Weekly BioML Digest [November 03, 2025]

Machine Learning × Computational Biology compilation from arXiv + bioRxiv

Hey! It's your weekly automated digest of machine learning papers in CompBio and Drug Discovery. Here is how it was created:

• Both arXiv and bioRxiv queried for new papers published in the past week [October 27, 2025 - November 02, 2025].
• Found 4671 new arXiv papers and 1343 new bioRxiv papers.
• 12 arXiv papers and 85 bioRxiv papers matched keyword filters.
• 30 papers are included in this digest after deduplication and ChatGPT relevance+novelty reranking.

Here are your top 30 papers:

• 🧬 SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology
  Gupta, A.; Wefers, Z.; Kahnert, K.; Hansen, J. N.; Misra, M. K.; Leineweber, W. D.; Cesnik, A.; Lu, D.; Axelsson, U.; Ballllosera Navarro, F.; Altman, R. B.; Karaletsos, T.; Lundberg, E. — bioRxiv:cell biology, 2025-10-30
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• 🧬 Large mRNA language foundation modeling with NUWA for unified sequence perception and generation
  Zhong, Y.; Yan, W.; Zhang, Y.; Tan, K.; Bian, B. — bioRxiv:bioinformatics, 2025-11-02
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• 🧬 From bench assays to bedside: context-embedding transformer predicts monoclonal antibody viscosity, clearance, and regulatory success
  Virk, S. S.; Virk, A. S. — bioRxiv:bioinformatics, 2025-11-01
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• 🧬 Design of multimodal antibiotics using deep learning
  Cesaro, A.; Wan, F.; Torres, M. D. T.; de la Fuente-Nunez, C. — bioRxiv:synthetic biology, 2025-10-31
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• 🧬 Accurately modelling RNase H-mediated antisense oligonucleotide efficacy
  Hill, B.; Jaques, M. R.; Nair, R. R.; Whiffin, N.; Wood, M. J. A.; Sanders, S. J.; Oliver, P. L.; Hill, A. C.; Rinaldi, C. — bioRxiv:bioinformatics, 2025-10-30
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• 🧬 From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models
  Pugh, C. W. J.; Nunez-Valencia, P. G.; Dias, M.; Frazer, J. — bioRxiv:bioinformatics, 2025-10-28
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• 🧬 CompleteBin: A transformer-based framework unlocks microbial dark matter through improved short contig binning
  Zou, B.; Zhang, Z.; Wang, X.; Tao, R.; Gu, N.; Kristiansen, K.; Han, M.; Zhang, L. — bioRxiv:bioinformatics, 2025-10-29
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• 📄 MolChord: Structure-Sequence Alignment for Protein-Guided Drug Design
  Wei Zhang, Zekun Guo, Yingce Xia, Peiran Jin, Shufang Xie, Tao Qin, Xiang-Yang Li — cs.AI, 2025-10-31
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• 📄 InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames
  Haorui Li, Weitao Du, Yuqiang Li, Hongyu Guo, Shengchao Liu — cs.LG, 2025-10-31
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• 🧬 Robust Prediction of Enzyme Variant Kinetics with RealKcat
  Sajeevan, K. A.; Osinuga, A.; B, A.; Ferdous, S.; Shahreen, N.; Noor, M.; Koneru, S.; Santa-Correa, L. M.; Salehi, R.; Chowdhury, N. B.; Aryee, R.; Calderon-Lopez, B.; Mali, A.; Saha, R.; Chowdhury, R. — bioRxiv:systems biology, 2025-10-30
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• 🧬 Deep learning assessment of nativeness and pairing likelihood for antibody and nanobody design with AbNatiV2
  Ramon, A.; Frassetto, N.; Zhao, H.; Xu, X.; Greenig, M.; Onuoha, S.; Sormanni, P. — bioRxiv:bioengineering, 2025-11-02
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• 🧬 CDR-aware masked language models for pairedantibodies enable state-of-the-art bindingprediction
  Talaei, M.; Walker, K. C.; Hao, B.; Jolley, E.; Jin, Y.; Kozakov, D.; Misasi, J.; Vajda, S.; Paschalidis, I. C.; Joseph-McCarthy, D. — bioRxiv:bioinformatics, 2025-10-31
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• 🧬 Fine-tuned Protein Language Model Identifies Antigen-specific B Cell Receptors from Immune Repertoires
  Paco, K.; Mendivil, M. P.; Zhang, Z.; Zebardast, S.; Davila, C.; Mooney, R. M.; Olatoyinbo, P.; Yang, T.; Bassi, S.; Gonzales, V.; Chen, E.; Ashraf, F. B.; Roman, I. C.; Felix, J. R.; Alam, R. M.; Lay, J. A.; Johal, M. S.; Le Roch, K. G.; Tolstorukov, I.; Hernandez, J. B.; da Silva, F. L. B.; Lonardi, S.; Sazinsky, M. H.; Ray, A. — bioRxiv:bioinformatics, 2025-10-31
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• 🧬 An Improved Systematic Method for Constructing ecGEMs using a Protein-Chemical Transformer
  Schooneveld, A.; Dewan, S.; Arad, N.; Genway, S.; Kalsi, S. K.; Bloznelyte, K.; Addison, W.; Berman, D. S. — bioRxiv:systems biology, 2025-10-30
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• 🧬 Decoding RNA-RNA Interactions: The Role of Low-Complexity Repeats and a Deep Learning Framework for Sequence-Based Prediction
  Setti, A.; Bini, G.; Maiorca, V.; Pellegrini, F.; Proietti, G.; Miltiadis-Vrachnos, D.; D'angelo, A.; Armaos, A.; Martone, J.; Monti, M.; Ruocco, G.; Rodola, E.; Bozzoni, I.; Colantoni, A.; Tartaglia, G. G. — bioRxiv:biochemistry, 2025-10-29
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• 🧬 Deciphering the Antigenic Evolution of Seasonal Influenza A Viruses with PREDAC-Transformer: From Antigenic Clustering to Key Site Identification
  Liu, J.; Wang, J.; Wang, C.; Ding, X.; Xie, W.; Qin, L.; Wu, A.; Meng, J.; Jiang, T. — bioRxiv:bioinformatics, 2025-10-29
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• 🧬 CellDiffusion: a generative model to annotate single-cell and spatial RNA-seq using bulk references
  Zhang, X.; Mao, J.; Le Cao, K.-A. — bioRxiv:bioinformatics, 2025-10-28
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• 🧬 Gradient-based Optimization for mRNA Sequence Design
  Li, H.; Terai, G.; Otagaki, T.; Asai, K. — bioRxiv:bioinformatics, 2025-10-30
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• 🧬 DCBK: A Fragment-Based Hybrid Simulation and Machine Learning Framework for Predicting Ligand Dissociation Kinetics
  Li, Y.; Wang, Y.; Zheng, X.; Guo, J.; Zhang, R. — bioRxiv:molecular biology, 2025-11-01
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• 🧬 AutoLead: An LLM-Guided Bayesian Optimization Framework for Multi-Objective Lead Optimization
  Zhang, Y.; Choong, J. j.; Madhawa, K.; Ozawa, K. — bioRxiv:bioinformatics, 2025-10-31
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• 🧬 ProAffinity++
  Xu, K.; Di, Z.; Zhao, J.; Zhang, H.; Bu, D. — bioRxiv:bioinformatics, 2025-11-01
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• 🧬 Mechanism-Aware Protein-Protein Interaction Prediction via Contact-Guided Dual Attention on Protein Language Models
  Deng, S.; Wan, X.; Mu, Z.; Huang, S.-Y.; Yan, C. — bioRxiv:bioinformatics, 2025-10-30
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• 📄 GeoPep: A geometry-aware masked language model for protein-peptide binding site prediction
  Dian Chen, Yunkai Chen, Tong Lin, Sijie Chen, Xiaolin Cheng — eess.SP, 2025-10-30
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• 🧬 ppLM-CO:Leveraging Pre-trained Protein Langauge Model for Codon Optimization
  Pathak, S.; Lin, G. — bioRxiv:bioinformatics, 2025-10-28
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• 🧬 Which pLM to choose?
  Senoner, T.; Koludarov, I.; Guenther, J.; Shehu, A.; Rost, B.; Bromberg, Y. — bioRxiv:bioinformatics, 2025-10-31
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• 🧬 AI-guided competitive docking for virtual screening and compound efficacy prediction
  Mirgaux, M.; Barcelli, V.; Chua, A. C. Y.; Bifani, P.; Wintjens, R. — bioRxiv:bioinformatics, 2025-10-29
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• 🧬 Structure-based Predictions of Conformational B Cell Epitopes by Protein Language Model and Deep Learning
  Zhang, Y.; Vilicich, F.; Kuang, X.; Liu, Y.; Zhang, G.; Su, Z.; Wu, Y. — bioRxiv:bioinformatics, 2025-10-30
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• 🧬 Dynamically Assembling Biological Intelligence to Predict Novel Cellular Phenotypes
  Pu, H.; Long, Y. — bioRxiv:bioengineering, 2025-10-30
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• 🧬 DomDiff: protein family and domain annotation via diffusion model and ESM2 embedding
  Zhang, C.; Xia, H.; Yin, P. — bioRxiv:genomics, 2025-10-28
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• 🧬 PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets
  Krzynowek, A.; Faust, K. — bioRxiv:bioinformatics, 2025-10-28
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