Weekly BioML Digest [December 01, 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 [November 24, 2025 - November 30, 2025].
• Found 4645 new arXiv papers and 1217 new bioRxiv papers.
• 24 arXiv papers and 70 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:

• 🧬 PULSAR: a Foundation Model for Multi-scale and Multicellular Biology
  Pang, K.; Rosen, Y.; Kedzierska, K.; He, Z.; Rajagopal, A.; Gustafson, C. E.; Huynh, G.; Leskovec, J. — bioRxiv:bioinformatics, 2025-11-26
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• 🧬 RNA-X: Modeling RNA interactions to design binder RNA and simultaneously target multiple molecules of different types
  Shukueian Tabrizi, S.; Hashemi Aghdam, H.; Cicek, A. E. — bioRxiv:bioinformatics, 2025-11-26
  abs · pdf

• 🧬 Discovery of molecular glues by modeling ternary complex conformational ensembles and thermodynamic stability
  Izaguirre, J. A.; McDargh, Z.; Trovato, F.; Wu, Y.; Palpant, T.; Razavi, A. M.; Koh, C.; Xu, H. — bioRxiv:bioinformatics, 2025-11-26
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• 🧬 Generalizable and scalable protein stability prediction with rewired protein generative models
  Li, Z.; Luo, Y. — bioRxiv:bioinformatics, 2025-11-26
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• 🧬 AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images
  Kawai, T.; Matsunaga, Y. — bioRxiv:biophysics, 2025-11-26
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• 📄 FoldSAE: Learning to Steer Protein Folding Through Sparse Representations
  Wojciech Zarzecki, Paulina Szymczak, Ewa Szczurek, Kamil Deja — q-bio.QM, 2025-11-27
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• 📄 Swarms of Large Language Model Agents for Protein Sequence Design with Experimental Validation
  Fiona Y. Wang, Di Sheng Lee, David L. Kaplan, Markus J. Buehler — cs.AI, 2025-11-27
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• 🧬 STODE: A Deep Generative Framework for Continuous Spatiotemporal Dynamics in Spatial Transcriptomics
  Majima, K.; Kojima, Y.; Shimamura, T. — bioRxiv:bioinformatics, 2025-11-26
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• 🧬 TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models
  Liu, S.; Tang, J.; Ma, J.; Liang, S. — bioRxiv:bioinformatics, 2025-11-27
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• 🧬 Expanding the RNA Virus Universe by Scalable Structure-Guided Discovery
  Luo, G.; Zang, Z.; Yuan, L.; Zhou, J.; Dong, A.; Huang, Y.; Li, S. Z.; Ju, F. — bioRxiv:bioinformatics, 2025-11-27
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• 🧬 PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA
  Del Vecchio, A.; Kapourani, C.-A.; Athar, A. M.; Dobrowolska, A.; Anighoro, A.; Tenmann, B.; Edwards, L.; Regep, C. — bioRxiv:genomics, 2025-11-29
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• 🧬 CodonTranslator: a conditional codon language model for codon optimization across all domains of life
  Chen, Y.; Zhang, Y.; Li, J.; Tian, B.; Huang, H. — bioRxiv:bioinformatics, 2025-11-27
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• 🧬 Rewriting protein alphabets with language models
  Pantolini, L.; Studer, G.; Engist, L.; Pudziuvelyte, I.; Pommerening, F.; Waterhouse, A. M.; Tauriello, G.; Steinegger, M.; Schwede, T.; Durairaj, J. — bioRxiv:bioinformatics, 2025-11-28
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• 🧬 Pangenome-Informed Language Models for Synthetic Genome Sequence Generation
  Huang, P.; Charton, F.; Schmelzle, J.-N. M.; Darnell, S. S.; Prins, P.; Garrison, E.; Suh, G. E. — bioRxiv:bioinformatics, 2025-11-25
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• 🧬 AI-driven discovery and optimization of antimicrobial peptides from extreme environments on global scale
  Kang, Z.; Zhang, H.; Zhou, Q.; Liu, J.; Zhou, K.; Chen, P.; Liu, B.-F.; Ning, K. — bioRxiv:bioinformatics, 2025-11-26
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• 🧬 ClsDiff-AMP30: Generating Antimicrobial Peptides by a Classifier Guidance Noise Predictor
  Yan, J.; Cai, J.; Li, Y.; Lin, Z.; Xian, W.; Wei, X.; Lei, I. F.; Zhou, M.; Campbell-Valois, F.-X.; Siu, S. W. I. — bioRxiv:bioinformatics, 2025-11-29
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• 📄 DeepPNI: Language- and graph-based model for mutation-driven protein-nucleic acid energetics
  Somnath Mondal, Tinkal Mondal, Soumajit Pramanik, Rukmankesh Mehra — q-bio.BM, 2025-11-27
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• 🧬 RoBep: A Region-Oriented Deep Learning Model for B-Cell Epitope Prediction
  Xu, Y.; Wei, G.; Zhou, J.; Huang, Y.; Yu, W.; Lin, Z.; LIU, R.; Fan, X. — bioRxiv:bioinformatics, 2025-11-25
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• 🧬 FusionProt: Fusing Sequence and Structural Information for Unified Protein Representation Learning
  Kalifa, D.; Singer, U.; Radinsky, K. — bioRxiv:bioinformatics, 2025-11-26
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• 🧬 Language may be all omics needs: Harmonizing multimodal data for omics understanding with CellHermes
  Gao, Y.; Wang, W.; Zhao, Y.; Dong, K.; Shan, C.; Zheng, W.; Richter, T.; Li, Z.; Chen, S.; Theis, F. J.; Liu, Q. — bioRxiv:bioinformatics, 2025-11-28
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• 🧬 Systematic discovery of single-cell protein networks in cancer with Shusi
  Zhang, T.; Yu, J.; Lou, S.; Liang, Z.; Liang, Y.; Li, Z.; Wang, H.; Pei, S.; Shen, N. — bioRxiv:bioinformatics, 2025-11-25
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• 🧬 LaCONIC: A Label-Aware and Graph-Guided Contrastive Multi-Omics Collaborative Learning Model for Cancer Risk Prediction
  Liu, P.; Liang, X.; Luo, J. — bioRxiv:bioinformatics, 2025-11-30
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• 🧬 An integrated platform for high-throughput phenospace learning of 3D multilineage organoid systems
  Okuda, R.; Harmel, C.; Xu, Q.; Mary, H.; Schulz, P.; Steinacher, L.; D'Arcangelo, E.; Gjeta, B.; Signer, M.; Cubela, I.; Bickle, M.; Lutolf, M. P.; Cabon, L.; Lukonin, I.; Camp, G. — bioRxiv:cancer biology, 2025-11-29
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• 🧬 High-resolution MRI Guided Whole Mouse Brain Cell Type Atlas using Deep Learning
  Han, X.; Hu, R.; Liu, Z.; Chen, J.; Jafry, M.; Song, H.; Zhao, Y.; Lin, M.; White, L. E.; Johnson, G. A.; Wang, N. — bioRxiv:neuroscience, 2025-11-28
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• 🧬 RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions
  Laverre, A.; Latrille, T.; Robinson-Rechavi, M. — bioRxiv:evolutionary biology, 2025-11-29
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• 📄 Flow Density Control: Generative Optimization Beyond Entropy-Regularized Fine-Tuning
  Riccardo De Santi, Marin Vlastelica, Ya-Ping Hsieh, Zebang Shen, Niao He, Andreas Krause — cs.LG, 2025-11-27
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• 🧬 Can We Extract Physics-like Energies from Generative Protein Diffusion Models?
  Sarma, S. S.; Truscott, H. H.; Xu, D.; Reid, K.; Chu, L.-S.; Chen, J.; Gray, J. J. — bioRxiv:biophysics, 2025-11-29
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• 🧬 Inferring Local Protein Structural Similarity from Sequence Alone
  Ma, Z.; Herrera, J. E.; Bethel, N. P.; Jinich, A. — bioRxiv:bioinformatics, 2025-11-27
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• 🧬 CrossPPI: A Cross - Fusion Based Model for Protein - Protein Binding Affinity Prediction.
  Singam, S. R.; Devarashetty, N. C. A.; Gogte, S.; Kondaparthi, V. — bioRxiv:bioinformatics, 2025-11-27
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• 📄 Aligning LLMs with Biomedical Knowledge using Balanced Fine-Tuning
  Zhenchao Tang, Fang Wang, Haohuai He, Jiale Zhou, Tianxu Lv, Jun Zhu, Shouzhi Chen, Minghao Yang, Yu Wang, Jiayang Wu, Yidong Song, Jianhua Yao — cs.LG, 2025-11-26
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