On Properties of Networks of Neuron-Like Elements. - Pierre Baldi; Santosh S. Venkatesh (NIPS, 1987)

Linear Learning: Landscapes and Algorithms. - Pierre Baldi (NIPS, 1988)

Group Actions and Learning for a Family of Automata. - Pierre Baldi (J. Comput. Syst. Sci., 1988)

Neural Networks, Acyclic Orientations of the Hypercube, and Sets of Orthogonal Vectors. - Pierre Baldi (SIAM J. Discret. Math., 1988)

Neural networks, orientations of the hypercube, and algebraic threshold functions. - Pierre Baldi (IEEE Trans. Inf. Theory, 1988)

On the Distribution of the Number of Local Minima of a Random Function on a Graph. - Pierre Baldi; Yosef Rinott; Charles Stein (NIPS, 1989)

Oscillations and Synchronizations in Neural Networks: an Exploration of the Labeling Hypothesis. - Amir F. Atiya; Pierre Baldi (Int. J. Neural Syst., 1989)

Neural networks and principal component analysis: Learning from examples without local minima. - Pierre Baldi; Kurt Hornik (Neural Networks, 1989)

Computing with Arrays of Bell-Shaped and Sigmoid Functions. - Pierre Baldi (NIPS, 1990)

On a generalized family of colorings. - Pierre Baldi (Graphs Comb., 1990)

Computing with Arrays of Coupled Oscillators: An Application to Preattentive Texture Discrimination. - Pierre Baldi; Ronny Meir (Neural Comput., 1990)

Programmed interactions in higher-order neural networks: Maximal capacity. - Santosh S. Venkatesh; Pierre Baldi (J. Complex., 1991)

Programmed interactions in higher-order neural networks: The outer-product algorithm. - Santosh S. Venkatesh; Pierre Baldi (J. Complex., 1991)

Temporal Evolution of Generalization during Learning in Linear Networks. - Pierre Baldi; Yves Chauvin (Neural Comput., 1991)

Contrastive Learning and Neural Oscillations. - Pierre Baldi; Fernando J. Pineda (Neural Comput., 1991)

Hidden Markov Models in Molecular Biology: New Algorithms and Applications. - Pierre Baldi; Yves Chauvin; Tim Hunkapiller; Marcella A. McClure (NIPS, 1992)

Trajectory learning using hierarchy of oscillatory modules. - Nikzad Benny Toomarian; Pierre Baldi (ESANN, 1993)

Learning trajectories with a hierarchy of oscillatory modules. - Pierre Baldi; Nikzad Benny Toomarian (ICNN, 1993)

Hidden Markov Models for Human Genes. - Pierre Baldi; Søren Brunak; Yves Chauvin; Jacob Engelbrecht; Anders Krogh (NIPS, 1993)

Neural Networks for Fingerprint Recognition. - Pierre Baldi; Yves Chauvin (Neural Comput., 1993)

Random interactions in higher order neural networks. - Pierre Baldi; Santosh S. Venkatesh (IEEE Trans. Inf. Theory, 1993)

Inferring Ground Truth from Subjective Labelling of Venus Images. - Padhraic Smyth; Usama M. Fayyad; Michael C. Burl; Pietro Perona; Pierre Baldi (NIPS, 1994)

Hidden Markov Models of the G-Protein-Coupled Receptor Family. - Pierre Baldi; Yves Chauvin (J. Comput. Biol., 1994)

Smooth On-Line Learning Algorithms for Hidden Markov Models. - Pierre Baldi; Yves Chauvin (Neural Comput., 1994)

How delays affect neural dynamics and learning. - Pierre Baldi; Amir F. Atiya (IEEE Trans. Neural Networks, 1994)

Periodic Sequence Patterns in Human Exons. - Pierre Baldi; Søren Brunak; Yves Chauvin; Jacob Engelbrecht; Anders Krogh (ISMB, 1995)

Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures. - Pierre Baldi; Yves Chauvin (ISMB, 1995)

Universal Approximnation and Learning of Trajectories Using Oscillators. - Pierre Baldi; Kurt Hornik (NIPS, 1995)

Substitution Matrices and Hidden Markov Models. - Pierre Baldi (J. Comput. Biol., 1995)

Gradient descent learning algorithm overview: a general dynamical systems perspective. - Pierre Baldi (IEEE Trans. Neural Networks, 1995)

Learning in linear neural networks: a survey. - Pierre Baldi; Kurt Hornik (IEEE Trans. Neural Networks, 1995)

Characterization of Prokaryotic and Eukaryotic Promoters Using Hidden Markov Models. - Anders Gorm Pedersen; Pierre Baldi; Søren Brunak; Yves Chauvin (ISMB, 1996)

Hybrid Modeling, HMM/NN Architectures, and Protein Applications. - Pierre Baldi; Yves Chauvin (Neural Comput., 1996)

Probabilistic Models of Neuronal Spike Trains. - Pierre Baldi (Summer School on Neural Networks, 1997)

Computational Applications of DNA Structural Scales. - Pierre Baldi; Søren Brunak; Yves Chauvin; Anders Gorm Pedersen (ISMB, 1998)

On the Use of Bayesian Methods for Evaluating Compartmental Neural Models. - Pierre Baldi; Michael C. Vanier; James M. Bower (J. Comput. Neurosci., 1998)

Structural basis for triplet repeat disorders: a computational analysis. - Pierre Baldi; Søren Brunak; Yves Chauvin; Anders Gorm Pedersen (Bioinform., 1999)

Exploiting the past and the future in protein secondary structure prediction. - Pierre Baldi; Søren Brunak; Paolo Frasconi; Giovanni Soda; Gianluca Pollastri (Bioinform., 1999)

The Biology of Eukaryotic Promoter Prediction - A Review. - Anders Gorm Pedersen; Pierre Baldi; Yves Chauvin; Søren Brunak (Comput. Chem., 1999)

Bioinformatics - the machine learning approach. - Pierre Baldi; Søren Brunak (MIT Press, 2000)

Protein β-Sheet Partner Prediction by Neural Networks. - Pierre Baldi; Gianluca Pollastri; Claus A. F. Andersen; Søren Brunak (ANNIMAB, 2000)

Matching Protein b-Sheet Partners by Feedforward and Recurrent Neural Networks. - Pierre Baldi; Gianluca Pollastri; Claus A. F. Andersen; Søren Brunak (ISMB, 2000)

Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods. - Steven Hampson; Pierre Baldi; Dennis F. Kibler; Suzanne B. Sandmeyer (ISMB, 2000)

On the convergence of a clustering algorithm for protein-coding regions in microbial genomes. - Pierre Baldi (Bioinform., 2000)

Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. - Pierre Baldi; Pierre-François Baisnée (Bioinform., 2000)

Assessing the accuracy of prediction algorithms for classification: an overview. - Pierre Baldi; Søren Brunak; Yves Chauvin; Claus A. F. Andersen; Henrik Nielsen (Bioinform., 2000)

Bioinformatics - the machine learning approach (2. ed.). - Pierre Baldi; Søren Brunak (MIT Press, 2001)

Improved prediction of the number of residue contacts in proteins by recurrent neural networks. - Gianluca Pollastri; Pierre Baldi; Piero Fariselli; Rita Casadio (ISMB (Supplement of Bioinformatics), 2001)

Bioethics, Fiction Science, and the Future of Mankind - Session Introduction. - Pierre Baldi; Søren Brunak (Pacific Symposium on Biocomputing, 2001)

DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression - Session Introduction. - Pierre Baldi; Richard H. Lathrop (Pacific Symposium on Biocomputing, 2001)

Bidirectional Dynamics for Protein Secondary Structure Prediction. - Pierre Baldi; Søren Brunak; Paolo Frasconi; Gianluca Pollastri; Giovanni Soda (Sequence Learning, 2001)

Flexibility of the genetic code with respect to DNA structure. - Pierre-François Baisnée; Pierre Baldi; Søren Brunak; Anders Gorm Pedersen (Bioinform., 2001)

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes. - Pierre Baldi; Anthony D. Long (Bioinform., 2001)

The Shattered Self - The End of Natural Evolution. - Pierre Baldi (MIT Press, 2002)

Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. - Gianluca Pollastri; Pierre Baldi (ISMB, 2002)

Prediction of Protein Topologies Using Generalized IOHMMS and RNNs. - Gianluca Pollastri; Pierre Baldi; Alessandro Vullo; Paolo Frasconi (NIPS, 2002)

Why are complementary DNA strands symmetric? - Pierre-François Baisnée; Steven Hampson; Pierre Baldi (Bioinform., 2002)

Distribution patterns of over-represented k-mers in non-coding yeast DNA. - Steven Hampson; Dennis F. Kibler; Pierre Baldi (Bioinform., 2002)

A Machine-Learning Strategy for Protein Analysis. - Pierre Baldi; Gianluca Pollastri (IEEE Intell. Syst., 2002)

Modeling and optimization of UWB communication networks through a flexible cost function. - Pierre Baldi; Luca De Nardis; Maria-Gabriella Di Benedetto (IEEE J. Sel. Areas Commun., 2002)

Modeling the Internet and the Web: Probabilistic Method and Algorithms - Pierre Baldi; Paolo Frasconi; Padhraic Smyth (John Wiley, 2003)

Machine Learning Methods for Computational Proteomics and Beyond. - Pierre Baldi (AI, 2003)

The Principled Design of Large-Scale Recursive Neural Network Architectures–DAG-RNNs and the Protein Structure Prediction Problem. - Pierre Baldi; Gianluca Pollastri (J. Mach. Learn. Res., 2003)

An Acoustic Identification Scheme for Location Systems. - Raja Jurdak; Cristina Videira Lopes; Pierre Baldi (ICPS, 2004)

Large-Scale Prediction of Disulphide Bond Connectivity. - Pierre Baldi; Jianlin Cheng; Alessandro Vullo (NIPS, 2004)

Structural proteomics of the poxvirus family. - Arlo Z. Randall; Pierre Baldi; Luis P. Villarreal (Artif. Intell. Medicine, 2004)

ICBS: a database of interactions between protein chains mediated by ?-sheet formation. - Yimeng Dou; Pierre-François Baisnée; Gianluca Pollastri; Yann Pécout; James Nowick; Pierre Baldi (Bioinform., 2004)

A survey, classification and comparative analysis of medium access control protocols for ad hoc networks. - Raja Jurdak; Cristina Videira Lopes; Pierre Baldi (IEEE Commun. Surv. Tutorials, 2004)

Combining protein secondary structure prediction models with ensemble methods of optimal complexity. - Yann Guermeur; Gianluca Pollastri; André Elisseeff; Dominique Zelus; Hélène Paugam-Moisy; Pierre Baldi (Neurocomputing, 2004)

Beep: 3D indoor positioning using audible sound. - Atri Mandal; Cristina V. Lopes; Tony Givargis; Amir Haghighat; Raja Jurdak; Pierre Baldi (CCNC, 2005)

A Principled Approach to Detecting Surprising Events in Video. - Laurent Itti; Pierre Baldi (CVPR (1), 2005)

SVM and pattern-enriched common fate graphs for the game of go. - Liva Ralaivola; Lin Wu; Pierre Baldi (ESANN, 2005)

State-Driven Energy Optimization in Wireless Sensor Networks. - Raja Jurdak; Pierre Baldi; Cristina Videira Lopes (Systems Communications, 2005)

Exploring chemical space with computers: challenges and opportunities. - Pierre Baldi (IJCNN, 2005)

Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms. - Jianlin Cheng; Pierre Baldi (ISMB (Supplement of Bioinformatics), 2005)

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. - Sanjay Joshua Swamidass; Jonathan H. Chen; Jocelyne Bruand; Peter Phung; Liva Ralaivola; Pierre Baldi (ISMB (Supplement of Bioinformatics), 2005)

Bayesian Surprise Attracts Human Attention. - Laurent Itti; Pierre Baldi (NIPS, 2005)

Statistical Distribution of Chemical Fingerprints. - Sanjay Joshua Swamidass; Pierre Baldi (WILF, 2005)

ChemDB: a public database of small molecules and related chemoinformatics resources. - Jonathan H. Chen; Sanjay Joshua Swamidass; Yimeng Dou; Jocelyne Bruand; Pierre Baldi (Bioinform., 2005)

Statistical detection of chromosomal homology using shared-gene density alone. - Steven E. Hampson; Brandon S. Gaut; Pierre Baldi (Bioinform., 2005)

Accurate Prediction of Protein Disordered Regions by Mining Protein Structure Data. - Jianlin Cheng; Michael J. Sweredoski; Pierre Baldi (Data Min. Knowl. Discov., 2005)

Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology. - Jianlin Cheng; Lucas Scharenbroich; Pierre Baldi; Eric Mjolsness (IEEE Intell. Syst., 2005)

How noisy and replicable are DNA microarray data? - Suman Sundaresh; She-pin Hung; G. Wesley Hatfield; Pierre Baldi (Int. J. Bioinform. Res. Appl., 2005)

MITOMAP: a human mitochondrial genome database - 2004 update. - Marty C. Brandon; Marie T. Lott; Kevin Cuong Nguyen; Syawal Spolim; Shamkant B. Navathe; Pierre Baldi; Douglas C. Wallace (Nucleic Acids Res., 2005)

SCRATCH: a protein structure and structural feature prediction server. - Jianlin Cheng; Arlo Z. Randall; Michael J. Sweredoski; Pierre Baldi (Nucleic Acids Res., 2005)

On the relationship between deterministic and probabilistic directed Graphical models: From Bayesian networks to recursive neural networks. - Pierre Baldi; Michal Rosen-Zvi (Neural Networks, 2005)

Graph kernels for chemical informatics. - Liva Ralaivola; Sanjay Joshua Swamidass; Hiroto Saigo; Pierre Baldi (Neural Networks, 2005)

U-MAC: a proactive and adaptive UWB medium access control protocol. - Raja Jurdak; Pierre Baldi; Cristina Videira Lopes (Wirel. Commun. Mob. Comput., 2005)

A Scalable Machine Learning Approach to Go. - Lin Wu; Pierre Baldi (NIPS, 2006)

Sourcerer: a search engine for open source code supporting structure-based search. - Sushil Krishna Bajracharya; Trung Chi Ngo; Erik Linstead; Yimeng Dou; Paul Rigor; Pierre Baldi; Cristina Videira Lopes (OOPSLA Companion, 2006)

A machine learning information retrieval approach to protein fold recognition. - Jianlin Cheng; Pierre Baldi (Bioinform., 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; Philip L. Felgner; Pierre Baldi (Bioinform., 2006)

DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. - Jianlin Cheng; Michael J. Sweredoski; Pierre Baldi (Data Min. Knowl. Discov., 2006)

Modular DAG-RNN Architectures for Assembling Coarse Protein Structures. - Gianluca Pollastri; Alessandro Vullo; Paolo Frasconi; Pierre Baldi (J. Comput. Biol., 2006)

Global landscape of recent inferred Darwinian selection for Homo sapiens. - Eric T. Wang; Greg Kodama; Pierre Baldi; Robert K. Moyzis (Proc. Natl. Acad. Sci. USA, 2006)

Localization of off-the-shelf mobile devices using audible sound: architectures, protocols and performance assessment. - Cristina Videira Lopes; Amir Haghighat; Atri Mandal; Tony Givargis; Pierre Baldi (ACM SIGMOBILE Mob. Comput. Commun. Rev., 2006)

Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. - Samuel A. Danziger; Sanjay Joshua Swamidass; Jue Zeng; Lawrence R. Dearth; Qiang Lu; Jonathan H. Chen; Jianlin Cheng; Vinh P. Hoang; Hiroto Saigo; Ray Luo 001; Pierre Baldi; Rainer K. Brachmann; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Machine Learning Challenges in Chemoinformatics and Drug Screening and Design. - Pierre Baldi (ICMLA, 2007)

From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. - Suman Sundaresh; Arlo Z. Randall; Berkay Unal; Jeannine M. Petersen; John T. Belisle; M. Gill Hartley; Melanie Duffield; Richard W. Titball; D. Huw Davies; Philip L. Felgner; Pierre Baldi (ISMB/ECCB (Supplement of Bioinformatics), 2007)

CodeGenie: using test-cases to search and reuse source code. - Otávio Augusto Lazzarini Lemos; Sushil Krishna Bajracharya; Joel Ossher; Ricardo Santos Morla; Paulo César Masiero; Pierre Baldi; Cristina Videira Lopes (ASE, 2007)

Mining concepts from code with probabilistic topic models. - Erik Linstead; Paul Rigor; Sushil Krishna Bajracharya; Cristina Videira Lopes; Pierre Baldi (ASE, 2007)

Learning and Charting Chemical Space with Strings and Graphs: Challenges and Opportunities for AI and Machine Learning. - Pierre Baldi (MLG, 2007)

Mining Eclipse Developer Contributions via Author-Topic Models. - Erik Linstead; Paul Rigor; Sushil Krishna Bajracharya; Cristina Videira Lopes; Pierre Baldi (MSR, 2007)

Mining Internet-Scale Software Repositories. - Erik Linstead; Paul Rigor; Sushil Krishna Bajracharya; Cristina Videira Lopes; Pierre Baldi (NIPS, 2007)

ChemDB update - full-text search and virtual chemical space. - Jonathan H. Chen; Erik Linstead; Sanjay Joshua Swamidass; Dennis Wang; Pierre Baldi (Bioinform., 2007)

Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling. - Michael J. Sweredoski; Kevin J. Donovan; Bao D. Nguyen; A. J. Shaka; Pierre Baldi (Bioinform., 2007)

Improved residue contact prediction using support vector machines and a large feature set. - Jianlin Cheng; Pierre Baldi (BMC Bioinform., 2007)

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. - Chloé-Agathe Azencott; Alexandre Ksikes; S. Joshua Swamidass; Jonathan H. Chen; Liva Ralaivola; Pierre Baldi (J. Chem. Inf. Model., 2007)

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval. - Pierre Baldi; Ryan W. Benz; Daniel S. Hirschberg; S. Joshua Swamidass (J. Chem. Inf. Model., 2007)

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. - S. Joshua Swamidass; Pierre Baldi (J. Chem. Inf. Model., 2007)

Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. - S. Joshua Swamidass; Pierre Baldi (J. Chem. Inf. Model., 2007)

An enhanced MITOMAP with a global mtDNA mutational phylogeny. - Eduardo Ruiz-Pesini; Marie T. Lott; Vincent Procaccio; Jason C. Poole; Marty C. Brandon; Dan Mishmar; Christina Yi; James Kreuziger; Pierre Baldi; Douglas C. Wallace (Nucleic Acids Res., 2007)

Adaptive Low Power Listening for Wireless Sensor Networks. - Raja Jurdak; Pierre Baldi; Cristina Videira Lopes (IEEE Trans. Mob. Comput., 2007)

Effective Compression of Monotone and Quasi-Monotone Sequences of Integers. - Daniel S. Hirschberg; Pierre Baldi (DCC, 2008)

An Application of Latent Dirichlet Allocation to Analyzing Software Evolution. - Erik Linstead; Cristina Videira Lopes; Pierre Baldi (ICMLA, 2008)

BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. - Pierre Baldi; Ryan W. Benz (ISMB, 2008)

A theory of aspects as latent topics. - Pierre Baldi; Cristina Videira Lopes; Erik Linstead; Sushil Krishna Bajracharya (OOPSLA, 2008)

TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. - Arlo Z. Randall; Jianlin Cheng; Michael J. Sweredoski; Pierre Baldi (Bioinform., 2008)

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. - Michael J. Sweredoski; Pierre Baldi (Bioinform., 2008)

Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive OR. - Pierre Baldi; Daniel S. Hirschberg; Ramzi Nasr (J. Chem. Inf. Model., 2008)

Discovery of Power-Laws in Chemical Space. - Ryan W. Benz; S. Joshua Swamidass; Pierre Baldi (J. Chem. Inf. Model., 2008)

Learning to play Go using recursive neural networks. - Lin Wu; Pierre Baldi (Neural Networks, 2008)

User contribution and trust in Wikipedia. - Sara Javanmardi; Yasser Ganjisaffar; Cristina Videira Lopes; Pierre Baldi (CollaborateCom, 2009)

Capturing Java naming conventions with first-order Markov models. - Erik Linstead; Lindsey Hughes; Cristina Videira Lopes; Pierre Baldi (ICPC, 2009)

Mining the coherence of GNOME bug reports with statistical topic models. - Erik Linstead; Pierre Baldi (MSR, 2009)

SourcererDB: An aggregated repository of statically analyzed and cross-linked open source Java projects. - Joel Ossher; Sushil Krishna Bajracharya; Erik Linstead; Pierre Baldi; Cristina Videira Lopes (MSR, 2009)

Software-driven sensor networks for short-range shallow water applications. - Raja Jurdak; Pierre Baldi; Cristina Videira Lopes (Ad Hoc Networks, 2009)

Data structures and compression algorithms for genomic sequence data. - Marty C. Brandon; Douglas C. Wallace; Pierre Baldi (Bioinform., 2009)

SOLpro: accurate sequence-based prediction of protein solubility. - Christophe N. Magnan; Arlo Z. Randall; Pierre Baldi (Bioinform., 2009)

MotifMap: a human genome-wide map of candidate regulatory motif sites. - Xiaohui Xie; Paul Rigor; Pierre Baldi (Bioinform., 2009)

Sourcerer: mining and searching internet-scale software repositories. - Erik Linstead; Sushil Krishna Bajracharya; Trung Chi Ngo; Paul Rigor; Cristina Videira Lopes; Pierre Baldi (Data Min. Knowl. Discov., 2009)

Large scale study of multiple-molecule queries. - Ramzi Nasr; Sanjay Joshua Swamidass; Pierre Baldi (J. Cheminformatics, 2009)

An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases. - Pierre Baldi; Daniel S. Hirschberg (J. Chem. Inf. Model., 2009)

No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms. - Jonathan H. Chen; Pierre Baldi (J. Chem. Inf. Model., 2009)

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. - S. Joshua Swamidass; Chloé-Agathe Azencott; Ting-Wan Lin; Hugo Gramajo; Shiou-Chuan Tsai; Pierre Baldi (J. Chem. Inf. Model., 2009)

A scalable reference-point based algorithm to efficiently search large chemical databases. - Francesco Napolitano; Roberto Tagliaferri; Pierre Baldi (IJCNN, 2010)

Information-Theoretic Metrics for Project-Level Scattering and Tangling. - Erik Linstead; Lindsey Hughes; Cristina Videira Lopes; Pierre Baldi (SEKE, 2010)

Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery. - Pierre Baldi; Chloé-Agathe Azencott; Sanjay Joshua Swamidass (WIRN, 2010)

High-throughput prediction of protein antigenicity using protein microarray data. - Christophe N. Magnan; Michael Zeller; Matthew A. Kayala; Adam Vigil; Arlo Z. Randall; Philip L. Felgner; Pierre Baldi (Bioinform., 2010)

A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. - Sanjay Joshua Swamidass; Chloé-Agathe Azencott; Kenny Daily; Pierre Baldi (Bioinform., 2010)

Data structures and compression algorithms for high-throughput sequencing technologies. - Kenny Daily; Paul Rigor; Scott Christley; Xiaohui Xie; Pierre Baldi (BMC Bioinform., 2010)

When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values. - Pierre Baldi; Ramzi Nasr (J. Chem. Inf. Model., 2010)

Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors. - Ramzi Nasr; Daniel S. Hirschberg; Pierre Baldi (J. Chem. Inf. Model., 2010)

Of bits and wows: A Bayesian theory of surprise with applications to attention. - Pierre Baldi; Laurent Itti (Neural Networks, 2010)

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors. - Thomas C. Whisenant; David T. Ho; Ryan W. Benz; Jeffrey S. Rogers; Robyn M. Kaake; Elizabeth A. Gordon; Lan Huang; Pierre Baldi; Lee Bardwell (PLoS Comput. Biol., 2010)

Modeling user reputation in wikis. - Sara Javanmardi; Cristina Videira Lopes; Pierre Baldi (Stat. Anal. Data Min., 2010)

DNA Microarrays and Gene Expression - From Experiments to Data Analysis and Modeling. - Pierre Baldi; G. Wesley Hatfield (Cambridge University Press, 2011)

Countering GATTACA: efficient and secure testing of fully-sequenced human genomes. - Pierre Baldi; Roberta Baronio; Emiliano De Cristofaro; Paolo Gasti; Gene Tsudik (CCS, 2011)

A Machine Learning Approach to Predict Chemical Reactions. - Matthew A. Kayala; Pierre Baldi (NIPS, 2011)

MotifMap: integrative genome-wide maps of regulatory motif sites for model species. - Kenneth Daily; Vishal R. Patel; Paul Rigor; Xiaohui Xie; Pierre Baldi (BMC Bioinform., 2011)

Privacy-Enhanced Methods for Comparing Compressed DNA Sequences - David Eppstein; Michael T. Goodrich; Pierre Baldi (CoRR, 2011)

Complex-Valued Autoencoders - Pierre Baldi; Sholeh Forouzan; Zhiqin Lu (CoRR, 2011)

Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. - Alessio Andronico; Arlo Z. Randall; Ryan W. Benz; Pierre Baldi (J. Chem. Inf. Model., 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 Centre. - Pierre Baldi (J. Chem. Inf. Model., 2011)

Learning to Predict Chemical Reactions. - Matthew A. Kayala; Chloé-Agathe Azencott; Jonathan H. Chen; Pierre Baldi (J. Chem. Inf. Model., 2011)

Deep Spatio-Temporal Architectures and Learning for Protein Structure Prediction. - Pietro Di Lena; Pierre Baldi; Ken Nagata (NIPS, 2012)

Deep architectures for protein contact map prediction. - Pietro di Lena; Ken Nagata; Pierre Baldi (Bioinform., 2012)

Boolean autoencoders and hypercube clustering complexity. - Pierre Baldi (Des. Codes Cryptogr., 2012)

The Universal Campus: An open virtual 3-D world infrastructure for research and education. - Pierre Baldi; Cristina Videira Lopes (eLearn Mag., 2012)

ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning. - Matthew A. Kayala; Pierre Baldi (J. Chem. Inf. Model., 2012)

Speeding Up Chemical Searches Using the Inverted Index: The Convergence of Chemoinformatics and Text Search Methods. - Ramzi Nasr; Rares Vernica; Chen Li 001; Pierre Baldi (J. Chem. Inf. Model., 2012)

Autoencoders, Unsupervised Learning, and Deep Architectures. - Pierre Baldi (ICML Unsupervised and Transfer Learning, 2012)

Cyber-T web server: differential analysis of high-throughput data. - Matthew A. Kayala; Pierre Baldi (Nucleic Acids Res., 2012)

Complex-valued autoencoders. - Pierre Baldi; Zhiqin Lu (Neural Networks, 2012)

Understanding Dropout. - Pierre Baldi; Peter J. Sadowski (NIPS, 2013)

An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases. - Francesco Napolitano; Roberto Tagliaferri; Pierre Baldi (WIRN, 2013)

A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions. - Ivan Chang; Pierre Baldi (Bioinform., 2013)

ReactionMap: An Efficient Atom-Mapping Algorithm for Chemical Reactions. - David Fooshee; Alessio Andronico; Pierre Baldi (J. Chem. Inf. Model., 2013)

Deep Architectures and Deep Learning in Chemoinformatics: The Prediction of Aqueous Solubility for Drug-Like Molecules. - Alessandro Lusci; Gianluca Pollastri; Pierre Baldi (J. Chem. Inf. Model., 2013)

Small-Molecule 3D Structure Prediction Using Open Crystallography Data. - Peter J. Sadowski; Pierre Baldi (J. Chem. Inf. Model., 2013)

Deep autoencoder neural networks for gene ontology annotation predictions. - Davide Chicco; Peter J. Sadowski; Pierre Baldi (BCB, 2014)

Deep Learning, Dark Knowledge, and Dark Matter. - Peter J. Sadowski; Julian Collado; Daniel Whiteson; Pierre Baldi (HEPML@NIPS, 2014)

Searching for Higgs Boson Decay Modes with Deep Learning. - Peter J. Sadowski; Daniel Whiteson; Pierre Baldi (NIPS, 2014)

Parallel Multicut Segmentation via Dual Decomposition. - Julian Yarkony; Thorsten Beier; Pierre Baldi; Fred A. Hamprecht (NFMCP, 2014)

The dropout learning algorithm. - Pierre Baldi; Peter J. Sadowski (Artif. Intell., 2014)

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. - Christophe N. Magnan; Pierre Baldi (Bioinform., 2014)

Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. - Ken Nagata; Arlo Z. Randall; Pierre Baldi (Bioinform., 2014)

Enhanced Higgs to $τ^+τ^-$ Searches with Deep Learning. - Pierre Baldi; Peter J. Sadowski; Daniel Whiteson (CoRR, 2014)

Deep Learning: Theory, Algorithms, and Applications (NII Shonan Meeting 2014-5). - Pierre Baldi; Kenji Fukumizu; Tomaso A. Poggio (NII Shonan Meet. Rep., 2014)

A Genomic Analysis Pipeline and Its Application to Pediatric Cancers. - Michael Zeller; Christophe N. Magnan; Vishal R. Patel; Paul Rigor; Leonard Sender; Pierre Baldi (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework. - Vishal R. Patel; Nicholas Ceglia; Michael Zeller; Kristin Eckel-Mahan; Paolo Sassone-Corsi; Pierre Baldi (Bioinform., 2015)

Learning Activation Functions to Improve Deep Neural Networks. - Forest Agostinelli; Matthew D. Hoffman; Peter J. Sadowski; Pierre Baldi (ICLR (Workshop), 2015)

The Ebb and Flow of Deep Learning: a Theory of Local Learning. - Pierre Baldi; Peter J. Sadowski (CoRR, 2015)

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. - Alessandro Lusci; Michael R. Browning; David Fooshee; S. Joshua Swamidass; Pierre Baldi (J. Cheminformatics, 2015)

Revealing Fundamental Physics from the Daya Bay Neutrino Experiment Using Deep Neural Networks. - Evan Racah; Seyoon Ko; Peter J. Sadowski; Wahid Bhimji; Craig Tull; Sang-Yun Oh; Pierre Baldi; Prabhat (ICMLA, 2016)

What time is it? Deep learning approaches for circadian rhythms. - Forest Agostinelli; Nicholas Ceglia; Babak Shahbaba; Paolo Sassone-Corsi; Pierre Baldi (Bioinform., 2016)

ISMB 2016 Proceedings. - Pierre Baldi; Teresa M. Przytycka (Bioinform., 2016)

VIRALpro: a tool to identify viral capsid and tail sequences. - Clovis Galiez; Christophe N. Magnan; François Coste; Pierre Baldi (Bioinform., 2016)

Parameterized Machine Learning for High-Energy Physics. - Pierre Baldi; Kyle Cranmer; Taylor Faucett; Peter J. Sadowski; Daniel Whiteson (CoRR, 2016)

Learning in the Machine: Random Backpropagation and the Learning Channel. - Pierre Baldi; Peter J. Sadowski; Zhiqin Lu (CoRR, 2016)

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction. - Peter J. Sadowski; David Fooshee; Niranjan Subrahmanya; Pierre Baldi (J. Chem. Inf. Model., 2016)

A theory of local learning, the learning channel, and the optimality of backpropagation. - Pierre Baldi; Peter J. Sadowski (Neural Networks, 2016)

From Reinforcement Learning to Deep Reinforcement Learning: An Overview. - Forest Agostinelli; Guillaume Hocquet; Sameer Singh 001; Pierre Baldi (Braverman Readings in Machine Learning, 2017)

Deep Learning in the Natural Sciences: Applications to Physics. - Peter J. Sadowski; Pierre Baldi (Braverman Readings in Machine Learning, 2017)

MotifMap-RNA: a genome-wide map of RBP binding sites. - Yu Liu; Sha Sun; Timothy Bredy; Marcelo A. Wood; Robert C. Spitale; Pierre Baldi (Bioinform., 2017)

A multi-resolution approach for spinal metastasis detection using deep Siamese neural networks. - Juan Wang 002; Zhiyuan Fang; Ning Lang; Huishu Yuan; Min-Ying Su; Pierre Baldi (Comput. Biol. Medicine, 2017)

Efficient Antihydrogen Detection in Antimatter Physics by Deep Learning. - Peter J. Sadowski; Balint Radics; Ananya; Yasunori Yamazaki; Pierre Baldi (CoRR, 2017)

Learning in the machine: The symmetries of the deep learning channel. - Pierre Baldi; Peter J. Sadowski; Zhiqin Lu (Neural Networks, 2017)

Detecting Cardiovascular Disease from Mammograms With Deep Learning. - Juan Wang 002; Huanjun Ding; Fatemeh Azamian Bidgoli; Brian Zhou; Carlos Iribarren; Sabee Molloi; Pierre Baldi (IEEE Trans. Medical Imaging, 2017)

On Neuronal Capacity. - Pierre Baldi; Roman Vershynin (NeurIPS, 2018)

Oreo: detection of clones in the twilight zone. - Vaibhav Saini; Farima Farmahinifarahani; Yadong Lu; Pierre Baldi; Cristina V. Lopes (ESEC/SIGSOFT FSE, 2018)

Learning in the machine: Random backpropagation and the deep learning channel. - Pierre Baldi; Peter J. Sadowski; Zhiqin Lu (Artif. Intell., 2018)

Solving the Rubik's Cube Without Human Knowledge. - Stephen McAleer; Forest Agostinelli; Alexander Shmakov; Pierre Baldi (CoRR, 2018)

The inner and outer approaches to the design of recursive neural architectures. - Pierre Baldi (Data Min. Knowl. Discov., 2018)

Inner and Outer Recursive Neural Networks for Chemoinformatics Applications. - Gregor Urban; Niranjan Subrahmanya; Pierre Baldi (J. Chem. Inf. Model., 2018)

CircadiOmics: circadian omic web portal. - Nicholas Ceglia; Yu Liu; Siwei Chen; Forest Agostinelli; Kristin Eckel-Mahan; Paolo Sassone-Corsi; Pierre Baldi (Nucleic Acids Res., 2018)

ClusterCAD: a computational platform for type I modular polyketide synthase design. - Clara H. Eng; Tyler W. H. Backman; Constance B. Bailey; Christophe N. Magnan; Héctor García Martín; Leonard Katz; Pierre Baldi; Jay D. Keasling (Nucleic Acids Res., 2018)

Learning in the machine: Recirculation is random backpropagation. - Pierre Baldi; Peter J. Sadowski (Neural Networks, 2018)

Efficient Neutrino Oscillation Parameter Inference with Gaussian Process. - Lingge Li; Nitish Nayak; Jianming Bian; Pierre Baldi (AAAI, 2019)

Solving the Rubik's Cube with Approximate Policy Iteration. - Stephen McAleer; Forest Agostinelli; Alexander Shmakov; Pierre Baldi (ICLR (Poster), 2019)

Towards automating precision studies of clone detectors. - Vaibhav Saini; Farima Farmahinifarahani; Yadong Lu; Di Yang 001; Pedro Martins 001; Hitesh Sajnani; Pierre Baldi; Cristina V. Lopes (ICSE, 2019)

Learning in the Machine: Random Backpropagation and the Deep Learning Channel (Extended Abstract). - Pierre Baldi; Peter J. Sadowski; Zhiqin Lu (IJCAI, 2019)

Modeling Dynamic Functional Connectivity with Latent Factor Gaussian Processes. - Lingge Li; Dustin S. Pluta; Babak Shahbaba; Norbert Fortin; Hernando Ombao; Pierre Baldi (NeurIPS, 2019)

Curiosity-Driven Multi-Criteria Hindsight Experience Replay. - John B. Lanier; Stephen McAleer; Pierre Baldi (CoRR, 2019)

ColosseumRL: A Framework for Multiagent Reinforcement Learning in N-Player Games. - Alexander Shmakov; John B. Lanier; Stephen McAleer; Rohan Achar; Cristina V. Lopes; Pierre Baldi (CoRR, 2019)

Neural network gradient Hamiltonian Monte Carlo. - Lingge Li; Andrew Holbrook; Babak Shahbaba; Pierre Baldi (Comput. Stat., 2019)

Solving the Rubik's cube with deep reinforcement learning and search. - Forest Agostinelli; Stephen McAleer; Alexander Shmakov; Pierre Baldi (Nat. Mach. Intell., 2019)

The capacity of feedforward neural networks. - Pierre Baldi; Roman Vershynin (Neural Networks, 2019)

Polynomial Threshold Functions, Hyperplane Arrangements, and Random Tensors. - Pierre Baldi; Roman Vershynin (SIAM J. Math. Data Sci., 2019)

Deep Learning for Drug Discovery and Cancer Research: Automated Analysis of Vascularization Images. - Gregor Urban; Kevin Bache; Duc T. T. Phan; Agua Sobrino; Alexander Shmakov; Stephanie J. Hachey; Christopher C. W. Hughes; Pierre Baldi (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Highly Accurate Machine Fault Diagnosis Using Deep Transfer Learning. - Siyu Shao; Stephen McAleer; Ruqiang Yan 001; Pierre Baldi (IEEE Trans. Ind. Informatics, 2019)

Continuous Representation of Molecules using Graph Variational Autoencoder. - Mohammadamin Tavakoli; Pierre Baldi (AAAI Spring Symposium: MLPS, 2020)

Pipeline PSRO: A Scalable Approach for Finding Approximate Nash Equilibria in Large Games. - Stephen McAleer; John B. Lanier; Roy Fox; Pierre Baldi (NeurIPS, 2020)

Quantity vs. Quality: On Hyperparameter Optimization for Deep Reinforcement Learning. - Lars Hertel; Pierre Baldi; Daniel L. Gillen (CoRR, 2020)

Permutationless Many-Jet Event Reconstruction with Symmetry Preserving Attention Networks. - Michael James Fenton; Alexander Shmakov; Ta-Wei Ho; Shih-Chieh Hsu; Daniel Whiteson; Pierre Baldi (CoRR, 2020)

Deep machine learning-assisted multiphoton microscopy to reduce light exposure and expedite imaging. - Stephen McAleer; Alex Fast; Yuntian Xue; Magdalene Seiler; William Tang 001; Mihaela Balu; Pierre Baldi; Andrew W. Browne (CoRR, 2020)

Deep-Learning-Based Kinematic Reconstruction for DUNE. - Junze Liu; Jordan Ott; Julian Collado; Benjamin Jargowsky; Wenjie Wu; Jianming Bian; Pierre Baldi (CoRR, 2020)

Learning in the machine: To share or not to share? - Jordan Ott; Erik Linstead; Nicholas LaHaye; Pierre Baldi (Neural Networks, 2020)

Development and validation of a deep neural network model to predict postoperative mortality, acute kidney injury, and reintubation using a single feature set. - Ira Hofer; Christine K. Lee; Eilon Gabel; Pierre Baldi; Maxime Cannesson (npj Digit. Medicine, 2020)

Sherpa: Robust hyperparameter optimization for machine learning. - Lars Hertel; Julian Collado; Peter J. Sadowski; Jordan Ott; Pierre Baldi (SoftwareX, 2020)

A Fortran-Keras Deep Learning Bridge for Scientific Computing. - Jordan Ott; Mike Pritchard; Natalie Best; Erik Linstead; Milan Curcic; Pierre Baldi (Sci. Program., 2020)

Deep Bucket Elimination. - Yasaman Razeghi; Kalev Kask; Yadong Lu; Pierre Baldi; Sakshi Agarwal; Rina Dechter (IJCAI, 2021)

XDO: A Double Oracle Algorithm for Extensive-Form Games. - Stephen McAleer; John B. Lanier; Kevin A. Wang; Pierre Baldi; Roy Fox (NeurIPS, 2021)

D-REX: Static Detection of Relevant Runtime Exceptions with Location Aware Transformer. - Farima Farmahinifarahani; Yadong Lu; Vaibhav Saini; Pierre Baldi; Cristina V. Lopes (SCAM, 2021)

Fold recognition by scoring protein maps using the congruence coefficient. - Pietro Di Lena; Pierre Baldi (Bioinform., 2021)

Detecting Pulmonary Coccidioidomycosis (Valley fever) with Deep Convolutional Neural Networks. - Jordan Ott; David Bruyette; Cody L. Arbuckle; Dylan Balsz; Silke Hecht; Lisa Shubitz; Pierre Baldi (CoRR, 2021)

A* Search Without Expansions: Learning Heuristic Functions with Deep Q-Networks. - Forest Agostinelli; Alexander Shmakov; Stephen McAleer; Roy Fox; Pierre Baldi (CoRR, 2021)

XDO: A Double Oracle Algorithm for Extensive-Form Games. - Stephen McAleer; John B. Lanier; Pierre Baldi; Roy Fox (CoRR, 2021)

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 (CoRR, 2021)

Improving Social Welfare While Preserving Autonomy via a Pareto Mediator. - Stephen McAleer; John B. Lanier; Michael Dennis 001; Pierre Baldi; Roy Fox (CoRR, 2021)

Tourbillon: a Physically Plausible Neural Architecture. - Mohammadamin Tavakoli; Peter J. Sadowski; Pierre Baldi (CoRR, 2021)

A theory of capacity and sparse neural encoding. - Pierre Baldi; Roman Vershynin (Neural Networks, 2021)

SPLASH: Learnable activation functions for improving accuracy and adversarial robustness. - Mohammadamin Tavakoli; Forest Agostinelli; Pierre Baldi (Neural Networks, 2021)

Development and validation of an interpretable neural network for prediction of postoperative in-hospital mortality. - Christine K. Lee; Muntaha Samad; Ira Hofer; Maxime Cannesson; Pierre Baldi (npj Digit. Medicine, 2021)

SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity. - Gregor Urban; Christophe N. Magnan; Pierre Baldi (Bioinform., 2022)

Rxn Hypergraph: a Hypergraph Attention Model for Chemical Reaction Representation. - Mohammadamin Tavakoli; Alexander Shmakov; Francesco Ceccarelli; Pierre Baldi (CoRR, 2022)

Anytime PSRO for Two-Player Zero-Sum Games. - Stephen McAleer; Kevin Wang 003; John B. Lanier; Marc Lanctot; Pierre Baldi; Tuomas Sandholm; Roy Fox (CoRR, 2022)

The Quarks of Attention. - Pierre Baldi; Roman Vershynin (CoRR, 2022)

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 (CoRR, 2022)

Self-Play PSRO: Toward Optimal Populations in Two-Player Zero-Sum Games. - Stephen McAleer; John B. Lanier; Kevin A. Wang; Pierre Baldi; Roy Fox; Tuomas Sandholm (CoRR, 2022)

Feasible Adversarial Robust Reinforcement Learning for Underspecified Environments. - John B. Lanier; Stephen McAleer; Pierre Baldi; Roy Fox (CoRR, 2022)

Geometry-aware Autoregressive Models for Calorimeter Shower Simulations. - Junze Liu; Aishik Ghosh; Dylan Smith; Pierre Baldi; Daniel Whiteson (CoRR, 2022)

Reproducible Hyperparameter Optimization. - Lars Hertel; Pierre Baldi; Daniel L. Gillen (J. Comput. Graph. Stat., 2022)

Call for a Public Open Database of All Chemical Reactions. - Pierre Baldi (J. Chem. Inf. Model., 2022)

Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity. - Mohammadamin Tavakoli; Aaron Mood; David Van Vranken; Pierre Baldi (J. Chem. Inf. Model., 2022)

Weakly Supervised Polyp Segmentation in Colonoscopy Images Using Deep Neural Networks. - Siwei Chen; Gregor Urban; Pierre Baldi (J. Imaging, 2022)

CircadiOmics: circadian omic web portal. - Muntaha Samad; Forest Agostinelli; Tomoki Sato; Kohei Shimaji; Pierre Baldi (Nucleic Acids Res., 2022)

Hippocampal ensembles represent sequential relationships among an extended sequence of nonspatial events. - Babak Shahbaba; Lingge Li; Forest Agostinelli; Mansi Saraf; Keiland W. Cooper; Derenik Haghverdian; Gabriel A. Elias; Pierre Baldi; Norbert J. Fortin (Zenodo, 2022)

Language Models can Solve Computer Tasks. - Geunwoo Kim; Pierre Baldi; Stephen McAleer (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 (NeurIPS, 2023)

AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learning. - Mohammadamin Tavakoli; Pierre Baldi; Ann Marie Carlton; Yin Ting T. Chiu; Alexander Shmakov; David Van Vranken (NeurIPS, 2023)

ClimSim: A large multi-scale dataset for hybrid physics-ML climate emulation. - Sungduk Yu; Walter M. Hannah; Liran Peng; Jerry Lin; Mohamed Aziz Bhouri; Ritwik Gupta; Björn Lütjens; Justus C. Will; Gunnar Behrens; Julius Busecke; Nora Loose; Charles Stern; et al. (NeurIPS, 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; Pierre Baldi (SNAMS, 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 L. Arbuckle; David Bruyette; Pierre Baldi (SNAMS, 2023)

Interpretable Joint Event-Particle Reconstruction for Neutrino Physics at NOvA with Sparse CNNs and Transformers. - Alexander Shmakov; Alejandro Yankelevich; Jianming Bian; Pierre Baldi (CoRR, 2023)

Generalizing to new calorimeter geometries with Geometry-Aware Autoregressive Models (GAAMs) for fast calorimeter simulation. - Junze Liu; Aishik Ghosh; Dylan Smith; Pierre Baldi; Daniel Whiteson (CoRR, 2023)

ClimSim: An open large-scale dataset for training high-resolution physics emulators in hybrid multi-scale climate simulators. - Sungduk Yu; Walter M. Hannah; Liran Peng; Mohamed Aziz Bhouri; Ritwik Gupta; Jerry Lin; Björn Lütjens; Justus C. Will; Tom Beucler; Bryce E. Harrop; Benjamin R. Hillman; Andrea M. Jenney; et al. (CoRR, 2023)

Selective Perception: Optimizing State Descriptions with Reinforcement Learning for Language Model Actors. - Kolby Nottingham; Yasaman Razeghi; Kyungmin Kim 002; JB Lanier; Pierre Baldi; Roy Fox; Sameer Singh 001 (CoRR, 2023)

Extended Symmetry Preserving Attention Networks for LHC Analysis. - Michael James Fenton; Alexander Shmakov; Hideki Okawa; Yuji Li; Ko-Yang Hsiao; Shih-Chieh Hsu; Daniel Whiteson; Pierre Baldi (CoRR, 2023)

Machine Learning-Enhanced Prediction of Surface Smoothness for Inertial Confinement Fusion Target Polishing Using Limited Data. - Antonios Alexos; Junze Liu; Akash Tiwari; Kshitij Bhardwaj; Sean Hayes; Pierre Baldi; Satish T. S. Bukkapatnam; Suhas Bhandarkar (CoRR, 2023)

Evaluating the Performance of Large Language Models for Spanish Language in Undergraduate Admissions Exams. - Sabino Miranda; Obdulia Pichardo-Lagunas; Bella Martínez-Seis; Pierre Baldi (Computación y Sistemas (CyS), 2023)

RMechDB: A Public Database of Elementary Radical Reaction Steps. - Mohammadamin Tavakoli; Yin Ting T. Chiu; Pierre Baldi; Ann Marie Carlton; David Van Vranken (J. Chem. Inf. Model., 2023)

The quarks of attention: Structure and capacity of neural attention building blocks. - Pierre Baldi; Roman Vershynin (Artif. Intell., 2023)

Toward Optimal Policy Population Growth in Two-Player Zero-Sum Games. - Stephen Marcus McAleer; JB Lanier; Kevin A. Wang; Pierre Baldi; Tuomas Sandholm; Roy Fox (ICLR, 2024)

Selective Perception: Learning Concise State Descriptions for Language Model Actors. - Kolby Nottingham; Yasaman Razeghi; Kyungmin Kim 002; JB Lanier; Pierre Baldi; Roy Fox; Sameer Singh 001 (NAACL (Short Papers), 2024)

Nuclear Fusion Diamond Polishing Dataset. - Antonios Alexos; Junze Liu; Shashank Galla; Sean Hayes; Kshitij Bhardwaj; Alexander Schwartz; Monika Biener; Pierre Baldi; Satish T. S. Bukkapatnam; Suhas Bhandarkar (NeurIPS, 2024)

FastStitch: Speech editing by hitch-hiking a pre-trained FastSpeech2 model. - Antonios Alexos; Pierre Baldi (NLDL, 2024)

Deep Learning Over-Parameterization: the Shallow Fallacy. - Pierre Baldi (NLDL, 2024)

AttentionStitch: How Attention Solves the Speech Editing Problem. - Antonios Alexos; Pierre Baldi (CoRR, 2024)

Unraveling the Molecular Magic: AI Insights on the Formation of Extraordinarily Stretchable Hydrogels. - Shahriar Hojjati Emmami; Ali Pilehvar Meibody; Lobat Tayebi; Mohammadamin Tavakoli; Pierre Baldi (CoRR, 2024)

Neural Erosion: Emulating Controlled Neurodegeneration and Aging in AI Systems. - Antonios Alexos; Yu-Dai Tsai; Ian Domingo; Maryam Pishgar; Pierre Baldi (CoRR, 2024)

Full Event Particle-Level Unfolding with Variable-Length Latent Variational Diffusion. - Alexander Shmakov; Kevin Greif; Michael James Fenton; Aishik Ghosh; Pierre Baldi; Daniel Whiteson (CoRR, 2024)

From Local to Global Order: A Theory of Neural Synaptic Balance. - Pierre Baldi; Alireza Rahmansetayesh (CoRR, 2024)

Make the Pertinent Salient: Task-Relevant Reconstruction for Visual Control with Distractions. - Kyungmin Kim 002; JB Lanier; Pierre Baldi; Charless C. Fowlkes; Roy Fox (CoRR, 2024)

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 B. Newman; et al. (CoRR, 2024)

PMechDB: A Public Database of Elementary Polar Reaction Steps. - Mohammadamin Tavakoli; Ryan J. Miller; Mirana Angel; Michael A. Pfeiffer; Eugene S. Gutman; Aaron Mood; David Van Vranken; Pierre Baldi (J. Chem. Inf. Model., 2024)

Improving Deep Learning Speed and Performance Through Synaptic Neural Balance. - Antonios Alexos; Ian Domingo; Pierre Baldi (AAAI, 2025)

Realizable Continuous-Space Shields for Safe Reinforcement Learning. - Kyungmin Kim 002; Davide Corsi; Andoni Rodríguez; JB Lanier; Benjami Parellada; Pierre Baldi; César Sánchez 001; Roy Fox (L4DC, 2025)

A theory of synaptic neural balance: From local to global order. - Pierre Baldi; Antonios Alexos; Ian Domingo; Alireza Rahmansetayesh (Artif. Intell., 2025)

Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction. - Mohammadamin Tavakoli; Yin Ting T. Chiu; Ann Marie Carlton; David Van Vranken; Pierre Baldi (J. Chem. Inf. Model., 2025)

Particle Hit Clustering and Identification Using Point Set Transformers in Liquid Argon Time Projection Chambers. - Edgar E. Robles; Alejandro Yankelevich; Wenjie Wu; Jianming Bian; Pierre Baldi (CoRR, 2025)

Memorization: A Close Look at Books. - Iris Ma; Ian Domingo; Alberto Krone-Martins; Pierre Baldi; Cristina V. Lopes (CoRR, 2025)

Interpretable Deep Learning for Polar Mechanistic Reaction Prediction. - Ryan J. Miller; Alexander E. Dashuta; Brayden Rudisill; David Van Vranken; Pierre Baldi (CoRR, 2025)

Antenna Near-Field Reconstruction from Far-Field Data Using Convolutional Neural Networks. - Sahar Bagherkhani; Jackson Christopher Earls; Franco De Flaviis; Pierre Baldi (CoRR, 2025)

Sparse Phased Array Optimization Using Deep Learning. - David Lu; Lior Maman; Jackson Earls; Amir Boag; Pierre Baldi (CoRR, 2025)