y. Mu, S. Hirst, D. M. Molina, D. Huw Davies, T. Milne, K. F. Griffin, P. Baldi, R. W. Titball, P. L. Felgner. Proteomics., 7, ( 13 ), 2172-2183, 2007.

Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set.   J. Cheng, P. Baldi. BMC Bioinformatics., 8, 113-121, 2007.

The fixed-size Luria–Delbruck model with a nonzero death rate.   N. Komarova, L. Wu, P. Baldi. Mathematical Biosciences., 210, ( 1 ), 253-290, 2007.

Minimizing the Overlap Problem in Protein NMR: A Computational Framework for Precision Amino Acid Labeling.   M. Sweredoski, K. Donovan, B. Nguyen, A. J. Shaka, P. Baldi. Bioinformatics., 23, ( 21 ), 2829-2835, 2007.

Assessment of Predictions Submitted for the CASP7 Domain Prediction Category.   M. Tress, J. Cheng, P. Baldi, K. Joo, J. Lee, J. Seo, J. Lee, D. Baker, D. Chivian, D. Kim, I. Ezkurdia. Proteins., 69, 137-151, 2007.

ChemDB Update—Full-Text Search and Virtual Chemical Space.   J. Chen, E. Linstead, S. J. Swamidass, D. Wang, P. Baldi. Bioinformatics., 23, 2348-2351, 2007.

From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis.   S. Sundaresh, A. Randall, B. Unal, J. M. Petersen, J. T. Belisle, M. Gill Hartley, M. Duffield, R. W. Titball, D. Huw Davies, P. L. Felgner, P. Baldi. Bioinformatics., 23, i508-i518, 2007.

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval.   P. Baldi, R. W. Benz, D. S. Hirschberg, S. Joshua Swamidass. Journal of Chemical Information and Modeling., 47, ( 6 ), 2098-2109, 2007.

Refereed Conference Proceedings
CodeGenie: Using Test-Cases to Search and Reuse Source Code.   O. Lemos, S. Bajracharya, J. Ossher, R. Morla, P. Masiero, P. Baldi, C. Lopes. Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering (ASE’07)., 525-526, 2007.

Software Modems for Underwater Sensor Networks.   R. Jurdak, P. Aguiar, P. Baldi, C. Lopes. Proceedings of IEEE/OES Oceans'07., 2007.

Mining Eclipse Developer Contributions via Author-Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Proceedings of the MSR 2007: International Workshop on Mining Software Repositories., 30-33, 2007.

Mining Concepts from Code with Probabilistic Topic Models.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering., 461-464, 2007.

Mining Internet-Scale Software Repositories.   E. Linstead, P. Rigor, S. Bajracharya, C. Lopes, P. Baldi. Advances in Neural Information Processing Systems 20., 929-936, 2007.

Book Chapters
Virtual High-Throughput Screening with Two-Dimensional Kernels.   A. Azencott, P. Baldi. Hands-On Pattern Recognition. Challenges in Data Representation, Model Selection, and Performance Prediction., 2007.

2006
Refereed Journals
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.   S. A. Danziger, S. J. Swamidass, J. Zeng, L. R. Dearth, Q. Lu, J. H. Chen, J. Cheng, V. P. Hoang, H. Saigo, R. Luo, P. Baldi, Rainer K. Brachmann, Richard H. Lathrop. IEEE Transactions on Computational Biology and Bioinformatics., 3, ( 2 ), 114-125, 2006.

Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.   J. Cheng, H. Saigo, P. Baldi. Proteins., 62, ( 3 ), 617-629, 2006.

Global Landscape of Recent Inferred Darwinian Selection for Homo Sapiens.   E. T. Wang, G. Kodama, P. Baldi, R. K. Moyzis. Proceedings of the National Academy of Sciences USA., 103, 135-140, 2006.

Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines.   J. Cheng, A. Randall, P. Baldi. Proteins., 62, ( 4 ), 1125-1132, 2006.

DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.   J. Cheng, M. J. Sweredoski, P. Baldi. Data Mining and Knowledge Discovery., 13, ( 1 ), 1-10, 2006.

Modular DAG-RNN Architectures for Assembling Coarse Protein Structures.   G. Pollastri, A. Vullo, P. Frasconi, P. Baldi. Journal of Computational Biology., 3, 631-650, 2006.

Structure-Based Inhibitor Design of AccD5, an Essential acyl-CoA Carboxylase Carboxyltransferase Domain of Mycobacterium tuberculosis.   T. Lin, M. Melgar, S. J. Swamidass, J. Purdon, T. Tseng, G. Gago, D. Kurth, P. Baldi, H. Gramajo, S. Tsai. Proceedings of the National Academy of Sciences USA., 103, ( 9 ), 3072-3077, 2006.

A tandem-affinity tag for two-step purification under fully denaturing conditions: Application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking.   C. Tagwerker, K. Flick1, M. Cui, C. Guerrero, Y. Dou, B. Auer, P. Baldi, L. Huang, Peter Kaiser. Molecular and Cellular Proteomics., 4, 737-748, 2006.

Localization of Off-the-Shelf Mobile Devices Using Audible Sound: Architectures, Protocols and Performance Assessment.   C. V. Lopes, A. Haghighat, A. Mandal, P. Baldi, T. Givargis. ACM SIGMOBILE Mobile Computing and Communications Review., 10, ( 2 ), 38-50, 2006.

A Machine Learning Information Retrieval Approach to Protein Fold Recognition.   J. Cheng, P. Baldi. Bioinformatics., 22, ( 12 ), 1456-1463, 2006.

Mitochondrial Mutations in Cancer.   M. Brandon, P. Baldi, D. C. Wallace. Oncogene., 25, 4647-4662, 2006.

Identification of Humoral Immune Responses in Protein Microarrays using DNA Microarray Data Analysis Techniques.   Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Phil Felgner, Pierre Baldi. Bioinformatics., 22, ( 14 ), 1760-1766, 2006.

Genomic Splice-Site Analysis Reveals Frequent Alternative Splicing Close to the Dominant Splice Site.   Y. Dou, K. Fox-Walsh, P. Baldi, K. Hertel. RNA., 12, ( 12 ), 2047-2056, 2006.

Refereed Conference Proceedings
Software Acoustic Modems for Short Range Mote-Based Underwater Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. In Proceedings of IEEE Oceans – Asia Pacific., 1-7, 2006.

A Comparative Analysis and Experimental Study on Wireless Aerial and Underwater Acoustic Communications.   R. Jurdak, C. Lopes, P. Aguiar, P. Baldi. Proceeding of the 2006 International Conference on Digital Telecommunications., 2006.

A Scalable Machine Learning Approach to Go.   L. Wu, P. Baldi. Advances in Neural Information Processing Systems 19., 1521-1528, 2006.

2005
Refereed Journals
Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   S. J. Swamidass, J. Chen, P. Phung, J. Bruand, L. Ralaivola, P. Baldi. Bioinformatics., 21, i359-368, 2005.

Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng, P. Baldi. Bioinformatics., 21, i75-84, 2005.

Statistical Detection of Chromosomal Homology Using Shared-Gene Density Alone.   S. Hampson, B. S. Gaut, P. Baldi. Bioinformatics., 21, ( 8 ), 1339-1348, 2005.

Polymodal sensory function of the C. elegans OCR-2 channel arises from distinct intrinsic determinants within the protein and is selectively conserved in human TRPV2.   I. Sokolchik, T. Tanabe, P. Baldi, J. Y. Sze. Journal of Neuroscience., 25, ( 4 ), 1015-1023, 2005.

MITOMAP: a human mitochondrial genome database - 2004 update.   M. Brandon, M. Lott, K. Nguyen, S. Spolim, S. Navathe, P. Baldi, D. Wallace. Nucleic Acids Research., 33, D611-613, 2005.

Sigmoid: Towards a Generative, Scalable Software Infrastructure for Pathway Bioinformatics and Systems Biology.   J. Cheng, L. Scharenbroich, P. Baldi, E. Mjolsness. IEEE Intelligent Systems., 20, ( 3 ), 68-75, 2005.

Profiling the Humoral Response to Infection by Using Proteome Microarrays: High-Throughput Vaccine and Diagnostic Antigen Discovery.   H. Davies, X. Liang, J. E. Hernandez, K. M. Romero, T. T. Nguyen, M. Kalantari-Dehaghi, S. Hirst, Y. Mu, A. Randall, P. Baldi, L. Villarreal, P. L. Felgner. Proceedings of the National Academy of Sciences USA., 102, ( 3 ), 547-552, 2005.

How Noisy and Replicable are DNA Microarray Data?   S. Sundaresh, S. Hung, G. W. Hatfield, P. Baldi. International Journal of Bioinformatics Research and Applications., 1, ( 1 ), 31-50, 2005.

U-MAC: A Proactive and Adaptive UWB Medium Access Control Protocol.   R. Jurdak, P. Baldi, C. Videira Lopes. Wireless Communications and Mobile Computing Journal (special Issue on "UWB Communications")., 5, ( 5 ), 551-566, 2005.

Global Gene Expression Profiling in Escherichia coli K12: The Effects of Oxygen Availability and ArcA.   K. A. Salmon, S. Hung, N. R. Steffen, R. Krupp, P. Baldi, G. Wesley Hatfield, R. P. Gunsalus. Journal of Biological Chemistry., 280, ( 15 ), 15084-15096, 2005.

Retroviruses and Yeast Retrotransposons Use Overlapping Sets of Host Genes.   B. Irwin, M. Aye, P. Baldi, N. Beliakova-Bethell, H. Cheng, Y. Dou, W. Liou, S. Sandmeyer. Genome Research., 15, 641-654, 2005.

Graph Kernels for Chemical Informatics.   L. Ralaivola, J. S. Swamidass, H. Saigo, P. Baldi. Neural Networks., 18, ( 8 ), 1093-1110, 2005.

On the Relationship Between Deterministic and Probabilistic Directed Graphical Models: from Bayesian Networks to Recursive Neural Networks.   P. Baldi, M. Rosen-Zvi. Neural Networks., 18, ( 8 ), 1080-1086, 2005.

SCRATCH: a Protein Structure and Structural Feature Prediction Server.   J. Cheng, A. Z. Randall, M. Sweredoski, P. Baldi. Nucleic Acids Research., 33, ( 9 ), W72-76, 2005.

Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data.   J. Cheng, M. J. Sweredoski, P. Baldi. Data Mining and Knowledge Discovery., 11, ( 3 ), 213-222, 2005.

The Absence of Favorable Aromatic Interactions between β-Sheet Peptides.   D. M. Chung, Y. Dou, P. Baldi, J. S. Nowick. Journal of the American Chemical Society., 127, ( 28 ), 9998-9999, 2005.

ChemDB: A Public Database of Small Molecules and Related Chemoinformatics Resources.   J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, P. Baldi. Bioinformatics., 21, 4133-4139, 2005.

The Architecture of pre-mRNAs Affects Mechanisms of Splice-Site Pairing.   Kristi L. Fox-Walsh1, Yimeng Dou, Bianca J. Lam1, She-pin Hung, Pierre F. Baldi, Klemens J. Hertel. Proceedings of the National Academy of Sciences USA., 102, 16176-16181, 2005.

Refereed Conference Proceedings
Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking., 2005.

State-Driven Energy Optimization in Wireless Sensor Networks.   R. Jurdak, P. Baldi, C. Lopes. Proceedings of the IEEE/IEE International Conference on Sensor Networks (SENET)., 356-363, 2005.

SVM and Pattern-Enriched Common Fate Graphs for the Game of GO.   L. Ralaivola, L. Wu, P. Baldi. European Symposium on Artificial Neural Networks (ESANN)., 2005.

A Principled Approach to Detecting Surprising Events in Video.   L. Itti, P. Baldi. Proc. IEEE Conference on Computer Vision and Pattern Recognition (CVPR)., 2005.

Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking., 2005.

Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity.   S. Swamidass, J. Chen, P. Phung, J. Bruand, L. Ralaivola, P. Baldi. 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 05)., 21, i359-368, 2005.

Three-Stage Prediction of Protein β-Sheets by Neural Networks, Alignments, and Graph Algorithms.   J. Cheng, P. Baldi. 2005 Conference on Intelligent Systems for Molecular Biology (ISMB 05)., i75-84, 2005.

Programming Model for Supporting Complex Optimizations in Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. Fourth International IEEE/ACM Conference on Information Processing in Sensor Networks (IPSN’05)., 2005.

Bayesian Surprise Attracts Human Attention.   L. Itti, P. Baldi. Advances in Neural Information Processing Systems 18, NIPS 2005., 547-554, 2005.

Attention: Bits versus Wows.   P. Baldi, L. Itti. Proceedings of the International Conference on Neural Networks and Brain., 1, PL56-PL61, 2005.

Exploring Chemical Space with Computers: Informatics Challenges for AI and Machine Learning.   P. Baldi. BIOMAT V Symposium., 2005.

Chemoinformatics, Drug Design, and Systems Biology.   P. Baldi. Proceedings of the 16th International Conference on Genome Informatics, (GIW 2005)., 2005.

Adaptive Low Power Listening for Sensor Networks.   R. Jurdak, C. Lopes, P. Baldi. 11th Annual International Conference on Mobile Computing and Networking., 2005.

Book Chapters
Surprise: A Shortcut for Attention?   P. Baldi. Neurobiology of Attention., 24-28, 2005.

Clustering Algorithms for Gene Expression Analysis.   P. Baldi, G. Wesley Hatfield, Li M. Fu. Handbook of Computational Molecular Biology., 2005.

Battery Lifetime Estimation and Optimization for Underwater Sensor Networks.   R. Jurdak, C. V. Lopes, P. Baldi. Sensor Network Operations., 2005.

Statistical Distribution of Chemical Fingerprints.   S. J. Swamidass, P. Baldi. Proceedings of WILF2005., 2005.

2004
Refereed Journals
ICBS: A Database of Interactions Between Protein Chains Mediated by β-Sheet Formation.   Y. Dou, P. Baisnee, G. Pollastri, Y. Pecout, J. Nowick, P. Baldi. Bioinformatics., 20, ( 16 ), 2767-2777, 2004.

Structural Proteomics of the Poxvirus Family.   A. Z. Randall, P. Baldi, L. P. Villareal. Artificial Intelligence in Medicine (special issue on “Data mining in Genomics and Proteomics”)., 31, ( 2 ), 105-115, 2004.

A Survey, Classification, and Comparative Analysis of Medium Access Control Protocols for Ad Hoc Networks.   R. Jurdak, C. Videira Lopes, P. Baldi. IEEE Communications Surveys and Tutorials., 6, ( 1 ), 2-16, 2004.

Refereed Conference Proceedings
An Identfication Scheme for Location Systems Using Robust Acoustic Signals.   R. Jurdak, C. Lopes, P. Baldi. Proceeding of the ACS/IEEE International Conference on Pervasive Services., 2004.

Large-Scale Prediction of Disulphide Bond Connectivity.   P. Baldi, J. Cheng, A. Vullo. Advances in Neural Information Processing Systems 17 (NIPS 2004)., 2004.

Beep: 3D Indoor Positioning Using Audible Sound.   A. Mandal, C. Lopes, T. Givargis, A. Haghighat, R. Jurdak, P. Baldi. Proceedings of the 2004 IEEE Consumer Communications and Networking Conference., 348-353, 2004.

Book Chapters
Hidden Markov Models and Neural Networks.   S. Kremer, P. Baldi. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics., 2004.

2003
Refereed Journals
What Genes are Made Of.   P. Baldi. Pathways., 2003.

Differential Analysis of DNA Microarray Gene Expression Data.   G. Wesley Hatfield, S. Hung, P. Baldi. Molecular Microbiology., 47, ( 4 ), 871-877, 2003.

Bounds on Variances of Estimators for Multinomial Processing Tree Models.   P. Baldi, W. H. Batchelder. Journal of Mathematical Psychology., 47, 467-470, 2003.

Combining Protein Secondary Structure Prediction Models With Ensemble Methods of Optimal Complexity.   Y. Guermeur, G. Pollastri, A. Elisseeff, D. Zelus, H. Paugam-Moisy, P. Baldi. Neurocomputing., 56, 305-327, 2003.

The Principled Design of Large-Scale Recursive Neural Network Architectures—DAG-RNNs and the Protein Structure Prediction Problem.   P. Baldi, G. Pollastri. Journal of Machine Learning Research., 4, 575-602, 2003.

Comprehensive Mutagenesis of the C-terminal Domain of the M13 Gene-3 Minor Coat Protein: The Requirements for Assembly into the Bacteriophage Particle.   G. A. Weiss, T. A. Roth, P. Baldi, S. S. Sidhu. Journal of Molecular Biology., 332, ( 4 ), 777-782, 2003.

LineUp : Statistical Detection of Chromosomal Homology with Applications to Plant Comparative Genomics.   S. Hampson, A. McLysaght, B. Gaut, P. Baldi. Genome Research., 13, ( 5 ), 1999-1010, 2003.

Global Gene Expression Profiling in Escherichia coli K12: The Effects of Oxygen Availability and FNR.   K. Salmon, K. Mekjian, R. P. Gunsalus, S. Hung, P. Baldi, G. Wesley Hatfield. Journal of Biological Chemistry., 278, ( 32 ), 29837-29855, 2003.

Extensive Gene Gain Associated With Adaptive Evolution of Poxviruses.   A. McLysaght, P. Baldi, B. S. Gaut. Proceedings of the National Academy of Sciences USA., 100, ( 26 ), 15655-15660, 2003.

Refereed Conference Proceedings
Prediction of Protein Topologies Using Generalized IOHMMs and RNNs.   G. Pollastri, P. Baldi, A. Vullo, P. Frasconi. Advances in Neural Information Processing Systems 15., 15, 2003.

Other
What Genes are Made Of.   P. Baldi. Review of edited book entitled: The Genomic Revolution: Unveiling the Unity of Life., 2003.

Books
Modeling the Internet and the Web: Probabilistic Methods and Algorithms.   P. Baldi, P. Frasconi, P. Smyth. , Wiley , 2003.

Book Chapters
New Machine Learning Methods for the Prediction of Protein Topologies.   P. Baldi, G. Pollastri, P. Frasconi, A. Vullo. Artificial Intelligence and Heuristic Methods in Bioinformatics., 51-73, 2003.

Understanding DNA Microarrays: Sources and Magnitudes of Variances in DNA Microarray Data Sets.   S. P. Hung, G. Wesley Hatfield, S. Sundaresh, P. Baldi. Genomics, Proteomics, and Vaccines., 2003.

2002
Refereed Journals
Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri, P. Baldi. Bioinformatics., 18, S62-S70, 2002.

Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles.   G. Pollastri, D. Przybylski, B. Rost, P. Baldi. Proteins., 47, 228-235, 2002.

Prediction of Coordination Number and Relative Solvent Accessibility in Proteins.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proteins., 47, 142-153, 2002.

Distribution Patterns of Over-Represented k-mers in Non-Coding Yeast DNA.   S. Hampson, D. Kibler, P. Baldi. Bioinformatics., 18, ( 4 ), 611-626, 2002.

A Machine Learning Strategy for Protein Analysis.   P. Baldi, G. Pollastri. IEEE Intelligent Systems (special Issue on "Intelligent Systems in Biology")., 17, ( 2 ), 28-35, 2002.

Why Are Complementary DNA Strands Symmetric?   P. Baisnee, S. Hampson, P. Baldi. Bioinformatics., 18, 1021-1033, 2002.

Global Gene Expression Profiling in Excherichia coli K12: The Effects of Leucine-responsive Regulatory Protein.   S. Hung, P. Baldi, G. Wesley Hatfield. Journal of Biological Chemistry., 277, ( 43 ), 40309-40323, 2002.

Modeling and Optimization of UWB Communication Networks Through a Flexible Cost Function.   P. Baldi, L. De Nardis, M. G. Di Benedetto. IEEE Journal on Selected Areas in Communications., 20, ( 9 ), 1733-1744, 2002.

Refereed Conference Proceedings
UWB Ad-Hoc Networks.   L. De Nardis, P. Baldi, M. Di Benedetto. Proceedings of the 2002 IEEE Conference on Ultra Wide Band Systems and Technologies (UWBST 2002)., 219-224, 2002.

Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation From All Four Cardinal Corners.   G. Pollastri, P. Baldi. Proceedings of the 2002 Conference on Intelligent Systems for Molecular Biology (ISMB 02)., 18, S62-S70, 2002.

Books
DNA Microarrays and Gene Expression: From Experiments to Data Analysis and Modeling.   P. Baldi, G. Wesley Hatfield. , Cambridge University Press , 2002.

Book Chapters
A Computational Theory of Surprise.   P. Baldi. Information, Coding, and Mathematics., 1-25, 2002.

2001
Refereed Journals
Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Bioinformatics., 17, S234-S242, 2001.

Flexibility of the Genetic Code with Respect to DNA Structure.   P. Baisnée, P. Baldi, S. Brunak, A. Gorm Pedersen. Bioinformatics., 17, 237-248, 2001.

A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Inference of Gene Changes.   P. Baldi, A. D. Long. Bioinformatics., 17, ( 6 ), 509-519, 2001.

Improved Statistical Inference from DNA Microarray Data Using Analysis of Variance and a Bayesian Statistical Framework.   A. D. Long, H. J. Mangalam, B. Y. P. Chan, L. Tolleri, G. W. Hatfield, P. Baldi. Journal of Biological Chemistry., 276, ( 23 ), 19937-19944, 2001.

Refereed Conference Proceedings
A Model for Self-Organizing Large Scale Wireless Networks.   M. Di Benedetto, P. Baldi. International Symposium on 3G Infrastructure and Services., 2001.

Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks.   G. Pollastri, P. Baldi, P. Fariselli, R. Casadio. Proceedings of the 2001 Conference on Intelligent Systems for Molecular Biology, (ISMB01)., 2001.

Books
The Shattered Self: The End of Natural Evolution.   P. Baldi. , MIT Press , 2001.

2000
Refereed Journals
Probabilistic Graphical Models in Computational Molecular Biology.   P. Baldi. Journal of the Italian Association for Artificial Intelligence., 1, 8-12, 2000.

On the Convergence of a Clustering Algorithm for Protein-Coding Regions in Microbial Genomes.   P. Baldi. Bioinformatics., 16, ( 4 ), 367-371, 2000.

Assessing the Accuracy of Prediction Algorithms for Classification: An Overview.   P. Baldi, S. Brunak, Y. Chauvin, H. Nielsen. Bioinformatics., 16, ( 5 ), 412-424, 2000.

Sequence Analysis by Additive Scales: DNA Structure for Sequences and Repeats of All Lenghts.   P. Baldi, P. Baisnée. Bioinformatics., 16, ( 10 ), 865-889, 2000.

Refereed Conference Proceedings
Protein β-Sheet Partner Prediction by Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, S. Brunak. Artifical Neural Networks in Medicine and Biology. Proceedings of the ANNIMAB-1 Conference., 2000.

Analysis of Yeast’s ORFs Upstream Regions by Parallel Processing, Microarrays, and Computational Methods.   S. Hampson, P. Baldi, D. Kibler, S. Sandmeyer. Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology (ISMB00)., 190-201, 2000.

Matching Protein β-Sheet Partners by Feedforward and Recurrent Neural Networks.   P. Baldi, G. Pollastri, C. A. F. Andersen, S. Brunak. Proceedings of the 2000 Conference on Intelligent Systems for Molecular Biology (ISMB00)., 25-36, 2000.

Book Chapters
Bidirectional IOHMMs and recurrent neural networks for protein secondary structure prediction.   P. Baldi, S. Brunak, G. Pollastri, P. Frasconi. Protein Sequence Analysis in the Genomic Era., 2000.

Bidirectional Dynamics for Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Pollastri, G. Soda. Sequence Learning: Paradigms, Algorithms, and Applications., 99-120, 2000.

1999
Refereed Journals
The Biology of Eukaryotic Promoter Prediction-a Review.   A. Gorm Pedersen, P. Baldi, S. Brunak, Y. Chauvin. Computers and Chemistry, Special Issue on Genome and Informatics., 23, 191-207, 1999.

Exploiting the Past and the Future in Protein Secondary Structure Prediction.   P. Baldi, S. Brunak, P. Frasconi, G. Soda, G. Pollastri. Bioinformatics., 15, ( 11 ), 937-946, 1999.

Structural Basis for Triplet Repeat Disorders: A Computational Analysis.   P. Baldi, S. Brunak, Y.Chauvin, A. Gorm Pedersen. Bioinformatics., 15, ( 11 ), 918-929, 1999.

1998
On the Use of Bayesian Methods for Evaluating Compartmental Neural Models.   P. Baldi, M. C. Vanier, J. M. Bower. Journal of Computational Neuroscience., 5, 285-314, 1998.

DNA Structure in Human RNA Polymerase II Promoters.   A. Gorm Pedersen, P. Baldi, Y. Chauvin, S. Brunak. Journal of Molecular Biology., 281, 663-673, 1998.

Refereed Conference Proceedings
Computational Applications of DNA Structural Scales.   P. Baldi, S. Brunak, Y. Chauvin, A. Gorm Pedersen. Proceedings of the 1998 Conference on Intelligent Systems for Molecular Biology (ISMB98)., 35-42, 1998.

Books
Bioinformatics: the Machine Learning Approach.   P. Baldi, S. Brunak. , MIT Press , 1998.

Book Chapters
Probabilistic Models of Neuronal Spike Trains.   P. Baldi. Adaptive Processing of Temporal Information., 198-228, 1998.

Software Foundation Libraries for the Design of Intelligent Systems.   P. Baldi, Y. Chauvin, V. Mittal Henkle. Neural Nets WIRN Vietri 98. Proceedings of the 10-th Italian Workshop on Neural Nets., 17-39, 1998.

1996
Refereed Journals
Hybrid Modeling, HMM/NN Architectures, and Protein Applications.   P. Baldi, Y. Chauvin. Neural Computation., 2, ( 3 ), 497-501, 1996.

Naturally Occurring Nucleosome Positioning Signals in Human Exons and Introns.   P. Baldi, S. Brunak, Y. Chauvin, A. Krogh. Journal of Molecular Biology., 263, ( 5 ), 503-510, 1996.

Refereed Conference Proceedings
Universal Approximation and Learning of Trajectories Using Oscillators.   P. Baldi, K. Hornik. Advances in Neural Information Processing Systems 8., 451-457, 1996.

Hidden Markov Models for Human Genes: Periodic Patterns in Exon Sequences.   P. Baldi, S. Brunak, Y. Chauvin, A. Krogh. Theoretical and Computational Methods in Genome Research., 1996.

Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models.   P. Baldi, A. Gorm Pedersen, S. Brunak, Y. Chauvin. Proceedings of the 1996 Conference on Intelligent Systems for Molecular Biology (ISMB96)., 182-191, 1996.

1995
Refereed Journals
Gradient Descent Learning Algorithms Overview: A General Dynamical Systems Perspective.   P. Baldi. IEEE Transactions on Neural Networks., 6, ( 1 ), 182-195, 1995.

Learning in Linear Networks: a Survey.   P. Baldi, K. Hornik. IEEE Transactions on Neural Networks., 6, ( 4 ), 837-858, 1995.

Substitution Matrices and Hidden Markov Models.   P. Baldi. Journal of Computational Biology., 2, ( 3 ), 497-501, 1995.

Refereed Conference Proceedings
Inferring Ground Truth from Subjective Labelling of Venus Images.   P. Smyth, U. Fayadd, P. Perona, M. Burl, P. Baldi. Advances in Neural Information Processing Systems., 1085-1092, 1995.

Periodic Sequence Patterns in Human Exons.   P. Baldi, Y. Chauvin, S. Brunak, J. Engelbrecht, A. Krogh. Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95)., 30-38, 1995.

Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures.   P. Baldi, Y. Chauvin. Proceedings of the 1995 Conference on Intelligent Systems for Molecular Biology (ISMB95)., 39-47, 1995.

Book Chapters
When Neural Networks Play Sherlock Holmes.   P. Baldi, Y. Chauvin. Back-Propagation: Theory, Architectures and Applications., ( 487 ), 1995.

Gradient Descent Learning Algorithms: A Unified Perspective.   P. Baldi. Back-Propagation: Theory, Architectures and Applications., 509-541, 1995.

Back-propagation and unsupervised learning in linear networks.   P. Baldi, Y. Chauvin, K. Hornik. Back-Propagation: Theory, Architectures and Applications., 389-432, 1995.

1994
Refereed Journals
How Delays Affect Neural Dynamics and Learning.   P. Baldi, A. Atiya. IEEE Transactions on Neural Networks., 5, ( 4 ), 626-635, 1994.

Smooth On-Line Learning Algorithms for Hidden Markov Models.   P. Baldi, Y. Chauvin. Neural Computation., 6, ( 2 ), 305-316, 1994.

Hidden Markov Models of Biological Primary Sequence Information.   P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. PNAS USA., 91, ( 3 ), 1059-1063, 1994.

Hidden Markov Models of the G-Protein Coupled Receptor Family.   P. Baldi, Y. Chauvin. Journal of Computational Biology., 1, ( 4 ), 311-335, 1994.

Refereed Conference Proceedings
Trading Decision Learning: from Theory to Personal Traders.   P. Baldi, Y. Chauvin. Proceedings of the Second International Conference on Neural Networks in the Capital Markets., 1994.

Modeling Protein Families and Human Genes: Hidden Markov Models and a Little Beyond.   P. Baldi, Y. Chauvin. Proceedings of the 1994 Fifth Generation Computing Symposium, Workshop on Fusion of Molecular Biology and Knowledge Processing., 1994.

Discrimination of Tyrosine and Serine/Threonine Kinase Sub-Families by Hidden Markov Models.   P. Baldi, Y. Chauvin. Proceedings of The Third International Conference on Bioinformatics and Genome Research., 1994.

Hidden Markov Models of Human Genes.   P. Baldi, S. Brunak, Y. Chauvin, J. Engelbrecht, A. Krogh. Advances in Neural Information Processing Systems., 761-768, 1994.

Book Chapters
Statistical Models of Proteins: an Application to the G-Protein-Coupled Receptor Family.   P. Baldi, Y. Chauvin. Modern Approaches in Molecular Bioinformatics., 53-102, 1994.

1993
Refereed Journals
Random Interactions in Higher-Orders Neural Networks.   P. Baldi, S.S. Venkatesh. IEEE Transactions on Information Theory., 39, ( 1 ), 274-283, 1993.

Neural Networks for Fingerprint Recognition.   P. Baldi, Y. Chauvin. Neural Computation., 5, ( 3 ), 402-418, 1993.

Refereed Conference Proceedings
Learning Trajectories with a Hierarchy of Oscillatory Modules.   P. Baldi, Nikzad Toomarian. Proceedings of the 1993 IEEE International Conference on Neural Networks., 1172-1176, 1993.

Hidden Markov Models in Molecular Biology: New Algorithms and Applications.   P. Baldi, Y. Chauvin, T. Hunkapiller, M. A. McClure. Advances in Neural Information Processing Systems., 747-754, 1993.

1992
A Modular Hierarchical Approach to Learning.   P. Baldi. Proceedings of the 2nd International Conference on Fuzzy Logic and Neural Networks., 2, 985-988, 1992.

Trading Decision Learning.   P. Baldi, Y. Chauvin. Neural Networks for Computing Conference (abstract)., 1992.

1991
Refereed Journals
Programmed Interactions in Higher-Orders Neural Networks: I. Maximal Capacity.   S.S. Venkatesh, P. Baldi. Journal of Complexity., 7, 316-337, 1991.

Programmed Interactions in Higher-Orders Neural Networks: II. The Outer-Product Algorithm.   S. S. Venkatesh, P. Baldi. Journal of Complexity., 7, 443-479, 1991.

Can Regulatory Peptides Be Regarded as Words of a Biological Language?   E. A. Mayer, J. Furness, P. Baldi. American Journal of Physiology., 261, G171-G184, 1991.

Temporal Evolution of Generalization during Learning in Linear Networks.   P. Baldi, Y. Chauvin. Neural Computation., 3, ( 4 ), 589-603, 1991.

Contrastive Learning and Neural Oscillations.   P. Baldi, F. Pineda. Neural Computation., 3, ( 4 ), 526-545, 1991.

1990
Graph Coloring Bounds for Cellular Radio.   P. Baldi, E.C. Posner. Computers and Mathematics with Applications., 19, ( 10 ), 91-97, 1990.

On a Generalized Family of Colorings.   P. Baldi. Graphs and Combinatorics., 6, 95-110, 1990.

Computing with Arrays of Coupled Oscillators: an Application to Preattentive Texture Discrimination.   P. Baldi, R. Meir. Neural Computation., 2, ( 4 ), 458-471, 1990.

Refereed Conference Proceedings
Computing with Arrays of Bell-Shaped and Sigmoid Functions.   P. Baldi. Proceedings of the 1990 conference on Advances in neural information processing systems 3., 735-742, 1990.

1989
Refereed Journals
Asymptotic Normality of Some Graph Related Statistics.   P. Baldi, Y. Rinott. Journal of Applied Probability., 26, 171-175, 1989.

On Normal Approximations of Distributions in Terms of Dependency Graphs.   P. Baldi, Y. Rinott. Annals of Probability., 17, ( 4 ), 1646-1650, 1989.

Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis.   P. Baldi, A. Atiya. International Journal of Neural Systems., 1, ( 2 ), 103-124, 1989.

Refereed Conference Proceedings
On the Distribution of the Number of Local Minima of a Random Function on a Graph.   P. Baldi, Y. Rinott, C. Stein. Proceedings of the 1989 Conference on Neural Information Processing Systems., 727-732, 1989.

Book Chapters
A Normal Approximation for the Number of Local Maxima of a Random Function on a Graph.   P. Baldi, Y. Rinott, C. Stein. Probability, Statistics and Mathematics: Papers in Honor of Samuel Karlin., 1989.

1988
Refereed Journals
Neural Networks and Principal Component Analysis: Learning from Examples without Local Minima.   P. Baldi, K. Hornik. Neural Networks., 2, ( 1 ), 53-58, 1988.

Neural Networks, Orientations of the Hypercube and Algebraic Threshold Functions.   P. Baldi. IEEE Transactions on Information Theory., 34, ( 3 ), 523-530, 1988.

Group Actions and Learning for a Family of Automata.   P. Baldi. Journal of Computer and System Sciences., 36, ( 2 ), 1-15, 1988.

Neural Networks, Acyclic Orientations of the Hypercube and Sets of Orthogonal Vectors.   P. Baldi. SIAM Journal of Discrete Mathematics., 1, ( 1 ), 1-13, 1988.

How Sensory Maps Could Enhance Resolution Through Ordered Arrangements of Broadly Tuned Receivers.   P. Baldi, W. Heiligenberg. Biological Cybernetics., 59, ( 4 ), 313-318, 1988.

Refereed Conference Proceedings
Neural Networks and Principal Component Analysis.   P. Baldi. Proceedings of the 1988 Conference on Neural Information Processing., 65-72, 1988.

1987
Refereed Journals
Number of Stable Points for Spin Glasses and Neural Networks of Higher Orders.   P. Baldi, S.S. Venkatesh. Physical Review Letters., 58, ( 9 ), 913-916, 1987.

Symmetries and Learning in Neural Network Models.   P. Baldi. Physical Review Letters., 59, ( 17 ), 1976-1978, 1987.

Embeddings of Ultrametric Spaces in Finite Dimensional Structures.   M. Aschbacher, P. Baldi, E. B. Baum, R.M. Wilson. SIAM Journal of Algebraic and Discrete Methods., 8, ( 4 ), 564-577, 1987.

Refereed Conference Proceedings
On Properties of Networks of Neuron-Like Elements: Complexity and Capacity.   P. Baldi, S.S. Venkatesh. Proceedings of the IEEE Conference on Neural Information Processing Systems., 1987.

1986
Refereed Journals
Bounds on the Size of Ultrametric Structures.   P. Baldi, E.B. Baum. Physical Review Letters., 56, ( 15 ), 1598-1600, 1986.

Refereed Conference Proceedings
Caging and Exhibiting Ultrametric Structures.   P. Baldi, E.B. Baum. Proceedings of the Conference on Neural Networks for Computing., 37, 232-246, 1986.
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