Paper Notes
Biology
Protein models, molecular design, and biomedical AI
NLP / Agents
LLMs, scientific agents, and language-model tooling
Vision
Video understanding, multimodal vision-language models
ML
Representation learning, graphs, and general ML methods
Software
Code models, summarization, and program analysis
Retrieval
Search, recommendation, and neural indexing
Systems
Distributed systems and systems for ML
2014
NeurIPS-2014 Two-Stream Convolutional Networks for Action Recognition in Videos
2014-11-12 · video, action-recognition
OSDI-2014 Scaling Distributed Machine Learning with the Parameter Server
2014-10-06 · distributed-dataflow
CVPR-2014 Large-scale Video Classification with Convolutional Neural Networks
2014-09-25 · video
2015
2016
2017
IJCNLP-2017 A parallel corpus of Python functions and documentation strings for automated code documentation and code generation
2017-11-02 · code-generation, code-documentation
ICML-2017 Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks
2017-07-18 · meta-learning
Bioinformatics-2017 DeepLoc：prediction of protein subcellular localization using deep learning
2017-07-07 · protein, subcellular localization
CVPR-2017 Quo Vadis, Action Recognition? A New Model and the Kinetics Dataset
2017-05-22 · vision-language, video, action-recognition
AAAI-2017 SeqGAN：Sequence Generative Adversarial Nets with Policy Gradient
2017-02-04 · LLM, NLP
2018
OpenAI-2018 Improving Language Understanding by Generative Pre-Training
2018-11-21 · LLM, NLP
ACL-2018 Improving Abstraction in Text Summarization
2018-10-23 · NLP
ICLR-2019 Graph2Seq：Graph to Sequence Learning with Attention-based Neural Networks
2018-09-28 · NLP, GNN
DeepMind-2018 Representation Learning with Contrastive Predictive Coding
2018-07-10 · vision-language, contrastive-learning
ICPC-2018 Deep code comment generation
2018-05-28 · code-comment
ICSE-2018 Deep code search
2018-05-27 · code-search
CVPR-2018 Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination
2018-05-01 · unsupervised-learning, contrastive-learning
CVPR-2018 Non-local Neural Networks
2018-04-13 · convolutional-neural-network
CVPR-2018 A Closer Look at Spatiotemporal Convolutions for Action Recognition
2018-04-12 · video, action-recognition
AAAI-2018 Generative Adversarial Network for Abstractive Text Summarization
2018-02-02 · NLP
2019
NeurIPS-2019 GPipe：Efficient Training of Giant Neural Networks using Pipeline Parallelism
2019-12-06 · pipeline-parallelism
ICCV-2019 SlowFast Networks for Video Recognition
2019-10-29 · vision-language, contrastive-learning
IJCAI-2019 Commit Message Generation for Source Code Changes
2019-08-10 · code-understanding
ACL-2019 Improving Robustness of Neural Machine Translation with Multi-task Learning
2019-08-01 · LLM, NLP
arXiv-2019 RoBERTa：A Robustly Optimized BERT Pretraining Approach
2019-07-26 · LLM, NLP
KDD-2019 MeLU：Meta-Learned User Preference Estimator for Cold-Start Recommendation
2019-07-25 · meta-learning, recommendation-system
OpenAI-2019 Language Models are Unsupervised Multitask Learners
2019-07-06 · LLM, NLP
ICSE-2019 A Neural Model for Generating Natural Language Summaries of Program Subroutines
2019-05-25 · code-summarization
ICSE-2019 A Novel Neural Source Code Representation Based on Abstract Syntax Tree
2019-05-25 · GNN, code-summarization
arXiv-2019 Unified Language Model Pre-training for Natural Language Understanding and Generation
2019-05-08 · LLM, NLP, transformer
CVPR-2019 Unsupervised Embedding Learning via Invariant and Spreading Instance Feature
2019-04-03 · unsupervised-learning
ICML-2019 Parameter-Efficient Transfer Learning for NLP
2019-02-02 · LLM, NLP
ACS Synthetic Biology-2019 Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima
2019-01-21 · protein, PLM
NeurIPS-2019 Evaluating Protein Transfer Learning with TAPE
2019-01-19 · protein, PLM, benchmark
2020
ECCV-2020 CMC: Contrastive Multiview Coding
2020-12-18 · contrastive-learning
NeurIPS-2020 Big Self-Supervised Models are Strong Semi-Supervised Learners
2020-12-06 · semi-supervised learning
NeurIPS-2020 Bootstrap your own latent：A new approach to self-supervised Learning
2020-12-06 · self-supervised learning
NeurIPS-2020 Graph Contrastive Learning with Augmentations
2020-12-06 · contrastive-learning, GNN
NeurIPS-2020 Unsupervised Learning of Visual Features by Contrasting Cluster Assignments
2020-12-01 · unsupervised-learning, contrastive-learning
MSR-2020 Improved Automatic Summarization of Subroutines via Attention to File Context
2020-11-18 · code-summarization
SC-2020 ZeRO：Memory Optimizations Toward Training Trillion Parameter Models
2020-11-09 · distributed-dataflow
arXiv-2020 BYOL works even without batch statistics
2020-10-20 · vision-language, transformer, contrastive-learning
KDD-2020 GCC：Graph Contrastive Coding for Graph Neural Network Pre-Training
2020-08-20 · contrastive-learning, GNN
SIGIR-2020 How to Retrain Recommender System？A Sequential Meta-Learning Method
2020-07-25 · meta-learning, recommendation-system
ACL-2020 Contrastive Code Representation Learning
2020-07-25 · code-understanding, contrastive-learning
NeurIPS-2020 Deep Graph Contrastive Representation Learning
2020-07-13 · contrastive-learning, GNN
ICML-2020 Graph-based, Self-Supervised Program Repair from Diagnostic Feedback
2020-07-13 · program-repair, GNN
arXiv-2020 Neural Subgraph Matching
2020-07-03 · GNN
ICML-2020 A Simple Framework for Contrastive Learning of Visual Representations
2020-07-01 · contrastive-learning
ICML-2020 Contrastive Multi-View Representation Learning on Graphs
2020-06-13 · contrastive-learning, GNN
ECCV-2020 End-to-End Object Detection with Transformers
2020-05-28 · transformer, object-detection
OpenAI-2020 Language Models are Few-Shot Learners
2020-05-14 · LLM, NLP
ACL-2020 A Transformer-based Approach for Source Code Summarization
2020-05-01 · code-summarization, transformer
ICLR-2020 DivideMix：Learning with Noisy Labels as Semi-supervised Learning
2020-04-26 · noisy label, semi-supervised, GMM, MixMatch
Transactions on Neural Networks and Learning Systems-2020 A Comprehensive Survey on Graph Neural Networks
2020-03-24 · GNN
CVPR-2020 Momentum Contrast for Unsupervised Visual Representation Learning
2020-03-23 · vision-language, contrastive-learning
GTC-2020 Megatron-LM：Training Multi-Billion Parameter Language Models Using Model Parallelism
2020-03-13 · model-parallelism
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 VLMo：Unified Vision-Language Pre-Training with Mixture-of-Modality-Experts
2021-12-01 · vision-language, contrastive-learning, transformer
NeurIPS-2021 Intriguing Properties of Vision Transformers
2021-11-25 · vision-language, transformer
NeurIPS-2021 Language models enable zero-shot prediction of the effects of mutations on protein function
2021-11-10 · protein, PLM, fitness-prediction
NeurIPS-2021 Align before Fuse：Vision and Language Representation Learning with Momentum Distillation
2021-11-10 · vision-language
Bioinformatics Advances-2021 Light attention predicts protein location from the language of life
2021-11-09 · protein, localization, PLM
CVPR-2021 Masked Autoencoders Are Scalable Vision Learners
2021-11-06 · vision-language, Transformer
EMNLP-2021 Rethinking Data Augmentation for Low-Resource Neural Machine Translation：A Multi-Task Learning Approach
2021-11-01 · LLM, NLP
NeurIPS-2021 FLIP：Benchmark tasks in fitness landscape inference for proteins
2021-10-11 · protein, benchmark
arXiv-2021 ActionCLIP：A New Paradigm for Video Action Recognition
2021-09-17 · video, action-recognition, contrastive-learning
ICLR-2021 GraphCodeBERT：Pre-training Code Representations with Data Flow
2021-09-13 · code-understanding, transformer, GNN
EMNLP-2021 CodeT5：Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation
2021-09-02 · code-understanding, transformer
bioRxiv-2021 Toward More General Embeddings for Protein Design：Harnessing Joint Representations of Sequence and Structure
2021-09-01 · protein, PLM, fitness-prediction
ICCV-2021 Swin Transformer：Hierarchical Vision Transformer using Shifted Windows
2021-08-17 · vision-language, transformer
ACL-2021 Learning Sequential and Structural Information for Source Code Summarization
2021-08-10 · Transformer, GNN
ICSME-2021 Ensemble Models for Neural Source Code Summarization of Subroutines
2021-07-23 · code-summarization
IJCAI-2021 Graph-Augmented Code Summarization in Computational Notebooks
2021-07-23 · code-summarization, GNN
Nature-2021 Highly accurate protein structure prediction with AlphaFold
2021-07-15 · protein, PLM, structure prediction
OpenAI-2021 Evaluating Large Language Models Trained on Code
2021-07-14 · LLM, code-generation
arXiv-2021 How Much Can CLIP Benefit Vision-and-Language Tasks？
2021-07-06 · vision-language, contrastive-learning
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
ICML-2021 Perceiver：General Perception with Iterative Attention
2021-06-23 · vision-language
arXiv-2021 CLIP4Clip：An Empirical Study of CLIP for End to End Video Clip Retrieval
2021-05-08 · Video, Contrastive Learning
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
ICCV-2021 An Empirical Study of Training Self-Supervised Vision Transformers
2021-04-05 · vision-language
ICPC-2021 A Multi-Modal Transformer-based Code Summarization Approach for Smart Contracts
2021-03-12 · transformer, code-summarization
ICML-2021 Learning Transferable Visual Models From Natural Language Supervision
2021-02-26 · vision-language, contrastive-learning
ICML-2021 E(n) Equivariant Graph Neural Networks
2021-02-19 · GNN
ICML-2021 MSA Transformer
2021-02-13 · protein, PLM
ICML-2021 ViLT：Vision-and-Language Transformer Without Convolution or Region Supervision
2021-02-05 · vision-language, contrastive-learning, transformer
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
Automated Software Engineering-2021 Automating just-in-time comment updating
2021-01-27 · code-summarization
GCPR-2021 AudioCLIP：Extending CLIP to Image, Text and Audio
2021-01-24 · vision-language, transformer, contrastive-learning
ICLR-2021 Learning from Protein Structure with Geometric Vector Perceptrons
2021-01-13 · protein, GNN, inverse folding
ICLR-2021 Supervised Contrastive Learning for Pre-trained Language Model Fine-tuning
2021-01-13 · LLM, NLP
ICLR-2021 An Image is Worth 16x16 Words：Transformers for Image Recognition at Scale
2021-01-13 · vision-language, transformer
ICML-2021 Is Space-Time Attention All You Need for Video Understanding
2021-01-09 · video, vision-language, transformer
ACL-2021 Code Summarization with Structure-induced Transformer
2021-01-01 · code-summarization, transformer
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 Transformer Memory as a Differentiable Search Index
2022-11-28 · transformer
EMNLP-2021 HAConvGNN：Hierarchical Attention Based Convolutional Graph Neural Network for Code Documentation Generation in Jupyter Notebooks
2022-11-10 · code-documentation, GNN
arXiv-2022 Holistic Evaluation of Language Models
2022-11-09 · LLM, NLP
NeurIPS-2022 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
2022-11-01 · protein, antibody, diffusion, GNN
NeurIPS-2022 A Neural Corpus Indexer for Document Retrieval
2022-11-01 · document-retrieval
PEDS-2022 Masked inverse folding with sequence transfer for protein representation learning
2022-10-26 · protein, PLM
ICPC-2022 HELoC：Hierarchical Contrastive Learning of Source Code Representation
2022-10-20 · contrastive-learning, GNN
MM-2022 Can Language Understand Depth？
2022-10-10 · vision-language, contrastive-learning
OpenAI-2022 Robust Speech Recognition via Large-Scale Weak Supervision
2022-10-06 · speech-recognition, transformer
Nature Biotechnology-2022 Single-sequence protein structure prediction using a language model and deep learning
2022-10-03 · protein, PLM, structure prediction
EMNLP-2020 CodeBERT：A Pre-Trained Model for Programming and Natural Languages
2022-09-18 · code-understanding, transformer
NeurIPS-2022 CoCa：Contrastive Captioners are Image-Text Foundation Models
2022-08-27 · vision-language, contrastive-learning
NAACL-2022 MoEBERT：from BERT to Mixture-of-Experts via Importance-Guided Adaptation
2022-07-29 · LLM, NLP
SIGGRAPH-2022 CLIPasso：Semantically-Aware Object Sketching
2022-07-22 · contrastive-learning
CVPR-2022 GroupViT：Semantic Segmentation Emerges from Text Supervision
2022-07-18 · video, vision-language
ECCV-2022 CDS：Contrastive Deep Supervision
2022-07-12 · contrastive-learning
ICSE-2022 AST-trans：code summarization with efficient tree-structured attention
2022-07-05 · code-summarization
ICSE-2022 Cross-Domain Deep Code Search with Few-Shot Meta Learning
2022-07-05 · code-search, meta-learning
AAAI-2022 Hierarchical Heterogeneous Graph Attention Network for Syntax-Aware Summarization
2022-06-28 · code-summarization, GNN
CVPR-2022 PointCLIP：Point Cloud Understanding by CLIP
2022-06-23 · vision-language, contrastive-learning
arXiv-2022 Learning code summarization from a small and local dataset
2022-06-08 · Transformer, GNN
arXiv-2022 GLIPv2：Unifying Localization and Vision-Language Understanding
2022-06-05 · vision-language, contrastive-learning, object-detection
Journal of Systems and Software-2022 Automatic source code summarization with graph attention networks
2022-06-01 · code-summarization, GNN
ICML-2022 Tranception：protein fitness prediction with autoregressive transformers and inference-time retrieval
2022-05-27 · protein, PLM, fitness-prediction
ICML-2016 A Convolutional Attention Network for Extreme Summarization of Source Code
2022-05-25 · convolutional-neural-network, code-summarization
ACL-2022 Impact of Evaluation Methodologies on Code Summarization
2022-05-20 · code-summarization
NAACL-2022 CODE-MVP：Learning to Represent Source Code from Multiple Views with Contrastive Pre-Training
2022-05-04 · code-summarization, transformer, contrastive-learning
arXiv-2022 A Survey of Deep Learning Models for Structural Code Understanding
2022-05-01 · code-understanding
NAR-2022 DeepLoc 2.0：multi-label subcellular localization prediction using protein language models
2022-04-30 · protein, localization, PLM
arXiv-2022 Training a Helpful and Harmless Assistant with Reinforcement Learning from Human Feedback
2022-04-16 · LLM, NLP, transformer
OpenAI-2022 Hierarchical Text-Conditional Image Generation with CLIP Latents
2022-04-13 · vision-language, contrastive-learning
MLSys-2022 Pathways：Asynchronous Distributed Dataflow for ML
2022-03-23 · distributed-dataflow
Nature Machine Intelligence-2022 Learning functional properties of proteins with language models
2022-03-21 · protein, PLM, functional prediction
OpenAI-2022 Training language models to follow instructions with human feedback
2022-03-16 · LLM, NLP, transformer
DeepMind-2022 Competition-Level Code Generation with AlphaCode
2022-03-07 · code-generation
Stanford-2022 AI Index Report
2022-03-02 · other
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
ICLR-2022 LoRA：Low-Rank Adaptation of Large Language Models
2022-01-29 · LLM, NLP
ICLR-2022 Open-vocabulary Object Detection via Vision and Language Knowledge Distillation
2022-01-29 · vision-language, contrastive-learning, object-detection
ICLR-2022 Perceiver IO：A General Architecture for Structured Inputs & Outputs
2022-01-29 · vision-language
NeurIPS-2022 Chain of Thought Prompting Elicits Reasoning in Large Language Models
2022-01-28 · LLM, NLP
ICML-2022 BLIP：Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation
2022-01-24 · vision-language, transformer, contrastive-learning
Nature Biotechnology-2022 Learning protein fitness models from evolutionary and assay-labeled data
2022-01-17 · protein, PLM, fitness-prediction
CVPR-2022 Grounded Language-Image Pre-trainin
2022-01-17 · LLM, NLP, vision-language
Journal of Machine Learning Research-2022 Switch Transformers：Scaling to Trillion Parameter Models with Simple and Efficient Sparsity
2022-01-16 · LLM, NLP, transformer
ICLR-2022 Language-driven Semantic Segmentation
2022-01-10 · LLM, NLP, vision-language
ACM Computing Surveys-2022 Deep Meta-learning in Recommendation Systems：A Survey
2022-01-09 · meta-learning, recommendation-system
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
CVPR-2020 Improved Baselines with Momentum Contrastive Learning
2023-03-09 · vision-language
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 AIM：Adapting Image Models for Efficient Video Action Recognition
2023-02-06 · video, action-recognition
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
CVPR-2023 Image as a Foreign Language：BEiT Pretraining for All Vision and Vision-Language Tasks
2023-01-15 · vision-language
WACV-2023 MixGen：A New Multi-Modal Data Augmentation
2023-01-09 · vision-language, data-augmentation
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
arXiv-2024 Movie Gen：A Cast of Media Foundation Models
2024-10-24 · video-generation
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
ACL Demo-2024 LlamaFactory：Unified Efficient Fine-Tuning of 100+ Language Models
2024-08-23 · LLM, NLP
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
AAAI-2024 T2I-Adapter：Learning Adapters to Dig out More Controllable Ability for Text-to-Image Diffusion Models
2024-02-20 · vision-language, diffusion
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
arXiv-2025 Evaluating Large Language Models in Scientific Discovery
2025-12-17 · Agent, LLM, NLP
NeurIPS-2025 AI-Researcher：Autonomous Scientific Innovation
2025-12-08 · Agent, NLP, LLM
EMNLP-2025 From Automation to Autonomy：A Survey on Large Language Models in Scientific Discovery
2025-11-04 · Agent, NLP, LLM
Nature Biotechnology-2025 Democratizing protein language model training, sharing and collaboration
2025-10-24 · protein
ACEBench：Who Wins the Match Point in Tool Usage
2025-09-08 · Agent, LLM, NLP
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 The AI Scientist-v2：Workshop-Level Automated Scientific Discovery via Agentic Tree Search
2025-04-10 · Agent, LLM, NLP
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
Nature Computational Science-2025 SciToolAgent：A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integration
2025-01-24 · Agent, LLM
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
ICLR-2025 ToolACE：Winning the Points of LLM Function Calling
2025-01-23 · LLM, NLP, Agent
Science-2025 Simulating 500 million years of evolution with a language model
2025-01-16 · protein, evolution, PLM, generative