SOTAVerified

Protein Function Prediction

For GO terms prediction, given the specific function prediction instruction and a protein sequence, models characterize the protein functions using the GO terms presented in three different domains (cellular component, biological process, and molecular function).

Papers

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Showing 1–50 of 79 papers

TitleStatusHype
Galactica: A Large Language Model for ScienceCode4
Robust deep learning based protein sequence design using ProteinMPNNCode3
Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language ModelsCode2
A Systematic Study of Joint Representation Learning on Protein Sequences and StructuresCode2
ProtBoost: protein function prediction with Py-Boost and Graph Neural Networks -- CAFA5 top2 solutionCode1
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence LearningCode1
Structure-Informed Protein Language ModelCode1
Endowing Protein Language Models with Structural KnowledgeCode1
Insights Into the Inner Workings of Transformer Models for Protein Function PredictionCode1
Prot2Text: Multimodal Protein's Function Generation with GNNs and TransformersCode1
MD-HIT: Machine learning for materials property prediction with dataset redundancy controlCode1
Deep learning-based rapid generation of broadly reactive antibodies against SARS-CoV-2 and its Omicron variantCode1
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence UnderstandingCode1
Multi-Scale Representation Learning on ProteinsCode1
Graph Self-supervised Learning with Accurate Discrepancy LearningCode1
OntoProtein: Protein Pretraining With Gene Ontology EmbeddingCode1
Coherent Hierarchical Multi-Label Classification NetworksCode1
Strategies for Pre-training Graph Neural NetworksCode1
AnnoDPO: Protein Functional Annotation Learning with Direct Preference OptimizationCode0
Into the Unknown: From Structure to Disorder in Protein Function Prediction—0
STELLA: Towards Protein Function Prediction with Multimodal LLMs Integrating Sequence-Structure Representations—0
MSNGO: multi-species protein function annotation based on 3D protein structure and network propagationCode0
evoBPE: Evolutionary Protein Sequence TokenizationCode0
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models—0
Computational Protein Science in the Era of Large Language Models (LLMs)—0
GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction—0
ProtCLIP: Function-Informed Protein Multi-Modal Learning—0
Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data SettingCode0
SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function PredictionCode0
Hashing for Protein Structure Similarity Search—0
Protein-Mamba: Biological Mamba Models for Protein Function Prediction—0
ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals—0
Autoregressive Enzyme Function Prediction with Multi-scale Multi-modality Fusion—0
A Vectorization Method Induced By Maximal Margin Classification For Persistent Diagrams—0
Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs—0
ProtFAD: Introducing function-aware domains as implicit modality towards protein function predictionCode0
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering—0
HeMeNet: Heterogeneous Multichannel Equivariant Network for Protein Multitask Learning—0
Advances of Deep Learning in Protein Science: A Comprehensive Survey—0
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction—0
InstructProtein: Aligning Human and Protein Language via Knowledge Instruction—0
Contrastive Learning for Non-Local Graphs with Multi-Resolution Structural Views—0
Biomedical Knowledge Graph Embeddings with Negative StatementsCode0
DeepGATGO: A Hierarchical Pretraining-Based Graph-Attention Model for Automatic Protein Function Prediction—0
Self-supervised Learning and Graph Classification under Heterophily—0
Linear-scaling kernels for protein sequences and small molecules outperform deep learning while providing uncertainty quantitation and improved interpretabilityCode0
Ankh: Optimized Protein Language Model Unlocks General-Purpose ModellingCode0
Reprogramming Pretrained Language Models for Protein Sequence Representation Learning—0
EurNet: Efficient Multi-Range Relational Modeling of Spatial Multi-Relational DataCode0
A Review of Deep Learning Techniques for Protein Function Prediction—0
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All datasetsCASPSimSeqPaenSeqUniProtSeq

Benchmark Results

#ModelMetricClaimedVerifiedStatus
1GAL 120BROUGE-L0.25—Unverified
2GAL 30BROUGE-L0.14—Unverified
3GAL 6.7BROUGE-L0.11—Unverified
4GAL 1.3BROUGE-L0.07—Unverified
5GAL 125MROUGE-L0.06—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 120BROUGE-L0.27—Unverified
2GAL 30BROUGE-L0.2—Unverified
3GAL 6.7BROUGE-L0.14—Unverified
4GAL 1.3BROUGE-L0.08—Unverified
5GAL 125MROUGE-L0.07—Unverified
#ModelMetricClaimedVerifiedStatus
1GAL 120BROUGE-L0.25—Unverified
2GAL 30BROUGE-L0.19—Unverified
3GAL 6.7BROUGE-L0.11—Unverified
4GAL 1.3BROUGE-L0.08—Unverified
5GAL 125MROUGE-L0.06—Unverified