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
2021-12-30 · protein, PLM, fitness-prediction
KDD-2021 Modeling Protein Using Large-scale Pretrain Language Model
2021-12-07 · protein, PLM
NeurIPS-2021 Language models enable zero-shot prediction of the effects of mutations on protein function
2021-11-10 · protein, PLM, fitness-prediction
Bioinformatics Advances-2021 Light attention predicts protein location from the language of life
2021-11-09 · protein, localization, PLM
NeurIPS-2021 FLIP：Benchmark tasks in fitness landscape inference for proteins
2021-10-11 · protein, benchmark
bioRxiv-2021 Toward More General Embeddings for Protein Design：Harnessing Joint Representations of Sequence and Structure
2021-09-01 · protein, PLM, fitness-prediction
Nature-2021 Highly accurate protein structure prediction with AlphaFold
2021-07-15 · protein, PLM, structure prediction
IEEE Transactions on Pattern Analysis and Machine Intelligence-2021 ProtTrans：Towards Cracking the Language of Life’s Code Through Self-Supervised Learning
2021-07-01 · protein, PLM, transformer, self-supervised
Proceedings of the National Academy of Sciences-2021 Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
2021-04-05 · protein, PLM
ICML-2021 E(n) Equivariant Graph Neural Networks
2021-02-19 · GNN
ICML-2021 MSA Transformer
2021-02-13 · protein, PLM
Bioinformatics-2021 DNABERT：pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
2021-02-04 · DNA, genomics, PLM
ICML-2021 Learning inverse folding from millions of predicted structures
2021-02-02 · protein, inverse folding, PLM, GNN
ICLR-2021 Learning from Protein Structure with Geometric Vector Perceptrons
2021-01-13 · protein, GNN, inverse folding
2022
NeurIPS-2022 PEER：A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
2022-12-01 · protein, benchmark, PLM
bioRxiv-2022 Fast protein structure searching using structure graph embeddings
2022-11-28 · protein, PLM, alignment
NeurIPS-2022 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
2022-11-01 · protein, antibody, diffusion, GNN
PEDS-2022 Masked inverse folding with sequence transfer for protein representation learning
2022-10-26 · protein, PLM
Nature Biotechnology-2022 Single-sequence protein structure prediction using a language model and deep learning
2022-10-03 · protein, PLM, structure prediction
ICML-2022 Tranception：protein fitness prediction with autoregressive transformers and inference-time retrieval
2022-05-27 · protein, PLM, fitness-prediction
NAR-2022 DeepLoc 2.0：multi-label subcellular localization prediction using protein language models
2022-04-30 · protein, localization, PLM
Nature Machine Intelligence-2022 Learning functional properties of proteins with language models
2022-03-21 · protein, PLM, functional prediction
Frontiers in Microbiology-2022 iThermo：A Sequence-Based Model for Identifying Thermophilic Proteins Using a Multi-Feature Fusion Strategy
2022-02-22 · protein
ICLR-2022 Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design
2022-01-29 · protein, antibody, GNN
ICLR-2022 OntoProtein：Protein Pretraining With Gene Ontology Embedding
2022-01-29 · protein, PLM
Nature Biotechnology-2022 Learning protein fitness models from evolutionary and assay-labeled data
2022-01-17 · protein, PLM, fitness-prediction
2023
bioRxiv-2023 IgDesign-In vitro validated antibody design against multiple therapeutic antigens using inverse folding
2023-12-08 · protein, antibody, inverse folding, protein-design
bioRxiv-2023 Learning sequence, structure, and function representations of proteins with language models
2023-11-26 · protein, PLM, function, MOE
Nature Biotechnology-2023 Protein remote homology detection and structural alignment using deep learning
2023-11-07 · protein, homology
NeurIPS-2023 PoET：A generative model of protein families as sequences-of-sequences
2023-11-01 · protein, PLM, fitness-prediction
EMNLP-2023 BioPlanner：Automatic Evaluation of LLMs on Protocol Planning in Biology
2023-10-08 · Agent, LLM
NeurIPS-2023 ProteinGym：Large-Scale Benchmarks for Protein Design and Fitness Prediction
2023-09-30 · protein, PLM, benchmark
NeurIPS-2023 Predicting a Protein’s Stability under a Million Mutations
2023-09-22 · protein, fitness-prediction
bioRxiv-2023 Protein generation with evolutionary diffusion：sequence is all you need
2023-09-11 · protein, PLM, protein-design
KDD-2023 Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design
2023-08-04 · protein, antibody, GNN, PLM
ICML-2023 End-to-End Full-Atom Antibody Design
2023-06-15 · protein, antibody, GNN
Nature Machine Intelligence-2023 Structure-inducing pre-training for generalizable representation learning
2023-06-01 · pre-training, PLM
Nature Biotechnology-2023 Fast and accurate protein structure search with Foldseek
2023-05-08 · protein, alignment
Science-2023 Evolutionary-scale prediction of atomic-level protein structure with a language model
2023-03-16 · protein, PLM, structure prediction
Bioinformatics-2023 Accurate and efficient protein sequence design through learning concise local environment of residues
2023-03-14 · protein, protein-design, GNN, PLM
ICLRw-2023 Enhancing Protein Language Models with Structure-based Encoder and Pre-training
2023-03-06 · PLM, GNN
ICML-2023 Structure-informed Language Models Are Protein Designers
2023-02-09 · protein, PLM, protein-design
ICLR-2023 Conditional Antibody Design as 3D Equivariant Graph Translation
2023-02-02 · protein, antibody, GNN
International Journal of Molecular Sciences-2023 DeepTP：A Deep Learning Model for Thermophilic Protein Prediction
2023-01-22 · protein
bioRxiv-2023 Ankh：Optimized Protein Language Model Unlocks General-Purpose Modelling
2023-01-16 · protein, PLM, language-model
bioRxiv-2023 When Geometric Deep Learning Meets Pretrained Protein Language Models
2023-01-05 · protein, PLM, GNN
2024
PLOS Computational Biology-2024 Large scale paired antibody language models
2024-12-06 · protein, antibody, PLM
bioRxiv-2024 Mixture of Experts Enable Efficient and Effective Protein Understanding and Design
2024-11-29 · protein, language-model
Bioinformatics-2024 Expert-guided protein language models enable accurate and blazingly fast fitness prediction
2024-11-22 · protein, fitness-prediction, PLM
Nature Communications-2024 A joint embedding of protein sequence and structure enables robust variant effect predictions
2024-11-07 · protein, fitness-prediction, PLM
Nature Computational Science-2025 Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy
2024-10-03 · GNN, protein, fitness-prediction
NeurIPS-2024 Multi-Scale Representation Learning for Protein Fitness Prediction
2024-09-26 · GNN, protein, fitness-prediction
Nature Biotechnology-2024 Multistate and functional protein design using RoseTTAFold sequence space diffusion
2024-09-25 · protein, diffusion, protein-design
ICML-2024 Feature Reuse and Scaling：Understanding Transfer Learning with Protein Language Models
2024-06-21 · protein, PLM, transfer learning
Nature Communications-2024 PLMSearch：Protein language model powers accurate and fast sequence search for remote homology
2024-03-30 · protein, PLM, alignment
Cell Systems-2024 Convolutions are competitive with transformers for protein sequence pretraining
2024-03-20 · protein, PLM, CNN, transformer
eLife-2024 Sensitive remote homology search by local alignment of small positional embeddings from protein language models
2024-03-15 · protein, homology, PLM
Journal of Chemical Information and Modeling-2024 TM-search：An Efficient and Effective Tool for Protein Structure Database Search
2024-01-25 · protein, structure search
ICLR-2024 SaProt：Protein Language Modeling with Structure-aware Vocabulary
2024-01-16 · protein, PLM
Bioinformatics-2024 Embedding-based alignment：combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone
2024-01-04 · protein, PLM, alignment
2025
Nature Biotechnology-2025 Democratizing protein language model training, sharing and collaboration
2025-10-24 · protein
Genome Biology-2025 Evaluating the representational power of pre-trained DNA language models for regulatory genomics
2025-06-14 · DNA, genomics, PLM
ICMLw-2025 ProteinCrow：A Language Model Agent That Can Design Proteins
2025-05-01 · protein, Agent
arXiv-2025 Scaling unlocks broader generation and deeper functional understanding of proteins
2025-04-15 · GNN, protein, protein-design, transformer
arXiv-2025 Prot42：a Novel Family of Protein Language Models for Target-aware Protein Binder Generation
2025-04-06 · GNN, protein, protein-design
COLING-2025 AutoProteinEngine：A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering
2025-01-24 · protein, Agent
ICLR-2025 Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions
2025-01-23 · protein, fitness-prediction, PPI
ICLR-2025 Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization
2025-01-23 · GNN, antibody
Science-2025 Simulating 500 million years of evolution with a language model
2025-01-16 · protein, evolution, PLM, generative