Paper Notes

Topic All
Venue All
Year All years

2019

NeurIPS-2019 GPipe：Efficient Training of Giant Neural Networks using Pipeline Parallelism

NeurIPS Systems 2019-12-06 pipeline-parallelism

ICCV-2019 SlowFast Networks for Video Recognition

ICCV Vision 2019-10-29 vision-language contrastive-learning

IJCAI-2019 Commit Message Generation for Source Code Changes

IJCAI Software 2019-08-10 code-understanding

ACL-2019 Improving Robustness of Neural Machine Translation with Multi-task Learning

ACL NLP / Agents 2019-08-01 LLM NLP

arXiv-2019 RoBERTa：A Robustly Optimized BERT Pretraining Approach

arXiv NLP / Agents 2019-07-26 LLM NLP

KDD-2019 MeLU：Meta-Learned User Preference Estimator for Cold-Start Recommendation

KDD Retrieval 2019-07-25 meta-learning recommendation-system

OpenAI-2019 Language Models are Unsupervised Multitask Learners

OpenAI NLP / Agents 2019-07-06 LLM NLP

ICSE-2019 A Neural Model for Generating Natural Language Summaries of Program Subroutines

ICSE Software 2019-05-25 code-summarization

ICSE-2019 A Novel Neural Source Code Representation Based on Abstract Syntax Tree

ICSE Software 2019-05-25 GNN code-summarization

arXiv-2019 Unified Language Model Pre-training for Natural Language Understanding and Generation

arXiv NLP / Agents 2019-05-08 LLM NLP transformer

CVPR-2019 Unsupervised Embedding Learning via Invariant and Spreading Instance Feature

CVPR Vision 2019-04-03 unsupervised-learning

ICML-2019 Parameter-Efficient Transfer Learning for NLP

ICML NLP / Agents 2019-02-02 LLM NLP

ACS Synthetic Biology-2019 Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima

ACS Synthetic Biology Biology 2019-01-21 protein PLM

NeurIPS-2019 Evaluating Protein Transfer Learning with TAPE

NeurIPS Biology 2019-01-19 protein PLM benchmark

2020

ECCV-2020 CMC: Contrastive Multiview Coding

ECCV Vision 2020-12-18 contrastive-learning

NeurIPS-2020 Big Self-Supervised Models are Strong Semi-Supervised Learners

NeurIPS Vision 2020-12-06 semi-supervised learning

NeurIPS-2020 Bootstrap your own latent：A new approach to self-supervised Learning

NeurIPS Vision 2020-12-06 self-supervised learning

NeurIPS-2020 Graph Contrastive Learning with Augmentations

NeurIPS ML 2020-12-06 contrastive-learning GNN

NeurIPS-2020 Unsupervised Learning of Visual Features by Contrasting Cluster Assignments

NeurIPS Vision 2020-12-01 unsupervised-learning contrastive-learning

MSR-2020 Improved Automatic Summarization of Subroutines via Attention to File Context

MSR Software 2020-11-18 code-summarization

SC-2020 ZeRO：Memory Optimizations Toward Training Trillion Parameter Models

SC Systems 2020-11-09 distributed-dataflow

arXiv-2020 BYOL works even without batch statistics

arXiv Vision 2020-10-20 vision-language transformer contrastive-learning

KDD-2020 GCC：Graph Contrastive Coding for Graph Neural Network Pre-Training

KDD ML 2020-08-20 contrastive-learning GNN

SIGIR-2020 How to Retrain Recommender System？A Sequential Meta-Learning Method

SIGIR Retrieval 2020-07-25 meta-learning recommendation-system

ACL-2020 Contrastive Code Representation Learning

ACL Software 2020-07-25 code-understanding contrastive-learning

NeurIPS-2020 Deep Graph Contrastive Representation Learning

NeurIPS ML 2020-07-13 contrastive-learning GNN

ICML-2020 Graph-based, Self-Supervised Program Repair from Diagnostic Feedback

ICML Software 2020-07-13 program-repair GNN

arXiv-2020 Neural Subgraph Matching

arXiv ML 2020-07-03 GNN

ICML-2020 A Simple Framework for Contrastive Learning of Visual Representations

ICML Vision 2020-07-01 contrastive-learning

ICML-2020 Contrastive Multi-View Representation Learning on Graphs

ICML ML 2020-06-13 contrastive-learning GNN

ECCV-2020 End-to-End Object Detection with Transformers

ECCV Vision 2020-05-28 transformer object-detection

OpenAI-2020 Language Models are Few-Shot Learners

OpenAI NLP / Agents 2020-05-14 LLM NLP

ACL-2020 A Transformer-based Approach for Source Code Summarization

ACL Software 2020-05-01 code-summarization transformer

ICLR-2020 DivideMix：Learning with Noisy Labels as Semi-supervised Learning

ICLR Vision 2020-04-26 noisy label semi-supervised GMM MixMatch

Transactions on Neural Networks and Learning Systems-2020 A Comprehensive Survey on Graph Neural Networks

Transactions on Neural Networks and Learning Systems ML 2020-03-24 GNN

CVPR-2020 Momentum Contrast for Unsupervised Visual Representation Learning

CVPR Vision 2020-03-23 vision-language contrastive-learning

GTC-2020 Megatron-LM：Training Multi-Billion Parameter Language Models Using Model Parallelism

GTC Systems 2020-03-13 model-parallelism

2021

Human Genetics-2021 Embeddings from protein language models predict conservation and variant effects

Human Genetics Biology 2021-12-30 protein PLM fitness-prediction

KDD-2021 Modeling Protein Using Large-scale Pretrain Language Model

KDD Biology 2021-12-07 protein PLM

NeurIPS-2021 VLMo：Unified Vision-Language Pre-Training with Mixture-of-Modality-Experts

NeurIPS Vision 2021-12-01 vision-language contrastive-learning transformer

NeurIPS-2021 Intriguing Properties of Vision Transformers

NeurIPS Vision 2021-11-25 vision-language transformer

NeurIPS-2021 Language models enable zero-shot prediction of the effects of mutations on protein function

NeurIPS Biology 2021-11-10 protein PLM fitness-prediction

NeurIPS-2021 Align before Fuse：Vision and Language Representation Learning with Momentum Distillation

NeurIPS Vision 2021-11-10 vision-language

Bioinformatics Advances-2021 Light attention predicts protein location from the language of life

Bioinformatics Advances Biology 2021-11-09 protein localization PLM

CVPR-2021 Masked Autoencoders Are Scalable Vision Learners

CVPR Vision 2021-11-06 vision-language Transformer

EMNLP-2021 Rethinking Data Augmentation for Low-Resource Neural Machine Translation：A Multi-Task Learning Approach

EMNLP NLP / Agents 2021-11-01 LLM NLP

NeurIPS-2021 FLIP：Benchmark tasks in fitness landscape inference for proteins

NeurIPS Biology 2021-10-11 protein benchmark

arXiv-2021 ActionCLIP：A New Paradigm for Video Action Recognition

arXiv Vision 2021-09-17 video action-recognition contrastive-learning

ICLR-2021 GraphCodeBERT：Pre-training Code Representations with Data Flow

ICLR Software 2021-09-13 code-understanding transformer GNN

EMNLP-2021 CodeT5：Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation

EMNLP Software 2021-09-02 code-understanding transformer

bioRxiv-2021 Toward More General Embeddings for Protein Design：Harnessing Joint Representations of Sequence and Structure

bioRxiv Biology 2021-09-01 protein PLM fitness-prediction

ICCV-2021 Swin Transformer：Hierarchical Vision Transformer using Shifted Windows

ICCV Vision 2021-08-17 vision-language transformer

ACL-2021 Learning Sequential and Structural Information for Source Code Summarization

ACL Software 2021-08-10 Transformer GNN

ICSME-2021 Ensemble Models for Neural Source Code Summarization of Subroutines

ICSME Software 2021-07-23 code-summarization

IJCAI-2021 Graph-Augmented Code Summarization in Computational Notebooks

IJCAI Software 2021-07-23 code-summarization GNN

Nature-2021 Highly accurate protein structure prediction with AlphaFold

Nature Biology 2021-07-15 protein PLM structure prediction

OpenAI-2021 Evaluating Large Language Models Trained on Code

OpenAI Software 2021-07-14 LLM code-generation

arXiv-2021 How Much Can CLIP Benefit Vision-and-Language Tasks？

arXiv Vision 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

IEEE Transactions on Pattern Analysis and Machine Intelligence Biology 2021-07-01 protein PLM transformer self-supervised

ICML-2021 Perceiver：General Perception with Iterative Attention

ICML Vision 2021-06-23 vision-language

arXiv-2021 CLIP4Clip：An Empirical Study of CLIP for End to End Video Clip Retrieval

arXiv Vision 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

Proceedings of the National Academy of Sciences Biology 2021-04-05 protein PLM

ICCV-2021 An Empirical Study of Training Self-Supervised Vision Transformers

ICCV Vision 2021-04-05 vision-language

ICPC-2021 A Multi-Modal Transformer-based Code Summarization Approach for Smart Contracts

ICPC Software 2021-03-12 transformer code-summarization

ICML-2021 Learning Transferable Visual Models From Natural Language Supervision

ICML Vision 2021-02-26 vision-language contrastive-learning

ICML-2021 E(n) Equivariant Graph Neural Networks

ICML Biology 2021-02-19 GNN

ICML-2021 MSA Transformer

ICML Biology 2021-02-13 protein PLM

ICML-2021 ViLT：Vision-and-Language Transformer Without Convolution or Region Supervision

ICML Vision 2021-02-05 vision-language contrastive-learning transformer

Bioinformatics-2021 DNABERT：pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

Bioinformatics Biology 2021-02-04 DNA genomics PLM

ICML-2021 Learning inverse folding from millions of predicted structures

ICML Biology 2021-02-02 protein inverse folding PLM GNN

Automated Software Engineering-2021 Automating just-in-time comment updating

Automated Software Engineering Software 2021-01-27 code-summarization

GCPR-2021 AudioCLIP：Extending CLIP to Image, Text and Audio

GCPR Vision 2021-01-24 vision-language transformer contrastive-learning

ICLR-2021 Learning from Protein Structure with Geometric Vector Perceptrons

ICLR Biology 2021-01-13 protein GNN inverse folding

ICLR-2021 Supervised Contrastive Learning for Pre-trained Language Model Fine-tuning

ICLR NLP / Agents 2021-01-13 LLM NLP

ICLR-2021 An Image is Worth 16x16 Words：Transformers for Image Recognition at Scale

ICLR Vision 2021-01-13 vision-language transformer

ICML-2021 Is Space-Time Attention All You Need for Video Understanding

ICML Vision 2021-01-09 video vision-language transformer

ACL-2021 Code Summarization with Structure-induced Transformer

ACL Software 2021-01-01 code-summarization transformer

2022

NeurIPS-2022 PEER：A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

NeurIPS Biology 2022-12-01 protein benchmark PLM

bioRxiv-2022 Fast protein structure searching using structure graph embeddings

bioRxiv Biology 2022-11-28 protein PLM alignment

NeurIPS-2022 Transformer Memory as a Differentiable Search Index

NeurIPS Retrieval 2022-11-28 transformer

EMNLP-2021 HAConvGNN：Hierarchical Attention Based Convolutional Graph Neural Network for Code Documentation Generation in Jupyter Notebooks

EMNLP Software 2022-11-10 code-documentation GNN

arXiv-2022 Holistic Evaluation of Language Models

arXiv NLP / Agents 2022-11-09 LLM NLP

NeurIPS-2022 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures

NeurIPS Biology 2022-11-01 protein antibody diffusion GNN

NeurIPS-2022 A Neural Corpus Indexer for Document Retrieval

NeurIPS Retrieval 2022-11-01 document-retrieval

PEDS-2022 Masked inverse folding with sequence transfer for protein representation learning

PEDS Biology 2022-10-26 protein PLM

ICPC-2022 HELoC：Hierarchical Contrastive Learning of Source Code Representation

ICPC Software 2022-10-20 contrastive-learning GNN

MM-2022 Can Language Understand Depth？

MM Vision 2022-10-10 vision-language contrastive-learning

OpenAI-2022 Robust Speech Recognition via Large-Scale Weak Supervision

NeurIPS ML 2022-10-06 speech-recognition transformer

Nature Biotechnology-2022 Single-sequence protein structure prediction using a language model and deep learning

Nature Biotechnology Biology 2022-10-03 protein PLM structure prediction

EMNLP-2020 CodeBERT：A Pre-Trained Model for Programming and Natural Languages

EMNLP Software 2022-09-18 code-understanding transformer

NeurIPS-2022 CoCa：Contrastive Captioners are Image-Text Foundation Models

NeurIPS Vision 2022-08-27 vision-language contrastive-learning

NAACL-2022 MoEBERT：from BERT to Mixture-of-Experts via Importance-Guided Adaptation

NAACL NLP / Agents 2022-07-29 LLM NLP

SIGGRAPH-2022 CLIPasso：Semantically-Aware Object Sketching

SIGGRAPH Vision 2022-07-22 contrastive-learning

CVPR-2022 GroupViT：Semantic Segmentation Emerges from Text Supervision

CVPR Vision 2022-07-18 video vision-language

ECCV-2022 CDS：Contrastive Deep Supervision

ECCV Vision 2022-07-12 contrastive-learning

ICSE-2022 AST-trans：code summarization with efficient tree-structured attention

ICSE Software 2022-07-05 code-summarization

ICSE-2022 Cross-Domain Deep Code Search with Few-Shot Meta Learning

ICSE Software 2022-07-05 code-search meta-learning

AAAI-2022 Hierarchical Heterogeneous Graph Attention Network for Syntax-Aware Summarization

AAAI Software 2022-06-28 code-summarization GNN

CVPR-2022 PointCLIP：Point Cloud Understanding by CLIP

CVPR Vision 2022-06-23 vision-language contrastive-learning

arXiv-2022 Learning code summarization from a small and local dataset

arXiv Software 2022-06-08 Transformer GNN

arXiv-2022 GLIPv2：Unifying Localization and Vision-Language Understanding

arXiv Vision 2022-06-05 vision-language contrastive-learning object-detection

Journal of Systems and Software-2022 Automatic source code summarization with graph attention networks

Journal of Systems and Software Software 2022-06-01 code-summarization GNN

ICML-2022 Tranception：protein fitness prediction with autoregressive transformers and inference-time retrieval

ICML Biology 2022-05-27 protein PLM fitness-prediction

ICML-2016 A Convolutional Attention Network for Extreme Summarization of Source Code

ICML Software 2022-05-25 convolutional-neural-network code-summarization

ACL-2022 Impact of Evaluation Methodologies on Code Summarization

ACL Software 2022-05-20 code-summarization

NAACL-2022 CODE-MVP：Learning to Represent Source Code from Multiple Views with Contrastive Pre-Training

NAACL Software 2022-05-04 code-summarization transformer contrastive-learning

arXiv-2022 A Survey of Deep Learning Models for Structural Code Understanding

arXiv Software 2022-05-01 code-understanding

NAR-2022 DeepLoc 2.0：multi-label subcellular localization prediction using protein language models

Nucleic Acids Research Biology 2022-04-30 protein localization PLM

arXiv-2022 Training a Helpful and Harmless Assistant with Reinforcement Learning from Human Feedback

arXiv NLP / Agents 2022-04-16 LLM NLP transformer

OpenAI-2022 Hierarchical Text-Conditional Image Generation with CLIP Latents

OpenAI Vision 2022-04-13 vision-language contrastive-learning

MLSys-2022 Pathways：Asynchronous Distributed Dataflow for ML

MLSys Systems 2022-03-23 distributed-dataflow

Nature Machine Intelligence-2022 Learning functional properties of proteins with language models

Nature Machine Intelligence Biology 2022-03-21 protein PLM functional prediction

OpenAI-2022 Training language models to follow instructions with human feedback

OpenAI NLP / Agents 2022-03-16 LLM NLP transformer

DeepMind-2022 Competition-Level Code Generation with AlphaCode

DeepMind Software 2022-03-07 code-generation

Stanford-2022 AI Index Report

Stanford ML 2022-03-02 other

Report: AI Index Report. Most statistics are drawn from Papers with Code. Because the report contains a large number of figures, individual screenshots are not included here.

Frontiers in Microbiology-2022 iThermo：A Sequence-Based Model for Identifying Thermophilic Proteins Using a Multi-Feature Fusion Strategy

Frontiers in Microbiology Biology 2022-02-22 protein

ICLR-2022 Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design

ICLR Biology 2022-01-29 protein antibody GNN

ICLR-2022 OntoProtein：Protein Pretraining With Gene Ontology Embedding

ICLR Biology 2022-01-29 protein PLM

ICLR-2022 LoRA：Low-Rank Adaptation of Large Language Models

ICLR NLP / Agents 2022-01-29 LLM NLP

ICLR-2022 Open-vocabulary Object Detection via Vision and Language Knowledge Distillation

ICLR Vision 2022-01-29 vision-language contrastive-learning object-detection

ICLR-2022 Perceiver IO：A General Architecture for Structured Inputs & Outputs

ICLR Vision 2022-01-29 vision-language

NeurIPS-2022 Chain of Thought Prompting Elicits Reasoning in Large Language Models

NeurIPS NLP / Agents 2022-01-28 LLM NLP

ICML-2022 BLIP：Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation

ICML Vision 2022-01-24 vision-language transformer contrastive-learning

Nature Biotechnology-2022 Learning protein fitness models from evolutionary and assay-labeled data

Nature Biotechnology Biology 2022-01-17 protein PLM fitness-prediction

CVPR-2022 Grounded Language-Image Pre-trainin

CVPR Vision 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

Journal of Machine Learning Research NLP / Agents 2022-01-16 LLM NLP transformer

ICLR-2022 Language-driven Semantic Segmentation

ICLR Vision 2022-01-10 LLM NLP vision-language

ACM Computing Surveys-2022 Deep Meta-learning in Recommendation Systems：A Survey

ACM Computing Surveys Retrieval 2022-01-09 meta-learning recommendation-system

2023

bioRxiv-2023 IgDesign-In vitro validated antibody design against multiple therapeutic antigens using inverse folding

bioRxiv Biology 2023-12-08 protein antibody inverse folding protein-design

bioRxiv-2023 Learning sequence, structure, and function representations of proteins with language models

bioRxiv Biology 2023-11-26 protein PLM function MOE

Nature Biotechnology-2023 Protein remote homology detection and structural alignment using deep learning

Nature Biotechnology Biology 2023-11-07 protein homology

NeurIPS-2023 PoET：A generative model of protein families as sequences-of-sequences

NeurIPS Biology 2023-11-01 protein PLM fitness-prediction

EMNLP-2023 BioPlanner：Automatic Evaluation of LLMs on Protocol Planning in Biology

EMNLP Biology 2023-10-08 Agent LLM

NeurIPS-2023 ProteinGym：Large-Scale Benchmarks for Protein Design and Fitness Prediction

NeurIPS Biology 2023-09-30 protein PLM benchmark

NeurIPS-2023 Predicting a Protein’s Stability under a Million Mutations

NeurIPS Biology 2023-09-22 protein fitness-prediction

bioRxiv-2023 Protein generation with evolutionary diffusion：sequence is all you need

bioRxiv Biology 2023-09-11 protein PLM protein-design

KDD-2023 Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design

KDD Biology 2023-08-04 protein antibody GNN PLM

ICML-2023 End-to-End Full-Atom Antibody Design

ICML Biology 2023-06-15 protein antibody GNN

Nature Machine Intelligence-2023 Structure-inducing pre-training for generalizable representation learning

Nature Machine Intelligence Biology 2023-06-01 pre-training PLM

Nature Biotechnology-2023 Fast and accurate protein structure search with Foldseek

Nature Biotechnology Biology 2023-05-08 protein alignment

Science-2023 Evolutionary-scale prediction of atomic-level protein structure with a language model

Science Biology 2023-03-16 protein PLM structure prediction

Bioinformatics-2023 Accurate and efficient protein sequence design through learning concise local environment of residues

Bioinformatics Biology 2023-03-14 protein protein-design GNN PLM

CVPR-2020 Improved Baselines with Momentum Contrastive Learning

CVPR Vision 2023-03-09 vision-language

ICLRw-2023 Enhancing Protein Language Models with Structure-based Encoder and Pre-training

ICLRw Biology 2023-03-06 PLM GNN

ICML-2023 Structure-informed Language Models Are Protein Designers

ICML Biology 2023-02-09 protein PLM protein-design

ICLR-2023 AIM：Adapting Image Models for Efficient Video Action Recognition

ICLR Vision 2023-02-06 video action-recognition

ICLR-2023 Conditional Antibody Design as 3D Equivariant Graph Translation

ICLR Biology 2023-02-02 protein antibody GNN

International Journal of Molecular Sciences-2023 DeepTP：A Deep Learning Model for Thermophilic Protein Prediction

International Journal of Molecular Sciences Biology 2023-01-22 protein

bioRxiv-2023 Ankh：Optimized Protein Language Model Unlocks General-Purpose Modelling

bioRxiv Biology 2023-01-16 protein PLM language-model

CVPR-2023 Image as a Foreign Language：BEiT Pretraining for All Vision and Vision-Language Tasks

CVPR Vision 2023-01-15 vision-language

WACV-2023 MixGen：A New Multi-Modal Data Augmentation

WACV Vision 2023-01-09 vision-language data-augmentation

bioRxiv-2023 When Geometric Deep Learning Meets Pretrained Protein Language Models

bioRxiv Biology 2023-01-05 protein PLM GNN

2024

PLOS Computational Biology-2024 Large scale paired antibody language models

PLOS Computational Biology Biology 2024-12-06 protein antibody PLM

bioRxiv-2024 Mixture of Experts Enable Efficient and Effective Protein Understanding and Design

bioRxiv Biology 2024-11-29 protein language-model

Bioinformatics-2024 Expert-guided protein language models enable accurate and blazingly fast fitness prediction

Bioinformatics Biology 2024-11-22 protein fitness-prediction PLM

Nature Communications-2024 A joint embedding of protein sequence and structure enables robust variant effect predictions

Nature Communications Biology 2024-11-07 protein fitness-prediction PLM

arXiv-2024 Movie Gen：A Cast of Media Foundation Models

arXiv Vision 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

Nature Computational Science Biology 2024-10-03 GNN protein fitness-prediction

NeurIPS-2024 Multi-Scale Representation Learning for Protein Fitness Prediction

NeurIPS Biology 2024-09-26 GNN protein fitness-prediction

Nature Biotechnology-2024 Multistate and functional protein design using RoseTTAFold sequence space diffusion

Nature Biotechnology Biology 2024-09-25 protein diffusion protein-design

ACL Demo-2024 LlamaFactory：Unified Efficient Fine-Tuning of 100+ Language Models

ACL NLP / Agents 2024-08-23 LLM NLP

ICML-2024 Feature Reuse and Scaling：Understanding Transfer Learning with Protein Language Models

ICML Biology 2024-06-21 protein PLM transfer learning

Nature Communications-2024 PLMSearch：Protein language model powers accurate and fast sequence search for remote homology

Nature Communications Biology 2024-03-30 protein PLM alignment

Cell Systems-2024 Convolutions are competitive with transformers for protein sequence pretraining

Cell Systems Biology 2024-03-20 protein PLM CNN transformer

eLife-2024 Sensitive remote homology search by local alignment of small positional embeddings from protein language models

eLife Biology 2024-03-15 protein homology PLM

AAAI-2024 T2I-Adapter：Learning Adapters to Dig out More Controllable Ability for Text-to-Image Diffusion Models

AAAI Vision 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

Journal of Chemical Information and Modeling Biology 2024-01-25 protein structure search

ICLR-2024 SaProt：Protein Language Modeling with Structure-aware Vocabulary

ICLR Biology 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

Bioinformatics Biology 2024-01-04 protein PLM alignment

2025

arXiv-2025 Evaluating Large Language Models in Scientific Discovery

arXiv NLP / Agents 2025-12-17 Agent LLM NLP

NeurIPS-2025 AI-Researcher：Autonomous Scientific Innovation

NeurIPS NLP / Agents 2025-12-08 Agent NLP LLM

EMNLP-2025 From Automation to Autonomy：A Survey on Large Language Models in Scientific Discovery

EMNLP NLP / Agents 2025-11-04 Agent NLP LLM

Nature Biotechnology-2025 Democratizing protein language model training, sharing and collaboration

Nature Biotechnology Biology 2025-10-24 protein

ACEBench：Who Wins the Match Point in Tool Usage

arXiv NLP / Agents 2025-09-08 Agent LLM NLP

Genome Biology-2025 Evaluating the representational power of pre-trained DNA language models for regulatory genomics

Genome Biology Biology 2025-06-14 DNA genomics PLM

ICMLw-2025 ProteinCrow：A Language Model Agent That Can Design Proteins

ICMLw Biology 2025-05-01 protein Agent

arXiv-2025 Scaling unlocks broader generation and deeper functional understanding of proteins

arXiv Biology 2025-04-15 GNN protein protein-design transformer

arXiv-2025 The AI Scientist-v2：Workshop-Level Automated Scientific Discovery via Agentic Tree Search

arXiv NLP / Agents 2025-04-10 Agent LLM NLP

arXiv-2025 Prot42：a Novel Family of Protein Language Models for Target-aware Protein Binder Generation

arXiv Biology 2025-04-06 GNN protein protein-design

COLING-2025 AutoProteinEngine：A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering

COLING Biology 2025-01-24 protein Agent

Nature Computational Science-2025 SciToolAgent：A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integration

Nature Computational Science NLP / Agents 2025-01-24 Agent LLM

ICLR-2025 Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions

ICLR Biology 2025-01-23 protein fitness-prediction PPI

ICLR-2025 Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization

ICLR Biology 2025-01-23 GNN antibody

ICLR-2025 ToolACE：Winning the Points of LLM Function Calling

ICLR NLP / Agents 2025-01-23 LLM NLP Agent

Science-2025 Simulating 500 million years of evolution with a language model

Science Biology 2025-01-16 protein evolution PLM generative