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DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

26 June 2023

Papers citing "DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome"

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Title
BMFM-RNA: An Open Framework for Building and Evaluating Transcriptomic Foundation Models Bharath Dandala Michael M. Danziger Ella Barkan Tanwi Biswas Viatcheslav Gurev ... Akira Koseki Tal Kozlovski Michal Rosen-Zvi Yishai Shimoni Ching-Huei Tsou AI4CE 25 0 0 17 Jun 2025
SLICK: Selective Localization and Instance Calibration for Knowledge-Enhanced Car Damage Segmentation in Automotive Insurance Teerapong Panboonyuen 161 0 0 12 Jun 2025
Predicting function of evolutionarily implausible DNA sequences Shiyu Jiang Xuyin Liu Zitong Jerry Wang 126 0 0 12 Jun 2025
Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics Ella Rannon David Burstein AI4TS 29 0 0 02 Jun 2025
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model Adibvafa Fallahpour Andrew Magnuson Purav Gupta Shihao Ma Jack Naimer ... Haonan Duan Omar Ibrahim Hani Goodarzi Chris J. Maddison Bo Wang SyDa AI4CE LRM 31 0 0 29 May 2025
Minimalist Softmax Attention Provably Learns Constrained Boolean Functions Jerry Yao-Chieh Hu Xiwen Zhang Maojiang Su Zhao Song Han Liu MLT 245 1 0 26 May 2025
DNAZEN: Enhanced Gene Sequence Representations via Mixed Granularities of Coding Units Lei Mao Yuanhe Tian Yan Song 34 0 0 04 May 2025
Multimodal Large Language Models for Medicine: A Comprehensive Survey Jiarui Ye Hao Tang LM&MA 191 0 0 29 Apr 2025
In-Context Learning can distort the relationship between sequence likelihoods and biological fitness Pranav Kantroo Günter P. Wagner Benjamin B. Machta 131 0 0 23 Apr 2025
NdLinear: Don't Flatten! Building Superior Neural Architectures by Preserving N-D Structure Alex Reneau Jerry Yao-Chieh Hu Zhongfang Zhuang Ting-Chun Liu Xiang He Judah Goldfeder Nadav Timor Allen Roush Ravid Shwartz-Ziv HAI 108 0 0 21 Mar 2025
Gene42: Long-Range Genomic Foundation Model With Dense Attention Kirill Vishniakov Boulbaba Ben Amor Engin Tekin Nancy A. ElNaker Karthik Viswanathan ... Tiago Magalhaes Natalia Vassilieva Dwarikanath Mahapatra Marco Pimentel and Shadab Khan 3DV 108 0 0 20 Mar 2025
HELM: Hierarchical Encoding for mRNA Language Modeling Mehdi Yazdani-Jahromi Mangal Prakash Tommaso Mansi Artem Moskalev Rui Liao 144 4 0 13 Mar 2025
Large Language Models in Bioinformatics: A Survey Ziyi Wang Zikang Wang Jiyue Jiang Pengan Chen Xiangyu Shi Yu Li LM&MA AI4CE 116 3 0 06 Mar 2025
Can Large Language Models Predict Antimicrobial Resistance Gene? Hyunwoo Yoo AI4CE LM&MA 70 0 0 06 Mar 2025
Enhancing DNA Foundation Models to Address Masking Inefficiencies Monireh Safari Pablo Millán Arias Joakim Bruslund Haurum Lila Kari Angel X. Chang Graham W. Taylor 137 0 0 25 Feb 2025
Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification Zicheng Liu Siyuan Li Zhiyuan Chen Lei Xin Fang Wu Chang Yu Qirong Yang Yucheng Guo Yifan Yang Stan Z. Li SyDa AI4CE 207 2 0 11 Feb 2025
TFBS-Finder: Deep Learning-based Model with DNABERT and Convolutional Networks to Predict Transcription Factor Binding Sites Nimisha Ghosh Pratik Dutta Daniele Santoni 72 0 0 03 Feb 2025
BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity Zahra Gharaee Joakim Bruslund Haurum ZeMing Gong Pablo Millán Arias Nicholas Pellegrino ... Lila Kari Lila Kari Graham W. Taylor Paul Fieguth Angel X. Chang 134 11 0 28 Jan 2025
A Comprehensive Survey of Foundation Models in Medicine Wasif Khan Seowung Leem Kyle B. See Joshua K. Wong Shaoting Zhang R. Fang AI4CE LM&MA VLM 290 27 0 17 Jan 2025
RapGuard: Safeguarding Multimodal Large Language Models via Rationale-aware Defensive Prompting Yilei Jiang Yingshui Tan Xiangyu Yue KELM LRM 148 10 0 25 Dec 2024
Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA Lifeng Qiao Peng Ye Yuchen Ren Weiqiang Bai Chaoqi Liang Xinzhu Ma Nanqing Dong W. Ouyang 153 3 0 18 Dec 2024
BarcodeMamba: State Space Models for Biodiversity Analysis Tiancheng Gao Graham W. Taylor Mamba 135 2 0 15 Dec 2024
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA Aman Patel Arpita Singhal Austin Wang Anusri Pampari Maya Kasowski Anshul Kundaje ELM 85 5 0 06 Dec 2024
Does your model understand genes? A benchmark of gene properties for biological and text models Yoav Kan-Tor Michael M. Danziger Eden Zohar Matan Ninio Yishai Shimoni 95 1 0 05 Dec 2024
Specialized Foundation Models Struggle to Beat Supervised Baselines Zongzhe Xu Ritvik Gupta Wenduo Cheng Alexander Shen Junhong Shen Ameet Talwalkar M. Khodak AI4CE 118 9 0 05 Nov 2024
Revisiting K-mer Profile for Effective and Scalable Genome Representation Learning Abdulkadir Celikkanat A. Masegosa Thomas D. Nielsen 64 2 0 04 Nov 2024
BSM: Small but Powerful Biological Sequence Model for Genes and Proteins Weixi Xiang Xueting Han Xiujuan Chai Jing Bai 45 1 0 15 Oct 2024
Plug-and-Play Controllable Generation for Discrete Masked Models Wei Guo Yuchen Zhu Molei Tao Yongxin Chen 80 5 0 03 Oct 2024
OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models Heng Yang Jack Cole Ke Li 53 0 0 02 Oct 2024
Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials Yizhen Zheng Huan Yee Koh M. Yang Li Li Lauren T. May Geoffrey I. Webb Shirui Pan George Church LM&MA 100 14 0 06 Sep 2024
Differentially Private Kernel Density Estimation Erzhi Liu Jerry Yao-Chieh Hu Alex Reneau Zhao Song Han Liu 147 3 0 03 Sep 2024
Genomic Language Models: Opportunities and Challenges Gonzalo Benegas Chengzhong Ye C. Albors Jianan Canal Li Yun S. Song AI4CE LM&MA ELM 133 26 0 16 Jul 2024
Multi-modal Transfer Learning between Biological Foundation Models Juan Jose Garau-Luis Patrick Bordes Liam Gonzalez Masa Roller Bernardo P. de Almeida ... Stefan Laurent Jan Grzegorzewski Maren Lang Thomas Pierrot Guillaume Richard AI4CE 99 6 0 20 Jun 2024
PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model Sajib Acharjee Dip Uddip Acharjee Shuvo Tran Chau Haoqiu Song Petra Choi Xuan Wang Liqing Zhang LM&MA 27 3 0 19 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 142 43 0 16 Jun 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 83 11 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 61 9 0 01 Jun 2024
DYNA: Disease-Specific Language Model for Variant Pathogenicity Huixin Zhan Zijun Zhang 64 0 0 31 May 2024
DocReLM: Mastering Document Retrieval with Language Model Gengchen Wei Xinle Pang Tianning Zhang Yu Sun Xun Qian Chen Lin Han-Sen Zhong Wanli Ouyang RALM 76 0 0 19 May 2024
An Embarrassingly Simple Approach to Enhance Transformer Performance in Genomic Selection for Crop Breeding Renqi Chen Wenwei Han Haohao Zhang Haoyang Su Zhefan Wang Xiaolei Liu Hao Jiang Wanli Ouyang Nanqing Dong 24 1 0 15 May 2024
Self-Distillation Improves DNA Sequence Inference Tong Yu Lei Cheng Ruslan Khalitov Erland Brandser Olsson Zhirong Yang SyDa 80 1 0 14 May 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 79 8 0 13 May 2024
Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity Zhufeng Li S. S. Cranganore Nicholas D. Youngblut Niki Kilbertus 117 2 0 09 May 2024
BiSHop: Bi-Directional Cellular Learning for Tabular Data with Generalized Sparse Modern Hopfield Model Chenwei Xu Yu-Chao Huang Jerry Yao-Chieh Hu Weijian Li Ammar Gilani H. Goan Han Liu 85 21 0 04 Apr 2024
Outlier-Efficient Hopfield Layers for Large Transformer-Based Models Jerry Yao-Chieh Hu Pei-Hsuan Chang Haozheng Luo Hong-Yu Chen Weijian Li Wei-Po Wang Han Liu 98 29 0 04 Apr 2024
Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling Yair Schiff Chia-Hsiang Kao Aaron Gokaslan Tri Dao Albert Gu Volodymyr Kuleshov Mamba 91 98 0 05 Mar 2024
RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks Rafael Josip Penić Tin Vlasic Roland G. Huber Yue Wan M. Šikić AI4CE 61 35 0 29 Feb 2024
FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics Chenrui Duan Z. Zang Yongjie Xu Hang He Zihan Liu Zijia Song Ju-Sheng Zheng Stan Z. Li 40 3 0 24 Feb 2024
Efficient and Scalable Fine-Tune of Language Models for Genome Understanding Huixin Zhan Ying Nian Wu Zijun Zhang ALM 42 1 0 12 Feb 2024
Progress and Opportunities of Foundation Models in Bioinformatics Qing Li Zhihang Hu Yixuan Wang Lei Li Yimin Fan Irwin King Le Song Yu Li AI4CE 85 18 0 06 Feb 2024