P. Baldi

Sushil Krishna Bajracharya, Cristina V. Lopes, Pierre Baldi, 2007, Fourth International Workshop on Mining Software Repositories (MSR'07:ICSE Workshops 2007).

Group Actions and Learning for a Family of Automata

Pierre Baldi, P. Baldi, 1988, J. Comput. Syst. Sci..

Boolean polynomial threshold functions and random tensors

P. Baldi, R. Vershynin, 2018, 1803.10868.

Random interactions in higher order neural networks

Pierre Baldi, Santosh S. Venkatesh, P. Baldi, 1993, IEEE Trans. Inf. Theory.

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity

Pierre Baldi, Sanjay Joshua Swamidass, Liva Ralaivola, 2005, ISMB.

State-driven energy optimization in wireless sensor networks

Cristina V. Lopes, Pierre Baldi, Raja Jurdak, 2005, 2005 Systems Communications (ICW'05, ICHSN'05, ICMCS'05, SENET'05).

ENERGY-AWARE ADAPTIVE LOW POWER LISTENING FOR SENSOR NETWORKS

P. Baldi, C. Lopes, R. Jurdak, 2005 .

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

Pierre Baldi, Anthony D. Long, P. Baldi, 2001, Bioinform..

What time is it? Deep learning approaches for circadian rhythms

Babak Shahbaba, Forest Agostinelli, Nicholas Ceglia, 2016, Bioinformatics.

Fold recognition by combining profile-profile alignment and support vector machine

Pierre Baldi, Sanjay Joshua Swamidass, Jonathan H. Chen, 2005, Bioinform..

The dropout learning algorithm

Pierre Baldi, Peter J. Sadowski, P. Baldi, 2014, Artif. Intell..

Sherpa: Hyperparameter Optimization for Machine Learning Models

Lars Hertel, Pierre Baldi, Julian Collado, 2018 .

A Framework for Modeling Sensor Networks

Pierre Baldi, Cristina Videira Lopes, Raja Jurdak, 2004 .

An Acoustic Identification Scheme for Location Systems

P. Baldi, C. Lopes, R. Jurdak, 2004, The IEEE/ACS International Conference on Pervasive Services.

The inner and outer approaches to the design of recursive neural architectures

Pierre Baldi, P. Baldi, 2017, Data Mining and Knowledge Discovery.

Jet flavor classification in high-energy physics with deep neural networks

P. Baldi, D. Whiteson, G. Urban, 2016, 1607.08633.

Caging and exhibiting ultrametric structures

P. Baldi, E. Baum, 1987 .

Prediction of protein stability changes for single‐site mutations using support vector machines

Arlo Z. Randall, P. Baldi, Jianlin Cheng, 2005, Proteins.

Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site.

Yimeng Dou, P. Baldi, K. J. Hertel, 2006, RNA.

On Normal Approximations of Distributions in Terms of Dependency Graphs

Pierre Baldi, Yosef Rinott, P. Baldi, 1989 .

SARM: Sparse Autoregressive Model for Scalable Generation of Sparse Images in Particle Physics

P. Baldi, D. Whiteson, Julian Collado, 2020, 2009.14017.

Jet Substructure Classification in High-Energy Physics with Deep Neural Networks

P. Baldi, Peter Sadowski, D. Whiteson, 2016, 1603.09349.

Training and Validation of Deep Neural Networks for the Prediction of 90-Day Post-Liver Transplant Mortality Using UNOS Registry Data.

P. Baldi, G. Urban, B. D. Ershoff, 2020, Transplantation proceedings.

Retrotransposon profiling of RNA polymerase III initiation sites.

P. Baldi, M. Johnston, R. Mitra, 2012, Genome research.

Gut microbiota directs PPARγ‐driven reprogramming of the liver circadian clock by nutritional challenge

Pierre Baldi, Paolo Sassone-Corsi, P. Baldi, 2016, EMBO reports.

Retroviruses and yeast retrotransposons use overlapping sets of host genes.

Pierre Baldi, Yimeng Dou, Michael Aye, 2005, Genome research.

Neural Network Gradient Hamiltonian Monte

Andrew J. Holbrook, P. Baldi, B. Shahbaba, 2017 .

A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions

Pierre Baldi, Lan Huang, Yimeng Dou, 2006, Molecular & Cellular Proteomics.

The fixed-size Luria-Delbruck model with a nonzero death rate.

Pierre Baldi, Natalia L Komarova, P. Baldi, 2007, Mathematical biosciences.

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes*

Arlo Z. Randall, Vishal R. Patel, P. Baldi, 2010, Molecular & Cellular Proteomics.

LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.

P. Baldi, S. Hampson, A. McLysaght, 2003, Genome research.

The architecture of pre-mRNAs affects mechanisms of splice-site pairing.

P. Baldi, K. J. Hertel, S. Hung, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Volume IV. The DUNE far detector single-phase technology

Jorge S. Díaz, V. P. Luzio, J. I. Crespo-Anadón, 2020, Journal of Instrumentation.

Genome Architecture Leads a Bifurcation in Cell Identity

Gerald A. Higgins, S. Smale, P. Baldi, 2017, bioRxiv.

Neutrino interaction classification with a convolutional neural network in the DUNE far detector

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2020, Physical Review D.

Volume I. Introduction to DUNE

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, Journal of Instrumentation.

Population-wide analysis of differences in disease progression patterns in men and women

P. Baldi, S. Brunak, P. Moseley, 2019, Nature Communications.

Profiling humoral immune responses to P. falciparum infection with protein microarrays

Arlo Z. Randall, P. Baldi, D. Freilich, 2008, Proteomics.

Mitochondrial mutations in cancer

Marty C. Brandon, P. Baldi, D. Wallace, 2006, Oncogene.

Visual Adaptation and Novelty Responses in the Superior Colliculus

Robert A. Marino, P. Baldi, L. Itti, 2022 .

The Influence Relevance Voter : An Accurate And Interpretable Virtual High Throughput Screening Method

S. Joshua Swamidass, P. Baldi, S. Joshua Joshua Swamidass, 2009 .

An automated machine learning-based model predicts postoperative mortality using readily-extractable preoperative electronic health record data.

Eran Halperin, Pierre Baldi, Sriram Sankararaman, 2019, British journal of anaesthesia.

Development and validation of an interpretable neural network for prediction of postoperative in-hospital mortality

P. Baldi, I. Hofer, Christine Lee, 2021, npj Digital Medicine.

Development and Validation of a Deep Neural Network Model for Prediction of Postoperative In-hospital Mortality

Pierre Baldi, Maxime Cannesson, P. Baldi, 2018, Anesthesiology.

A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray

Pierre Baldi, Denise L. Doolan, Philip L. Felgner, 2010, Proceedings of the National Academy of Sciences.

First results on ProtoDUNE-SP liquid argon time projection chamber performance from a beam test at the CERN Neutrino Platform

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, Journal of Instrumentation.

A 3-Dimensional Trimeric β-Barrel Model for Chlamydia MOMP Contains Conserved and Novel Elements of Gram-Negative Bacterial Porins

Rommie E. Amaro, Arlo Z. Randall, P. Baldi, 2013, PloS one.

Transmembrane beta-barrel protein structure prediction

Arlo Z. Randall, P. Baldi, A. Randall, 2010 .

TMBpro : Secondary Structure , β-contact , and Tertiary Structure Prediction of Transmembrane β-Barrel Proteins

Pierre Baldi, Jianlin Cheng, Arlo Randall, 2007 .

Appendix A: Mathematical Complements

P. Baldi, Padhraic Smyth, P. Frasconi, 2003 .

AN EXPERIMENT FOR ZSCAN EFFICIENCY IN SURFACE MONITORING

P. Baldi, G. Casula, F. Loddo, 2009 .

Large Scale Immune Profiling of Infected Humans and Goats Reveals Differential Recognition of Brucella melitensis Antigens

Matthew A. Kayala, P. Baldi, R. Gilman, 2010, PLoS neglected tropical diseases.

Simple jury predicts protein secondary structure best

James A. Cuff, David T. Jones, P. Baldi, 2003 .

Long-baseline neutrino oscillation physics potential of the DUNE experiment

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2020, The European Physical Journal C.

A Study of Ranking Schemes in Internet-Scale Code Search

Pierre Baldi, Erik Linstead, Paul Rigor, 2007 .

Title Improved residue contact prediction using support vector machines and a large feature set Permalink

P. Baldi, Jianlin Cheng, 2007 .

Circadian Control of Fatty Acid Elongation by SIRT1 Protein-mediated Deacetylation of Acetyl-coenzyme A Synthetase 1*

P. Baldi, W. C. Hallows, J. Denu, 2014, The Journal of Biological Chemistry.

of Acetyl-coenzyme A Synthetase 1 by SIRT 1 Protein-mediated Deacetylation Circadian Control of Fatty Acid Elongation Gene Regulation :

P. Baldi, W. C. Hallows, J. Denu, 2014 .

Coordination of the transcriptome and metabolome by the circadian clock

Pierre Baldi, Paolo Sassone-Corsi, Vishal R. Patel, 2012, Proceedings of the National Academy of Sciences.

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume II: DUNE Physics

R. Hatcher, R. Illingworth, A. Rappoldi, 2020, 2002.03005.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2020, The European physical journal. C, Particles and fields.

Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception

P. Baldi, J. Arthur, N. Ceglia, 2017, Nature Communications.

MiR‐29 coordinates age‐dependent plasticity brakes in the adult visual cortex

P. Baldi, A. Cellerino, T. Pizzorusso, 2020, EMBO reports.

Improved energy reconstruction in NOvA with regression convolutional neural networks

Lars Hertel, Pierre Baldi, P. Baldi, 2018, Physical Review D.

Pierre Baldi, Chase Shimmin, Peter Sadowski, 2017, Physical Review D.

Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks

P. Baldi, P. Magistretti, V. Orlando, 2018, Cell.

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time.

Pierre Baldi, S. Joshua Swamidass, P. Baldi, 2007 .

Search for slow magnetic monopoles with the NOvA detector on the surface

D. A. Wickremasinghe, D. P. Méndez, P. Baldi, 2020, Physical Review D.

The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental temporal lobe epilepsy

P. Baldi, W. Löscher, A. Becker, 2020, Science Advances.

The circadian dynamics of the hippocampal transcriptome and proteome is altered in experimental epilepsy

P. Baldi, W. Löscher, A. Becker, 2020 .

The circadian hippocampus and its reprogramming in epilepsy: impact for chronotherapeutics

P. Baldi, W. Löscher, C. Bernard, 2017, bioRxiv.

Information-Theoretic Metrics for Project-Level Scattering and Tangling

Cristina V. Lopes, Pierre Baldi, Erik Linstead, 2010, SEKE.

Ty3 Capsid Mutations Reveal Early and Late Functions of the Amino-Terminal Domain

G. W. Hatfield, Liza S. Z. Larsen, P. Baldi, 2007, Journal of Virology.

Sigmoid : Towards an Intelligent , Scalable , Software Infrastructure for Pathway Bioinformatics and Systems Biology

P. Baldi, E. Mjolsness, Jianlin Cheng, 2005 .

Sums of dependent 0-1 (indicator) or bounded random variables arise often in statistics, random graphs theory and other areas of applied probability. Since such

P. Baldi, Y. Rinott, 1989 .

Backpropagation and unsupervised learning in linear networks

Kurt Hornik, Pierre Baldi, Yves Chauvin, 1995 .

Defining the Independence of the Liver Circadian Clock

P. Baldi, P. Sassone-Corsi, Patrick-Simon Welz, 2019, Cell.

Deep Learning: Theory, Algorithms, and Applications (NII Shonan Meeting 2014-5)

Kenji Fukumizu, Pierre Baldi, Tomaso A. Poggio, 2014, NII Shonan Meet. Rep..

First results on ProtoDUNE-SP liquid argon time projection chamber performance from a beam test at the CERN Neutrino Platform

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2007.06722.

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume IV Far Detector Single-phase Technology

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2002.03010.

Patterns of cilia gene dysregulations in major psychiatric disorders

P. Baldi, M. Vawter, S. Nauli, 2021, Progress in Neuro-Psychopharmacology and Biological Psychiatry.

Efficient neutrino oscillation parameter inference using Gaussian processes

P. Baldi, J. Bian, L. Li, 2020 .

How pervasive are circadian oscillations?

P. Baldi, P. Sassone-Corsi, K. Eckel-Mahan, 2014, Trends in cell biology.

In press, Infection and Immunity A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi 5 Running title: Immunogens of Borrelia burgdorferi in natural infections

Matthew A. Kayala, P. Baldi, A. Steere, 2008 .

The role of bottom-up and top-down influences in directing primate gaze shifts

Pierre Baldi, Laurent Itti, Robert A. Marino, 2010 .

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures

Pierre Baldi, Arlo Z. Randall, Ken Nagata, 2014, Bioinform..

Interrogating Metabolic Interactions Between Skeletal Muscle and Liver Circadian Clocks In Vivo

P. Baldi, V. Orlando, P. Sassone-Corsi, 2022, bioRxiv.

Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle.

P. Baldi, A. Ballabio, N. Ceglia, 2018, Cell reports.

Distinct Circadian Signatures in Liver and Gut Clocks Revealed by Ketogenic Diet.

P. Baldi, E. Verdin, P. Sassone-Corsi, 2017, Cell metabolism.

Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia

Matthew A. Kayala, P. Baldi, J. Wingard, 2010, PLoS pathogens.

Light Entrains Diurnal Cha nges in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons Graphical

P. Baldi, R. Coppari, P. Sassone-Corsi, 2019 .

Light Entrains Diurnal Changes in Insulin Sensitivity of Skeletal Muscle via Ventromedial Hypothalamic Neurons.

P. Baldi, R. Coppari, P. Sassone-Corsi, 2019, Cell reports.

Search for Active-Sterile Antineutrino Mixing Using Neutral-Current Interactions with the NOvA Experiment.

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2021, Physical review letters.

Supernova neutrino detection in NOvA

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2020, Journal of Cosmology and Astroparticle Physics.

Deep Learning in High-Energy Physics: Improving the Search for Exotic Particles

P. Baldi, D. Whiteson, P. Sadowski, 2014 .

A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens

Matthew A. Kayala, P. Baldi, G. Bancroft, 2009, Proceedings of the National Academy of Sciences.

Matching Protein -Sheet Partners by Neural Networks

P. Baldi, G. Pollastri, 2000 .

Create standalone simulation tools to facilitate collaboration between HEP and machine learning community

Gilles Louppe, Pierre Baldi, Balázs Kégl, 2016 .

Reshaping circadian metabolism in the suprachiasmatic nucleus and prefrontal cortex by nutritional challenge

P. Baldi, P. Sassone-Corsi, M. Moisan, 2020, Proceedings of the National Academy of Sciences.

Development of an in-situ calibration device of firn properties for Askaryan neutrino detectors

P. Baldi, A. Nelles, S. Barwick, 2021 .

Deep learning reconstruction of the neutrino energy with a shallow Askaryan detector

P. Baldi, S. Barwick, C. Glaser, 2021, Proceedings of 37th International Cosmic Ray Conference — PoS(ICRC2021).

Rationally selected single-site mutants of the Thermoascus aurantiacus endoglucanase increase hydrolytic activity on cellulosic substrates.

Arlo Z. Randall, P. Baldi, N. D. Da Silva, 2012, Biotechnology and bioengineering.

Deep learning reconstruction of the neutrino direction and energy from in-ice radio detector data

P. Baldi, S. Barwick, C. Glaser, 2022 .

Protocol Features I E E E C O M M U N I C a T I O N S a Survey, Classification and Comparative Analysis of Medium Access Control Protocols for Ad Hoc Networks

P. Baldi, C. Lopes, R. Jurdak, 2004 .

Improved Modeling of the Discrete Component of the Galactic Interstellar Gamma-ray Emission and Implications for the Fermi-LAT Galactic Center Excess

P. Baldi, Mohammadamin Tavakoli, Alexander Shmakov, 2022, 2206.02809.

Deep Learning Models of the Discrete Component of the Galactic Interstellar Gamma-Ray Emission

P. Baldi, Mohammadamin Tavakoli, Alexander Shmakov, 2022, ArXiv.

Weakly Supervised Polyp Segmentation in Colonoscopy Images Using Deep Neural Networks

P. Baldi, G. Urban, Siwei Chen, 2022, J. Imaging.

Sterile Protective Immunity to Malaria is Associated with a Panel of Novel P. falciparum Antigens*

Matthew A. Kayala, P. Baldi, Angela Trieu, 2011, Molecular & Cellular Proteomics.

Obtaining Approximately Admissible Heuristic Functions through Deep Reinforcement Learning and A* Search

P. Baldi, Roy Fox, Forest Agostinelli, 2021 .

Fold recognition by scoring protein map similarities using the congruence coefficient

P. Baldi, Pietro Di Lena, 2020, bioRxiv.

GRHL3/GET1 and Trithorax Group Members Collaborate to Activate the Epidermal Progenitor Differentiation Program

Michael D. Zeller, P. Baldi, B. Andersen, 2012, PLoS genetics.

FKBP10 Regulates Protein Translation to Sustain Lung Cancer Growth.

P. Baldi, A. Charollais, R. Coppari, 2020, Cell reports.

CircadiOmics: circadian omic web portal

P. Baldi, Forest Agostinelli, M. Samad, 2022, Nucleic Acids Res..

White Paper: ARIANNA-200 high energy neutrino telescope

P. Baldi, A. Nelles, S. Barwick, 2020, 2004.09841.

An atlas of posttranslational modifications on RNA binding proteins

Ryan A. Flynn, P. Baldi, R. Spitale, 2022, Nucleic acids research.

S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling

P. Baldi, E. Gratton, H. Okamura, 2020, Science advances.

Gap Junction Channels of Innexins and Connexins: Relations and Computational Perspectives

P. Baldi, Carlos Castro, D. Flores, 2019, International journal of molecular sciences.

Characterizing the Skin and Gut Microbiome of Alopecia Areata Patients

P. Baldi, N. Mesinkovska, C. Ekelem, 2020 .

Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis.

P. Baldi, J. Holst, A. Walch, 2020, Cell metabolism.

Feasible Adversarial Robust Reinforcement Learning for Underspecified Environments

P. Baldi, Roy Fox, S. McAleer, 2022, ArXiv.

Self-Play PSRO: Toward Optimal Populations in Two-Player Zero-Sum Games

P. Baldi, Roy Fox, T. Sandholm, 2022, ArXiv.

Brain histone beta-hydroxy-butyrylation couples metabolism with gene expression

P. Baldi, T. Pizzorusso, Raffaele Mazziotti, 2021, bioRxiv.

Metabolic changes associated with methionine stress sensitivity in MDA-MB-468 breast cancer cells

Michael D. Zeller, P. Baldi, O. Fiehn, 2016, Cancer & Metabolism.

Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock

Pierre Baldi, Paolo Sassone-Corsi, Henriette Pilegaard, 2013, Molecular metabolism.

Reinforcement Learning and Deep Reinforcement Learning

Pierre Baldi, P. Baldi, 2021, Deep Learning in Science.

Commerce on the Web: Models and Applications

Pierre Baldi, Paolo Frasconi, Padhraic Smyth, 2003 .

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.

Pierre Baldi, Vishal R. Patel, Lee Bardwell, 2013, Cellular signalling.

Bioethics, Fiction Science, and the Future of Mankind - Session Introduction

Pierre Baldi, Søren Brunak, P. Baldi, 2000, Pacific Symposium on Biocomputing.

Distinct metabolic adaptation of liver circadian pathways to acute and chronic patterns of alcohol intake

P. Baldi, N. Ceglia, P. Sassone-Corsi, 2019, Proceedings of the National Academy of Sciences.

SPANet: Generalized Permutationless Set Assignment for Particle Physics using Symmetry Preserving Attention

P. Baldi, D. Whiteson, Alexander Shmakov, 2021, SciPost Physics.

Advanced Crawling Techniques

Pierre Baldi, Paolo Frasconi, Padhraic Smyth, 2003 .

Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity

Michael D. Zeller, P. Baldi, S. Sandmeyer, 2016, PloS one.

Hidden Markov Models: The Theory

Søren Brunak, Pierre Baldi, P. Baldi, 2001 .

Neural Networks: The Theory

Søren Brunak, Pierre Baldi, P. Baldi, 2001 .

Bioinformatics - the machine learning approach (2. ed.)

Pierre Baldi, Søren Brunak, P. Baldi, 2001 .

Probabilistic Graphical Models in Bioinformatics

Søren Brunak, Pierre Baldi, P. Baldi, 2001 .

Hidden Markov Models: Applications

Søren Brunak, Pierre Baldi, P. Baldi, 2001 .

The formation of extinction memory requires the accumulation of N6-methyl-2-deoxyadenosine in DNA

P. Baldi, T. Bredy, R. Spitale, 2016 .

Global Gene Expression Profiling in Escherichia coli K12

G. W. Hatfield, P. Baldi, R. Krupp, 2005, Journal of Biological Chemistry.

The Absence of Favorable Aromatic Interactions between β-Sheet Peptides

P. Baldi, J. Nowick, Yimeng Dou, 2005 .

Deep-learning-based reconstruction of the neutrino direction and energy for in-ice radio detectors

P. Baldi, S. Barwick, C. Glaser, 2022, Astroparticle Physics.

Resolving extreme jet substructure

P. Baldi, D. Whiteson, Yadong Lu, 2022, Journal of High Energy Physics.

Deep Underground Neutrino Experiment (DUNE) Near Detector Conceptual Design Report

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2021, Instruments.

Volume III. DUNE far detector technical coordination

Jorge S. Díaz, V. P. Luzio, J. I. Crespo-Anadón, 2020, Journal of Instrumentation.

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume III DUNE Far Detector Technical Coordination

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2002.03008.

Gaussian Process Accelerated Feldman-Cousins Approach for Physical Parameter Inference

P. Baldi, Lingge Li, J. Bian, 2018, 1811.07050.

Erratum to "Muscle insulin sensitivity and glucose metabolism are controlled by the intrinsic muscle clock" [Mol Metab 3 (2014) 29-41].

P. Baldi, S. Bicciato, M. Forcato, 2014, Molecular metabolism.

Homo sapiens Global landscape of recent inferred Darwinian selection for

P. Baldi, R. Moyzis, E. Wang, 2006 .

Feasible Adversarial Robust Reinforcement Learning for Underspecified Environments

P. Baldi, Roy Fox, S. McAleer, 2022, ArXiv.

Latent Factor Gaussian Processes with Log-Euclidean Metric for Dynamic Covariance Modeling

P. Baldi, B. Shahbaba, Lingge Li, 2019 .

Deep learning techniques for a real-time neutrino classifier

P. Baldi, A. Nelles, S. Barwick, 2021 .

Deducing Neutron Star Equation of State Parameters Directly From Telescope Spectra with Uncertainty-Aware Machine Learning

P. Baldi, D. Whiteson, L. Lindblom, 2022, 2209.02817.

Subsampling needlet coefﬁcients on the sphere

P. Baldi, G. Kerkyacharian, D. Picard, 2009 .

Probabilistic Modeling and Inference: Examples

Søren Brunak, Pierre Baldi, P. Baldi, 2001 .

Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

P. Baldi, G. Abbott, A. Alachkar, 2020, Communications Biology.

Learning to identify electrons

P. Baldi, D. Whiteson, Taylor Faucett, 2020, 2011.01984.

Capabilities of ARIANNA: Neutrino Pointing Resolution and Implications for Future Ultra-high Energy Neutrino Astronomy

S. W. Barwick, D. Z. Besson, P. Baldi, 2021, Proceedings of 37th International Cosmic Ray Conference — PoS(ICRC2021).

The Gag3 spacer controls intracellular condensation and

Arlo Z. Randall, Liza S. Z. Larsen, P. Baldi, 2011 .

Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein.

G. W. Hatfield, P. Baldi, S. Hung, 2002, The Journal of biological chemistry.

Deep Networks and Backpropagation

Pierre Baldi, P. Baldi, 2021, Deep Learning in Science.

Global Gene Expression Profiling in Escherichia coliK12

Pierre Baldi, G. W. Hatfield, G Wesley Hatfield, 2002, The Journal of Biological Chemistry.

Enhanced Higgs to $τ^+τ^-$ Searches with Deep Learning pdf

Pierre Baldi, Daniel Whiteson, Peter J. Sadowski, 2014, ArXiv.

DNA Microarrays and Gene Expression: Statistical analysis of array data: Dimensionality reduction, clustering, and regulatory regions

Pierre Baldi, G. W. Hatfield, G. Wesley Hatfield, 2002 .

Solving the Rubik's Cube with Approximate Policy Iteration

Pierre Baldi, Forest Agostinelli, Stephen McAleer, 2018, ICLR.

The Stability and Complexity of Antibody Responses to the Major Surface Antigen of Plasmodium falciparum Are Associated with Age in a Malaria Endemic Area*

Pierre Baldi, Denise L. Doolan, Philip L. Felgner, 2011, Molecular & Cellular Proteomics.

Neural Network Regression with Beta, Dirichlet, and Dirichlet-Multinomial Outputs

Pierre Baldi, Peter Sadowski, P. Baldi, 2018 .

A surprise theory of early attention

Pierre Baldi, Laurent Itti, P. Baldi, 2005 .

Mapping the Structural Topology of the Yeast 19S Proteasomal Regulatory Particle Using Chemical Cross-linking and Probabilistic Modeling*

Pierre Baldi, Arlo Z. Randall, Vishal R. Patel, 2012, Molecular & Cellular Proteomics.

Reproducible Hyperparameter Optimization

Pierre Baldi, Daniel L. Gillen, Lars Hertel, 2021, J. Comput. Graph. Stat..

Comparative Circadian Metabolomics Reveal Differential Effects of Nutritional Challenge in the Serum and Liver*

Pierre Baldi, Paolo Sassone-Corsi, P. Baldi, 2015, The Journal of Biological Chemistry.

MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences

Pierre Baldi, Vincent Procaccio, Eduardo Ruiz-Pesini, 2009, Human mutation.

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.

Pierre Baldi, Liva Ralaivola, S. Joshua Swamidass, 2007 .

Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis

Amir F. Atiya, Pierre Baldi, P. Baldi, 1991, Int. J. Neural Syst..

The Deep Learning Channel

Pierre Baldi, P. Baldi, 2021, Deep Learning in Science.

A neural network with modular hierarchical learning

Pierre Baldi, Nikzad Toomarian, P. Baldi, 1994 .

Pierre Baldi, Siddiqua Hirst, Yunxiang Mu, 2007, Proteomics.

Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis

Pierre Baldi, Paolo Sassone-Corsi, P. Baldi, 2016, Cell.

Detecting Pulmonary Coccidioidomycosis (Valley fever) with Deep Convolutional Neural Networks pdf

Pierre Baldi, Jordan Ott, Silke Hecht, 2021, ArXiv.

SPANet: Generalized Permutationless Set Assignment for Particle Physics using Symmetry Preserving Attention pdf

Pierre Baldi, Ta-Wei Ho, Michael James Fenton, 2021, SciPost Physics.

Trajectory learning using hierarchy of oscillatory modules

Pierre Baldi, Nikzad Benny Toomarian, P. Baldi, 1993, ESANN.

Reaction Explorer:Towards a Knowledge Map of Organic Chemistry To Support Dynamic Assessment and Personalized Instruction

Pierre Baldi, Jonathan H. Chen, Matthew A. Kayala, 2010 .

Circadian acetylome reveals regulation of mitochondrial metabolic pathways

Pierre Baldi, Paolo Sassone-Corsi, Vishal R. Patel, 2013, Proceedings of the National Academy of Sciences.

Mitochondrial Mutations and Polymorphisms in Psychiatric Disorders

Pierre Baldi, Fabio Macciardi, Douglas C. Wallace, 2012, Front. Gene..

Modeling and Understanding Human Behavior on the Web

Pierre Baldi, Paolo Frasconi, Padhraic Smyth, 2003 .

Gradient descent learning algorithms: a unified perspective

Pierre Baldi, P. Baldi, 1995 .

Methyl Anion Affinities of the Canonical Organic Functional Groups.

Pierre Baldi, Mohammadamin Tavakoli, Aaron D. Mood, 2020, The Journal of organic chemistry.

DNA Microarrays and Gene Expression: The design, analysis, and interpretation of gene expression profiling experiments

Pierre Baldi, G. W. Hatfield, G. Wesley Hatfield, 2002 .

Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis.

Pierre Baldi, S Joshua Swamidass, S. Joshua Swamidass, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Learning in the Machine: Random Backpropagation and the Deep Learning Channel (Extended Abstract)

Pierre Baldi, Peter J. Sadowski, Zhiqin Lu, 2019, IJCAI.

Machine learning of physiological waveforms and electronic health record data to predict, diagnose and treat haemodynamic instability in surgical patients: protocol for a retrospective study

Pierre Baldi, Artur Dubrawski, Joseph Rinehart, 2019, BMJ Open.

Detecting pulmonary Coccidioidomycosis with deep convolutional neural networks

Pierre Baldi, Jordan Ott, Silke Hecht, 2021 .

Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity pdf

Pierre Baldi, Mohammadamin Tavakoli, Aaron D. Mood, 2021, J. Chem. Inf. Model..

Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery.

Pierre Baldi, Siddiqua Hirst, Yunxiang Mu, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Seasonal variation of multiple-muon cosmic ray air showers observed in the NOvA detector on the surface

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2021, Physical Review D.

Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability

Arlo Z. Randall, P. Baldi, Z. Guan, 2010, Proceedings of the National Academy of Sciences.

Parameterized neural networks for high-energy physics

P. Baldi, D. Whiteson, K. Cranmer, 2016, The European Physical Journal C.

Time of Exercise Specifies the Impact on Muscle Metabolic Pathways and Systemic Energy Homeostasis.

Pierre Baldi, Paolo Sassone-Corsi, Ali Altıntaş, 2019, Cell metabolism.

Symmetric-APL Activations: Training Insights and Robustness to Adversarial Attacks

Pierre Baldi, Forest Agostinelli, Mohammadamin Tavakoli, 2019 .

Deducing neutron star equation of state parameters directly from telescope spectra with uncertainty-aware machine learning

P. Baldi, D. Whiteson, L. Lindblom, 2022, Journal of Cosmology and Astroparticle Physics.

ClusterCAD: a computational platform for type I modular polyketide synthase design

Tyler W. H. Backman, Jay D. Keasling, Héctor García Martín, 2017, Nucleic Acids Res..

Deep Learning from Four Vectors

P. Baldi, D. Whiteson, Peter Sadowski, 2022, Artificial Intelligence for High Energy Physics.

Deep Bucket Elimination

Pierre Baldi, Yadong Lu, Rina Dechter, 2021, IJCAI.

A* Search Without Expansions: Learning Heuristic Functions with Deep Q-Networks pdf

Pierre Baldi, Roy Fox, Forest Agostinelli, 2021, ArXiv.

The capacity of feedforward neural networks

Pierre Baldi, Roman Vershynin, P. Baldi, 2019, Neural Networks.

From Reinforcement Learning to Deep Reinforcement Learning: An Overview

Pierre Baldi, Sameer Singh, Forest Agostinelli, 2017, Braverman Readings in Machine Learning.

Revealing Fundamental Physics from the Daya Bay Neutrino Experiment Using Deep Neural Networks

Prabhat, Pierre Baldi, Sang-Yun Oh, 2016, 2016 15th IEEE International Conference on Machine Learning and Applications (ICMLA).

Deep Learning, Dark Knowledge, and Dark Matter

Pierre Baldi, Daniel Whiteson, Peter J. Sadowski, 2014, HEPML@NIPS.

Polarization Reconstruction of Cosmic Rays with the ARIANNA Neutrino Radio Detector

P. Baldi, A. Nelles, S. Barwick, 2021, Proceedings of 37th International Cosmic Ray Conference — PoS(ICRC2021).

A novel trigger based on neural networks for radio neutrino detectors

P. Baldi, A. Nelles, S. Barwick, 2021, Proceedings of 37th International Cosmic Ray Conference — PoS(ICRC2021).

A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition.

Pierre Baldi, Christof Koch, Laurent Itti, 2007, Journal of vision.

Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants

Pierre Baldi, Ray Luo, Sanjay Joshua Swamidass, 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The Neuron-specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory

Pierre Baldi, Christophe N. Magnan, Gary Lynch, 2013, Nature Neuroscience.

Circadian clock regulates the host response to Salmonella

Pierre Baldi, Paolo Sassone-Corsi, Michael D. George, 2013, Proceedings of the National Academy of Sciences.

High-throughput prediction of protein antigenicity using protein microarray data

Pierre Baldi, Michael Zeller, Philip L. Felgner, 2010, Bioinform..

Bidirectional IOHMMs and Recurrent Neural Networks for Protein Secondary Structure Prediction

Paolo Frasconi, Gianluca Pollastri, Søren Brunak, 2000 .

Vitreoretinal Surgical Instrument Tracking in Three Dimensions Using Deep Learning

P. Baldi, J. Liu, A. Browne, 2023, Translational vision science & technology.

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values

Pierre Baldi, Ramzi Nasr, P. Baldi, 2010, J. Chem. Inf. Model..

BLASTing small molecules—statistics and extreme statistics of chemical similarity scores

Pierre Baldi, Ryan W. Benz, P. Baldi, 2008, ISMB.

Improving Social Welfare While Preserving Autonomy via a Pareto Mediator pdf

Pierre Baldi, Roy Fox, Michael Dennis, 2021, ArXiv.

SCRATCH: a protein structure and structural feature prediction server

Pierre Baldi, Jianlin Cheng, Michael J. Sweredoski, 2005, Nucleic Acids Res..

Graph kernels for chemical informatics

Pierre Baldi, Sanjay Joshua Swamidass, Hiroto Saigo, 2005, Neural Networks.

Modeling the Internet and the Web: Probabilistic Method and Algorithms

Pierre Baldi, Paolo Frasconi, Padhraic Smyth, 2002 .

Combining Deep Learning With Optical Coherence Tomography Imaging to Determine Scalp Hair and Follicle Counts

Gregor Urban, Pierre Baldi, Nate Feil, 2020, Lasers in surgery and medicine.

Combining protein secondary structure prediction models with ensemble methods of optimal complexity

Gianluca Pollastri, Hélène Paugam-Moisy, Yann Guermeur, 2004, Neurocomputing.

Detecting Cardiovascular Disease from Mammograms With Deep Learning

Sabee Molloi, Juan Wang, Pierre Baldi, 2017, IEEE Transactions on Medical Imaging.

Modeling the Internet and the Web: Probabilistic Method and Algorithms

Pierre Baldi, Paolo Frasconi, Padhraic Smyth, 2003 .

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume II: DUNE Physics

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2002.03005.

A machine learning information retrieval approach to protein fold recognition.

Pierre Baldi, Jianlin Cheng, P. Baldi, 2006, Bioinformatics.

Of bits and wows: A Bayesian theory of surprise with applications to attention

Pierre Baldi, Laurent Itti, P. Baldi, 2010, Neural Networks.

Safety of Quark/Gluon Jet Classification

P. Baldi, D. Whiteson, Julian Collado, 2021, 2103.09103.

Bioinformatics - the machine learning approach (2. ed.)

Pierre Baldi, Søren Brunak, P. Baldi, 2000 .

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

Pierre Baldi, Paolo Sassone-Corsi, Vishal R. Patel, 2013, Nature Structural &Molecular Biology.

Functional Conservation of lncRNA JPX despite Sequence and Structural Divergence.

P. Baldi, R. Spitale, Shan Sun, 2020, Journal of molecular biology.

A Genomic Analysis Pipeline and Its Application to Pediatric Cancers

Pierre Baldi, Michael Zeller, Paul Rigor, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Mutation of neuron-specific chromatin remodeling subunit BAF53b: rescue of plasticity and memory by manipulating actin remodeling

Richard T Dang, P. Baldi, G. Lynch, 2017, Learning & memory.

The Biology of Eukaryotic Promoter Prediction - A Review

Pierre Baldi, Yves Chauvin, Søren Brunak, 1999, Comput. Chem..

Reprogramming of the Circadian Clock by Nutritional Challenge

Pierre Baldi, Paolo Sassone-Corsi, Vishal R. Patel, 2013, Cell.

Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites

P. Baldi, S. Sandmeyer, X. Qi, 2019, Genome research.

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

Pierre Baldi, Christophe N. Magnan, P. Baldi, 2014, Bioinform..

Function and Regulation of Cph2 in Candida albicans

P. Baldi, S. Lane, Haopin Liu, 2015, Eukaryotic Cell.

A non-pharmacological therapeutic approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced dysfunctions encompassed by metabolic syndrome

P. Baldi, P. Sassone-Corsi, Yu Liu, 2020, Scientific Reports.

Why are complementary DNA strands symmetric?

Pierre Baldi, Steven E. Hampson, Pierre-François Baisnée, 2002, Bioinform..

Deep autoencoder neural networks for gene ontology annotation predictions

Pierre Baldi, Davide Chicco, Peter J. Sadowski, 2014, BCB.

Structural basis for triplet repeat disorders: a computational analysis

Pierre Baldi, Yves Chauvin, Søren Brunak, 1999, Bioinform..

A WNT/p21 Circuit Directed by the C-Clamp, a Sequence-Specific DNA Binding Domain in TCFs

P. Baldi, M. Waterman, S. Sundaresh, 2012, Molecular and Cellular Biology.

Statistical detection of chromosomal homology using shared-gene density alone

Pierre Baldi, Steven E. Hampson, B. S. Gaut, 2005, Bioinform..

Extensive gene gain associated with adaptive evolution of poxviruses

Brandon S. Gaut, P. Baldi, A. McLysaght, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Global landscape of recent inferred Darwinian selection for Homo sapiens

Pierre Baldi, Eric T Wang, Greg Kodama, 2006, Proc. Natl. Acad. Sci. USA.

Cocaine-mediated circadian reprogramming in the striatum through dopamine D2R and PPARγ activation

P. Baldi, K. Brami-Cherrier, E. Borrelli, 2020, Nature Communications.

Assessing the accuracy of prediction algorithms for classification: an overview

Pierre Baldi, Yves Chauvin, Søren Brunak, 2000, Bioinform..

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

Xiaohui Xie, Pierre Baldi, Paul Rigor, 2011, BMC Bioinformatics.

MotifMap: a human genome-wide map of candidate regulatory motif sites

Xiaohui Xie, Pierre Baldi, Paul Rigor, 2009, Bioinform..

Improved Statistical Inference from DNA Microarray Data Using Analysis of Variance and A Bayesian Statistical Framework

A D Long, H J Mangalam, B Y Chan, 2001, The Journal of Biological Chemistry.

Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells

Matthew A. Kayala, P. Baldi, Yu-Han Chen, 2019, Scientific Reports.

A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia.

Bogi Andersen, Hsiang Ho, Michael D. Zeller, 2014, The Journal of clinical investigation.

Mitochondrial Mutations in Subjects with Psychiatric Disorders

P. Baldi, R. Myers, H. Akil, 2015, PloS one.

Periodic Sequence Patterns in Human Exons

Pierre Baldi, Yves Chauvin, Søren Brunak, 1995, ISMB.

Hidden Markov Models for Human Genes

Pierre Baldi, Yves Chauvin, Søren Brunak, 1993, NIPS.

Functional conservation of lncRNA JPX despite sequence and structural divergence

P. Baldi, R. Spitale, Shan Sun, 2019, bioRxiv.

Large‐scale prediction of disulphide bridges using kernel methods, two‐dimensional recursive neural networks, and weighted graph matching

Pierre Baldi, Jianlin Cheng, Hiroto Saigo, 2005, Proteins.

MotifMap‐RNA: a genome‐wide map of RBP binding sites

Yu Liu, Pierre Baldi, Sha Sun, 2017, Bioinform..

Dynamic Changes of Brain Cilia Transcriptomes across the Human Lifespan

P. Baldi, S. Nauli, A. Alachkar, 2021, International journal of molecular sciences.

Large‐scale analysis reveals spatiotemporal circadian patterns of cilia transcriptomes in the primate brain

P. Baldi, A. Alachkar, Siwei Chen, 2021, Journal of neuroscience research.

Genome-Wide Identification of Bcl11b Gene Targets Reveals Role in Brain-Derived Neurotrophic Factor Signaling

P. Baldi, L. Schaffer, S. Head, 2011, PloS one.

Distribution patterns of over-represented k-mers in non-coding yeast DNA

Pierre Baldi, Steven E. Hampson, Dennis F. Kibler, 2002, Bioinform..

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors

Pierre Baldi, Lan Huang, Jeffrey S. Rogers, 2010, PLoS Comput. Biol..

The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction

P. Baldi, T. Bredy, R. Spitale, 2019, Nature Neuroscience.

Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae.

P. Baldi, B. Gaut, Nan Wang, 2007, Molecular phylogenetics and evolution.

Enhanced Higgs boson to τ(+)τ(-) search with deep learning.

P Baldi, P Sadowski, D Whiteson, 2014, Physical review letters.

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

Pierre Baldi, Michael J. Sweredoski, Michael J. Sweredoski, 2008, Bioinform..

An enhanced MITOMAP with a global mtDNA mutational phylogeny

Pierre Baldi, Vincent Procaccio, Marie T. Lott, 2006, Nucleic Acids Res..

MITOMAP: a human mitochondrial genome database—2004 update

Shamkant B. Navathe, Pierre Baldi, Marie T. Lott, 2004, Nucleic Acids Res..

Title An enhanced MITOMAP with a global mtDNA mutational phylogeny Permalink

Marty C. Brandon, P. Baldi, D. Wallace, 2006 .

Development and validation of a deep neural network model to predict postoperative mortality, acute kidney injury, and reintubation using a single feature set

P. Baldi, I. Hofer, Eilon Gabel, 2020, npj Digital Medicine.

Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in creatine transporter deficiency

P. Baldi, T. Pizzorusso, Raffaele Mazziotti, 2023, Acta Neuropathologica Communications.

Mapping the Protein Interaction Network of the Human COP9 Signalosome Complex Using a Label-free QTAX Strategy*

Vishal R. Patel, Robyn M. Kaake, P. Baldi, 2012, Molecular & Cellular Proteomics.

The hidden link between circadian entropy and mental health disorders

P. Baldi, E. Mayer, A. Alachkar, 2022, Translational Psychiatry.

ChemDB update - full-text search and virtual chemical space

Pierre Baldi, Sanjay Joshua Swamidass, Dennis Wang, 2007, Bioinform..

Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress

Pierre Baldi, Arlo Z. Randall, Ryan W. Benz, 2011, J. Chem. Inf. Model..

SOLpro: accurate sequence-based prediction of protein solubility

Pierre Baldi, Arlo Z. Randall, Christophe N. Magnan, 2009, Bioinform..

On Properties of Networks of Neuron-Like Elements

Pierre Baldi, Santosh S. Venkatesh, P. Baldi, 1987, NIPS.

P. Baldi, A. Alachkar, Siwei Chen, 2021, ACS chemical neuroscience.

Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data

Pierre Baldi, Jianlin Cheng, Michael J. Sweredoski, 2005, Data Mining and Knowledge Discovery.

The accumulation of N6-methyl-2’-deoxyadenosine in DNA drives activity-induced gene expression and is required for the extinction of conditioned fear

P. Baldi, T. Bredy, R. Spitale, 2018, bioRxiv.

DNA Microarrays and Gene Expression: A brief history of genomics

G. W. Hatfield, P. Baldi, 2002 .

Population-wide analysis of differences in disease progression patterns in men and women

P. Baldi, S. Brunak, P. Moseley, 2019, Nature Communications.

Partitioning Circadian Transcription by SIRT6 Leads to Segregated Control of Cellular Metabolism

Pierre Baldi, Paolo Sassone-Corsi, Paul Rigor, 2014, Cell.

Cyber-T web server: differential analysis of high-throughput data

Pierre Baldi, Matthew A. Kayala, P. Baldi, 2012, Nucleic Acids Res..

Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming

Pierre Baldi, Alfred Hero, Gerald A. Higgins, 2018, iScience.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2020, The European Physical Journal. C, Particles and Fields.

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume II: DUNE Physics

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2002.03005.

A Genome-Wide Proteome Array Reveals a Limited Set of Immunogens in Natural Infections of Humans and White-Footed Mice with Borrelia burgdorferi

Pierre Baldi, D. Huw Davies, Philip L. Felgner, 2008, Infection and Immunity.

Supernova Neutrino Burst Detection with the Deep Underground Neutrino Experiment

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2020, 2008.06647.

Deep-Learning-Based Kinematic Reconstruction for DUNE pdf

Wenjie Wu, Pierre Baldi, Jianming Bian, 2020, ArXiv.

Long-baseline neutrino oscillation physics potential of the DUNE experiment

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2020, 2006.16043.

First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NOvA.

D. P. Méndez, P. Baldi, R. Nichol, 2019, Physical review letters.

Deep Underground Neutrino Experiment (DUNE) Near Detector Conceptual Design Report

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2021, 2103.13910.

Countering GATTACA: efficient and secure testing of fully-sequenced human genomes

Emiliano De Cristofaro, Gene Tsudik, Paolo Gasti, 2011, CCS '11.

Guidelines for Genome-Scale Analysis of Biological Rhythms

Pierre Baldi, Andrew J. Millar, Francis J. Doyle, 2017, Journal of biological rhythms.

Structure, self-assembly, and properties of a truncated reflectin variant

Zhijing Feng, Qiyin Lin, Atrouli Chatterjee, 2020, Proceedings of the National Academy of Sciences.

Identification of Immunodominant Antigens by Probing a Whole Chlamydia trachomatis Open Reading Frame Proteome Microarray Using Sera from Immunized Mice

Matthew A. Kayala, P. Baldi, D. Molina, 2010, Infection and Immunity.

Machine Learning Methods for Protein Structure Prediction

Jianlin Cheng, P. Baldi, A.N. Tegge, 2008, IEEE Reviews in Biomedical Engineering.

From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis

Pierre Baldi, Suman Sundaresh, Berkay Unal, 2007, ISMB/ECCB.

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques

Pierre Baldi, Suman Sundaresh, Denise L. Doolan, 2006, Bioinform..

Cocaine induces paradigm-specific changes to the transcriptome within the ventral tegmental area

P. Baldi, V. Swarup, D. Matheos, 2021, Neuropsychopharmacology.

A multi-resolution approach for spinal metastasis detection using deep Siamese neural networks

Min-Ying Su, Pierre Baldi, Juan Wang, 2017, Comput. Biol. Medicine.

Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms

P. Baldi, P. Sassone-Corsi, P. Muñoz-Cánoves, 2021, Science advances.

COBEpro: a novel system for predicting continuous B-cell epitopes.

Pierre Baldi, Michael J. Sweredoski, Michael J Sweredoski, 2009, Protein engineering, design & selection : PEDS.

Intergenerational Stress Transmission is Associated with Brain Metabotranscriptome Remodeling and Mitochondrial Dysfunction

Emily C. Shapiro, P. Baldi, L. Mutesa, 2021, bioRxiv.

Hippocampal gene expression patterns linked to late-life physical activity oppose age and AD-related transcriptional decline

P. Baldi, C. Cotman, N. Berchtold, 2019, Neurobiology of Aging.

Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory

P. Baldi, P. Sassone-Corsi, Yu Liu, 2018, Nature Communications.

Biomimetic Design of Protein Nanomaterials for Hydrophobic Molecular Transport

Arlo Z. Randall, P. Baldi, Dongmei Ren, 2012, Advanced functional materials.

Transcriptome Profiling of Dysregulated GPCRs Reveals Overlapping Patterns across Psychiatric Disorders and Age-Disease Interactions

P. Baldi, O. Civelli, A. Alachkar, 2021, Cells.

Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths

Pierre Baldi, Pierre-François Baisnée, P. Baldi, 2000, Bioinform..

A theory of local learning, the learning channel, and the optimality of backpropagation

Pierre Baldi, Peter J. Sadowski, P. Baldi, 2015, Neural Networks.

The Ebb and Flow of Deep Learning: a Theory of Local Learning pdf

Pierre Baldi, Peter J. Sadowski, P. Baldi, 2015, ArXiv.

SIRT6 Suppresses Cancer Stem-like Capacity in Tumors with PI3K Activation Independently of Its Deacetylase Activity

P. Baldi, A. Charollais, R. Coppari, 2017, Cell reports.

Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin.

Vishal R. Patel, P. Baldi, Linh Vong, 2013, Cell metabolism.

host genes Retroviruses and yeast retrotransposons use overlapping sets of Material Supplemental

P. Baldi, B. Irwin, Yimeng Dou, 2005 .

Parallel Multicut Segmentation via Dual Decomposition

Pierre Baldi, Julian Yarkony, Fred A. Hamprecht, 2014, NFMCP.

Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors

Pierre Baldi, Daniel S. Hirschberg, Ramzi Nasr, 2010, J. Chem. Inf. Model..

Accurate Identification of the Trabecular Meshwork under Gonioscopic View in Real Time Using Deep Learning

P. Baldi, G. Urban, W. Alward, 2021, Ophthalmology Glaucoma.

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions

Pierre Baldi, Ivan Chang, P. Baldi, 2013, Bioinform..

Deep Learning in Biomedical Data Science

Pierre Baldi, P. Baldi, 2018, Annual Review of Biomedical Data Science.

Computing with Arrays of Coupled Oscillators: An Application to Preattentive Texture Discrimination

Pierre Baldi, Ron Meir, P. Baldi, 1990, Neural Computation.

Computing with Arrays of Coupled Oscillators

Joachim M. Buhmann, Pierre Baldi, Ron Meir, 1990 .

DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks

Pierre Baldi, Jianlin Cheng, Michael J. Sweredoski, 2006, Data Mining and Knowledge Discovery.

Hippocampal ensembles represent sequential relationships among an extended sequence of nonspatial events

P. Baldi, Forest Agostinelli, B. Shahbaba, 2022, Nature communications.

Hippocampal ensembles represent sequential relationships among discrete nonspatial events

Babak Shahbaba, Forest Agostinelli, Pierre Baldi, 2019, bioRxiv.

Measurement of neutrino-induced neutral-current coherent π0 production in the NOvA near detector

D. P. Méndez, P. Baldi, R. Nichol, 2020, Physical Review D.

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume IV Far Detector Single-phase Technology

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2002.03010.

Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction

Emily C. Shapiro, P. Baldi, L. Mutesa, 2021, Communications Biology.

Highly Accurate Machine Fault Diagnosis Using Deep Transfer Learning

Ruqiang Yan, Pierre Baldi, Stephen McAleer, 2019, IEEE Transactions on Industrial Informatics.

Adjusting neutrino interaction models and evaluating uncertainties using NOvA near detector data

Astrophysics, Faculty of Mathematics, Statistics, 2020, The European Physical Journal C.

Improved residue contact prediction using support vector machines and a large feature set

Pierre Baldi, Jianlin Cheng, P. Baldi, 2007, BMC Bioinformatics.

Improved prediction of the number of residue contacts in proteins by recurrent neural networks

Piero Fariselli, Pierre Baldi, Gianluca Pollastri, 2001, ISMB.

The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition

Pierre Baldi, Anke Busch, Michael D. Zeller, 2014, Nucleic acids research.

U-MAC: a proactive and adaptive UWB medium access control protocol

Cristina V. Lopes, Pierre Baldi, Raja Jurdak, 2005, Wirel. Commun. Mob. Comput..

An acoustic identification scheme for location systems

Cristina V. Lopes, Pierre Baldi, Raja Jurdak, 2004, The IEEE/ACS International Conference onPervasive Services, 2004. ICPS 2004. Proceedings..

A survey, classification and comparative analysis of medium access control protocols for ad hoc networks

Cristina V. Lopes, Pierre Baldi, Raja Jurdak, 2004, IEEE Communications Surveys & Tutorials.

Polynomial Threshold Functions, Hyperplane Arrangements, and Random Tensors

Pierre Baldi, Roman Vershynin, P. Baldi, 2018, SIAM J. Math. Data Sci..

Search for multimessenger signals in NOvA coincident with LIGO/Virgo detections

Astrophysics, Faculty of Mathematics, Statistics, 2020, Physical Review D.

Deep Learning in the Natural Sciences: Applications to Physics

Pierre Baldi, Peter J. Sadowski, P. Baldi, 2017, Braverman Readings in Machine Learning.

Extended search for supernovalike neutrinos in NOvA coincident with LIGO/Virgo detections

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2021, Physical Review D.

Learning to isolate muons

P. Baldi, D. Whiteson, Taylor Faucett, 2021, Journal of High Energy Physics.

SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity

P. Baldi, G. Urban, C. Magnan, 2022, Bioinform..

Deep Underground Neutrino Experiment (DUNE), Far Detector Technical Design Report, Volume III DUNE Far Detector Technical Coordination

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, 2002.03008.

How to GAN Higher Jet Resolution

P. Baldi, D. Whiteson, G. Kasieczka, 2020, SciPost Physics.

Permutationless Many-Jet Event Reconstruction with Symmetry Preserving Attention Networks pdf

Daniel Whiteson, Pierre Baldi, Shih-Chieh Hsu, 2020, Physical Review D.

Sparse autoregressive models for scalable generation of sparse images in particle physics

P. Baldi, D. Whiteson, Julian Collado, 2021, Physical Review D.

Language Models can Solve Computer Tasks

P. Baldi, S. McAleer, Geunwoo Kim, 2023, ArXiv.

Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays.

P. Baldi, D. Molina, P. Felgner, 2010, Vaccine.

How delays affect neural dynamics and learning

Amir F. Atiya, Pierre Baldi, P. Baldi, 1994, IEEE Trans. Neural Networks.

Seasonal variation of multiple-muon cosmic ray air showers observed in the NOvA detector on the surface

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2021, Physical Review D.

Deep learning for chemical reaction prediction

Gregor Urban, Pierre Baldi, David Fooshee, 2018 .

Efficient antihydrogen detection in antimatter physics by deep learning pdf

Pierre Baldi, Yasunori Yamazaki, Peter J. Sadowski, 2017, ArXiv.

What time is it? Deep learning approaches for circadian rhythms

Babak Shahbaba, Forest Agostinelli, Nicholas Ceglia, 2016, Bioinform..

Metabolomic and transcriptomic signatures of prenatal excessive methionine support nature rather than nurture in schizophrenia pathogenesis

P. Baldi, G. Abbott, A. Alachkar, 2020, Communications Biology.

The central clock suffices to drive the majority of circulatory metabolic rhythms

P. Baldi, P. Sassone-Corsi, P. Muñoz-Cánoves, 2022, bioRxiv.

Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA.

Pierre Baldi, G. W. Hatfield, Nicholas R. Steffen, 2005, The Journal of biological chemistry.

Solving the Rubik’s cube with deep reinforcement learning and search

Pierre Baldi, Forest Agostinelli, Stephen McAleer, 2019, Nat. Mach. Intell..

The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework

Pierre Baldi, Michael Zeller, Paolo Sassone-Corsi, 2015, Bioinform..

Surprise: A Shortcut for Attention?

Pierre Baldi, P. Baldi, 2005 .

VIRALpro: a tool to identify viral capsid and tail sequences

Pierre Baldi, Clovis Galiez, François Coste, 2016, Bioinform..

Deep machine learning-assisted multiphoton microscopy to reduce light exposure and expedite imaging pdf

Pierre Baldi, Yuntian Xue, William Tang, 2020, ArXiv.

The TY3 Gag3 Spacer Controls Intracellular Condensation and Uncoating

Arlo Z. Randall, Liza S. Z. Larsen, P. Baldi, 2011, Journal of Virology.

Learning to Predict Chemical Reactions

Pierre Baldi, Jonathan H. Chen, Chloé-Agathe Azencott, 2011, J. Chem. Inf. Model..

CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics

Pierre Baldi, Paolo Sassone-Corsi, Kristin Eckel-Mahan, 2012, Nature Methods.

Characterizing surprise in humans and monkeys

Robert A. Marino, P. Baldi, L. Itti, 2010 .

Gradient descent learning algorithm overview: a general dynamical systems perspective

Pierre Baldi, P. Baldi, 1995, IEEE Trans. Neural Networks.

Modeling of Mitochondria Bioenergetics Using a Composable Chemiosmotic Energy Transduction Rate Law: Theory and Experimental Validation

Pierre Baldi, Douglas Wallace, Ivan Chang, 2011, PloS one.

Enforcing Analytic Constraints in Neural Networks Emulating Physical Systems.

Pierre Baldi, Pierre Gentine, Tom Beucler, 2019, Physical review letters.

Learning in the Machine: To Share or Not to Share?

Pierre Baldi, Erik Linstead, Jordan Ott, 2019, Neural Networks.

Generalizing to new calorimeter geometries with Geometry-Aware Autoregressive Models (GAAMs) for fast calorimeter simulation

P. Baldi, D. Whiteson, Junze Liu, 2023, ArXiv.

End-To-End Latent Variational Diffusion Models for Inverse Problems in High Energy Physics

P. Baldi, D. Whiteson, Alexander Shmakov, 2023, NeurIPS.

Geometry-aware Autoregressive Models for Calorimeter Shower Simulations

P. Baldi, D. Whiteson, Junze Liu, 2022, ArXiv.

Sourcerer: a search engine for open source code supporting structure-based search

Sushil Krishna Bajracharya, Cristina V. Lopes, Pierre Baldi, 2006, OOPSLA '06.

Boolean autoencoders and hypercube clustering complexity

Pierre Baldi, P. Baldi, 2012, Designs, Codes and Cryptography.

A Computational Theory of Surprise

Pierre Baldi, P. Baldi, 2002 .

133 - Computer-Assisted Polyp Detection Identifies all Polyps Found by Expert Colonoscopists – And then Some

Andrew Q. Ninh, Kenneth J. Chang, P. Baldi, 2018 .

Clinical Knowledge and Reasoning Abilities of AI Large Language Models in Anesthesiology: A Comparative Study on the ABA Exam

P. Baldi, J. Rinehart, M. Ángel, 2023, medRxiv.

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties

Pierre Baldi, Sanjay Joshua Swamidass, Liva Ralaivola, 2007, J. Chem. Inf. Model..

Statistical Distribution of Chemical Fingerprints

Pierre Baldi, Sanjay Joshua Swamidass, P. Baldi, 2005, WILF.

On the Use of Bayesian Methods for Evaluating Compartmental Neural Models

Pierre Baldi, James M. Bower, Michael C. Vanier, 1998, Journal of Computational Neuroscience.

Probabilistic Models of Neuronal Spike Trains

Pierre Baldi, P. Baldi, 1997, Summer School on Neural Networks.

Sourcerer: mining and searching internet-scale software repositories

Sushil Krishna Bajracharya, Cristina V. Lopes, Pierre Baldi, 2008, Data Mining and Knowledge Discovery.

An Application of Latent Dirichlet Allocation to Analyzing Software Evolution

Cristina V. Lopes, Pierre Baldi, Erik Linstead, 2008, 2008 Seventh International Conference on Machine Learning and Applications.

Mining Internet-Scale Software Repositories

Sushil Krishna Bajracharya, Cristina V. Lopes, Pierre Baldi, 2007, NIPS.

Mining concepts from code with probabilistic topic models

Sushil Krishna Bajracharya, Cristina V. Lopes, Pierre Baldi, 2007, ASE.

Language Models can Solve Computer Tasks

P. Baldi, S. McAleer, Geunwoo Kim, 2023, ArXiv.

Learning to play Go using recursive neural networks

Lin Wu, Pierre Baldi, P. Baldi, 2008, Neural Networks.

A Normal Approximation for the Number of Local Maxima of a Random Function on a Graph

Pierre Baldi, Yosef Rinott, Charles Stein, 1989 .

A model for self-organizing large scale wireless networks

Maria-Gabriella Di Benedetto, Pierre Baldi, P. Baldi, 2001 .

Searching for solar KDAR with DUNE

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2021, 2107.09109.

Software Foundation Libraries for Intelligent Systems

Yves Chauvin, Pierre Baldi, Van Mittal-Henkle, 1999 .

Experiment Simulation Configurations Approximating DUNE TDR

J. I. Crespo-Anad'on, V. P. Luzio, P. Baldi, 2021, 2103.04797.

XDO: A Double Oracle Algorithm for Extensive-Form Games

P. Baldi, Roy Fox, S. McAleer, 2021, NeurIPS.

Pipeline PSRO: A Scalable Approach for Finding Approximate Nash Equilibria in Large Games pdf

Roy Fox, Pierre Baldi, Stephen McAleer, 2020, NeurIPS.

CFR-DO: A Double Oracle Algorithm for Extensive-Form Games

P. Baldi, Roy Fox, S. McAleer, 2021 .

A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval

Pierre Baldi, Sanjay Joshua Swamidass, S. Joshua Swamidass, 2010, Bioinform..

An end-to-end CNN with attentional mechanism applied to raw EEG in a BCI classification task

P. Baldi, U. Maoz, J. Ott, 2021, Journal of neural engineering.

Anytime Optimal PSRO for Two-Player Zero-Sum Games pdf

Pierre Baldi, Roy Fox, Marc Lanctot, 2022 .

Quantity vs. Quality: On Hyperparameter Optimization for Deep Reinforcement Learning pdf

Lars Hertel, Pierre Baldi, Daniel L. Gillen, 2020, ArXiv.

CircadiOmics: circadian omic web portal

Pierre Baldi, Yu Liu, Forest Agostinelli, 2018, Nucleic Acids Res..

DNA Microarrays and Gene Expression - From Experiments to Data Analysis and Modeling

Pierre Baldi, G. Wesley Hatfield, G. W. Hatfield, 2002 .

Liver and muscle circadian clocks cooperate to support glucose tolerance in mice.

P. Baldi, V. Orlando, P. Sassone-Corsi, 2023, Cell reports.

Adaptive Low Power Listening for Wireless Sensor Networks

Cristina V. Lopes, Pierre Baldi, Raja Jurdak, 2007, IEEE Transactions on Mobile Computing.

Neural Networks: Applications

Pierre Baldi, Søren Brunak, P. Baldi, 2001 .

Neural networks, orientations of the hypercube, and algebraic threshold functions

Pierre Baldi, P. Baldi, 1988, IEEE Trans. Inf. Theory.

Computational Applications of DNA Structural Scales

Pierre Baldi, Yves Chauvin, Søren Brunak, 1998, ISMB.

Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models

Pierre Baldi, Yves Chauvin, Søren Brunak, 1996, ISMB.

Privacy-Enhanced Methods for Comparing Compressed DNA Sequences pdf

David Eppstein, Michael T. Goodrich, Pierre Baldi, 2011, ArXiv.

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction

Pierre Baldi, Niranjan A. Subrahmanya, Peter J. Sadowski, 2016, J. Chem. Inf. Model..

A theory of aspects as latent topics

Sushil Krishna Bajracharya, Cristina V. Lopes, Pierre Baldi, 2008, OOPSLA.

Epigenetic regulation of the circadian gene Per1 in the hippocampus mediates age-related changes in memory and synaptic plasticity

P. Baldi, P. Sassone-Corsi, Yu Liu, 2018, bioRxiv.

Title A GRHL 3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia

Michael D. Zeller, P. Baldi, B. Andersen, 2022 .

The Quarks of Attention

P. Baldi, R. Vershynin, 2022, ArXiv.

A* Search Without Expansions: Learning Heuristic Functions with Deep Q-Networks

P. Baldi, Roy Fox, Forest Agostinelli, 2021, ArXiv.

Deep Semi-Supervised Learning Improves Universal Peptide Identification of Shotgun Proteomics Data

Pierre Baldi, David M. Rocke, Gregor Urban, 2020 .

Deep Learning Models of the Discrete Component of the Galactic Interstellar Gamma-Ray Emission

P. Baldi, Mohammadamin Tavakoli, Alexander Shmakov, 2022, Physical Review D.

A Fortran-Keras Deep Learning Bridge for Scientific Computing

Erik J. Linstead, P. Baldi, E. Linstead, 2020, Sci. Program..

SPLASH: Learnable Activation Functions for Improving Accuracy and Adversarial Robustness pdf

Pierre Baldi, Forest Agostinelli, Mohammadamin Tavakoli, 2020, Neural Networks.

Sherpa: Robust Hyperparameter Optimization for Machine Learning

Lars Hertel, Pierre Baldi, Jordan Ott, 2020, SoftwareX.

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method

Pierre Baldi, Sanjay Joshua Swamidass, Chloé-Agathe Azencott, 2009, J. Chem. Inf. Model..

Data structures and compression algorithms for genomic sequence data

Pierre Baldi, Douglas C. Wallace, Marty C. Brandon, 2009, Bioinform..

ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning

Pierre Baldi, Matthew A. Kayala, P. Baldi, 2012, J. Chem. Inf. Model..

On neuronal capacity

Pierre Baldi, Roman Vershynin, P. Baldi, 2019, NeurIPS.

Assessing the Potential of Deep Learning for Emulating Cloud Superparameterization in Climate Models With Real‐Geography Boundary Conditions

P. Baldi, P. Gentine, M. Pritchard, 2020, Journal of Advances in Modeling Earth Systems.

Assessment of predictions submitted for the CASP7 domain prediction category

David Kim, Keehyoung Joo, Jinwoo Lee, 2007, Proteins.

Spatiotemporal Mapping of Brain Cilia Length and Orientation Reveals Region-Specific Oscillation

P. Baldi, S. Nauli, A. Alachkar, 2023, bioRxiv.

ReactionMap: An Efficient Atom-Mapping Algorithm for Chemical Reactions

Pierre Baldi, David Fooshee, Alessio Andronico, 2013, J. Chem. Inf. Model..

Solving the Rubik's Cube Without Human Knowledge pdf

Pierre Baldi, Forest Agostinelli, Stephen McAleer, 2018, ArXiv.

Adaptation and habituation of visual responses in the superficial and intermediate layers of the superior colliculus (SC)

Pierre Baldi, Laurent Itti, Susan E. Boehnke, 2010 .

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time

Pierre Baldi, Sanjay Joshua Swamidass, S. Joshua Swamidass, 2007, J. Chem. Inf. Model..

Learning in the machine: The symmetries of the deep learning channel

Pierre Baldi, Peter J. Sadowski, Zhiqin Lu, 2017, Neural Networks.

General Terms Languages

Erik J. Linstead, P. Baldi, C. Lopes, 2022 .

Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images

Pierre Baldi, Chris Hughes, Gregor Urban, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter

Pierre Baldi, Sanjay Joshua Swamidass, S. Joshua Swamidass, 2015, Journal of Cheminformatics.

Modeling the Internet and the Web: Probabilistic Methods and Algorithms: Baldi/Probabilistic

Pierre Baldi, Paolo Frasconi, Padhraic Smyth, 2002 .

Call for a Public Open Database of All Chemical Reactions

P. Baldi, 2021, J. Chem. Inf. Model..

Selective Perception: Optimizing State Descriptions with Reinforcement Learning for Language Model Actors

P. Baldi, Roy Fox, Sameer Singh, 2023, ArXiv.

Software Modems for Underwater Sensor Networks

P. Baldi, C.V. Lopes, R. Jurdak, 2007, OCEANS 2007 - Europe.

Beep: 3D indoor positioning using audible sound

A. Haghighat, C.V. Lopes, R. Jurdak, 2005, Second IEEE Consumer Communications and Networking Conference, 2005. CCNC. 2005.

Generalizing to new geometries with Geometry-Aware Autoregressive Models (GAAMs) for fast calorimeter simulation

P. Baldi, D. Whiteson, Junze Liu, 2023, 2305.11531.

Oreo: detection of clones in the twilight zone

Cristina V. Lopes, Pierre Baldi, Yadong Lu, 2018, ESEC/SIGSOFT FSE.

A theory of capacity and sparse neural encoding

Pierre Baldi, Roman Vershynin, P. Baldi, 2021, Neural Networks.

Real-time reconstruction of high energy, ultrafast laser pulses using deep learning

P. Baldi, Christopher A Mancuso, J. Ott, 2022, Scientific Reports.

Real-time reconstruction of intense, ultrafast laser pulses using deep learning

P. Baldi, J. Ott, F. Dollar, 2021, 2104.08372.

Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms

Pierre Baldi, Jianlin Cheng, P. Baldi, 2005, ISMB.

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.

Arlo Z. Randall, P. Baldi, 2008, BMC structural biology.

Search for Active-Sterile Antineutrino Mixing Using Neutral-Current Interactions with the NOvA Experiment.

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2021, Physical review letters.

Observation of seasonal variation of atmospheric multiple-muon events in the NOvA Near Detector

D. P. Méndez, P. Baldi, R. Nichol, 2019, Physical Review D.

Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory

P. Baldi, P. Sassone-Corsi, Yu Liu, 2018, Nature Communications.

Statistical machine learning and data mining for chemoinformatics and drug discovery

Pierre Baldi, Chloé-Agathe Azencott, P. Baldi, 2010 .

Improved modeling of the discrete component of the Galactic interstellar γ -ray emission and implications for the Fermi –LAT Galactic Center excess

P. Baldi, Mohammadamin Tavakoli, Alexander Shmakov, 2022, Physical Review D.

ISMB 2016 Proceedings

Pierre Baldi, Teresa M. Przytycka, P. Baldi, 2016, Bioinform..

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins

Pierre Baldi, Jianlin Cheng, Michael J. Sweredoski, 2008, Bioinform..

Dysregulation of the hypothalamic‐pituitary‐adrenal (HPA) axis in irritable bowel syndrome

P. Baldi, L. Chang, B. Naliboff, 2009, Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society.

Curiosity-Driven Multi-Criteria Hindsight Experience Replay pdf

Pierre Baldi, Stephen McAleer, John B. Lanier, 2019, ArXiv.

Towards Automating Precision Studies of Clone Detectors

Cristina V. Lopes, Pierre Baldi, Hitesh Sajnani, 2018, 2019 IEEE/ACM 41st International Conference on Software Engineering (ICSE).

Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells

Matthew A. Kayala, P. Baldi, Yu-Han Chen, 2019, Scientific Reports.

RMechDB: A Public Database of Elementary Radical Reaction Steps

P. Baldi, Mohammadamin Tavakoli, D. V. Vranken, 2023, Journal of Chemical Information and Modeling.

Continuous Representation of Molecules using Graph Variational Autoencoder pdf

Pierre Baldi, Mohammadamin Tavakoli, P. Baldi, 2020, AAAI Spring Symposium: MLPS.

Protein profiles: Biases and protocols

Gianluca Pollastri, Gregor Urban, Mirko Torrisi, 2020, bioRxiv.

Flexibility of the genetic code with respect to DNA structure

Pierre Baldi, Søren Brunak, Anders Gorm Pedersen, 2001, Bioinform..

Tree and Hashing Data Structures to Speed up Chemical Searches: Analysis and Experiments

Pierre Baldi, Ramzi Nasr, Thomas Kristensen, 2011, Molecular informatics.

An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases

Pierre Baldi, Daniel S. Hirschberg, P. Baldi, 2009, J. Chem. Inf. Model..

Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive OR

Pierre Baldi, Daniel S. Hirschberg, Ramzi Nasr, 2008, J. Chem. Inf. Model..

Deep learning to enable color vision in the dark

P. Baldi, A. Browne, Josiah K To, 2022, PloS one.

New Machine Learning Methods for the Prediction of Protein Topologies

Paolo Frasconi, Alessandro Vullo, Gianluca Pollastri, 2002 .

Prediction of Contact Maps by Recurrent Neural Network Architectures and Hidden Context Propagation From All Four Cardinal Corners

Gianluca Pollastri, Pierre Baldi, P. Baldi, 2002 .

Speeding Up Chemical Searches Using the Inverted Index: The Convergence of Chemoinformatics and Text Search Methods

Pierre Baldi, Chen Li, Rares Vernica, 2012, J. Chem. Inf. Model..

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling

Pierre Baldi, Michael J. Sweredoski, Kevin J. Donovan, 2007, Bioinform..

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs

Pierre Baldi, Arlo Z. Randall, Arlo Randall, 2008, BMC Structural Biology.

Searching for exotic particles in high-energy physics with deep learning

P. Baldi, Peter Sadowski, D. Whiteson, 2014, Nature Communications.

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures

Arlo Z. Randall, P. Baldi, Ken Nagata, 2014, Bioinform..

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

P. Baldi, C. Magnan, 2014, Bioinform..

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method

S. Joshua Swamidass, P. Baldi, Chloé-Agathe Azencott, 2009, J. Chem. Inf. Model..

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

Michael J. Sweredoski, P. Baldi, 2008, Bioinform..

Reanalysis of primate brain circadian transcriptomics reveals connectivity-related oscillations

P. Baldi, Siwei Chen, Pieter Derdeyn, 2023, iScience.

Visual adaptation and novelty responses in the superior colliculus

Robert A. Marino, P. Baldi, L. Itti, 2011, The European journal of neuroscience.

Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery

Pierre Baldi, Sanjay Joshua Swamidass, S. Joshua Swamidass, 2011, WIRN.

Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis.

P. Baldi, J. Holst, A. Walch, 2022, Cell metabolism.

A Scalable Machine Learning Approach to Go

Lin Wu, Pierre Baldi, P. Baldi, 2006, NIPS.

On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks

P. Baldi, M. Rosen-Zvi, 2005, Neural Networks.

First measurement of neutrino oscillation parameters using neutrinos and antineutrinos by NOvA.

D. P. Méndez, P. Baldi, R. Nichol, 2019, Physical review letters.

Deducing the EOS of dense neutron star matter with machine learning

P. Baldi, D. Whiteson, A. Steiner, 2023, Astronomical Notes - Astronomische Nachrichten.

Sigmoid: a software infrastructure for pathway bioinformatics and systems biology

Pierre Baldi, Eric Mjolsness, Jianlin Cheng, 2005, IEEE Intelligent Systems.

Classifying shoulder implants in X-ray images using deep learning

Kazunori Okada, Gregor Urban, Saman Porhemmat, 2020, Computational and structural biotechnology journal.

A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia.

Michael D. Zeller, P. Baldi, B. Andersen, 2014, The Journal of clinical investigation.

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques

P. Baldi, P. Felgner, S. Sundaresh, 2006, Bioinform..

Volume I. Introduction to DUNE

V. P. Luzio, J. I. Crespo-Anadón, P. Baldi, 2020, Journal of Instrumentation.

Supernova neutrino detection in NOvA

D. A. Wickremasinghe, P. Baldi, R. Nichol, 2020, Journal of Cosmology and Astroparticle Physics.

Bayesian Causality

P. Baldi, B. Shahbaba, 2019, The American statistician.

Comprehensive mutagenesis of the C-terminal domain of the M13 gene-3 minor coat protein: the requirements for assembly into the bacteriophage particle.

P. Baldi, G. Weiss, S. Sidhu, 2003, Journal of molecular biology.

Generalizing to new geometries with Geometry-Aware Autoregressive Models (GAAMs) for fast calorimeter simulation

P. Baldi, D. Whiteson, Junze Liu, 2023, Journal of Instrumentation.

Editorial: Charting Chemical Space: Challenges and Opportunities for Artificial Intelligence and Machine Learning

Klaus-Robert Müller, Pierre Baldi, Gisbert Schneider, 2011, Molecular informatics.

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval

Pierre Baldi, Sanjay Joshua Swamidass, Daniel S. Hirschberg, 2007, J. Chem. Inf. Model..

Discovery of Power-Laws in Chemical Space

Pierre Baldi, Sanjay Joshua Swamidass, S. Joshua Swamidass, 2008, J. Chem. Inf. Model..

Bioinformatics Original Paper a Machine Learning Information Retrieval Approach to Protein Fold Recognition

P. Baldi, Jianlin Cheng, 2022 .

A theory of local learning, the learning channel, and the optimality of backpropagation

P. Baldi, Peter Sadowski, 2015, Neural Networks.

Tourbillon: a Physically Plausible Neural Architecture pdf

Pierre Baldi, Peter Sadowski, Mohammadamin Tavakoli, 2021, ArXiv.

Learning in the machine: Recirculation is random backpropagation

Pierre Baldi, Peter J. Sadowski, P. Baldi, 2018, Neural Networks.

Neural network gradient Hamiltonian Monte Carlo

Babak Shahbaba, Pierre Baldi, Lingge Li, 2017, Computational Statistics.

Learning in the Machine: Random Backpropagation and the Learning Channel pdf

Pierre Baldi, Peter J. Sadowski, Zhiqin Lu, 2016, ArXiv.

Clinical Knowledge and Reasoning Abilities of AI Large Language Models in Pharmacy: A Comparative Study on the NAPLEX Exam

P. Baldi, A. Alachkar, Mirana Angel, 2023, bioRxiv.

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs

Arlo Z. Randall, P. Baldi, 2008, BMC Structural Biology.

Retrotransposon profiling of RNA polymerase III initiation sites.

P. Baldi, M. Johnston, R. Mitra, 2012, Genome research.

Deducing neutron star equation of state from telescope spectra with machine-learning-derived likelihoods

P. Baldi, D. Whiteson, L. Lindblom, 2023, Journal of Cosmology and Astroparticle Physics.

A machine learning information retrieval approach to protein fold recognition

P. Baldi, Jianlin Cheng, 2006, Bioinform..

A scalable and integrative system for pathway bioinformatics and systems biology.

Pierre Baldi, Eric Mjolsness, Jianlin Cheng, 2010, Advances in experimental medicine and biology.