Weekly BioML Digest [February 09, 2026]

Machine Learning × Computational Biology paper compilation

Hey! It's your weekly digest of machine learning papers in CompBio and Drug Discovery.

This weeks digest contains only preprint section due to technical issues.

Feedback? Email me at biomldigest@gmail.com.

🧬 Preprints (arXiv + bioRxiv)

154 papers matched filters → 20 selected after LLM relevance + novelty ranking.

• 🧬 Decoding the Molecular Language of Proteins with Evolla
  Zhou, X.; Han, C.; Zhang, Y.; Du, H.; Tian, J.; Su, J.; Liu, R.; Zhuang, K.; Jiang, S.; Gitter, A.; Liu, L.; Li, H.; Wu, M.; You, S.; Yuan, Z.; Ju, F.; Zhang, H.; Zheng, W.; Dai, F.; Zhou, Y.; Tao, Y.; Wu, D.; Shao, Z.; Liu, Y.; Lu, H.; Yuan, F. — bioRxiv, 2026-02-03
  abs

• 🧬 Large mRNA language foundation modeling with NUWA for unified sequence perception and generation
  Zhong, Y.; Yan, W.; Zhang, Y.; Tan, K.; Saito, Y.; Bian, B. — bioRxiv, 2026-02-04
  abs

• 🧬 Ophiuchus-Ab: A Versatile Generative Foundation Model for Advanced Antibody-Based Immunotherapy
  Zhu, Y.; Ma, J.; Yin, M.; Wu, J.; Tang, L.; Zhang, Z.; Li, Q.; Feng, S.; Liu, H.; Qin, T.; Yan, J.; Hsieh, C.-Y.; Hou, T. — bioRxiv, 2026-02-04
  abs

• 📄 Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics
  Nima Shoghi, Yuxuan Liu, Yuning Shen, Rob Brekelmans, Pan Li, Quanquan Gu — arXiv, 2026-02-02
  abs

• 🧬 A Unified Framework for Model-Informed and Agentic RNA Design
  Riley, A. T.; Vlasity, M.; Becicka, W. M.; Huang, J. Z.; Pang, S.; Wong, W. W.; Grinstaff, M. W.; Green, A. A. — bioRxiv, 2026-02-07
  abs

• 🧬 GCP-VQVAE: A Geometry-Complete Language for Protein 3D Structure
  Pourmirzaei, M.; Morehead, A.; Esmaili, F.; Ren, J.; Pourmirzaei, M.; Xu, D. — bioRxiv, 2026-02-03
  abs

• 🧬 Visual-like 2D Geometric Template Diffusion for Boosting Single-Sequence Protein Structure Prediction
  Wang, X.; Zhang, T.; Cui, Z.; Guo, X.; Wang, F.; Wang, Y.; Cai, X.; Zheng, W. — bioRxiv, 2026-02-07
  abs

• 🧬 Deconvolving mutation effects on protein stability and function with disentangled protein language models
  Ding, K.; Li, Z.; Tu, T.; Luo, J.; Luo, Y. — bioRxiv, 2026-02-05
  abs

• 🧬 Designing protein/non-protein binding interactions using a full-atom diffusion model
  Kundert, K.; Church, G. — bioRxiv, 2026-02-04
  abs

• 📄 MoLF: Mixture-of-Latent-Flow for Pan-Cancer Spatial Gene Expression Prediction from Histology
  Susu Hu, Stefanie Speidel — arXiv, 2026-02-02
  abs

• 📄 Repurposing Protein Language Models for Latent Flow-Based Fitness Optimization
  Amaru Caceres Arroyo, Lea Bogensperger, Ahmed Allam, Michael Krauthammer, Konrad Schindler, Dominik Narnhofer — arXiv, 2026-02-02
  abs

• 🧬 Macro-Equi-Diff (MED): Scaffold-based Macrocycles Generation Using Equivariant Diffusion
  Kambampati, S. S.; Anumandla, S.; Guttula, S. L.; Kavadi, V. R.; Gogte, S.; Kondaparthi, V. — bioRxiv, 2026-02-06
  abs

• 📄 All-Atom GPCR-Ligand Simulation via Residual Isometric Latent Flow
  Jiying Zhang, Shuhao Zhang, Pierre Vandergheynst, Patrick Barth — arXiv, 2026-02-03
  abs

• 🧬 Joint Modeling of Transcriptomic and Morphological Phenotypes for Generative Molecular Design
  Verma, S.; Wang, M.; Jayasundara, S.; Malusare, A. M.; Wang, L.; Grama, A.; Kazemian, M.; Lanman, N. A. — bioRxiv, 2026-02-04
  abs

• 🧬 DecoderTCR: Compositional Pretraining and Entropy-Guided Decoding for TCR-pMHC Interactions
  Lai, B.; Englund, M.; Bharanikumar, R.; Nocedal, I.; Davariashtiyani, A.; Perera, J.; Khan, A. A. — bioRxiv, 2026-02-06
  abs

• 🧬 Separating selection from mutation in antibody language models
  Matsen, F. A.; Dumm, W.; Sung, K.; Johnson, M. M.; Rich, D.; Starr, T.; Song, Y. S.; Fukuyama, J.; Haddox, H. K. — bioRxiv, 2026-02-03
  abs

• 🧬 Efficient, Few-shot Directed Evolution with Energy Rank Alignment
  Ibarraran, S.; Chennakesavalu, S.; Hu, F.; Rotskoff, G. M. — bioRxiv, 2026-02-06
  abs

• 📄 Synthesizable Molecular Generation via Soft-constrained GFlowNets with Rich Chemical Priors
  Hyeonah Kim, Minsu Kim, Celine Roget, Dionessa Biton, Louis Vaillancourt, Yves V. Brun, Yoshua Bengio, Alex Hernandez-Garcia — arXiv, 2026-02-04
  abs

• 🧬 Decoupling Structure and Property in Discrete Protein Diffusion: Alignment Dynamics and Collapse Mechanisms
  Wu, J.; Dong, L.; Jia, N.; Li, L.; Zhang, H. — bioRxiv, 2026-02-08
  abs

• 🧬 Learning millisecond protein dynamics from what is missing in NMR spectra
  Wayment-Steele, H. K.; El Nesr, G.; Hettiarachchi, R.; Ojoawo, A. M.; Kariyawasam, H.; Ovchinnikov, S.; Kern, D. — bioRxiv, 2026-02-07
  abs