Weekly BioML Digest [December 08, 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 [December 01, 2025 - December 07, 2025].
• Found 4663 new arXiv papers and 1353 new bioRxiv papers.
• 36 arXiv papers and 79 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:

• 🧬 Generative design and construction of functional plasmids with a DNA language model
  Cunningham, A. G.; Dekker, L.; Shcherbakova, A.; Barnes, C. P. — bioRxiv:synthetic biology, 2025-12-07
  abs · pdf

• 📄 Atomic Diffusion Models for Small Molecule Structure Elucidation from NMR Spectra
  Ziyu Xiong, Yichi Zhang, Foyez Alauddin, Chu Xin Cheng, Joon Soo An, Mohammad R. Seyedsayamdost, Ellen D. Zhong — cs.LG, 2025-12-02
  abs · pdf

• 🧬 DeepRank-Ab: a dedicated scoring function for antibody-antigen complexes based on geometric deep learning
  Xu, X.; Coratella, I.; Bonvin, A. M. — bioRxiv:bioinformatics, 2025-12-06
  abs · pdf

• 🧬 Disobind: a sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions
  Majila, K.; Ullanat, V.; Viswanath, S. — bioRxiv:bioinformatics, 2025-12-07
  abs · pdf

• 🧬 A Unified Multi-modal LLM for Dynamic Protein-Ligand Interactions and Generative Molecular Design
  Jing, H.; Miao, Y. — bioRxiv:bioinformatics, 2025-12-03
  abs · pdf

• 🧬 Modeling the structure-conditioned sequence landscape for large-scale protein design with TriFlow
  Srinivasan, H.; Yuan, R.; Cong, Q.; Zhou, J. — bioRxiv:bioinformatics, 2025-12-02
  abs · pdf

• 🧬 GCP-VQVAE: A Geometry-Complete Language for Protein 3D Structure
  Pourmirzaei, M.; Morehead, A.; Esmaili, F.; Ren, J.; Pourmirzaei, M.; Xu, D. — bioRxiv:bioinformatics, 2025-12-04
  abs · pdf

• 📄 NEAT: Neighborhood-Guided, Efficient, Autoregressive Set Transformer for 3D Molecular Generation
  Daniel Rose, Roxane Axel Jacob, Johannes Kirchmair, Thierry Langer — cs.LG, 2025-12-05
  abs · pdf

• 📄 Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time
  Daniel D. Richman, Jessica Karaguesian, Carl-Mikael Suomivuori, Ron O. Dror — q-bio.BM, 2025-12-02
  abs · pdf

• 📄 Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training
  Felix Teufel, Aaron W. Kollasch, Yining Huang, Ole Winther, Kevin K. Yang, Pascal Notin, Debora S. Marks — q-bio.BM, 2025-12-02
  abs · pdf

• 📄 OMTRA: A Multi-Task Generative Model for Structure-Based Drug Design
  Ian Dunn, Liv Toft, Tyler Katz, Juhi Gupta, Riya Shah, Ramith Hettiarachchi, David R. Koes — cs.LG, 2025-12-04
  abs · pdf

• 🧬 De Novo Computational Design of VHH Nanobodies Against LGR5
  Xu, C.; Li, Y.; Nguyen, T.; Zhou, Y.; Cong, L.; Lee, T.-H.; Lang, Y.; Shek, R.; Yi, L.; Greisen, P. — bioRxiv:bioengineering, 2025-12-05
  abs · pdf

• 🧬 Improving nanobody structure prediction with self-distillation
  Ali, M.; Greenig, M.; Jaskolowski, M.; Crnogaj, M.; Smorodina, E.; Zhao, H.; Greiff, V.; Sormanni, P. — bioRxiv:bioengineering, 2025-12-02
  abs · pdf

• 📄 Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
  Danny Reidenbach, Zhonglin Cao, Zuobai Zhang, Kieran Didi, Tomas Geffner, Guoqing Zhou, Jian Tang, Christian Dallago, Arash Vahdat, Emine Kucukbenli, Karsten Kreis — q-bio.BM, 2025-12-01
  abs · pdf

• 🧬 InfluenceNet: Encoding Motif Influence for Interpretable Modeling of Cis-Regulatory Syntax
  Hu, J.; Fetter, J.; Koes, D. R.; Chikina, M. — bioRxiv:bioinformatics, 2025-12-04
  abs · pdf

• 📄 STAR-GO: Improving Protein Function Prediction by Learning to Hierarchically Integrate Ontology-Informed Semantic Embeddings
  Mehmet Efe Akça, Gökçe Uludoğan, Arzucan Özgür, İnci M. Baytaş — q-bio.BM, 2025-12-04
  abs · pdf

• 🧬 Mechanism-Aware Inductive Bias Enhances Generalization in Protein-Protein Interaction Prediction
  Deng, S.; Wan, X.; Mu, Z.; Huang, S.-Y.; Yan, C. — bioRxiv:bioinformatics, 2025-12-05
  abs · pdf

• 🧬 Pseudodynamics+: Reconstructing Population Dynamics from Time-Resolved Single Cell Landscapes with Physics Informed Neural Networks
  Zheng, W.; Barile, M.; Wilson, N. K.; Huang, Y.; Theis, F. J.; Gottgens, B. — bioRxiv:bioinformatics, 2025-12-02
  abs · pdf

• 🧬 End-to-end single-stranded DNA sequence design with all-atom structure reconstruction
  si, y.; chen, l. — bioRxiv:molecular biology, 2025-12-05
  abs · pdf

• 🧬 Designing Convergent Overlapping Genes with Transformer Encoder Models and Lightweight Structural Proxies
  Morgan, J. K. — bioRxiv:synthetic biology, 2025-12-05
  abs · pdf

• 📄 Teaching Language Models Mechanistic Explainability Through Arrow-Pushing
  Théo A. Neukomm, Zlatko Jončev, Philippe Schwaller — cs.LG, 2025-12-05
  abs · pdf

• 📄 Graph VQ-Transformer (GVT): Fast and Accurate Molecular Generation via High-Fidelity Discrete Latents
  Haozhuo Zheng, Cheng Wang, Yang Liu — cs.LG, 2025-12-02
  abs · pdf

• 🧬 MS4MS: LLMs-driven Multi-agent System for Small-molecule Identification via LC-MS/MS
  Guo, N.; Guo, J.; Liu, Y.; Wei, S.; Dong, L.; Du, H.; Bai, Y.; Zhao, Y.; Wang, X.; Yang, H.; Zeng, D. — bioRxiv:bioinformatics, 2025-12-05
  abs · pdf

• 🧬 Machine learning inference of natural product chemistry across biosynthetic gene cluster types
  Larralde, M.; Zeller, G. — bioRxiv:bioinformatics, 2025-12-07
  abs · pdf

• 🧬 Genomic foundation models reveal RNA-binding proteins regulating translation and mRNA degradation during Drosophila development
  Brase, L.; Creamer, D. R.; Shapovalova, Y.; Ashe, M. P.; Ashe, H. L.; Rattray, M. — bioRxiv:bioinformatics, 2025-12-06
  abs · pdf

• 🧬 A flaw in using pre-trained pLLMs in protein-protein interaction inference models
  Szymborski, J.; Emad, A. — bioRxiv:bioinformatics, 2025-12-05
  abs · pdf

• 📄 Generalization Beyond Benchmarks: Evaluating Learnable Protein-Ligand Scoring Functions on Unseen Targets
  Jakub Kopko, David Graber, Saltuk Mustafa Eyrilmez, Stanislav Mazurenko, David Bednar, Jiri Sedlar, Josef Sivic — cs.LG, 2025-12-05
  abs · pdf

• 📄 Fine-Tuning ChemBERTa for Predicting Inhibitory Activity Against TDP1 Using Deep Learning
  Baichuan Zeng — cs.LG, 2025-12-03
  abs · pdf

• 🧬 DPCMHC: efficient prediction of MHC-peptide binding affinity by deep learning based on dual-padding convolution
  Lu, Y.; Mi, L.; Zhang, S. — bioRxiv:bioinformatics, 2025-12-02
  abs · pdf

• 🧬 Modeling TCR-pMHC Binding with Dual Encoders and Cross-Attention Fusion
  Wang, W.; Qi, C.; Wei, Z. — bioRxiv:bioinformatics, 2025-12-02
  abs · pdf