BEND: Benchmarking DNA Language Models on biologically meaningful tasks

BEND: Benchmarking DNA Language Models on biologically meaningful tasks

21 November 2023

Frederikke Isa Marin

Papers citing "BEND: Benchmarking DNA Language Models on biologically meaningful tasks"

10 / 10 papers shown

Title
Revisiting Convolution Architecture in the Realm of DNA Foundation Models Yu Bo Weian Mao Yanjun Shao Weiqiang Bai Peng Ye Xinzhu Ma Junbo Zhao Hao Chen Chunhua Shen 3DV 60 1 0 25 Feb 2025
BarcodeMamba: State Space Models for Biodiversity Analysis Tiancheng Gao Graham W. Taylor Mamba 82 2 0 15 Dec 2024
Recent advances in deep learning and language models for studying the microbiome Binghao Yan Yunbi Nam Lingyao Li Rebecca A Deek Hongzhe Li Siyuan Ma 16 1 0 15 Sep 2024
Genomic Language Models: Opportunities and Challenges Gonzalo Benegas Chengzhong Ye C. Albors Jianan Canal Li Yun S. Song AI4CE LM&MA ELM 41 18 0 16 Jul 2024
M5: A Whole Genome Bacterial Encoder at Single Nucleotide Resolution Agust Egilsson 23 0 0 03 Jul 2024
BEACON: Benchmark for Comprehensive RNA Tasks and Language Models Yuchen Ren Zhiyuan Chen Lifeng Qiao Hongtai Jing Yuchen Cai ... Siqi Sun Hongliang Yan Dong Yuan Wanli Ouyang Xihui Liu 36 9 0 14 Jun 2024
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models Zicheng Liu Jiahui Li Siyuan Li Z. Zang Cheng Tan Yufei Huang Yajing Bai Stan Z. Li ELM 29 8 0 01 Jun 2024
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling Siyuan Li Zedong Wang Zicheng Liu Di Wu Cheng Tan Jiangbin Zheng Yufei Huang Stan Z. Li 40 7 0 13 May 2024
Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation Ofir Press Noah A. Smith M. Lewis 250 695 0 27 Aug 2021
Big Bird: Transformers for Longer Sequences Manzil Zaheer Guru Guruganesh Kumar Avinava Dubey Joshua Ainslie Chris Alberti ... Philip Pham Anirudh Ravula Qifan Wang Li Yang Amr Ahmed VLM 274 2,015 0 28 Jul 2020