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2007.06225
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ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing
13 July 2020
Ahmed Elnaggar
M. Heinzinger
Christian Dallago
Ghalia Rehawi
Yu Wang
Llion Jones
Tom Gibbs
Tamas B. Fehér
Christoph Angerer
Martin Steinegger
D. Bhowmik
B. Rost
DRL
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Papers citing
"ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing"
48 / 48 papers shown
Title
Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A Hemagglutinin
Ella Barkan
Ibrahim Siddiqui
Kevin J. Cheng
Alex Golts
Yoel Shoshan
J. Weber
Yailin Campos Mota
Michal Ozery-Flato
Giuseppe A. Sautto
AI4CE
56
0
0
02 Feb 2025
Recent advances in deep learning and language models for studying the microbiome
Binghao Yan
Yunbi Nam
Lingyao Li
Rebecca A Deek
Hongzhe Li
Siyuan Ma
16
1
0
15 Sep 2024
DisorderUnetLM: Validating ProteinUnet for efficient protein intrinsic disorder prediction
Krzysztof Kotowski
I. Roterman
Katarzyna Stapor
16
0
0
11 Apr 2024
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
Lirong Wu
Yijun Tian
Yufei Huang
Siyuan Li
Haitao Lin
Nitesh V. Chawla
Stan Z. Li
28
22
0
22 Feb 2024
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
Zuobai Zhang
Jiarui Lu
Vijil Chenthamarakshan
Aurélie C. Lozano
Payel Das
Jian Tang
23
1
0
10 Feb 2024
Language models in molecular discovery
Chaoqi Wang
Yibo Jiang
Chenghao Yang
Han Liu
Yuxin Chen
23
7
0
28 Sep 2023
Materials Informatics Transformer: A Language Model for Interpretable Materials Properties Prediction
Hongshuo Huang
Rishikesh Magar
Chang Xu
A. Farimani
AI4CE
35
4
0
30 Aug 2023
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction
Y. Tan
Bingxin Zhou
Yuanhong Jiang
Yu Wang
Liang Hong
21
2
0
08 Jun 2023
Accurate and Definite Mutational Effect Prediction with Lightweight Equivariant Graph Neural Networks
Bingxin Zhou
Outongyi Lv
Kai Yi
Xinye Xiong
P. Tan
Liang Hong
Yu Wang
26
4
0
13 Apr 2023
A Text-guided Protein Design Framework
Shengchao Liu
Yanjing Li
Zhuoxinran Li
A. Gitter
Yutao Zhu
...
Arvind Ramanathan
Chaowei Xiao
Jian Tang
Hongyu Guo
Anima Anandkumar
67
61
0
09 Feb 2023
The geometry of hidden representations of large transformer models
L. Valeriani
Diego Doimo
F. Cuturello
A. Laio
A. Ansuini
Alberto Cazzaniga
MILM
21
48
0
01 Feb 2023
On Pre-trained Language Models for Antibody
Danqing Wang
Fei Ye
Zhou Hao
33
10
0
28 Jan 2023
ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts
Minghao Xu
Xinyu Yuan
Santiago Miret
Jian Tang
AI4TS
27
95
0
28 Jan 2023
PlasmoFAB: A Benchmark to Foster Machine Learning for Plasmodium falciparum Protein Antigen Candidate Prediction
Jonas C. Ditz
Jacqueline Wistuba-Hamprecht
Timo Maier
Rolf Fendel
N. Pfeifer
Bernhard Reuter
16
1
0
16 Jan 2023
A Survey on Protein Representation Learning: Retrospect and Prospect
Lirong Wu
Yu-Feng Huang
H. Lin
Stan Z. Li
AI4TS
26
12
0
31 Dec 2022
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering
Mingchen Li
Liqi Kang
Y. Xiong
Yu Wang
Guisheng Fan
P. Tan
Liang Hong
16
22
0
29 Dec 2022
Unsupervised language models for disease variant prediction
Allan Zhou
Nicholas C. Landolfi
Daniel C. O’Neill
22
0
0
07 Dec 2022
Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks
Fang Wu
Yujun Tao
Dragomir R. Radev
Jinbo Xu
Stan Z. Li
AI4CE
30
32
0
07 Dec 2022
Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design
Kaiyuan Gao
Lijun Wu
Jinhua Zhu
Tianbo Peng
Yingce Xia
...
Shufang Xie
Tao Qin
Haiguang Liu
Kun He
Tie-Yan Liu
24
9
0
26 Oct 2022
MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Prediction
Zhonglin Cao
Rishikesh Magar
Yuyang Wang
A. Farimani
AI4CE
23
88
0
25 Oct 2022
AlphaFold Distillation for Protein Design
Igor Melnyk
A. Lozano
Payel Das
Vijil Chenthamarakshan
12
1
0
05 Oct 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
Zhuoran Qiao
Weili Nie
Arash Vahdat
Thomas F. Miller
Anima Anandkumar
DiffM
33
84
0
30 Sep 2022
Exploiting Pretrained Biochemical Language Models for Targeted Drug Design
Gökçe Uludogan
Elif Özkirimli
K. Ülgen
N. Karalı
Arzucan Özgür
17
15
0
02 Sep 2022
PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction
Sirui Liu
Jun Zhang
Haotian Chu
Min Wang
Boxin Xue
...
Zidong Wang
Lijiang Yang
Fan Yu
Lei Chen
Y. Gao
3DV
14
13
0
24 Jun 2022
Evaluating Self-Supervised Learning for Molecular Graph Embeddings
Hanchen Wang
Jean Kaddour
Shengchao Liu
Jian Tang
Joan Lasenby
Qi Liu
27
20
0
16 Jun 2022
Exploring evolution-aware & -free protein language models as protein function predictors
Min Hu
Fajie Yuan
Kevin Kaichuang Yang
Fusong Ju
Jingyu Su
Hongya Wang
Fei Yang
Qiuyang Ding
15
36
0
14 Jun 2022
Contrastive Representation Learning for 3D Protein Structures
Pedro Hermosilla
Timo Ropinski
3DV
46
51
0
31 May 2022
Simple Recurrence Improves Masked Language Models
Tao Lei
Ran Tian
Jasmijn Bastings
Ankur P. Parikh
77
4
0
23 May 2022
Multi-segment preserving sampling for deep manifold sampler
Daniel Berenberg
Jae Hyeon Lee
S. Kelow
Ji Won Park
Andrew Watkins
Vladimir Gligorijević
Richard Bonneau
Stephen Ra
Kyunghyun Cho
MedIm
19
5
0
09 May 2022
SNP2Vec: Scalable Self-Supervised Pre-Training for Genome-Wide Association Study
Samuel Cahyawijaya
Tiezheng Yu
Zihan Liu
Tiffany Mak
Xiaopu Zhou
N. Ip
Pascale Fung
13
8
0
14 Apr 2022
Few Shot Protein Generation
Soumya Ram
Tristan Bepler
26
6
0
03 Apr 2022
Prompt-Guided Injection of Conformation to Pre-trained Protein Model
Qiang Zhang
Zeyuan Wang
Yuqiang Han
Haoran Yu
Xurui Jin
Huajun Chen
23
3
0
07 Feb 2022
Mitigating cold start problems in drug-target affinity prediction with interaction knowledge transferring
T. Nguyen
Thin Nguyen
T. Tran
8
14
0
16 Jan 2022
Deciphering antibody affinity maturation with language models and weakly supervised learning
Jeffrey A. Ruffolo
Jeffrey J. Gray
Jeremias Sulam
10
130
0
14 Dec 2021
Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model
Liang He
Shizhuo Zhang
Lijun Wu
Huanhuan Xia
Fusong Ju
...
Jianwei Zhu
Pan Deng
Bin Shao
Tao Qin
Tie-Yan Liu
26
31
0
29 Oct 2021
Deciphering the Language of Nature: A transformer-based language model for deleterious mutations in proteins
Theodore Jiang
Li Fang
Kai Wang
MedIm
25
17
0
27 Oct 2021
Unifying Likelihood-free Inference with Black-box Optimization and Beyond
Dinghuai Zhang
Jie Fu
Yoshua Bengio
Aaron Courville
31
13
0
06 Oct 2021
Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs
Fang Wu
Dragomir R. Radev
Huabin Xing
ViT
33
54
0
04 Oct 2021
Deep Generative Modeling for Protein Design
Alexey Strokach
Philip M. Kim
AI4CE
179
90
0
31 Aug 2021
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties
Jerret Ross
Brian M. Belgodere
Vijil Chenthamarakshan
Inkit Padhi
Youssef Mroueh
Payel Das
AI4CE
24
272
0
17 Jun 2021
TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks
Anna Weber
Jannis Born
María Rodríguez Martínez
11
129
0
21 Apr 2021
Neural representation and generation for RNA secondary structures
Zichao Yan
William L. Hamilton
Mathieu Blanchette
37
2
0
01 Feb 2021
Align-gram : Rethinking the Skip-gram Model for Protein Sequence Analysis
Nabil Ibtehaz
S. Sourav
Md. Shamsuzzoha Bayzid
M. S. Rahman
19
2
0
06 Dec 2020
Generative Capacity of Probabilistic Protein Sequence Models
Francisco McGee
Quentin Novinger
R. Levy
Vincenzo Carnevale
A. Haldane
24
34
0
03 Dec 2020
Profile Prediction: An Alignment-Based Pre-Training Task for Protein Sequence Models
Pascal Sturmfels
Jesse Vig
Ali Madani
Nazneen Rajani
13
24
0
01 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
274
2,015
0
28 Jul 2020
BERTology Meets Biology: Interpreting Attention in Protein Language Models
Jesse Vig
Ali Madani
L. Varshney
Caiming Xiong
R. Socher
Nazneen Rajani
26
288
0
26 Jun 2020
Megatron-LM: Training Multi-Billion Parameter Language Models Using Model Parallelism
M. Shoeybi
M. Patwary
Raul Puri
P. LeGresley
Jared Casper
Bryan Catanzaro
MoE
245
1,817
0
17 Sep 2019
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