Weekly BioML Digest [October 13, 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 were queried for new papers published in the past week [October 06, 2025 - October 13, 2025].
• Found 7459 new arXiv papers and 1565 new bioRxiv.
• 16 arXiv papers and 104 bioRxiv papers matched keyword filters.
• 30 papers are included in this digest after ChatGPT relevance+novelty reranking.

Here are your top 30 papers:

• 🧬 Base-editing a single missense mutation in A20 enhances CAR-T cell efficacy
  Blaisdell, A.; Bachl, S.; Sandoval, L. R.; Ching, C.; Bowman, C. J.; Kale, N.; Prabandham, M.; Diolaiti, M.; Havig, C.; Advincula, R.; Lenci, N.; Li, Z.; Yamashita, E.; Wang, C. H.; Zhang, S.; Liu, Q.; Achacoso, P.; Stibor, D.; Oynebraten, I.; Seo, J.; Ashworth, A.; Marson, A.; Ye, C. J.; Malynn, B. A.; Eyquem, J.; Carnevale, J.; Ma, A. — bioRxiv:immunology, 2025-10-06
  abs · pdf

• 📄 Protenix-Mini+: efficient structure prediction model with scalable pairformer
  Bo Qiang, Chengyue Gong, Xinshi Chen, Yuxuan Zhang, Wenzhi Xiao — q-bio.QM, 2025-10-13
  abs · pdf

• 🧬 FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling
  Zhu, J.; Shi, Y.; Bi, R.; Jin, P.; Liu, C.; Zhang, Z.; Huang, H.; Guo, Z.; Hu, P.; Ju, F.; Huang, L.; Tai, X.; Li, C.; Gao, K.; Wei, X.; Xia, H.; Zhang, J.; Min, Y.; Wang, Z.; Wang, Y.; He, L.; Liu, H.; Qin, T. — bioRxiv:molecular biology, 2025-10-10
  abs · pdf

• 🧬 Unified Sampling and Ranking for Protein Docking with DFMDock
  Chu, L.-S.; Sarma, S.; Xu, D.; Gray, J. J. — bioRxiv:bioinformatics, 2025-10-08
  abs · pdf

• 📄 Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
  Zishen Zhang, Xiangzhe Kong, Wenbing Huang, Yang Liu — cs.LG, 2025-10-12
  abs · pdf

• 🧬 Towards a universal foundation model for biobank-scale human genome variation
  Xu, A. G.; Xu, Y.; Xing, Y.; Luo, P.; Yang, J.; Bai, Y.; Tang, K. — bioRxiv:genomics, 2025-10-11
  abs · pdf

• 🧬 RNA sequence design and protein-DNA specificity prediction with NA-MPNN
  Kubaney, A.; Favor, A. H.; McHugh, L.; Mitra, R.; Pecoraro, R.; Dauparas, J.; Glasscock, C.; Baker, D. — bioRxiv:biochemistry, 2025-10-08
  abs · pdf

• 🧬 Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning
  Seitz, E.; McCandlish, D. M.; Kinney, J. B.; Koo, P. — bioRxiv:genomics, 2025-10-08
  abs · pdf

• 🧬 Protein Hunter: exploiting structure hallucination within diffusion for protein design
  Cho, Y.; Rangel, G.; Bhardwaj, G.; Ovchinnikov, S. — bioRxiv:molecular biology, 2025-10-10
  abs · pdf

• 📄 PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
  Sazan Mahbub, Souvik Kundu, Eric P. Xing — q-bio.QM, 2025-10-12
  abs · pdf

• 📄 ProteinAE: Protein Diffusion Autoencoders for Structure Encoding
  Shaoning Li, Le Zhuo, Yusong Wang, Mingyu Li, Xinheng He, Fandi Wu, Hongsheng Li, Pheng-Ann Heng — cs.LG, 2025-10-12
  abs · pdf

• 🧬 SLAE: Strictly Local All-atom Environment for Protein Representation
  Chen, Y.; Lu, T.; Zhao, C.; Wayment-Steele, H. K.; Huang, P. — bioRxiv:bioinformatics, 2025-10-06
  abs · pdf

• 🧬 GREmLN: A Cellular Graph Structure Aware Transcriptomics Foundation Model
  Zhang, M.; Swamy, V.; Cassius, R.; Dupire, L.; Kanatsoulis, C.; Paull, E.; AlQuraishi, M.; Karaletsos, T.; Califano, A. — bioRxiv:bioinformatics, 2025-10-11
  abs · pdf

• 🧬 Evolutionary and geometric signatures reveal ligand-binding sites across proteomes
  Tarasi, S.; Malo, L.; Molina, A. — bioRxiv:bioinformatics, 2025-10-07
  abs · pdf

• 🧬 Paraplume: A fast and accurate paratope prediction method provides insights into repertoire-scale binding dynamics
  Athenes, G.; Woolfe, A.; Mora, T.; Walczak, A. M. — bioRxiv:bioinformatics, 2025-10-06
  abs · pdf

• 🧬 DeepEmbCas9: Cas9 coevolution and sgRNA structural information for CRISPR-Cas9 cleavage activity prediction
  Mak, J. K.; Minary, P. — bioRxiv:bioinformatics, 2025-10-08
  abs · pdf

• 🧬 SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process
  Cai, J.; Chen, Y.; Fang, L.; Zhong, W.; Yuan, G.-C.; Ma, P. — bioRxiv:bioinformatics, 2025-10-08
  abs · pdf

• 🧬 Leveraging protein representations to explore uncharted fold spaces with generative models
  Miao, Y.; Pacesa, M.; georgeon, s.; Schmidt, J.; Lu, T.; Huang, P.; Correia, B. — bioRxiv:bioinformatics, 2025-10-10
  abs · pdf

• 🧬 Learning Protein Representations with Conformational Dynamics
  Kalifa, D.; Horvitz, E.; Radinsky, K. — bioRxiv:bioinformatics, 2025-10-06
  abs · pdf

• 📄 Reasoning-Enhanced Large Language Models for Molecular Property Prediction
  Jiaxi Zhuang, Yaorui Shi, Jue Hou, Yunong He, Mingwei Ye, Mingjun Xu, Yuming Su, Linfeng Zhang, Linfeng Zhang, Guolin Ke, Hengxing Cai — cs.LG, 2025-10-11
  abs · pdf

• 🧬 Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation
  Luo, E.; Wei, L.; Hao, M.; Zhang, X.; Liu, Q. — bioRxiv:bioinformatics, 2025-10-08
  abs · pdf

• 📄 Hierarchical Bayesian Flow Networks for Molecular Graph Generation
  Yida Xiong, Jiameng Chen, Kun Li, Hongzhi Zhang, Xiantao Cai, Wenbin Hu — cs.LG, 2025-10-11
  abs · pdf

• 📄 Trustworthy Retrosynthesis: Eliminating Hallucinations with a Diverse Ensemble of Reaction Scorers
  Michal Sadowski, Tadija Radusinović, Maria Wyrzykowska, Lukasz Sztukiewicz, Jan Rzymkowski, Paweł Włodarczyk-Pruszyński, Mikołaj Sacha, Piotr Kozakowski, Ruard van Workum, Stanislaw Kamil Jastrzebski — cs.LG, 2025-10-12
  abs · pdf

• 📄 Protein as a Second Language for LLMs
  Xinhui Chen, Zuchao Li, Mengqi Gao, Yufeng Zhang, Chak Tou Leong, Haoyang Li, Jiaqi Chen — cs.LG, 2025-10-13
  abs · pdf

• 📄 Fast and Interpretable Protein Substructure Alignment via Optimal Transport
  Zhiyu Wang, Bingxin Zhou, Jing Wang, Yang Tan, Weishu Zhao, Pietro Liò, Liang Hong — q-bio.QM, 2025-10-12
  abs · pdf

• 📄 Enhancing Diffusion-Based Sampling with Molecular Collective Variables
  Juno Nam, Bálint Máté, Artur P. Toshev, Manasa Kaniselvan, Rafael Gómez-Bombarelli, Ricky T. Q. Chen, Brandon Wood, Guan-Horng Liu, Benjamin Kurt Miller — physics.chem-ph, 2025-10-13
  abs · pdf

• 🧬 Cancer target discovery enabled by transcriptome-based virtual CRISPR screening
  Sadagopan, A.; Li, B.; Li, J.; Cui, Y.; Deodhar, R.; Yang, D.; Wu, Y.; Konda, P.; Biji, C.; Thapa, D. R.; Thakur, M.; Weiss, C.; Choueiri, T.; Cheah, J.; Doench, J.; Drapkin, B. J.; Viswanathan, S. — bioRxiv:cancer biology, 2025-10-13
  abs · pdf

• 🧬 Generative design of antibody Fc-variants with synthetic and programmable functional profiles
  Irvine, E. B.; Bikias, T.; Stamkopoulos, E.; Frei, L.; Schuermann, N.; Warrender, A. K.; Schmid, H.; Coukos, D.; Yang, H.; Minot, M.; Kelton, W.; Reddy, S. T. — bioRxiv:bioengineering, 2025-10-11
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• 📄 ST2HE: A Cross-Platform Framework for Virtual Histology and Annotation of High-Resolution Spatial Transcriptomics Data
  Zhentao Liu, Arun Das, Wen Meng, Yu-Chiao Chiu, Shou-Jiang Gao, Yufei Huang — q-bio.QM, 2025-10-13
  abs · pdf

• 🧬 Calibration-free single-frame super-resolution fluorescence microscopy
  Dostalova, A.; Vasinka, D.; Starek, R.; Jezek, M. — bioRxiv:molecular biology, 2025-10-13
  abs · pdf