Weekly BioML Digest [January 05, 2026]

Machine Learning × Computational Biology paper compilation

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

Due to technical issues with Springer Nature API this week's digest only has arXiv and bioRxiv preprints.

Feedback? Email me at biomldigest@gmail.com.

🧬 Preprints (arXiv + bioRxiv)

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

• 🧬 A Generative Foundation Model for Cryo-EM Densities
  Li, Y.; Yuan, J.; Zhou, Y.; Wang, Z.; Chen, S.; Yang, F.; Ling, H.; Kovalsky, S. Z.; Zheng, X.; Gu, Q. — bioRxiv, 2025-12-29
  abs

• 🧬 Phenotype-Guided In Silico Molecular Generation Using Large Language Models
  Jiang, Q.; Ye, X.; Guo, Z.; Xia, Y.; Liu, Z.; Xu, J.; Jin, P.; Ju, F.; Xia, H.; Feng, S.; Liu, H.; Qin, T.; Deng, P.; Shao, S. — bioRxiv, 2026-01-03
  abs

• 📄 SeedProteo: Accurate De Novo All-Atom Design of Protein Binders
  Wei Qu, Yiming Ma, Fei Ye, Chan Lu, Yi Zhou, Kexin Zhang, Lan Wang, Minrui Gui, Quanquan Gu — arXiv, 2025-12-30
  abs

• 📄 Physio-DPO: Aligning Large Language Models with the Protein Energy Landscape to Eliminate Structural Hallucinations
  QiWei Meng — arXiv, 2026-01-02
  abs

• 🧬 Multimodal AI for Single cfDNA Profiling and Cancer Screening
  Wang, B.; Song, L.; Li, H.; Lin, N.; Xin, Y.; He, X.; Liu, W.; Liu, L.; Cui, J.; Li, X.; Mei, Y.; You, Q.; Zhu, H.; Zhao, G.; Chen, G.; Liu, J.; Zhu, B.; Sun, X.; Wu, X.; Gao, Z.; Ye, Y. — bioRxiv, 2025-12-30
  abs

• 🧬 Intrinsic DNA sequence determinants and tissue-specific regulation of human replication origins
  Veiner, M.; Salvadores, M.; Galvan-Femenia, I.; Supek, F. — bioRxiv, 2025-12-29
  abs

• 🧬 A machine learning framework for predicting and modulating condition-dependent protein phase separation
  Bae, J.; Kang, M.; Lee, D.; Yoon, K.-J.; Jung, Y. — bioRxiv, 2025-12-29
  abs

• 🧬 Fast, accurate construction of multiple sequence alignments from protein language embeddings
  Hoang, M.; Armour-Garb, I.; Singh, M. — bioRxiv, 2026-01-02
  abs

• 🧬 Viral Sentry AI (VirSentAI) - Automated Zoonotic Surveillance & Drug Repurposing Agent
  Munteanu, C. R.; Vazquez-Naya, J. M.; Tejera, E. — bioRxiv, 2025-12-29
  abs

• 🧬 NetMedGPT - A network medicine foundation model for extensive disease mechanism mining and drug repurposing
  Firoozbakht, F.; Suwer, S.; Elkjaer, M. L.; Handy, D. E.; Maier, A.; Li, J.; Lancashire, L.; Loscalzo, J.; Baumbach, J. — bioRxiv, 2026-01-04
  abs

• 🧬 Generative AI-based design of hybrid transcriptional activator proteins with new DNA-binding specificity
  Okuda, S.; Minami, A.; Aiko, M.; Uetsuka, K.; Miyazaki, K.; Ohtake, K.; Kiga, D. — bioRxiv, 2025-12-31
  abs

• 🧬 Combinatorial Optimization of Antibody Libraries via Constrained Integer Programming
  Hayes, C. F.; Goncalves, A.; Magana-Zook, S. A.; Pettit, J.; Solak, A. C.; Faissol, D.; Landajuela, M. — bioRxiv, 2025-12-31
  abs

• 🧬 Statistical design of a synthetic microbiome that suppresses diverse gut pathogens
  Oliveira, R.; McSpadden, E.; Pandey, B.; Lee, K.; Yousef, M.; Chen, R. Y.; Triebold, C.; Haro, F.; Aksianiuk, V.; Patel, R.; Shriram, K.; Ramanujam, R.; Kuehn, S.; Raman, A. — bioRxiv, 2025-12-31
  abs

• 🧬 BABAPPAlign: A Multiple Sequence Alignment Engine with a Learned Residue-Level Scoring Function
  Sinha, K. — bioRxiv, 2025-12-29
  abs

• 🧬 Bento: Benchmarking Classical and AI Docking on Drug Design-Relevant Data
  Pak, M. A.; Frolova, D.; Nikolenko, S. A.; Daulbaev, T.; Ryabchenko, D.; Litvin, A.; Gurevich, P.; Garifullin, K.; Shapeev, A.; Oseledets, I.; Ivankov, D. N. — bioRxiv, 2025-12-30
  abs

• 🧬 Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens
  Kim, J.; Correy, G. J.; Hall, B. W.; Rachman, M. M.; Mailhot, O.; Togo, T.; Gonciarz, R. L.; Jaishankar, P.; Neitz, R. J.; Hantz, E. R.; Doruk, Y. U.; Stevens, M. G. V.; Diolaiti, M. E.; Reid, R.; Gopalkrishnan, S.; Krogan, N. J.; Renslo, A. R.; Ashworth, A.; Shoichet, B. K.; Fraser, J. S. — bioRxiv, 2025-12-29
  abs

• 📄 HELM-BERT: A Transformer for Medium-sized Peptide Property Prediction
  Seungeon Lee, Takuto Koyama, Itsuki Maeda, Shigeyuki Matsumoto, Yasushi Okuno — arXiv, 2025-12-29
  abs

• 🧬 PeptiVerse: A Unified Platform for Therapeutic Peptide Property Prediction
  Zhang, Y.; Tang, S.; Chen, T.; Mahood, E.; Vincoff, S.; Chatterjee, P. — bioRxiv, 2026-01-03
  abs

• 📄 AceFF: A State-of-the-Art Machine Learning Potential for Small Molecules
  Stephen E. Farr, Stefan Doerr, Antonio Mirarchi, Francesc Sabanes Zariquiey, Gianni De Fabritiis — arXiv, 2026-01-02
  abs

• 🧬 CholBindNet: Interpretable Neural Networks for Cholesterol Binding Site Prediction
  Hernamdez, A.; Bhatt, A.; Revilla, I.; Levine, J. E.; Kosaraju, S. C.; Luo, Y. L. — bioRxiv, 2026-01-02
  abs