Cell-ontology guided transcriptome foundation model

v1v2 (latest)

Cell-ontology guided transcriptome foundation model

22 August 2024

Jian Tang

ArXiv (abs)PDF HTML

Papers citing "Cell-ontology guided transcriptome foundation model"

19 / 19 papers shown

Title
The cell as a token: high-dimensional geometry in language models and cell embeddings William Gilpin 119 0 0 26 Mar 2025
Generalized Neural Collapse for a Large Number of Classes Jiachen Jiang Jinxin Zhou Peng Wang Qing Qu Dustin Mixon Chong You Zhihui Zhu AI4CE 73 28 0 09 Oct 2023
scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain Gyutaek Oh B. Choi Inkyung Jung Jong Chul Ye 53 5 0 04 Oct 2023
A Survey on Oversmoothing in Graph Neural Networks T. Konstantin Rusch Michael M. Bronstein Siddhartha Mishra 89 213 0 20 Mar 2023
Hyena Hierarchy: Towards Larger Convolutional Language Models Michael Poli Stefano Massaroli Eric Q. Nguyen Daniel Y. Fu Tri Dao S. Baccus Yoshua Bengio Stefano Ermon Christopher Ré VLM 119 307 0 21 Feb 2023
A single-cell gene expression language model Will Connell Umair W Khan Michael J. Keiser 39 9 0 25 Oct 2022
Emergent Abilities of Large Language Models Jason W. Wei Yi Tay Rishi Bommasani Colin Raffel Barret Zoph ... Tatsunori Hashimoto Oriol Vinyals Percy Liang J. Dean W. Fedus ELM ReLM LRM 286 2,511 0 15 Jun 2022
Perfectly Balanced: Improving Transfer and Robustness of Supervised Contrastive Learning Mayee F. Chen Daniel Y. Fu A. Narayan Michael Zhang Zhao Song Kayvon Fatahalian Christopher Ré SSL 62 51 0 15 Apr 2022
A Survey on Graph Representation Learning Methods Shima Khoshraftar A. An GNN AI4TS 83 121 0 04 Apr 2022
GraphFormers: GNN-nested Transformers for Representation Learning on Textual Graph Junhan Yang Zheng Liu Shitao Xiao Chaozhuo Li Defu Lian Sanjay Agrawal Amit Singh Guangzhong Sun Xing Xie AI4CE 52 159 0 06 May 2021
Dissecting Supervised Contrastive Learning Florian Graf Christoph Hofer Marc Niethammer Roland Kwitt SSL 156 74 0 17 Feb 2021
Contrastive Representation Learning: A Framework and Review Phúc H. Lê Khắc Graham Healy Alan F. Smeaton SSL AI4TS 313 712 0 10 Oct 2020
Targeted sampling from massive block model graphs with personalized PageRank Fan Chen Yini Zhang Karl Rohe 30 12 0 04 Oct 2019
TabNet: Attentive Interpretable Tabular Learning Sercan O. Arik Tomas Pfister LMTD 206 1,355 0 20 Aug 2019
BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding Jacob Devlin Ming-Wei Chang Kenton Lee Kristina Toutanova VLM SSL SSeg 1.8K 95,175 0 11 Oct 2018
Graph Attention Networks Petar Velickovic Guillem Cucurull Arantxa Casanova Adriana Romero Pietro Lio Yoshua Bengio GNN 481 20,233 0 30 Oct 2017
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 730 132,363 0 12 Jun 2017
Inductive Representation Learning on Large Graphs William L. Hamilton Z. Ying J. Leskovec 514 15,319 0 07 Jun 2017
Semi-Supervised Classification with Graph Convolutional Networks Thomas Kipf Max Welling GNN SSL 657 29,154 0 09 Sep 2016