Weekly BioML Digest [June 08, 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)

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

• Flow matching for fast, multi-purpose structure-based ligand generation for drug discovery
  — Nature Computational Science, 2026-06-02
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• SyntheMol-RL: a flexible reinforcement learning framework for designing easily synthesizable antibiotics
  Swanson, Kyle, Liu, Gary, Catacutan, Denise B, McLellan, Stewart, Arnold, Autumn, Tu, Megan M, Brown, Eric D, Zou, James, Stokes, Jonathan M — Molecular Systems Biology, 2026-06-02
  abs

• DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning
  Xu, Xiaotong, Coratella, Ilaria, Reys, Victor, Bonvin, Alexandre MJJ — Communications Biology, 2026-06-02
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• EPIC: Multi-objective Guided Diffusion for Epitope Design in TCR-pMHC Complexes
  Yueshan Huang, Gufeng Yu, Letian Chen, Haoyang Luan, Yang Yang — Bioinformatics, 2026-06-04
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• Deep docking, part 2: an amplified DDU platform for ultra-large virtual screening
  Mohit Pandey, Tanvir Sajed, Ivan Semenov, Renfei Zhang, Fuqiang Ban, Ekaterina Manskaia, Martin Ester, Artem Cherkasov — Chemical Science, 2026-06-05
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• LLMs uncover 6M1@C60’s therapeutic targets: inhibiting atherosclerotic progression via NRF2/HO-1/GPX4 axis-mediated ferroptosis suppression
  Liu, Wenhao, Zhou, Guofeng, Gao, Xin, Li, Bo, Zhao, Yingjie — Journal of Nanobiotechnology, 2026-06-02
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• Optimizing drug combinations to resurrect the potency of failed antibody therapy against emerging COVID-19 variants using IDentif.AI
  Peter Wang, Kui You, Zi Wei Chia, L. Hooi, Li Ming Chong, D. Chye, Angelina Moh, Z. Lee, E. Lim, Alrick Zi Xin Kok, Stephen Chua, Isaiah Zhuang, Ella Chang, B. Tan, Gladys Tan, Shawn Vasoo, C. E. Chan, Edward Kai-Hua Chow, Dean Ho — Frontiers in Digital Health, 2026-06-02
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• Genome-wide modelling of plant transcription factor binding captures regulatory variants associated with phenotypic traits
  F. F. Peleke, S. Zumkeller, D. Schirmer, Gernot Schmitz, Thomas Hartwig, J. Engelhorn, Sergius Weizel, A. Schmitt, Tobias Jores, J. Szymanski — Nature Communications, 2026-06-03
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• Metab8D: a metabolic regulome network from multiomics and machine learning
  Schildcrout, Ryan, Smith, Kirk, Bhowmick, Rupa, Lu, Yuntao, Menon, Suraj, Kapadia, Minali, Kurtz, Emily, Coffeen-Vandeven, Anya, Nelakuditi, Srikar, Chandrasekaran, Sriram — Communications Biology, 2026-06-02
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• ProSiteHunter: A Unified Framework for Sequence‐Based Prediction of Protein‐Nucleic Acid and Protein‐Protein Binding Sites
  Dongliang Hou, Qihang Zhen, Zexin Lv, Xinyue Cui, Suhui Wang, Minghua Hou, Zhan Zhou, Xiaogen Zhou, Guijun Zhang — Advanced Science, 2026-06-02
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• A multiscale, Bayesian inference approach to augment mechanistic models of cell signaling with machine-learning predictions of binding affinity
  H. Huber, Stacey D. Finley — PLOS Computational Biology, 2026-06-05
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• NbBayesLM: bayesian prediction of nanobody thermostability using protein language model
  F. S. Shishir, Rokunuzjahan Rudro, Bishnu Sarker, Cuncong Zhong, S. Shomaji — Frontiers in Bioinformatics, 2026-06-03
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• Exploring the conformational landscape of adenylate kinase and beyond with protein folding models
  Bhasin, Aryan, Delaunay, Antoine, Saccon, Francesco, Fu, Yunguan — Scientific Reports, 2026-06-01
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• Relevance of 3D Rotationally Equivariant Neural Networks for Predicting Protein-Ligand Binding Affinities
  Li, Gaili, Yuan, Yongna, Zhang, Ruisheng — Interdisciplinary Sciences: Computational Life Sciences, 2026-06-01
  abs

• A Bond-Level Sequence Framework for Molecular Representation Learning with Structural Constraints
  Haoran Fan, Haoqiang Qi, Xin Huang, Dongyang Zhu, Na Wang, Ting Wang, Hongxun Hao — Molecules, 2026-06-05
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• A Reinforcement Learning-driven Transformer GAN for Molecular Generation
  Li, Chen, Tang, Huidong, Zhu, Ye, Yamanishi, Yoshihiro — Machine Intelligence Research, 2026-06-01
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• Accurate prediction of activity cliff compounds based on bioactivity profiles depends on assay nearest neighbor relationships
  Abe, Ryuto, Miyao, Tomoyuki, Bajorath, Jürgen — Journal of Cheminformatics, 2026-06-03
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• Oral bioavailability property prediction based on task similarity transfer learning
  Zeng, Chen, Xu, Chengcheng, Liu, Yingxu, Jiang, Yunya, Zheng, Lidan, Liu, Yang, Zhang, Yanmin, Chen, Yadong, Liu, Haichun, Gu, Rui — Molecular Diversity, 2026-06-01
  abs

• Machine Learning Model for Predicting Molecular Surface Area and Volume Defined by the Kohn-Sham One-electron Potential
  Meng, Peiran, Feng, Jiayi, Song, Jiaqing, Kong, Xianghe, Zhao, Jian, Yu, Chunyang, Gong, Lidong — Chemical Research in Chinese Universities, 2026-06-01
  abs

• A dual-critic network architecture for personalized tumor treatment under a dynamical tumor model
  Weiye Wang, Ru-ru Ma, Dakui Luo, Jie Chen, Xue Wang, Jie Wu, Zhendong Gao — Physica Scripta, 2026-06-02
  abs

🧬 Preprints (arXiv + bioRxiv)

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

• 📄 AlloGen: Conformation-Selective Binder Generation with Differential State Scoring
  Hanqun Cao, Zachary Quinn, Aastha Pal, Sumi Kimura, Jingjie Zhang, Pheng Ann Heng, Pranam Chatterjee — arXiv, 2026-06-03
  abs

• 🧬 CryoDiff: An uncertainty-aware diffusion model for Cryo-EM map enhancement
  Wen, B.; He, B.; Cheng, Y.; Zhou, S.; Han, R.; Zhang, F. — bioRxiv, 2026-06-06
  abs

• 📄 AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design
  Sahil Rahman, Maxx Richard Rahman — arXiv, 2026-06-01
  abs

• 📄 EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning
  Mansoor Ahmed, Huirong Chai, Haoxin Wang, Hemanth Venkateswara, Murray Patterson — arXiv, 2026-06-02
  abs

• 📄 Structure-Aware Prediction of PROTAC-Mediated Protein Degradability via Graph Neural Networks
  Bryan Cheng, Austin Jin — arXiv, 2026-06-01
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• 📄 SpliceBind: Isoform-Aware Prediction of Binding Pocket Druggability
  Bryan Cheng, Austin Jin, Joshua Chang — arXiv, 2026-06-01
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• 🧬 scMTG reconstructs single-cell temporal dynamics with Markov transition generators
  Cui, X.; Wang, H.; Gao, Z.; Jiang, R.; Wong, W. H.; Liu, Q. — bioRxiv, 2026-06-06
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• 🧬 Decoding Hierarchical Cell-Cell Communication in Spatial Multi-Omics with CellSTIC
  Wang, S.; Wang, J.; Wang, J.; Yuan, Z.; Xu, Y. — bioRxiv, 2026-06-05
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• 🧬 IMAS enables target-aware integration of tumour multiomics to resolve communication-guided regulatory mechanisms
  Deyang, W.; Yamashiro, T.; Inubushi, T. — bioRxiv, 2026-06-05
  abs

• 🧬 Learning residue-level context for modeling protein-protein interactions
  Zhang, Z.; Yang, Z.; Liu, A.; Yu, K.-H.; Zhao, J.; Yang, Y.; Neale, B.; Chen, S. — bioRxiv, 2026-06-04
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• 📄 Uncertainty-Calibrated Diffusion for Reliable 3D Molecular Graph Generation
  Fang Wan, Jingxiang Qu, Yi Liu — arXiv, 2026-06-01
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• 📄 Plug-and-Play Guidance for Discrete Diffusion Models via Gradient-Informed Logit Correction
  Hongkun Dou, Zike Chen, Fengji Li, Hongjue Li, Yue Deng — arXiv, 2026-06-04
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• 📄 Generative Molecular Morphing for Flexible-Size Design via Unbalanced Optimal Transport
  Malte Franke, Stefan P. Schmid, Zarko Ivkovic, Kjell Jorner, Andreas Krause — arXiv, 2026-06-05
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• 📄 Equivariant Neural Belief Propagation
  Zehua Cheng, Wei Dai, Jiahao Sun — arXiv, 2026-06-04
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• 🧬 Species- and Topic-aware Representation Learning for Antimicrobial Peptide Discovery
  Padi, S.; Mondal, K.; Kaur, N.; Hoogerheide, D. P.; Heinrich, F.; Mihailescu, E.; Klauda, J. B.; Cardone, A.; Keyrouz, W. — bioRxiv, 2026-06-01
  abs

• 📄 Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling
  Keyue Qiu, Xintong Wang, Zhilong Zhang, Hao Zhou, Wei-Ying Ma — arXiv, 2026-06-01
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• 📄 Mos-Gen: A Generative Molecular Framework for Mosquito Insecticide Design
  Lina Wang, Yaning Cui — arXiv, 2026-06-01
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• 🧬 AI-Guided Structure-Aware Modeling and Thermal Proteomics Reveal Direct Demethylzeylasteral-ACLY Interaction
  Wang, Q.; Yu, N.; Song, Y.; Fan, X.; Tian, J.; Chang, S.; Guo, Y.; Tan, C. S. H.; Ji, H. — bioRxiv, 2026-06-01
  abs

• 🧬 Convergent genome- and gene-level constraints shape repeated environmental adaptation in grasses
  Hsu, S.-K.; Schulz, A. J.; Hale, C. O.; Costa-Neto, G.; Miller, Z. R.; stitzer, M. C.; Wrightsman, T.; Zhai, J.; Lai, W.-Y.; Dawson, H. D.; Wang, Q.; AuBuchon-Elder, T. M.; Brindisi, L. J.; Oren, E.; Luo, Y.; Konadu, B. A.; Ojeda-Rivera, J. O.; Pennell, M.; Kellogg, E. A.; Romay, M. C.; Buckler, E. S. — bioRxiv, 2026-06-03
  abs

• 📄 Cross-scale spatially-aware generative modeling of transcriptomic programs underlying neurodegenerative brain organization
  Krishnakumar Vaithianathan — arXiv, 2026-06-04
  abs