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Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins.
Central dogma of molecular biology
Francis Crick · 1970
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Hidden markov models and their applications in biological sequence analysis
Byung-Jun Yoon · 2009
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Understanding transcriptional regulation by integrative analysis of transcription factor binding data
Chao Cheng, Roger Alexander, Renqiang Min, Jing Leng, Kevin Y Yip, Joel Rozowsky, Koon-Kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, et al · 2012
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Review the cancer genome atlas (tcga): an immeasurable source of knowledge
Katarzyna Tomczak, Patrycja Czerwińska, and Maciej Wiznerowicz · 2015
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Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation
Alvaro J González, Manu Setty, and Christina S Leslie · 2015
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Gmap and gsnap for genomic sequence alignment: enhancements to speed, accuracy, and functionality
Thomas D Wu, Jens Reeder, Michael Lawrence, Gabe Becker, and Matthew J Brauer · 2016
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Multi-omics approaches to disease
Yehudit Hasin, Marcus Seldin, and Aldons Lusis · 2017
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Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova · 2018
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Sequential regulatory activity prediction across chromosomes with convolutional neural networks
David R Kelley, Yakir A Reshef, Maxwell Bileschi, David Belanger, Cory Y McLean, and Jasper Snoek · 2018
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Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
Jian Zhou, Chandra L Theesfeld, Kevin Yao, Kathleen M Chen, Aaron K Wong, and Olga G Troyanskaya · 2018
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Tuning of mrna stability through altering 3’-utr sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations
Woo Seuk Koh, Joshua R Porter, and Eric Batchelor · 2019
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Proteomicsdb: a multi-omics and multi-organism resource for life science research
Patroklos Samaras, Tobias Schmidt, Martin Frejno, Siegfried Gessulat, Maria Reinecke, Anna Jarzab, Jana Zecha, Julia Mergner, Piero Giansanti, Hans-Christian Ehrlich, et al · 2020
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Computational methods for predicting functions at the mrna isoform level
Sambit K Mishra, Viraj Muthye, and Gaurav Kandoi · 2020
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Language models are few-shot learners
Tom Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared D Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, et al · 2020
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Highly accurate protein structure prediction with alphafold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, et al · 2021
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Effective gene expression prediction from sequence by integrating long-range interactions
Žiga Avsec, Vikram Agarwal, Daniel Visentin, Joseph R Ledsam, Agnieszka Grabska-Barwinska, Kyle R Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R Kelley · 2021
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Learning transferable visual models from natural language supervision
Alec Radford, Jong Wook Kim, Chris Hallacy, Aditya Ramesh, Gabriel Goh, Sandhini Agarwal, Girish Sastry, Amanda Askell, Pamela Mishkin, Jack Clark, et al · 2021
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Less is more: Clipbert for video-and-language learning via sparse sampling
Jie Lei, Linjie Li, Luowei Zhou, Zhe Gan, Tamara L. Berg, Mohit Bansal, and Jingjing Liu · 2021
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Perceiver: General perception with iterative attention
Andrew Jaegle, Felix Gimeno, Andy Brock, Oriol Vinyals, Andrew Zisserman, and Joao Carreira · 2021
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Selective upregulation of sirt1 expression in retinal ganglion cells by aav-mediated gene delivery increases neuronal cell survival and alleviates axon demyelination associated with optic neuritis
Ahmara G Ross, Brahim Chaqour, Devin S McDougald, Kimberly E Dine, Thu T Duong, Ryan E Shindler, Jipeng Yue, Tehui Liu, and Kenneth S Shindler · 2022
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Flamingo: a visual language model for few-shot learning
Jean-Baptiste Alayrac, Jeff Donahue, Pauline Luc, Antoine Miech, Iain Barr, Yana Hasson, Karel Lenc, Arthur Mensch, Katherine Millican, Malcolm Reynolds, et al · 2022
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Zerocap: Zero-shot image-to-text generation for visual-semantic arithmetic
Yoad Tewel, Yoav Shalev, Idan Schwartz, and Lior Wolf · 2022
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Protein–rna interaction prediction with deep learning: structure matters
Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, and Yu Li · 2022
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Video-text modeling with zero-shot transfer from contrastive captioners
Shen Yan, Tao Zhu, Zirui Wang, Yuan Cao, Mi Zhang, Soham Ghosh, Yonghui Wu, and Jiahui Yu · 2022
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Coca: Contrastive captioners are image-text foundation models
Jiahui Yu, Zirui Wang, Vijay Vasudevan, Legg Yeung, Mojtaba Seyedhosseini, and Yonghui Wu · 2022
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Language is not all you need: Aligning perception with language models
Shaohan Huang, Li Dong, Wenhui Wang, Yaru Hao, Saksham Singhal, Shuming Ma, Tengchao Lv, Lei Cui, Owais Khan Mohammed, Barun Patra, Qiang Liu, Kriti Aggarwal, Zewen Chi, Nils Johan Bertil Bjorck, Vishrav Chaudhary, Subhojit Som, Xia Song, and Furu Wei · 2023
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BLIP-2: bootstrapping language-image pre-training with frozen image encoders and large language models
Junnan Li, Dongxu Li, Silvio Savarese, and Steven C. H. Hoi · 2023
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Self-chained image-language model for video localization and question answering
Shoubin Yu, Jaemin Cho, Prateek Yadav, and Mohit Bansal · 2023
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Maivar-t: Multimodal audio-image and video action recognizer using transformers
Muhammad Bilal Shaikh, Douglas Chai, Syed Mohammed Shamsul Islam, and Naveed Akhtar · 2023
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Self-supervised contrastive learning for audio-visual action recognition
Yang Liu, Ying Tan, and Haoyuan Lan · 2023
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alphaXiv searches the wider corpus for related work and actual follow-ups.
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Yi Wang, Kunchang Li, Yizhuo Li, Yinan He, Bingkun Huang, Zhiyu Zhao, Hongjie Zhang, Jilan Xu, Yi Liu, Zun Wang, Sen Xing, Guo Chen, Junting Pan, Jiashuo Yu, Yali Wang, Limin Wang, and Yu Qiao · 2022
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Blip: Bootstrapping language-image pre-training for unified vision-language understanding and generation
Junnan Li, Dongxu Li, Caiming Xiong, and Steven Hoi · 2022
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Evolutionary-scale prediction of atomic-level protein structure with a language model
Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Robert Verkuil, Ori Kabeli, Yaniv Shmueli, et al · 2023
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The nucleotide transformer: Building and evaluating robust foundation models for human genomics
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza Revilla, Nicolas Lopez Carranza, Adam Henryk Grzywaczewski, Francesco Oteri, Christian Dallago, Evan Trop, Hassan Sirelkhatim, Guillaume Richard, Marcin Skwark, Karim Beguir, Marie Lopez, and Thomas Pierrot · 2023
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Dnabert-2: Efficient foundation model and benchmark for multi-species genome
Zhihan Zhou, Yanrong Ji, Weijian Li, Pratik Dutta, Ramana Davuluri, and Han Liu · 2023
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Accurate proteome-wide missense variant effect prediction with alphamissense
Jun Cheng, Guido Novati, Joshua Pan, Clare Bycroft, Akvilė Žemgulytė, Taylor Applebaum, Alexander Pritzel, Lai Hong Wong, Michal Zielinski, Tobias Sargeant, Rosalia G. Schneider, Andrew W. Senior, John Jumper, Demis Hassabis, Pushmeet Kohli, and Žiga Avsec · 2023
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Scaling deep learning for materials discovery
Amil Merchant, Simon Batzner, Samuel S Schoenholz, Muratahan Aykol, Gowoon Cheon, and Ekin Dogus Cubuk · 2023
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Honeybee: Locality-enhanced projector for multimodal llm
Junbum Cha, Wooyoung Kang, Jonghwan Mun, and Byungseok Roh · 2023
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Predicting rna-seq coverage from dna sequence as a unifying model of gene regulation
Johannes Linder, Divyanshi Srivastava, Han Yuan, Vikram Agarwal, and David R Kelley · 2023
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Ensembl 2023
Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, et al · 2023
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Kosmos-2: Grounding multimodal large language models to the world
Zhiliang Peng, Wenhui Wang, Li Dong, Yaru Hao, Shaohan Huang, Shuming Ma, and Furu Wei · 2023
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Sequence modeling and design from molecular to genome scale with evo
Eric Nguyen, Michael Poli, Matthew G. Durrant, Armin W. Thomas, Brian Kang, Jeremy Sullivan, Madelena Y. Ng, Ashley Lewis, Aman Patel, Aaron Lou, Stefano Ermon, Stephen A. Baccus, Tina Hernandez-Boussard, Christopher Ré, Patrick D. Hsu, and Brian L. Hie · 2024
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Rna language models predict mutations that improve rna function
Yekaterina Shulgina, Marena I Trinidad, Conner J Langeberg, Hunter Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J Nissley, Jaymin Patel, Ron S Boger, Honglue Shi, et al · 2024
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Visual instruction tuning
Haotian Liu, Chunyuan Li, Qingyang Wu, and Yong Jae Lee · 2024
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Omnivec: Learning robust representations with cross modal sharing
Siddharth Srivastava and Gaurav Sharma · 2024
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A visual-language foundation model for computational pathology
Ming Y. Lu, Bowen Chen, Drew F. K. Williamson, Richard J. Chen, Ivy Liang, Tong Ding, Guillaume Jaume, Igor Odintsov, Long Phi Le, Georg Gerber, Anil V. Parwani, Andrew Zhang, and Faisal Mahmood · 2024
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Caduceus: Bi-directional equivariant long-range dna sequence modeling
Yair Schiff, Chia-Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, and Volodymyr Kuleshov · 2024
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Avsegformer: Audio-visual segmentation with transformer
Shengyi Gao, Zhe Chen, Guo Chen, Wenhai Wang, and Tong Lu · 2024
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Prompting segmentation with sound is generalizable audio-visual source localizer
Yaoting Wang, Weisong Liu, Guangyao Li, Jian Ding, Di Hu, and Xi Li · 2024
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Chatnt: A multimodal conversational agent for dna, rna and protein tasks
Guillaume Richard, Bernardo P de Almeida, Hugo Dalla-Torre, Christopher Blum, Lorenz Hexemer, Priyanka Pandey, Stefan Laurent, Marie P Lopez, Alexander Laterre, Maren Lang, et al · 2024
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Are genomic language models all you need? exploring genomic language models on protein downstream tasks
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