mlsanityData to 14 Oct 2026

VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning

arXiv 2503.15438 ↗First posted 19 Mar 2025cs.CL cs.AI q-bio.QMcited by 3

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Abstract (arXiv)

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating 40+ protein-related datasets and 40+ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

Key facts. Cited by 3 papers in the map (data through 14 Oct 2026). Builds on 18 of its 59 references that are in the map. First posted on arXiv 19 Mar 2025.

Builds on

18 of 59 references.

References · 18

  1. 2020Language Models are Few-Shot Learnerscited by 32,419
  2. 2019PyTorch: An Imperative Style, High-Performance Deep Learning Librarycited by 20,305
  3. 2023Judging LLM-as-a-Judge with MT-Bench and Chatbot Arenacited by 8,626
  4. 2017Neural Discrete Representation Learningcited by 4,712
  5. 2023QLoRA: Efficient Finetuning of Quantized LLMscited by 3,418
  6. 2017Decoupled Weight Decay Regularizationcited by 1,831
  7. 2024LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Modelscited by 1,464
  8. 2022Few-Shot Parameter-Efficient Fine-Tuning is Better and Cheaper than In-Context Learningcited by 896
  9. 2024DoRA: Weight-Decomposed Low-Rank Adaptationcited by 758
  10. 2023AdaLoRA: Adaptive Budget Allocation for Parameter-Efficient Fine-Tuningcited by 357
  11. 2019Evaluating Protein Transfer Learning with TAPEcited by 231
  12. 2019Gradio: Hassle-Free Sharing and Testing of ML Models in the Wildcited by 178
6 more
  1. 2023LMFlow: An Extensible Toolkit for Finetuning and Inference of Large Foundation Modelscited by 60
  2. 2023Ankh: Optimized Protein Language Model Unlocks General-Purpose Modellingcited by 45
  3. 2023The Janus Interface: How Fine-Tuning in Large Language Models Amplifies the Privacy Riskscited by 36
  4. 2022Exploring evolution-aware & -free protein language models as protein function predictorscited by 20
  5. 2024Large scale paired antibody language modelscited by 16
  6. 2024DrugWatch: A Comprehensive Multi-Source Data Visualisation Platform for Drug Safety Informationcited by 2

Built on by

Cited by year (2026 to 14 Oct)

Citing papers per year: 2025: 2; 2026: 1.

3 papers.

  1. 2025VenusX: Unlocking Fine-Grained Functional Understanding of Proteinscited by 5
  2. 2025PFMBench: Protein Foundation Model Benchmarkcited by 4
  3. 2026MIMIC: A Generative Multimodal Foundation Model for Biomoleculescited by 0