Itsik Pe'er

70 papers A* 3A 6B 11Misc 1Journal 40Unranked 9
YearRankTypeTitle / Venue / Authors
2026 J jnl
Efficient algorithms for simulating sequences along a phylogenetic tree.
Bioinform.
Elya Wygoda, Asher Moshe, Nimrod Serok, Edo Dotan, Noa Ecker, Naiel Jabareen, Omer Israeli, Itsik Pe'er, Tal Pupko
2025 J jnl
Even Faster Hyperbolic Random Forests: A Beltrami-Klein Wrapper Approach.
CoRR
Philippe Chlenski, Itsik Pe'er
2025 A* conf
Hyperbolic Genome Embeddings.
ICLR
Raiyan R. Khan, Philippe Chlenski, Itsik Pe'er
2025 J jnl
Hyperbolic Genome Embeddings.
CoRR
Raiyan R. Khan, Philippe Chlenski, Itsik Pe'er
2025 J jnl
Manify: A Python Library for Learning Non-Euclidean Representations.
CoRR
Philippe Chlenski, Kaizhu Du, Dylan Satow, Itsik Pe'er
2025 A* conf
Mixed-curvature decision trees and random forests.
ICML
Philippe Chlenski, Quentin Chu, Raiyan R. Khan, Kaizhu Du, Antonio Khalil Moretti, Itsik Pe'er
2025 A conf
Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space.
AISTATS
Alex Chen, Philippe Chlenski, Kenneth Munyuza, Antonio Khalil Moretti, Christian A. Naesseth, Itsik Pe'er
2025 J jnl
Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetics in Hyperbolic Space.
CoRR
Alex Chen, Philippe Chlenski, Kenneth Munyuza, Antonio Khalil Moretti, Christian A. Naesseth, Itsik Pe'er
2024 J jnl
Distributional bias compromises leave-one-out cross-validation.
CoRR
George I. Austin, Itsik Pe'er, Tal Korem
2024 A* conf
Fast Hyperboloid Decision Tree Algorithms.
ICLR
Philippe Chlenski, Ethan Turok, Antonio Khalil Moretti, Itsik Pe'er
2024 J jnl
Mixed-curvature decision trees and random forests.
CoRR
Philippe Chlenski, Quentin Chu, Raiyan R. Khan, Antonio Khalil Moretti, Itsik Pe'er
2024 J jnl
Variational Pseudo Marginal Methods for Jet Reconstruction in Particle Physics.
CoRR
Hanming Yang, Antonio Khalil Moretti, Sebastian Macaluso, Philippe Chlenski, Christian A. Naesseth, Itsik Pe'er
2024 J jnl
Variational Pseudo Marginal Methods for Jet Reconstruction in Particle Physics.
Trans. Mach. Learn. Res.
Hanming Yang, Antonio Khalil Moretti, Sebastian Macaluso, Philippe Chlenski, Christian A. Naesseth, Itsik Pe'er
2023 J jnl
Fast hyperboloid decision tree algorithms.
CoRR
Philippe Chlenski, Ethan Turok, Antonio Khalil Moretti, Itsik Pe'er
2022 — conf
ICLR 2022 Challenge for Computational Geometry & Topology: Design and Results.
TAG-ML
Adele Myers, Saiteja Utpala, Shubham Talbar, Sophia Sanborn, Christian Shewmake, Claire Donnat, Johan Mathe, Rishi Sonthalia, Xinyue Cui, Tom Szwagier, Arthur Pignet, Andri Bergsson, Søren Hauberg, Dmitriy Nielsen, Stefan Sommer, David A. Klindt, Erik Hermansen, Melvin Vaupel, Benjamin A. Dunn, Jeffrey Xiong, Noga Aharony, Itsik Pe'er, Felix Ambellan, Martin Hanik, Esfandiar Nava-Yazdani, Christoph von Tycowicz, Nina Miolane
2022 J jnl
ICLR 2022 Challenge for Computational Geometry and Topology: Design and Results.
CoRR
Adele Myers, Saiteja Utpala, Shubham Talbar, Sophia Sanborn, Christian Shewmake, Claire Donnat, Johan Mathe, Umberto Lupo, Rishi Sonthalia, Xinyue Cui, Tom Szwagier, Arthur Pignet, Andri Bergsson, Søren Hauberg, Dmitriy Nielsen, Stefan Sommer, David A. Klindt, Erik Hermansen, Melvin Vaupel, Benjamin A. Dunn, Jeffrey Xiong, Noga Aharony, Itsik Pe'er, Felix Ambellan, Martin Hanik, Esfandiar Nava-Yazdani, Christoph von Tycowicz, Nina Miolane
2022 B ed.
Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings
RECOMB
Itsik Pe'er
2022 J jnl
Special Issue: RECOMB 2022, Part 1.
J. Comput. Biol.
Itsik Pe'er
2022 J jnl
Special Issue: RECOMB 2022, Part 2.
J. Comput. Biol.
Itsik Pe'er
2022 — conf
Unclonable Polymers and Their Cryptographic Applications.
EUROCRYPT (1)
Ghada Almashaqbeh, Ran Canetti, Yaniv Erlich, Jonathan Gershoni, Tal Malkin, Itsik Pe'er, Anna Roitburd-Berman, Eran Tromer
2022 J jnl
Unclonable Polymers and Their Cryptographic Applications.
IACR Cryptol. ePrint Arch.
Ghada Almashaqbeh, Ran Canetti, Yaniv Erlich, Jonathan Gershoni, Tal Malkin, Itsik Pe'er, Anna Roitburd-Berman, Eran Tromer
2021 — conf
A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group Testing Under the Probabilistic Framework.
AlCoB
Yining Liu, Sachin Kadyan, Itsik Pe'er
2021 J jnl
SICaRiO: short indel call filtering with boosting.
Briefings Bioinform.
Md Shariful Islam Bhuyan, Itsik Pe'er, M. Sohel Rahman
2021 J jnl
Variational Combinatorial Sequential Monte Carlo Methods for Bayesian Phylogenetic Inference.
CoRR
Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth, Hadiah Venner, David M. Blei, Itsik Pe'er
2021 A conf
variational combinatorial sequential monte carlo methods for bayesian phylogenetic inference.
UAI
Antonio Khalil Moretti, Liyi Zhang, Christian A. Naesseth, Hadiah Venner, David M. Blei, Itsik Pe'er
2020 J jnl
Compositional Lotka-Volterra describes microbial dynamics in the simplex.
PLoS Comput. Biol.
Tyler A. Joseph, Liat Shenhav, João B. Xavier, Eran Halperin, Itsik Pe'er
2020 B conf
Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count Data.
RECOMB
Tyler A. Joseph, Amey P. Pasarkar, Itsik Pe'er
2020 A conf
Variational Objectives for Markovian Dynamics with Backward Simulation.
ECAI
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Iddo Drori, Itsik Pe'er
2020 J jnl
arcasHLA: high-resolution HLA typing from RNAseq.
Bioinform.
Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er, Raul Rabadan
2019 J jnl
Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations.
CoRR
Iddo Drori, Darshan Thaker, Arjun Srivatsa, Daniel Jeong, Yueqi Wang, Linyong Nan, Fan Wu, Dimitri Leggas, Jinhao Lei, Weiyi Lu, Weilong Fu, Yuan Gao, Sashank Karri, Anand Kannan, Antonio Khalil Moretti, Mohammed AlQuraishi, Chen Keasar, Itsik Pe'er
2019 J jnl
Autoencoding Topographic Factors.
J. Comput. Biol.
Antonio Khalil Moretti, Andrew Stirn, Gabriel Marks, Itsik Pe'er
2019 J jnl
Particle Smoothing Variational Objectives.
CoRR
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Iddo Drori, Itsik Pe'er
2019 — conf
Smoothing Nonlinear Variational Objectives with Sequential Monte Carlo.
DGS@ICLR
Antonio Khalil Moretti, Zizhao Wang, Luhuan Wu, Itsik Pe'er
2018 J jnl
High Quality Prediction of Protein Q8 Secondary Structure by Diverse Neural Network Architectures.
CoRR
Iddo Drori, Isht Dwivedi, Pranav Shrestha, Jeffrey Wan, Yueqi Wang, Yunchu He, Anthony Mazza, Hugh Krogh-Freeman, Dimitri Leggas, Kendal Sandridge, Linyong Nan, Kaveri A. Thakoor, Chinmay Joshi, Sonam Goenka, Chen Keasar, Itsik Pe'er
2018 B conf
Inference of Population Structure from Ancient DNA.
RECOMB
Tyler A. Joseph, Itsik Pe'er
2017 J jnl
Parkinson's Disease Digital Biomarker Discovery with Optimized Transitions and Inferred Markov Emissions.
CoRR
Avinash Bukkittu, Baihan Lin, Trung Vu, Itsik Pe'er
2016 J jnl
Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.
J. Comput. Biol.
Shuo Yang, Shai Carmi, Itsik Pe'er
2015 B conf
Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.
RECOMB
Shuo Yang, Shai Carmi, Itsik Pe'er
2013 J jnl
Inference of historical migration rates via haplotype sharing.
Bioinform.
Pier Francesco Palamara, Itsik Pe'er
2013 Misc conf
MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association Studies.
Pacific Symposium on Biocomputing
Angad Pal Singh, Samreen Zafer, Itsik Pe'er
2011 J jnl
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data.
BMC Bioinform.
Yufeng Shen, Yiwei Gu, Itsik Pe'er
2011 — conf
A parametric Bayesian method to test the association of rare variants.
BIBM Workshops
Yufeng Shen, Yee Him Cheung, Shuang Wang, Itsik Pe'er
2011 — conf
CONDEX: Copy number detection in exome sequences.
BIBM Workshops
Arthi Ramachandran, Mariann Micsinai, Itsik Pe'er
2011 J jnl
Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.
Bioinform.
Yufeng Shen, Ruijie Song, Itsik Pe'er
2011 J jnl
HLA Type Inference via Haplotypes Identical by Descent.
J. Comput. Biol.
Manu N. Setty, Alexander Gusev, Itsik Pe'er
2011 — conf
Poster: A Hidden Markov Model for Copy Number Variant prediction from Whole genome resequencing data.
ICCABS
Yufeng Shen, Yiwei Gu, Itsik Pe'er
2011 — conf
Workshop: Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.
ICCABS
Yufeng Shen, Ruijie Song, Itsik Pe'er
2010 B conf
HLA Type Inference via Haplotypes Identical by Descent.
RECOMB
Manu N. Setty, Alexander Gusev, Itsik Pe'er
2010 J jnl
Power to detect selective allelic amplification in genome-wide scans of tumor data.
Bioinform.
Ninad Dewal, Matthew L. Freedman, Thomas LaFramboise, Itsik Pe'er
2009 B conf
Overlapping Pools for High Throughput Targeted Resequencing.
RECOMB
Snehit Prabhu, Itsik Pe'er
2008 J jnl
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er
2008 J jnl
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data.
Bioinform.
Julia Stoyanovich, Itsik Pe'er
2004 B conf
Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs.
CPM
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er
2004 J jnl
Incomplete Directed Perfect Phylogeny.
SIAM J. Comput.
Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan
2003 B conf
Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples.
RECOMB
Itsik Pe'er, Jacques S. Beckmann
2002 J jnl
A Structural EM Algorithm for Phylogenetic Inference.
J. Comput. Biol.
Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
2002 J jnl
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families.
Bioinform.
Tal Pupko, Itsik Pe'er, Masami Hasegawa, Dan Graur, Nir Friedman
2002 J jnl
On the Complexity of Positional Sequencing by Hybridization.
J. Comput. Biol.
Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan
2002 — conf
On the Generality of Phylogenies from Incomplete Directed Characters.
SWAT
Itsik Pe'er, Ron Shamir, Roded Sharan
2001 B conf
A structural EM algorithm for phylogenetic inference.
RECOMB
Nir Friedman, Matan Ninio, Itsik Pe'er, Tal Pupko
2001 J jnl
On the Complexity of Positional Sequencing by Hybridization
Electron. Colloquium Comput. Complex.
Piotr Berman, Amir Ben-Dor, Itsik Pe'er, Roded Sharan, Ron Shamir
2000 J jnl
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping.
J. Comput. Biol.
Richard M. Karp, Itsik Pe'er, Ron Shamir
2000 B conf
Incomplete Directed Perfect Phylogeny.
CPM
Itsik Pe'er, Ron Shamir, Roded Sharan
2000 A conf
Spectrum Alignment: Efficient Resequencing by Hybridization.
ISMB
Itsik Pe'er, Ron Shamir
1999 A conf
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping.
ISMB
Richard M. Karp, Itsik Pe'er, Ron Shamir
1999 B conf
On the Complexity of Positional Sequencing by Hybridization.
CPM
Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan
1998 J jnl
The median problems for breakpoints are NP-complete
Electron. Colloquium Comput. Complex.
Itsik Pe'er, Ron Shamir
1997 J jnl
Realizing Interval Graphs with Size and Distance Constraints.
SIAM J. Discret. Math.
Itsik Pe'er, Ron Shamir
1997 J jnl
Satisfiability Problems on Intervals and Unit Intervals.
Theor. Comput. Sci.
Itsik Pe'er, Ron Shamir
1995 A conf
Interval Graphs with Side (and Size) Constraints.
ESA
Itsik Pe'er, Ron Shamir