A Phylogenetic Approach to Genomic Language Modeling - Carlos Albors; Jianan Canal Li; Gonzalo Benegas; Chengzhong Ye; Yun S. Song (Research in Computational Molecular Biology - 29th International Conference, RECOMB 2025, Seoul, South Korea, April 26-29, 2025, Proceedings, 2025)

Tree Reconstruction Guarantees from CRISPR-Cas9 Lineage Tracing Data Using Neighbor-Joining - Sebastian Prillo; Kevin An; Wilson Wu; Ivan Kristanto; Matthew G. Jones; Yun S. Song; Nir Yosef (Research in Computational Molecular Biology - 29th International Conference, RECOMB 2025, Seoul, South Korea, April 26-29, 2025, Proceedings, 2025)

A Phylogenetic Approach to Genomic Language Modeling - Carlos Albors; Jianan Canal Li; Gonzalo Benegas; Chengzhong Ye; Yun S. Song (CoRR, 2025)

CELL-E: A Text-to-Image Transformer for Protein Image Prediction - Emaad Khwaja; Yun S. Song; Bo Huang (Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings, 2024)

Genomic Language Models: Opportunities and Challenges - Gonzalo Benegas; Chengzhong Ye; Carlos Albors; Jianan Canal Li; Yun S. Song (CoRR, 2024)

A fast machine-learning-guided primer design pipeline for selective whole genome amplification - Jane A. Dwivedi-Yu; Zachary J. Oppler; Matthew W. Mitchell; Yun S. Song; Dustin Brisson (PLoS Comput. Biol., 2023)

Enzyme Activity Prediction of Sequence Variants on Novel Substrates using Improved Substrate Encodings and Convolutional Pooling - Zhiqing Xu; Jinghao Wu; Yun S. Song; Radhakrishnan Mahadevan (Machine Learning in Computational Biology Meeting, MLCB 2021, online, November 22-23, 2021, 2021)

Parallelizing Contextual Linear Bandits - Jeffrey Chan; Aldo Pacchiano; Nilesh Tripuraneni; Yun S. Song; Peter L. Bartlett; Michael I. Jordan (CoRR, 2021)

Evaluating Protein Transfer Learning with TAPE - Roshan Rao; Nicholas Bhattacharya; Neil Thomas; Yan Duan; Xi Chen; John F. Canny; Pieter Abbeel; Yun S. Song (Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, NeurIPS 2019, December 8-14, 2019, Vancouver, BC, Canada, 2019)

Evaluating Protein Transfer Learning with TAPE - Roshan Rao; Nicholas Bhattacharya; Neil Thomas; Yan Duan; Xi Chen; John F. Canny; Pieter Abbeel; Yun S. Song (CoRR, 2019)

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks - Jeffrey Chan; Valerio Perrone; Jeffrey P. Spence; Paul A. Jenkins; Sara Mathieson; Yun S. Song (Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, NeurIPS 2018, December 3-8, 2018, Montréal, Canada, 2018)

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks - Jeffrey Chan; Valerio Perrone; Jeffrey P. Spence; Paul A. Jenkins; Sara Mathieson; Yun S. Song (CoRR, 2018)

Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD) - Miaoyan Wang; Yun S. Song (Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, AISTATS 2017, 20-22 April 2017, Fort Lauderdale, FL, USA, 2017)

SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes - Matthias Steinrücken; Ethan M. Jewett; Yun S. Song (Bioinform., 2016)

Prediction of ribosome footprint profile shapes from transcript sequences - Tzu-Yu Liu; Yun S. Song (Bioinform., 2016)

Deep Learning for Population Genetic Inference - Sara Sheehan; Yun S. Song (PLoS Comput. Biol., 2016)

Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads - Shishi Luo; Jane A. Yu; Yun S. Song (PLoS Comput. Biol., 2016)

Orthogonal Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD) - Miaoyan Wang; Yun S. Song (CoRR, 2016)

SMaSH: a benchmarking toolkit for human genome variant calling - Ameet Talwalkar; Jesse Liptrap; Julie Newcomb; Christopher Hartl; Jonathan Terhorst; Kristal Curtis; Ma'ayan Bresler; Yun S. Song; Michael I. Jordan; David A. Patterson (Bioinform., 2014)

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals - Paula Tataru; Jasmine A. Nirody; Yun S. Song (Bioinform., 2014)

Changepoint Analysis for Efficient Variant Calling - Adam E. Bloniarz; Ameet Talwalkar; Jonathan Terhorst; Michael I. Jordan; David A. Patterson; Bin Yu; Yun S. Song (Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings, 2014)

Decoding Coalescent Hidden Markov Models in Linear Time - Kelley Harris; Sara Sheehan; John A. Kamm; Yun S. Song (Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings, 2014)

Blockwise HMM computation for large-scale population genomic inference - Joshua S. Paul; Yun S. Song (Bioinform., 2012)

Telescoper: de novo assembly of highly repetitive regions - Ma'ayan Bresler; Sara Sheehan; Andrew H. Chan; Yun S. Song (Bioinform., 2012)

naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing - Wei-Chun Kao; Yun S. Song (J. Comput. Biol., 2011)

On the Genealogy of Asexual Diploids - Fumei Lam; Charles H. Langley; Yun S. Song (J. Comput. Biol., 2011)

Application of a reconfigurable computing cluster to ultra high throughput genome resequencing (abstract only) - Kristian Stevens; Henry Chen; Terry Filiba; Peter L. McMahon; Yun S. Song (Proceedings of the ACM/SIGDA 18th International Symposium on Field Programmable Gate Arrays, FPGA 2010, Monterey, California, USA, February 21-23, 2010, 2010)

SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing - Kristian Stevens; Henry Chen; Terry Filiba; Peter L. McMahon; Yun S. Song (International Conference on Field Programmable Logic and Applications, FPL 2010, August 31 2010 - September 2, 2010, Milano, Italy, 2010)

naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing - Wei-Chun Kao; Yun S. Song (Research in Computational Molecular Biology, 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings, 2010)

On the Genealogy of Asexual Diploids - Fumei Lam; Charles H. Langley; Yun S. Song (Research in Computational Molecular Biology, 14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings, 2010)

Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models - Anand Bhaskar; Yun S. Song (Bioinform., 2009)

Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data - Junming Yin; Michael I. Jordan; Yun S. Song (Bioinform., 2009)

Efficient whole-genome association mapping using local phylogenies for unphased genotype data - Zhihong Ding; Thomas Mailund; Yun S. Song (Bioinform., 2008)

Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony - Rune B. Lyngsø; Yun S. Song; Jotun Hein (Research in Computational Molecular Biology, 12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008. Proceedings, 2008)

A Decomposition Theory for Phylogenetic Networks and Incompatible Characters - Dan Gusfield; Vikas Bansal; Vineet Bafna; Yun S. Song (J. Comput. Biol., 2007)

Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations - Yun S. Song; Zhihong Ding; Dan Gusfield; Charles H. Langley; Yufeng Wu (J. Comput. Biol., 2007)

A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree - Yun S. Song (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics - Yun S. Song; Rune B. Lyngsø; Jotun Hein (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations - Yun S. Song; Zhihong Ding; Dan Gusfield; Charles H. Langley; Yufeng Wu (Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings, 2006)

Constructing Minimal Ancestral Recombination Graphs - Yun S. Song; Jotun Hein (J. Comput. Biol., 2005)

Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution - Yun S. Song; Yufeng Wu; Dan Gusfield (Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005, 2005)

Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event - Yun S. Song; Yufeng Wu; Dan Gusfield (Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings, 2005)

Minimum Recombination Histories by Branch and Bound - Rune B. Lyngsø; Yun S. Song; Jotun Hein (Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings, 2005)

An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees - Gerton Lunter; István Miklós; Yun S. Song; Jotun Hein (J. Comput. Biol., 2003)

Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks - Yun S. Song; Jotun Hein (Algorithms in Bioinformatics, Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003, Proceedings, 2003)