Weekly BioML Digest [November 10, 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 03, 2025 - November 09, 2025].
• Found 4221 new arXiv papers and 1349 new bioRxiv papers.
• 18 arXiv papers and 94 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:

• 📄 SigmaDock: Untwisting Molecular Docking With Fragment-Based SE(3) Diffusion
  Alvaro Prat, Leo Zhang, Charlotte M. Deane, Yee Whye Teh, Garrett M. Morris — cs.LG, 2025-11-06
  abs · pdf

• 📄 FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation
  Jiameng Chen, Yida Xiong, Kun Li, Hongzhi Zhang, Xiantao Cai, Wenbin Hu, Jia Wu — cs.LG, 2025-11-05
  abs · pdf

• 🧬 HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence design
  Fang, M.; Wang, C.; Shi, J.; Lian, F.; JIn, Q.; Wang, Z.; Zhang, Y.; Cui, Z.; Wang, Y.; Ke, Y.; Han, Q.; Cao, L. — bioRxiv:bioinformatics, 2025-11-09
  abs · pdf

• 🧬 SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design
  Zhang, P.; Han, R.; Kong, X.; Chen, T.; Ma, J. — bioRxiv:bioinformatics, 2025-11-08
  abs · pdf

• 🧬 De novo design of light-regulated dynamic proteins using deep learning
  Scutteri, L.; Abriata, L.; Zhang, S.; Hacisuleyman, A.; Lau, K.; Pojer, F.; Rahi, S. J.; Barth, P. — bioRxiv:biophysics, 2025-11-05
  abs · pdf

• 🧬 CycleVI: Isolating cell cycle variation with an interpretable deep generative model
  Mozdzanowski, P.; Tarbier, M.; S. Jeuken, G. — bioRxiv:systems biology, 2025-11-05
  abs · pdf

• 🧬 Context-aware geometric deep learning for RNA sequence design
  Bibekar, P.; Krapp, L. F.; Dal Peraro, M. — bioRxiv:bioinformatics, 2025-11-05
  abs · pdf

• 📄 STAR-VAE: Latent Variable Transformers for Scalable and Controllable Molecular Generation
  Bum Chul Kwon, Ben Shapira, Moshiko Raboh, Shreyans Sethi, Shruti Murarka, Joseph A Morrone, Jianying Hu, Parthasarathy Suryanarayanan — cs.LG, 2025-11-04
  abs · pdf

• 📄 Discrete Bayesian Sample Inference for Graph Generation
  Ole Petersen, Marcel Kollovieh, Marten Lienen, Stephan Günnemann — cs.LG, 2025-11-04
  abs · pdf

• 🧬 EVOSYNTH: Enabling Multi-Target Drug Discovery through Latent Evolutionary Optimization and Synthesis-Aware Prioritization
  Nguyen, V. T. D.; Pham, P.; Hy, T.-S. — bioRxiv:bioinformatics, 2025-11-05
  abs · pdf

• 🧬 Ultrahigh throughput screening to train generative protein models for engineering specificity into unspecific peroxygenases
  Nair, P. M.; Steinberg, D. M.; Resende, T.; Suarez, A. F.; Power, H.; Ong, C. S.; Sairam, V.; Cheng, S. H.-Y.; Fragata, L.; Serafini, A.; Oh, V.; Tan, S. H.; Speight, R. E.; Vahidi, A. K. — bioRxiv:bioengineering, 2025-11-04
  abs · pdf

• 🧬 Uncertainty-Aware Deep Learning for Multi-Metric and Dose-Specific Prediction of Drug Synergy
  Heydari, M. J.; Lye, B.; Masouri, P.; Marsland, T.; Lock, J.; McKenna, J.; Vafaee, F. G. — bioRxiv:bioinformatics, 2025-11-07
  abs · pdf

• 📄 DGTN: Graph-Enhanced Transformer with Diffusive Attention Gating Mechanism for Enzyme DDG Prediction
  Abigail Lin — cs.LG, 2025-11-07
  abs · pdf

• 📄 Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
  Xinheng He, Yijia Zhang, Haowei Lin, Xingang Peng, Xiangzhe Kong, Mingyu Li, Jianzhu Ma — cs.LG, 2025-11-07
  abs · pdf

• 🧬 HyperBind2: Multi-Shot Learning Enables Progressive Improvement in Computational Antibody Discovery
  Dell'uomo, D.; Satz, A.; Averso, B. — bioRxiv:bioengineering, 2025-11-06
  abs · pdf

• 🧬 Iterative immunogen optimization to focus elicited responses on a conserved, subdominant influenza hemagglutinin epitope
  Marston, D. J.; Watanabe, A.; Kapingidza, A. B.; Harris, C.; Van Itallie, E.; Devkota, K.; Christopher, J.; Liu, P.; Pun, B.; Rhodes, B.; Frazier, M.; Winters, K.; Burre, H.; Kannan, P.; Liang, X.; Kelsoe, G.; Wiehe, K.; Singh, R.; Wrapp, D.; Kuraoka, M.; Azoitei, M. L. — bioRxiv:immunology, 2025-11-06
  abs · pdf

• 🧬 Physics-Diffusion-Driven Multiscale Aggregation for Drug-Target Interaction Prediction
  Liu, J.; Le, J.; Wei, C.; Liu, M.; Yin, Z.; Luo, Y.; Qin, H.; Yu, G. — bioRxiv:bioinformatics, 2025-11-04
  abs · pdf

• 🧬 ECLIPSE: Exploration of Complex Ligand-Protein Interactions through Learning from Systems-level Heterogeneous Biomedical Knowledge Graphs
  Atas Guvenilir, H.; Dogan, T. — bioRxiv:bioinformatics, 2025-11-07
  abs · pdf

• 🧬 qcGEM: a graph-based molecular representation with quantum chemistry awareness
  Wang, H.; Gong, H. — bioRxiv:biophysics, 2025-11-04
  abs · pdf

• 🧬 Benchmarking Real-World Applicability of Molecular Generative Models from De novo Design to Lead Optimization with MolGenBench
  Cao, D.; Fan, Z.; Yu, J.; Chen, M.; Jiang, X.; Wang, X.; Sheng, X.; Luo, X.; Teng, D.; Zheng, M. — bioRxiv:bioinformatics, 2025-11-04
  abs · pdf

• 🧬 Data-optimal scaling of paired antibody language models
  Neyestanak, M. S.; Burbach, S. M.; Ng, K.; Gangavarapu, P.; Hurtado, J.; Magura, J.; Ismail, N.; Muema, D.; Ndung'u, T.; Ward, A.; Briney, B. — bioRxiv:immunology, 2025-11-05
  abs · pdf

• 🧬 H3BERTa: A CDR-H3 specific language model for antibody repertoire analysis
  Rodella, C.; Lemmin, T. — bioRxiv:immunology, 2025-11-05
  abs · pdf

• 📄 SPECTRA: Spectral Target-Aware Graph Augmentation for Imbalanced Molecular Property Regression
  Brenda Nogueira, Meng Jiang, Nitesh V. Chawla, Nuno Moniz — cs.LG, 2025-11-06
  abs · pdf

• 📄 A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification
  Sebastian Ojeda, Rafael Velasquez, Nicolás Aparicio, Juanita Puentes, Paula Cárdenas, Nicolás Andrade, Gabriel González, Sergio Rincón, Carolina Muñoz-Camargo, Pablo Arbeláez — cs.LG, 2025-11-06
  abs · pdf

• 📄 POEMS: Product of Experts for Interpretable Multi-omic Integration using Sparse Decoding
  Mihriban Kocak Balik, Pekka Marttinen, Negar Safinianaini — cs.LG, 2025-11-05
  abs · pdf

• 🧬 MotifAE Reveals Functional Motifs from Protein Language Model: Unsupervised Discovery and Interpretability Analysis
  Hou, C.; Liu, D.; Shen, Y. — bioRxiv:bioinformatics, 2025-11-05
  abs · pdf

• 🧬 SKiM-GPT: Combining Biomedical Literature-Based Discovery with Large Language Model Hypothesis Evaluation
  Freeman, J.; Millikin, R. J.; Xu, L.; Sharma, I.; Moore, B. M.; Lock, C.; George, K. S.; Bal, A.; Mohanty, C.; Stewart, R. — bioRxiv:bioinformatics, 2025-11-05
  abs · pdf

• 🧬 Cross-Molecular Active Learning for the Discovery of Antimicrobial Polyacrylamides
  Williams, S. C.; Greenstein, G.; Liu, X.; Fragasso, A.; Eckman, N.; Prossnitz, A.; Dong, C.; Makar-Limanov, A.; Jacobs-Wagner, C.; Cegelski, L.; Lopez Hernandez, H.; Appel, E. — bioRxiv:microbiology, 2025-11-07
  abs · pdf

• 🧬 Multi-Dimensional Spatiotemporal Attention Neural Network for Next Generation Sequencing Basecalling
  Peng, K.; Chen, W.; Yao, T.; Xia, H.; Fu, G.; Li, G.; Bao, Y.; Liu, E.; Zhao, L.; Wang, G. — bioRxiv:bioinformatics, 2025-11-08
  abs · pdf

• 🧬 Pro4S: prediction of protein solubility by fusing sequence, structure, and surface
  Qian, J.; Yang, L.; Wang, R.; Qi, Y. — bioRxiv:bioinformatics, 2025-11-07
  abs · pdf