Yun S. Song
- Evaluating Protein Transfer Learning with TAPE
2019/06/19 by Roshan Rao, Rao, Roshan, Nicholas Bhattacharya +13 · 32 citations
Biochemistry, Genetics and Molecular Biology · #Machine Learning in Bioinformatics #RNA and protein synthesis mechanisms #Protein Structure and Dynamics
- Genomic Language Models: Opportunities and Challenges
2024/07/16 by Gonzalo Benegas, Chengzhong Ye, Benegas, Gonzalo +7 · 2 voices · 17 citations
Biochemistry, Genetics and Molecular Biology · #68T07 #68T50 #92-08 #92B20 #FOS: Biological sciences #FOS: Computer and information sciences #Genomics (q-bio.GN) #Machine Learning (cs.LG) #Machine Learning (stat.ML)
- A DNA language model based on multispecies alignment predicts the effects of genome-wide variants
2025/01/02 by Gonzalo Benegas, Carlos Albors, Alan J. Aw +2 · 2 voices · 12 citations
Biochemistry, Genetics and Molecular Biology · #Genomics and Rare Diseases #Genomics and Phylogenetic Studies #Genetic Associations and Epidemiology
- CherryML: scalable maximum likelihood estimation of phylogenetic models
2023/06/29 by Sebastian Prillo, Yun Deng, Pierre Boyeau +4 · 1 voice · 4 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #Evolution and Paleontology Studies #Genomics and Phylogenetic Studies #Morphological variations and asymmetry
- Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
2025/09/01 by Yun Deng, Rasmus Nielsen, Yun S. Song · 1 voice · 15 citations
Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #Genetic diversity and population structure #RNA and protein synthesis mechanisms
- Benchmarking DNA Sequence Models for Causal Regulatory Variant Prediction in Human Genetics
2025/02/12 by Gonzalo Benegas, Gökçen Eraslan, Yun S. Song · 1 voice · 4 citations
Biochemistry, Genetics and Molecular Biology · #Genomics and Rare Diseases #Genetics, Bioinformatics, and Biomedical Research #Genetic Associations and Epidemiology
- Two-Locus Likelihoods under Variable Population Size and Fine-Scale\n Recombination Rate Estimation
2015/10/20 by Jack Kamm, Kamm, John A., Jeffrey P. Spence +5 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #Genetic diversity and population structure #Genomics and Phylogenetic Studies
- A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact
2024/12/16 by Yun Deng, Rasmus Nielsen, Yun S. Song · 1 voice · 2 citations
Social Sciences · Earth and Planetary Sciences · Arts and Humanities · #Pleistocene-Era Hominins and Archaeology #Archaeology and ancient environmental studies #Paleopathology and ancient diseases
- A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder
2025/07/30 by F. A. Matsen, Kevin Sung, Mackenzie M. Johnson +7 · 2 voices · 2 citations
Medicine · Biochemistry, Genetics and Molecular Biology · #Monoclonal and Polyclonal Antibodies Research #Gene Regulatory Network Analysis #Receptor Mechanisms and Signaling
- Exact and efficient phylodynamic simulation from arbitrarily large populations
2025/05/14 by Michael Celentano, William S. DeWitt, Sebastian Prillo +1 · 2 voices
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Genetic diversity and population structure #Evolution and Paleontology Studies #Genomics and Phylogenetic Studies