Yun S. Song

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 15

Top Topics

Transfer Learning

Tensor Decomposition

Diffusion Processes

Top Venues

PLoS Comput. Biol.

Publications

Emaad Khwaja, Yun S. Song, Bo Huang
CELL-E: A Text-to-Image Transformer for Protein Image Prediction. RECOMB (2024)
Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S. Song
Genomic Language Models: Opportunities and Challenges. CoRR (2024)
Jane A. Dwivedi-Yu, Zachary J. Oppler, Matthew W. Mitchell, Yun S. Song, Dustin Brisson
A fast machine-learning-guided primer design pipeline for selective whole genome amplification. PLoS Comput. Biol. 19 (4) (2023)
Zhiqing Xu, Jinghao Wu, Yun S. Song, Radhakrishnan Mahadevan
Enzyme Activity Prediction of Sequence Variants on Novel Substrates using Improved Substrate Encodings and Convolutional Pooling. MLBC (2021)
Jeffrey Chan, Aldo Pacchiano, Nilesh Tripuraneni, Yun S. Song, Peter L. Bartlett, Michael I. Jordan
Parallelizing Contextual Linear Bandits. CoRR (2021)
Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John F. Canny, Pieter Abbeel, Yun S. Song
Evaluating Protein Transfer Learning with TAPE. NeurIPS (2019)
Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John F. Canny, Pieter Abbeel, Yun S. Song
Evaluating Protein Transfer Learning with TAPE. CoRR (2019)
Jeffrey Chan, Valerio Perrone, Jeffrey P. Spence, Paul A. Jenkins, Sara Mathieson, Yun S. Song
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. CoRR (2018)
Jeffrey Chan, Valerio Perrone, Jeffrey P. Spence, Paul A. Jenkins, Sara Mathieson, Yun S. Song
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. NeurIPS (2018)
Miaoyan Wang, Yun S. Song
Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). AISTATS (2017)
Shishi Luo, Jane A. Yu, Yun S. Song
Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads. PLoS Comput. Biol. 12 (9) (2016)
Matthias Steinrücken, Ethan M. Jewett, Yun S. Song
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes. Bioinform. 32 (5) (2016)
Miaoyan Wang, Yun S. Song
Orthogonal Tensor Decompositions via Two-Mode Higher-Order SVD (HOSVD). CoRR (2016)
Tzu-Yu Liu, Yun S. Song
Prediction of ribosome footprint profile shapes from transcript sequences. Bioinform. 32 (12) (2016)
Sara Sheehan, Yun S. Song
Deep Learning for Population Genetic Inference. PLoS Comput. Biol. 12 (3) (2016)
Ameet Talwalkar, Jesse Liptrap, Julie Newcomb, Christopher Hartl, Jonathan Terhorst, Kristal Curtis, Ma'ayan Bresler, Yun S. Song, Michael I. Jordan, David A. Patterson
SMaSH: a benchmarking toolkit for human genome variant calling. Bioinform. 30 (19) (2014)
Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song
Decoding Coalescent Hidden Markov Models in Linear Time. RECOMB (2014)
Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David A. Patterson, Bin Yu, Yun S. Song
Changepoint Analysis for Efficient Variant Calling. RECOMB (2014)
Paula Tataru, Jasmine A. Nirody, Yun S. Song
diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals. Bioinform. 30 (23) (2014)
Ma'ayan Bresler, Sara Sheehan, Andrew H. Chan, Yun S. Song
assembly of highly repetitive regions. Bioinform. 28 (18) (2012)
Joshua S. Paul, Yun S. Song
Blockwise HMM computation for large-scale population genomic inference. Bioinform. 28 (15) (2012)
Wei-Chun Kao, Yun S. Song
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. J. Comput. Biol. 18 (3) (2011)
Fumei Lam, Charles H. Langley, Yun S. Song
On the Genealogy of Asexual Diploids. J. Comput. Biol. 18 (3) (2011)
Fumei Lam, Charles H. Langley, Yun S. Song
On the Genealogy of Asexual Diploids. RECOMB (2010)
Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song
SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing. FPL (2010)
Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song
Application of a reconfigurable computing cluster to ultra high throughput genome resequencing (abstract only). FPGA (2010)
Wei-Chun Kao, Yun S. Song
naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing. RECOMB (2010)
Anand Bhaskar, Yun S. Song
Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models. Bioinform. 25 (12) (2009)
Junming Yin, Michael I. Jordan, Yun S. Song
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinform. 25 (12) (2009)
Zhihong Ding, Thomas Mailund, Yun S. Song
Efficient whole-genome association mapping using local phylogenies for unphased genotype data. Bioinform. 24 (19) (2008)
Rune B. Lyngsø, Yun S. Song, Jotun Hein
Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. RECOMB (2008)
Dan Gusfield, Vikas Bansal, Vineet Bafna, Yun S. Song
A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. J. Comput. Biol. 14 (10) (2007)
Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. J. Comput. Biol. 14 (10) (2007)
Yun S. Song, Rune B. Lyngsø, Jotun Hein
Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (3) (2006)
Yun S. Song, Zhihong Ding, Dan Gusfield, Charles H. Langley, Yufeng Wu
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. RECOMB (2006)
Yun S. Song
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (2) (2006)
Yun S. Song, Yufeng Wu, Dan Gusfield
Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. WABI (2005)
Yun S. Song, Yufeng Wu, Dan Gusfield
Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. ISMB (Supplement of Bioinformatics) (2005)
Rune B. Lyngsø, Yun S. Song, Jotun Hein
Minimum Recombination Histories by Branch and Bound. WABI (2005)
Yun S. Song, Jotun Hein
Constructing Minimal Ancestral Recombination Graphs. J. Comput. Biol. 12 (2) (2005)
Yun S. Song, Jotun Hein
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks. WABI (2003)
Gerton Lunter, István Miklós, Yun S. Song, Jotun Hein
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees. J. Comput. Biol. 10 (6) (2003)