Title
Efficient Time Series Processing for Transformers and State-Space Models through Token Merging Leon Götz Marcel Kollovieh Stephan Günnemann Leo Schwinn 32 2 0 28 May 2024
CLIBD: Bridging Vision and Genomics for Biodiversity Monitoring at Scale ZeMing Gong Austin T. Wang Joakim Bruslund Haurum Scott C. Lowe Graham W. Taylor Angel X. Chang Angel X. Chang 39 5 0 27 May 2024
Self-Distillation Improves DNA Sequence Inference Tong Yu Lei Cheng Ruslan Khalitov Erland Brandser Olsson Zhirong Yang SyDa 40 0 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 45 7 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 47 2 0 09 May 2024
Mamba-360: Survey of State Space Models as Transformer Alternative for Long Sequence Modelling: Methods, Applications, and Challenges Badri N. Patro Vijay Srinivas Agneeswaran Mamba 48 38 0 24 Apr 2024
Locating and Editing Factual Associations in Mamba Arnab Sen Sharma David Atkinson David Bau KELM 79 28 0 04 Apr 2024
Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions Yuting He Fuxiang Huang Xinrui Jiang Yuxiang Nie Minghao Wang Jiguang Wang Hao Chen LM&MA AI4CE 84 28 0 04 Apr 2024
Mechanistic Design and Scaling of Hybrid Architectures Michael Poli Armin W. Thomas Eric N. D. Nguyen Pragaash Ponnusamy Bjorn Deiseroth ... Brian Hie Stefano Ermon Christopher Ré Ce Zhang Stefano Massaroli MoE 57 21 0 26 Mar 2024
Holographic Global Convolutional Networks for Long-Range Prediction Tasks in Malware Detection Mohammad Mahmudul Alam Edward Raff Stella Biderman Tim Oates James Holt AAML 38 3 0 23 Mar 2024
AI for Biomedicine in the Era of Large Language Models Zhenyu Bi Sajib Acharjee Dip Daniel Hajialigol Sindhura Kommu Hanwen Liu Meng Lu Xuan Wang LM&MA AI4CE 34 8 0 23 Mar 2024
Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling Yair Schiff Chia-Hsiang Kao Aaron Gokaslan Tri Dao Albert Gu Volodymyr Kuleshov Mamba 27 81 0 05 Mar 2024
Recent Advances, Applications, and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2023 Symposium Hyewon Jeong Sarah Jabbour Yuzhe Yang Rahul Thapta Hussein Mozannar ... Linying Zhang Harvineet Singh Tom Hartvigsen Helen Zhou Chinasa T. Okolo VLM AI4TS OOD 43 2 0 03 Mar 2024
Beyond Language Models: Byte Models are Digital World Simulators Shangda Wu Xu Tan Zili Wang Rui Wang Xiaobing Li Maosong Sun 35 12 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 13 2 0 24 Feb 2024
Assessing the importance of long-range correlations for deep-learning-based sleep staging Tiezhi Wang Nils Strodthoff 32 1 0 22 Feb 2024
Personalised Drug Identifier for Cancer Treatment with Transformers using Auxiliary Information A. Jayagopal Hansheng Xue Ziyang He R. J. Walsh K. K. Hariprasannan D. S. P. Tan T. Z. Tan J. J. Pitt A. D. Jeyasekharan Vaibhav Rajan 13 1 0 16 Feb 2024
Graph Mamba: Towards Learning on Graphs with State Space Models Ali Behrouz Farnoosh Hashemi AI4CE 112 61 0 13 Feb 2024
DiscDiff: Latent Diffusion Model for DNA Sequence Generation Zehui Li Yuhao Ni W. Beardall Guoxuan Xia Akashaditya Das Guy-Bart Stan Yiren Zhao 35 6 0 08 Feb 2024
QuIP#: Even Better LLM Quantization with Hadamard Incoherence and Lattice Codebooks Albert Tseng Jerry Chee Qingyao Sun Volodymyr Kuleshov Christopher De Sa MQ 128 101 0 06 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 43 9 0 06 Feb 2024
Repeat After Me: Transformers are Better than State Space Models at Copying Samy Jelassi David Brandfonbrener Sham Kakade Eran Malach 103 80 0 01 Feb 2024
Graph-Mamba: Towards Long-Range Graph Sequence Modeling with Selective State Spaces Chloe X. Wang Oleksii Tsepa Jun Ma Bo Wang Mamba 38 88 0 01 Feb 2024
Finetuning Foundation Models for Joint Analysis Optimization M. Vigl N. Hartman L. Heinrich 43 13 0 24 Jan 2024
Large Language Models in Plant Biology H. Lam Xing Er Ong Marek Mutwil 11 16 0 05 Jan 2024
On the Long Range Abilities of Transformers Itamar Zimerman Lior Wolf 35 7 0 28 Nov 2023
BEND: Benchmarking DNA Language Models on biologically meaningful tasks Frederikke Isa Marin Felix Teufel Marc Horlacher Dennis Madsen Dennis Pultz Ole Winther Wouter Boomsma 22 34 0 21 Nov 2023
A Multi-Center Study on the Adaptability of a Shared Foundation Model for Electronic Health Records L. Guo Jason Alan Fries E. Steinberg Scott L. Fleming Keith Morse Catherine Aftandilian J. Posada Nigam Shah L. Sung OOD 26 13 0 20 Nov 2023
To Transformers and Beyond: Large Language Models for the Genome Micaela Elisa Consens Cameron Dufault Michael Wainberg Duncan Forster Mehran Karimzadeh Hani Goodarzi Fabian J. Theis Alan Moses Bo Wang LM&MA MedIm 26 28 0 13 Nov 2023
FlashFFTConv: Efficient Convolutions for Long Sequences with Tensor Cores Daniel Y. Fu Hermann Kumbong Eric N. D. Nguyen Christopher Ré VLM 43 29 0 10 Nov 2023
Understanding the Natural Language of DNA using Encoder-Decoder Foundation Models with Byte-level Precision Aditya Malusare Harish Kothandaraman Dipesh Tamboli N. Lanman Vaneet Aggarwal AI4CE 43 2 0 04 Nov 2023
Splicing Up Your Predictions with RNA Contrastive Learning Phil Fradkin Ruian Shi Bo Wang Brendan Frey Leo J. Lee SSL 29 0 0 12 Oct 2023
scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain Gyutaek Oh B. Choi Inkyung Jung Jong Chul Ye 30 5 0 04 Oct 2023
Multi-Dimensional Hyena for Spatial Inductive Bias Itamar Zimerman Lior Wolf ViT 30 4 0 24 Sep 2023
Embed-Search-Align: DNA Sequence Alignment using Transformer Models Pavan Holur Kenneth C. Enevoldsen Shreyas Rajesh L. Mboning Thalia Georgiou Louis-S. Bouchard Matteo Pellegrini V. Roychowdhury 27 0 0 20 Sep 2023
DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation Z. Zang Hao Luo Kaidi Wang Panpan Zhang F. Wang Stan. Z Li Yang You 35 5 0 10 Sep 2023
A Survey on Generative Modeling with Limited Data, Few Shots, and Zero Shot Milad Abdollahzadeh Touba Malekzadeh Christopher T. H. Teo Keshigeyan Chandrasegaran Guimeng Liu Ngai-man Cheung VLM MedIm 47 21 0 26 Jul 2023
Math Agents: Computational Infrastructure, Mathematical Embedding, and Genomics M. Swan Takashi Kido Eric Roland R. P. D. Santos AI4CE 29 10 0 04 Jul 2023
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome Zhihan Zhou Yanrong Ji Weijian Li Pratik Dutta R. Davuluri Han Liu 24 174 0 26 Jun 2023
FlexConv: Continuous Kernel Convolutions with Differentiable Kernel Sizes David W. Romero Robert-Jan Bruintjes Jakub M. Tomczak Erik J. Bekkers Mark Hoogendoorn Jan van Gemert 80 82 0 15 Oct 2021
The Power of Scale for Parameter-Efficient Prompt Tuning Brian Lester Rami Al-Rfou Noah Constant VPVLM 280 3,872 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 255 4,805 0 24 Feb 2021
Shortformer: Better Language Modeling using Shorter Inputs Ofir Press Noah A. Smith M. Lewis 230 89 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 288 2,023 0 28 Jul 2020
Wavelet Networks: Scale-Translation Equivariant Learning From Raw Time-Series David W. Romero Erik J. Bekkers Jakub M. Tomczak Mark Hoogendoorn 13 3 0 09 Jun 2020