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2306.15794
Cited By
HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution
27 June 2023
Eric N. D. Nguyen
Michael Poli
Marjan Faizi
A. Thomas
Callum Birch-Sykes
Michael Wornow
Aman Patel
Clayton M. Rabideau
Stefano Massaroli
Yoshua Bengio
Stefano Ermon
S. Baccus
Christopher Ré
MedIm
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Papers citing
"HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution"
25 / 25 papers shown
Title
Efficient Unstructured Pruning of Mamba State-Space Models for Resource-Constrained Environments
Ibne Farabi Shihab
Sanjeda Akter
Anuj Sharma
Mamba
36
0
0
13 May 2025
DNAZEN: Enhanced Gene Sequence Representations via Mixed Granularities of Coding Units
Lei Mao
Yuanhe Tian
Yan Song
14
0
0
04 May 2025
Fast and Low-Cost Genomic Foundation Models via Outlier Removal
Haozheng Luo
Chenghao Qiu
Maojiang Su
Zhihan Zhou
Zoe Mehta
Guo Ye
Jerry Yao-Chieh Hu
Han Liu
AAML
55
0
0
01 May 2025
Beating Transformers using Synthetic Cognition
Alfredo Ibias
Miguel Rodriguez-Galindo
Hector Antona
Guillem Ramirez-Miranda
Enric Guinovart
26
0
0
10 Apr 2025
Leveraging State Space Models in Long Range Genomics
Matvei Popov
Aymen Kallala
Anirudha Ramesh
Narimane Hennouni
Shivesh Khaitan
Rick Gentry
Alain-Sam Cohen
Mamba
60
0
0
07 Apr 2025
HELM: Hierarchical Encoding for mRNA Language Modeling
Mehdi Yazdani-Jahromi
Mangal Prakash
Tommaso Mansi
Artem Moskalev
Rui Liao
84
2
0
13 Mar 2025
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
58
1
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
Y. Yang
Stan Z. Li
SyDa
AI4CE
87
0
0
11 Feb 2025
Longer Attention Span: Increasing Transformer Context Length with Sparse Graph Processing Techniques
Nathaniel Tomczak
Sanmukh Kuppannagari
91
0
0
31 Jan 2025
BIOSCAN-5M: A Multimodal Dataset for Insect Biodiversity
Zahra Gharaee
Scott C. Lowe
ZeMing Gong
Pablo Millán Arias
Nicholas Pellegrino
...
Lila Kari
Dirk Steinke
Graham W. Taylor
Paul Fieguth
Angel X. Chang
44
7
0
28 Jan 2025
State-space models are accurate and efficient neural operators for dynamical systems
Zheyuan Hu
Nazanin Ahmadi Daryakenari
Qianli Shen
Kenji Kawaguchi
George Karniadakis
Mamba
AI4CE
64
10
0
28 Jan 2025
Can linguists better understand DNA?
Wang Liang
82
1
0
20 Jan 2025
Context Clues: Evaluating Long Context Models for Clinical Prediction Tasks on EHRs
Michael Wornow
Suhana Bedi
Miguel Angel Fuentes Hernandez
E. Steinberg
Jason Alan Fries
Christopher Ré
Sanmi Koyejo
N. Shah
95
4
0
09 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
38
6
0
05 Nov 2024
Differentially Private Kernel Density Estimation
Erzhi Liu
Jerry Yao-Chieh Hu
Alex Reneau
Zhao Song
Han Liu
56
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
37
18
0
16 Jul 2024
Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity
Zhufeng Li
S. S. Cranganore
Nicholas D. Youngblut
Niki Kilbertus
34
2
0
09 May 2024
Assessing the importance of long-range correlations for deep-learning-based sleep staging
Tiezhi Wang
Nils Strodthoff
27
1
0
22 Feb 2024
Splicing Up Your Predictions with RNA Contrastive Learning
Phil Fradkin
Ruian Shi
Bo Wang
Brendan Frey
Leo J. Lee
SSL
24
0
0
12 Oct 2023
Embed-Search-Align: DNA Sequence Alignment using Transformer Models
Pavan Holur
K. Enevoldsen
Shreyas Rajesh
L. Mboning
Thalia Georgiou
Louis-S. Bouchard
Matteo Pellegrini
V. Roychowdhury
8
0
0
20 Sep 2023
FlexConv: Continuous Kernel Convolutions with Differentiable Kernel Sizes
David W. Romero
Robert-Jan Bruintjes
Jakub M. Tomczak
Erik J. Bekkers
Mark Hoogendoorn
J. C. V. Gemert
74
81
0
15 Oct 2021
The Power of Scale for Parameter-Efficient Prompt Tuning
Brian Lester
Rami Al-Rfou
Noah Constant
VPVLM
280
3,835
0
18 Apr 2021
Zero-Shot Text-to-Image Generation
Aditya A. Ramesh
Mikhail Pavlov
Gabriel Goh
Scott Gray
Chelsea Voss
Alec Radford
Mark Chen
Ilya Sutskever
VLM
253
4,764
0
24 Feb 2021
Shortformer: Better Language Modeling using Shorter Inputs
Ofir Press
Noah A. Smith
M. Lewis
219
88
0
31 Dec 2020
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
249
2,009
0
28 Jul 2020
1