Protein Function Prediction

Description from the archive archive 2025-07-28.

Benchmarks archive 2025-07-28

3 leaderboard tables shown for this task, 3 with rows (a “benchmark” on this site is a table with at least one row, as on /sota), ordered by row count. “Best model” is the first row in the archive's own order at snapshot; nothing is re-ranked here and metric direction is not recorded in the archive. PwC's Trend sparklines are not in the archive, so that column is omitted.

Syntology column: samples harvested from the paper's repositories and executed on synthesized fixtures; “ran” is not a correctness claim and does not order the table. A dash means no Syntology record for that paper, not a recorded non-run. Read from the graph 2026-09-24.

Libraries

Not in the archive: the export carries no per-task library table, so there is nothing to show at snapshot 2025-07-28.

Datasets archive 2025-07-28

2 datasets whose archive record lists this task, ordered by the archive's paper count.

Subtasks archive 2025-07-28

1 subtask in the archive's task tree.

Most implemented papers archive 2025-07-28

30 shown of 31 papers with code (79 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• Strategies for Pre-training Graph Neural Networks
  29 May 2019 11 repositories listed Syntology ran 10 of 14 samples · 4 unverified · 2 pointer-only (licence)
  Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training.
• Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations
  12 Jun 2019 4 repositories listed Syntology ran 4 of 11 samples · 7 unverified
  Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis.
• A Systematic Study of Joint Representation Learning on Protein Sequences and Structures
  11 Mar 2023 3 repositories listed Syntology ran 1 of 3 samples · 2 unverified · 3 pointer-only (licence)
  Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge.
• ProtFAD: Introducing function-aware domains as implicit modality towards protein function prediction
  24 May 2024 2 repositories listed
  Protein function prediction is currently achieved by encoding its sequence or structure, where the sequence-to-function transcendence and high-quality structural data scarcity lead to obvious performance bottlenecks.
• Linear-scaling kernels for protein sequences and small molecules outperform deep learning while providing uncertainty quantitation and improved interpretability
  7 Feb 2023 2 repositories listed Syntology ran 0 of 2 samples · 2 unverified
  We compare the performance of xGPR with the reported performance of various deep learning models on 20 benchmarks, including small molecule, protein sequence and tabular data.
• AnnoDPO: Protein Functional Annotation Learning with Direct Preference Optimization
  8 Jun 2025 1 repository listed
  Deciphering protein function remains a fundamental challenge in protein representation learning.
• MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation
  29 Mar 2025 1 repository listed
  While single-species protein function prediction methods have achieved remarkable success, multi-species protein function prediction methods are still in the stage of using PPI networks and sequence features.
• evoBPE: Evolutionary Protein Sequence Tokenization
  11 Mar 2025 1 repository listed
  Recent advancements in computational biology have drawn compelling parallels between protein sequences and linguistic structures, highlighting the need for sophisticated tokenization methods that capture the intricate…
• ProtBoost: protein function prediction with Py-Boost and Graph Neural Networks -- CAFA5 top2 solution
  5 Dec 2024 1 repository listed
  Py-Boost is the first gradient boosting method capable of predicting thousands of targets simultaneously, making it an ideal fit for tasks like the CAFA challange.
• SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction
  18 Nov 2024 1 repository listed
  Existing approaches mostly focus on protein sequences or topological structures, while rarely exploiting the spatial properties and ignoring the relevance between sequence and structure information.
• DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
  2 Oct 2024 1 repository listed
  Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions.
• Structure-Informed Protein Language Model
  7 Feb 2024 1 repository listed
  To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input.
• Endowing Protein Language Models with Structural Knowledge
  26 Jan 2024 1 repository listed
  Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules.
• Insights Into the Inner Workings of Transformer Models for Protein Function Prediction
  7 Sep 2023 1 repository listed
  Motivation: We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of…
• Biomedical Knowledge Graph Embeddings with Negative Statements
  7 Aug 2023 1 repository listed
  Explicitly considering negative statements has been shown to improve performance on tasks such as entity summarization and question answering or domain-specific tasks such as protein function prediction.
• Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers
  25 Jul 2023 1 repository listed Syntology ran 3 of 3 samples · 0 unverified · 3 pointer-only (licence)
  These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate function prediction of existing as well as…
• MD-HIT: Machine learning for materials property prediction with dataset redundancy control
  10 Jul 2023 1 repository listed
  This issue is well known in the field of bioinformatics for protein function prediction, in which a redundancy reduction procedure (CD-Hit) is always applied to reduce the sample redundancy by ensuring no pair of…
• Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models
  13 Jun 2023 1 repository listed Syntology ran 2 of 2 samples · 0 unverified
  Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields.
• Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling
  16 Jan 2023 1 repository listed
  As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization.
• EurNet: Efficient Multi-Range Relational Modeling of Spatial Multi-Relational Data
  23 Nov 2022 1 repository listed Syntology ran 1 of 9 samples · 8 unverified
  We study EurNets in two important domains for image and protein structure modeling.
• Galactica: A Large Language Model for Science
  16 Nov 2022 1 repository listed Syntology ran 0 of 2 samples · 2 unverified
  We believe these results demonstrate the potential for language models as a new interface for science.
• Deep learning-based rapid generation of broadly reactive antibodies against SARS-CoV-2 and its Omicron variant
  27 Sep 2022 1 repository listed
  The COVID-19 pandemic has been ongoing for nearly two and half years, and new variants of concern (VOCs) of SARS-CoV-2 continue to emerge, which urges the development of broadly neutralizing antibodies.
• PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
  5 Jun 2022 1 repository listed Syntology ran 0 of 2 samples · 2 unverified
  However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field.
• Robust deep learning based protein sequence design using ProteinMPNN
  4 Jun 2022 1 repository listed
  While deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta.
• Multi-Scale Representation Learning on Proteins
  4 Apr 2022 1 repository listed Syntology ran 0 of 7 samples · 7 unverified
  This paper introduces a multi-scale graph construction of a protein -- HoloProt -- connecting surface to structure and sequence.
• Graph Self-supervised Learning with Accurate Discrepancy Learning
  7 Feb 2022 1 repository listed Syntology ran 2 of 3 samples · 1 unverified · 3 pointer-only (licence)
  Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two…
• OntoProtein: Protein Pretraining With Gene Ontology Embedding
  23 Jan 2022 1 repository listed Syntology ran 1 of 1 samples · 0 unverified
  We construct a novel large-scale knowledge graph that consists of GO and its related proteins, and gene annotation texts or protein sequences describe all nodes in the graph.
• Encoding protein dynamic information in graph representation for functional residue identification
  15 Dec 2021 1 repository listed
  Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions.
• Structure-Enhanced Meta-Learning For Few-Shot Graph Classification
  5 Mar 2021 1 repository listed
  Graph classification is a highly impactful task that plays a crucial role in a myriad of real-world applications such as molecular property prediction and protein function prediction.
• Coherent Hierarchical Multi-Label Classification Networks
  20 Oct 2020 1 repository listed
  Hierarchical multi-label classification (HMC) is a challenging classification task extending standard multi-label classification problems by imposing a hierarchy constraint on the classes.

Syntology lines on 12 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.