Biology — Paper Notes
Protein models, molecular design, and biomedical AI
2019
2021
Human Genetics-2021 Embeddings from protein language models predict conservation and variant effects
KDD-2021 Modeling Protein Using Large-scale Pretrain Language Model
NeurIPS-2021 Language models enable zero-shot prediction of the effects of mutations on protein function
Bioinformatics Advances-2021 Light attention predicts protein location from the language of life
NeurIPS-2021 FLIP：Benchmark tasks in fitness landscape inference for proteins
bioRxiv-2021 Toward More General Embeddings for Protein Design：Harnessing Joint Representations of Sequence and Structure
Nature-2021 Highly accurate protein structure prediction with AlphaFold
IEEE Transactions on Pattern Analysis and Machine Intelligence-2021 ProtTrans：Towards Cracking the Language of Life’s Code Through Self-Supervised Learning
Proceedings of the National Academy of Sciences-2021 Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
ICML-2021 E(n) Equivariant Graph Neural Networks
ICML-2021 MSA Transformer
Bioinformatics-2021 DNABERT：pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
ICML-2021 Learning inverse folding from millions of predicted structures
ICLR-2021 Learning from Protein Structure with Geometric Vector Perceptrons
2022
NeurIPS-2022 PEER：A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
bioRxiv-2022 Fast protein structure searching using structure graph embeddings
NeurIPS-2022 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
PEDS-2022 Masked inverse folding with sequence transfer for protein representation learning
Nature Biotechnology-2022 Single-sequence protein structure prediction using a language model and deep learning
ICML-2022 Tranception：protein fitness prediction with autoregressive transformers and inference-time retrieval
NAR-2022 DeepLoc 2.0：multi-label subcellular localization prediction using protein language models
Nature Machine Intelligence-2022 Learning functional properties of proteins with language models
Frontiers in Microbiology-2022 iThermo：A Sequence-Based Model for Identifying Thermophilic Proteins Using a Multi-Feature Fusion Strategy
ICLR-2022 Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design
ICLR-2022 OntoProtein：Protein Pretraining With Gene Ontology Embedding
Nature Biotechnology-2022 Learning protein fitness models from evolutionary and assay-labeled data
2023
bioRxiv-2023 IgDesign-In vitro validated antibody design against multiple therapeutic antigens using inverse folding
bioRxiv-2023 Learning sequence, structure, and function representations of proteins with language models
Nature Biotechnology-2023 Protein remote homology detection and structural alignment using deep learning
NeurIPS-2023 PoET：A generative model of protein families as sequences-of-sequences
EMNLP-2023 BioPlanner：Automatic Evaluation of LLMs on Protocol Planning in Biology
NeurIPS-2023 ProteinGym：Large-Scale Benchmarks for Protein Design and Fitness Prediction
NeurIPS-2023 Predicting a Protein’s Stability under a Million Mutations
bioRxiv-2023 Protein generation with evolutionary diffusion：sequence is all you need
KDD-2023 Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design
ICML-2023 End-to-End Full-Atom Antibody Design
Nature Machine Intelligence-2023 Structure-inducing pre-training for generalizable representation learning
Nature Biotechnology-2023 Fast and accurate protein structure search with Foldseek
Science-2023 Evolutionary-scale prediction of atomic-level protein structure with a language model
Bioinformatics-2023 Accurate and efficient protein sequence design through learning concise local environment of residues
ICLRw-2023 Enhancing Protein Language Models with Structure-based Encoder and Pre-training
ICML-2023 Structure-informed Language Models Are Protein Designers
ICLR-2023 Conditional Antibody Design as 3D Equivariant Graph Translation
International Journal of Molecular Sciences-2023 DeepTP：A Deep Learning Model for Thermophilic Protein Prediction
bioRxiv-2023 Ankh：Optimized Protein Language Model Unlocks General-Purpose Modelling
bioRxiv-2023 When Geometric Deep Learning Meets Pretrained Protein Language Models
2024
PLOS Computational Biology-2024 Large scale paired antibody language models
bioRxiv-2024 Mixture of Experts Enable Efficient and Effective Protein Understanding and Design
Bioinformatics-2024 Expert-guided protein language models enable accurate and blazingly fast fitness prediction
Nature Communications-2024 A joint embedding of protein sequence and structure enables robust variant effect predictions
Nature Computational Science-2025 Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy
NeurIPS-2024 Multi-Scale Representation Learning for Protein Fitness Prediction
Nature Biotechnology-2024 Multistate and functional protein design using RoseTTAFold sequence space diffusion
ICML-2024 Feature Reuse and Scaling：Understanding Transfer Learning with Protein Language Models
Nature Communications-2024 PLMSearch：Protein language model powers accurate and fast sequence search for remote homology
Cell Systems-2024 Convolutions are competitive with transformers for protein sequence pretraining
eLife-2024 Sensitive remote homology search by local alignment of small positional embeddings from protein language models
Journal of Chemical Information and Modeling-2024 TM-search：An Efficient and Effective Tool for Protein Structure Database Search
ICLR-2024 SaProt：Protein Language Modeling with Structure-aware Vocabulary
Bioinformatics-2024 Embedding-based alignment：combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone
2025
Nature Biotechnology-2025 Democratizing protein language model training, sharing and collaboration
Genome Biology-2025 Evaluating the representational power of pre-trained DNA language models for regulatory genomics
ICMLw-2025 ProteinCrow：A Language Model Agent That Can Design Proteins
arXiv-2025 Scaling unlocks broader generation and deeper functional understanding of proteins
arXiv-2025 Prot42：a Novel Family of Protein Language Models for Target-aware Protein Binder Generation
COLING-2025 AutoProteinEngine：A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering
ICLR-2025 Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions
ICLR-2025 Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization
Science-2025 Simulating 500 million years of evolution with a language model
Related Open Projects
ProSST
Quantized structure meets disentangled attention
ProtSSN
Sequence–structure fusion for zero-shot protein engineering
VenusX
Unlocking fine-grained functional understanding of proteins
VenusREM
Retrieval-enhanced mutation effect prediction
VenusFactory
An integrated system for protein engineering
VenusFactory2
Self-evolving agents for protein discovery
ProtLOCA
Structure-only local geometry alignment
ProtSolM
Multimodal protein solubility prediction
VenusVaccine
Immunogenicity prediction for vaccine target selection
SES-Adapter
Structure-aware adapters for fitness prediction
PETA
Sub-word tokenization for protein transfer learning