Weekly BioML Digest [June 15, 2026]

Machine Learning × Computational Biology paper compilation

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

Feedback? Email me at biomldigest@gmail.com.

📚 Peer-Reviewed Journals (Top 20)

192 matched filters -> 20 selected after LLM relevance + novelty ranking.

• Single‐Sequence Deep Learning Delivers Crystal‐Quality Models of Covalent K‐Ras G12 Hotspot Complexes
  Sungwon Jung, Qinheng Zheng, K. Shokat — Iubmb Life, 2026-06-13
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• Void-X: A generative void-filling model for predicting atomic packing in proteins.
  Jing Yang, Junying Yuan, James J. Chou — Proceedings of the National Academy of Sciences of the United States of America, 2026-06-09
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• Pushing the Limits of One-Dimensional NMR Spectroscopy for Automated Structure Elucidation Using Artificial Intelligence.
  Frank Hu, Jonathan M. Tubb, Dimitris Argyropoulos, S. Golotvin, M. Elyashberg, Grant M. Rotskoff, M. Kanan, T. Markland — Journal of chemical information and modeling, 2026-06-09
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• Quantitative prediction of siRNA complexation by ionizable drugs enables their codelivery in nanoparticles
  Kai V Slaughter, Mickael Dang, E. Donders, Austin H. Cheng, Gary Tom, Xiang Olivia Li, Sangwoo Han, Eric S Y Chiu, O. Roland, Alán Aspuru-Guzik, Molly S. Shoichet — Science Advances, 2026-06-12
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• PathTIGR: A pathway topology-informed graph representation learning framework for immunotherapy response prediction
  Xiangmei Li, Yalan He, Jiashuo Wu, Ziyi Wang, Xilong Zhao, Yongbao Zhang, Bingyue Pan, Yujie Tang, Junwei Han — Science Advances, 2026-06-10
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• Overcoming Data Starvation: Automated Virtual Reaction Exploration and Machine Learning Discovery of p-Block Metal Catalysts for Borrowing Hydrogen.
  Zhe Chen, Xiaoyu Zhou, Chuanyi Xiong, Yubang Liu, Ruzhao Chen, Fuyi Yang, Huayu Liang, Jiaxin Lin, Ji Su, Yinwu Li, Zhuofeng Ke — Angewandte Chemie, 2026-06-11
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• Comprehensive multi-omics and single-cell analysis reveals a ferroptosis signature associated with tumor microenvironment remodeling and therapeutic decision-making across pan-cancer
  Yanan Qu, Qiuxia Wei, Chaoling Wu, Nigmat Rahim, Jiahao Luo, Jinhai Deng, Wenping Hu, Jing Liu, Liqun Wang, Xiaoyan Lin, Jinyuan Xiao, Zining Yu, Changjian Yan, Xiaoni Liu, Xiaoliang Yuan, Jianlin Tong, Jing Wang, Mingxia Zhu, Ping Yang, Yingtong Chen, Shuang Gao, Hongsen Zhang, Haibo Zhou, Qilong Tan, W. Wan, Hongmei Jing, Weilong Zhang — International Journal of Surgery, 2026-06-10
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• PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.
  Xu Zhang, Songyan Xue, Jing Geng, Xiehuizhi Wen, Lingwei Lai, Lvwen Huang, Jiantao Yu — Journal of computational biology : a journal of computational molecular cell biology, 2026-06-09
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• CMA-DTI: a cross-modal fusion and attentive interaction network for interpretable drug-target interaction prediction
  Chi Qin, Denggao Zheng, Ziyang Wang, Yu Li, Jingrui Cao, Houchun Qiu, Hongxing Kan, Liping Sun, Yu Liu, Jili Hu — Frontiers in Bioinformatics, 2026-06-11
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• Diffusion-enhanced Fine-grained Cross Semantic Fusion for Drug-disease Association Prediction.
  Shijie Zhang, Xiangmei Cao, Xianhao Huo, Xin Wang, Zhenhua Yu, Fang Du — IEEE journal of biomedical and health informatics, 2026-06-09
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• Machine Learning-Enhanced Ultrasensitive Immuno-CRISPR Array Facilitates Early Diagnosis of Alzheimer's Disease by Detecting Multiple Plasma Biomarkers.
  Liding Zhang, Changwen Yang, Qian Yao, Xuewei Du, Shuai Ding, Yaoqiang Shi, Can Sheng, Ming Wang, Ying Han, Haiming Luo — Advanced science, 2026-06-09
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• NToxSEM: Enhancing prediction of neurotoxic peptides and neurotoxins using a stacked ensemble‐based multimodal framework
  Watshara Shoombuatong, N. Schaduangrat, S. H. Mahmud, Saeed Ahmed — Protein Science : A Publication of the Protein Society, 2026-06-09
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• Identification of G4-regulated immune-related drug targets for prostate cancer based on G4 screen and machine learning
  Liu Ge, Yue Hou, Xuan Huang, Jiawei Zhang, Lin Yao, Saisai Chen, Likai Mao, Wei Ning, Han Liang, Nini Shi, Changbin Yang, Dongfang Jiang, Yuanji Shen, Bing Zheng, Chuanjun Shu, Minhao Zhang — Frontiers in Immunology, 2026-06-10
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• Deep learning-based prediction of gene expression from histopathology identifies NR5A1 as a candidate biomarker and druggable target in high-grade serous ovarian carcinoma
  Prakash Lingasamy, Marta Ostrowska-Leśko, Pantelis Tsakalis, Naisarg Patel, Ilias Chamatidis, Sajitha Lulu Sudhakaran, J. Kubik, M. Bobiński, N. Lagaros, A. Salumets, V. Modhukur — Journal of Ovarian Research, 2026-06-11
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• Artificial intelligence-guided MOF immobilization of Leloir glycosyltransferases for enhanced catalytic efficiency.
  Mengting Chang, Yuan Ji, Qiu Sun, Meng Qiao, Jie Zheng, Xing Zhang — Colloids and surfaces. B, Biointerfaces, 2026-06-09
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• Librarian of Alexandria: A Modular Chemical Data Extraction Pipeline to Compare LLM Performance.
  Morgan Grougan, J. Subasinghe, M. Hix, Alice R. Walker — Journal of chemical information and modeling, 2026-06-09
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• BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool.
  Vicente Ramos, Sundous Hussein, Mohamed Abdel-Hafiz, Arunangshu Sarkar, Weixuan Liu, K. Kechris, R. Bowler, Leslie A Lange, F. Banaei-Kashani — Bioinformatics, 2026-06-11
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• Digital Hydrogel Fluorescent-Enhancing Microspheres via CRISPR/Cas12a for Amplification-Free Relative Quantification of Nucleic Acids.
  Xueer Yin, Qiangyuan Xiong, Taowei Shu, Sichen Yan, Jun Zhao, Zhenyu Wang, Guoqing Deng, Yong Liu, Ling Zhu, Cancan Zhu — Analytical chemistry, 2026-06-09
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• Integrated Pharmacophore, Docking, Machine Learning, and Molecular Dynamics Approach for the Discovery and Validation of LuxS Quorum-Sensing Inhibitors to Combat Antibiotic Resistance.
  Mariyam Nawaz, Mahmood Ahmed, K. Raheem, M. Mughram, Muhammad Jadoon Khan, K. Alzahrani, M. Muddassar — ChemPlusChem, 2026-06-10
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• Data‐driven insights into photocatalytic dye degradation: Ensemble learning and SHAP ‐based mechanistic interpretation
  M. T. Amin — Journal of Chemical Technology & Biotechnology, 2026-06-11
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🧬 Preprints (arXiv + bioRxiv)

84 matched filters -> 20 selected after LLM relevance + novelty ranking.

• 🧬 Combinatorial docking and molecular generation to navigate over 100-billion molecules for prospective ligand discovery
  Zhang, J.; Yang, C.; Zhang, Y.; Chen, X.; Lam, B.; Bryant, C.; Pidathala, S.; Wang, Y.; Moroz, Y.; Radchenko, D.; Alon, A.; Lee, C.-H.; Zhang, Z.; Lyu, J. — bioRxiv, 2026-06-11
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• 🧬 HoloCell: A Generative Foundation Model for Holistic Cellular Modeling
  Jiang, Q.; Li, Z.; Hu, B.; Bie, Y.; Li, K.; Li, Q.; Jin, P.; He, Y.; Deng, P.; Wang, Z.; Chen, X.; Qin, T.; Liu, H.; Jiang, R.; Yin, Q. — bioRxiv, 2026-06-11
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• 📄 OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction
  Danning Jiang, Zheming An, Yalong Zhao, Lipeng Lai — arXiv, 2026-06-11
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• 🧬 SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology
  Gupta, A.; Wefers, Z.; Kahnert, K.; Hansen, J. N.; Misra, M. K.; Leineweber, W. D.; Cesnik, A.; Lu, D.; Axelsson, U.; Ballllosera Navarro, F.; Altman, R. B.; Karaletsos, T.; Lundberg, E. — bioRxiv, 2026-06-08
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• 🧬 ProtGPT3: an Open-source family of Promptable and Aligned Protein Language Models
  Garibbo, M.; Boxo Corominas, G.; Stocco, F.; Illanes Vicioso, R.; Middendorf, L.; Ferruz, N. — bioRxiv, 2026-06-08
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• 🧬 Controlling metal-carbonate phase, form, and function through de novo protein design
  Kwon, P. S.; Li, X.; Yu, L. T.; Pyles, H.; Lewis, T. H.; Weidle, C.; Borst, A. J.; Bodinger, C. C.; Kang, A.; Nguyen, H.; Mendoza, J.; Carr, K. D.; Coventry, B.; Hsia, Y.; Molnar, Z.; Li, D.; Zhang, B.; Cossairt, B. M.; Zhang, S.; Bera, A. K.; De Yoreo, J.; Baker, D. — bioRxiv, 2026-06-11
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• 📄 MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback
  Zehong Wang, Yijun Ma, Connor R. Schmidt, Tianyi Ma, Weixiang Sun, Ziming Li, Xiaoguang Guo, Chuxu Zhang, Matthew J. Webber, Yanfang Ye — arXiv, 2026-06-11
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• 📄 Flexible Flows for Biological Sequence Design
  Yogesh Verma, Dani Korpela, Harri Lähdesmäki, Vikas Garg — arXiv, 2026-06-09
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• 📄 GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction
  Emily Nguyen, Yongchan Hong, Harsh Toshniwal, Yan Liu, Andreas Luttens — arXiv, 2026-06-09
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• 📄 Probabilistic Contrastive Pretraining for Multi-task ADME Property Prediction
  Yifan Xue, Srimukh Prasad Veccham, Saee Paliwal, Tyler Shimko, Micha Livne — arXiv, 2026-06-09
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• 🧬 Deciphering cross-omics complexity of tissues via diagonal integration of unpaired spatial multi-omics data
  Zhou, X.; Kangning, D.; Xiao, J.; Chen, L.; Zhang, S. — bioRxiv, 2026-06-12
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• 🧬 Robust integration of weakly anchored spatial multi-omics
  Wang, C.; Liu, Y.; Wang, Z.; Sun, P.; Li, Z.; Li, J.; Wang, X.; Chen, K.; Zou, Q.; Daoliang, Z.; Hu, Z.; Du, Y.; Qian, B.; Feng, X.; Yuan, Z.; Guan, R. — bioRxiv, 2026-06-14
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• 🧬 TaxoFormer: Hierarchical Transformer for Predicting the Full Taxonomic Lineage of Protein Sequences
  Parsa, M.; Azimian, K.; Wei, K. Y. — bioRxiv, 2026-06-09
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• 🧬 Decoding the Grammar of Protein-Protein Interaction Interfaces with Multimodal Representations
  Gardinazzi, Y.; Villegas Garcia, E. N.; Senci, S.; Di Vora, D.; Feltrin, A.; Cuturello, F. — bioRxiv, 2026-06-09
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• 📄 Interpretable enzyme function prediction via sparse autoencoder features of ESMC across the microbial protein universe
  Yue Hu, Wanyu Cheng, Junqing Wang, Yingchao Liu — arXiv, 2026-06-10
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• 📄 Uncertainty Estimation for Molecular Diffusion Models
  Paul Seij, Christian A. Naesseth, Stephan Mandt, Metod Jazbec — arXiv, 2026-06-11
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• 📄 Smoothing Dark Areas in Molecular Latent Diffusion
  Xi Wang, Jiahan Li, Yuxuan Xia, Yingcheng Wu, Shaoyi Zheng, Shengjie Wang — arXiv, 2026-06-11
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• 📄 Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction
  Peng-Fei Sun, Chuan-Xian Ren, Hong Yan — arXiv, 2026-06-12
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• 📄 Curvature-Guided Geometric Representation for Protein-Ligand Binding Affinity Prediction
  Shuai Li, Chuan-Xian Ren, Yuhao Li, Ziqi Huang, Yue Pan, Mingzhe Tang, Hong Yan — arXiv, 2026-06-12
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• 📄 PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion
  Junming Zhang, Siyu Yi, Wei Ju, Zhonghui Gu — arXiv, 2026-06-12
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