Weekly BioML Digest [March 23, 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)

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

• Manufacturing-aware generative models enable petascale synthesis of designed DNA
  Weinstein, Eli N., Gollub, Mattia G., Slabodkin, Andrei, Dobbs, Kerry, Cui, Xiao-Bing, Gardner, Cameron L., Grant, Ryan J., Gurung, Kristina, Bailey, Amira, Amin, Alan N., Church, George M., Wood, Elizabeth B. — Nature Biotechnology, 2026-03-17
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• Artificial intelligence-guided design of LNPs for in vivo targeted mRNA delivery via analysis of the spatial conformation of ionizable lipids
  Su, Lin-Jia, Wang, Nan-Nan, Luo, Rui, Ji, Zi-Han, Gu, Haiyan, Yang, Chao, Xu, Mo-Xi, Zhang, Juchen, Chen, Qinghua, Yu, Meng-Zhen, Li, Chenglin, Fan, Kelong, Mei, Lin, Zhao, Yuliang, Wang, Yi, Gao, Yurui, Wang, Hao, Lin, Yao-Xin — Nature Biomedical Engineering, 2026-03-18
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• Sample-efficient generative molecular design using memory manipulation
  Guo, Jeff, Chen, Junwu, GX-Chen, Anthony, Schwaller, Philippe — Nature Machine Intelligence, 2026-03-17
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• Functional protein design and enhancement with ontology reinforcement iteration
  He, Bing, Qin, Chenchen, Zhao, Yu, Huang, Long-Kai, Wu, Zihan, Wang, Fang, Wu, Fandi, Yang, Fan, Yao, Jianhua — Nature Communications, 2026-03-19
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• FineST: contrastive learning integrates histology and spatial transcriptomics for nuclei-resolved ligand-receptor analysis
  Li, Lingyu, Wang, Tianjie, Liang, Zhuo, Yu, Huajian, Ma, Stephanie, Yu, Lequan, Huang, Yuanhua — Nature Communications, 2026-03-16
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• High-resolution phage-host assignment through key proteins using large language models
  Du, Zhihua, Li, Min, Lin, Kaihuang, Xing, Bo, Ou, Yuehua, Lin, Zihao, Song, Wenchen, Chen, Jie, Li, Junhua, Li, Jianqiang, Xiao, Minfeng — Nature Communications, 2026-03-20
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• Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries.
  K. Antonopoulos, Olof Nordenstorm, Avlant Nilsson — PLoS computational biology, 2026-03-18
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• VEDA: Generation of 3D Molecules via Variance-Exploding Diffusion with Annealing
  Peining Zhang, Jinbo Bi, Minghu Song — Proceedings of the AAAI Conference on Artificial Intelligence, 2026-03-18
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• An end-to-end framework for reactivity in heterogeneous catalysis
  Morandi, Santiago, Loveday, Oliver, Renningholtz, Tim, Pablo-García, Sergio, Vargas-Hernández, Rodrigo A., Seemakurthi, Ranga Rohit, Sanz Berman, Pol, García-Muelas, Rodrigo, Aspuru-Guzik, Alán, López, Núria — Nature Chemical Engineering, 2026-03-19
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• ProAR: Probabilistic Autoregressive Modeling for Molecular Dynamics
  Kaiwen Cheng, Yutian Liu, Zhiwei Nie, Mujie Lin, Yanzhen Hou, Yiheng Tao, Chang Liu, Jie Chen, Youdong Mao, Yonghong Tian — Proceedings of the AAAI Conference on Artificial Intelligence, 2026-03-17
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• Beyond Conservation: Flexible Molecular Assembly with Unbalanced Diffusion Bridge
  Rongchao Zhang, Yiwei Lou, Yu Huang, Yi Xin, Yongzhi Cao, Hanping Wang — Proceedings of the AAAI Conference on Artificial Intelligence, 2026-03-18
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• Structural evolution of carbon frameworks realizes in vitro interfacial transport in metabolically reprogrammed senescent cells for senolysis
  Wang, Xuelian, Ma, Hanyu, Li, Yongqiang, Chen, Liangfeng, Ye, Caichao, Zhao, Yuhao, Wang, Hang, Fu, Wanting, Yu, Chen, Wang, Fei, Yang, Siwei, Kang, Yuli, Ding, Guqiao, Li, Zhen — Nature Communications, 2026-03-17
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• Multiscale-Aware Graph Embedding Approach Uncovers LC-61, a Potent Anti-Leishmania infantum Compound.
  Vinícius Alexandre Fiaia Costa, Alexandra Maria dos Santos Carvalho, R. Chelucci, Felipe da Silva Mendonça de Melo, Gustavo Santos Sandes Felizardo, Clarissa Alves Carneiro Bernardes, H. Martin, R. Braga, Sébastien Charneau, Eugene N. Muratov, A. Andricopulo, I. D. Bastos, B. J. Neves — Journal of chemical information and modeling, 2026-03-17
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• Graph Machine Learning Can Estimate Drug Concentrations in Whole Blood from Forensic Screening Results.
  Tetiana Lutchyn, M. Mardal, Michael Nedahl, Benjamin Ricaud — Analytical chemistry, 2026-03-18
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• Accurate Hydration Free Energy Calculations for Diverse Organic Molecules With a Machine Learning Force Field.
  Xiaowei Xie, John L. Weber, Mats Svensson, Ryne C. Johnston, Edward D Harder, Leif D Jacobson — Journal of chemical theory and computation, 2026-03-19
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• Evolutionary digital twin framework for optimal aminoglycoside dosing in neonates with suspected sepsis
  Prunella, Michela, Romano, Chiara, Borri, Alessandro, Altini, Nicola, Benedetto, Maria Domenica, Annaert, Pieter, Allegaert, Karel, Smits, Anne, Bevilacqua, Vitoantonio — npj Digital Medicine, 2026-03-21
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• Network model for alignment, stitching and slice-to-volume 3D reconstruction of large-scale spatially resolved slices
  Wang, Yu, Liu, Zaiyi, Ma, Xiaoke — Nature Communications, 2026-03-20
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• Dynamic Geometric Equivariant Network for Full-Atom Antibody Design
  Weihong Huang, Fengjie Yang, Qiang Zhang, Juan Liu — Proceedings of the AAAI Conference on Artificial Intelligence, 2026-03-17
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• DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design
  Yanting Li, Zikang Wang, Jiyue Jiang, Ziqian Lin, Dongchen He, Yuheng Shan, Yanruisheng Shao, Jiayi Li, Xiangyu Shi, Jiuming Wang, Yanyu Chen, Yimin Fan, Han Li, Yu Li — Proceedings of the AAAI Conference on Artificial Intelligence, 2026-03-17
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• EPO: Diverse and Realistic Protein Ensemble Generation via Energy Preference Optimization
  Yuancheng Sun, Yuxuan Ren, Zhaoming Chen, Xu Han, Kang Liu, Qiwei Ye — Proceedings of the AAAI Conference on Artificial Intelligence, 2026-03-17
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🧬 Preprints (arXiv + bioRxiv)

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

• 🧬 De novo design of metalloproteases for targeted amyloid-β cleavage
  Qu, Y.; Wang, C.; Zhu, H.; Wang, Y.; Cao, L. — bioRxiv, 2026-03-16
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• 🧬 AetherCell: A generative engine for virtual cell perturbation and in vivo drug discovery
  Xie, Z.; Li, W.; Chen, Y.; Peng, Z.; Xiang, L.; Wang, D. — bioRxiv, 2026-03-16
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• 🧬 X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models
  Wang, C.; Karimzadeh, M.; Ravindra, N. G.; Bounds, L. R.; Alerasool, N.; Huang, A. C.; Ma, S.; Gulbranson, D. R.; Cui, H.; Lee, Y.; Arjavalingam, A.; MacKrell, E. J.; Wilken, M. S.; Chen, J.; Herken, B. W.; Weber, J. A.; Onesto, M. M.; Gonzalez-Teran, B.; Leung, N. F.; Shi, S. Y.; Smith, B. J.; Lam, S. K.; Barner, A.; Wright, P.; Rumsey, E. M.; Kim, S.; Sit, R. V.; Litterman, A. J.; Chu, C.; Wang, B. — bioRxiv, 2026-03-20
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• 🧬 Learning Universal Representations of Intermolecular Interactions with ATOMICA
  Fang, A.; Desgagne, M.; Zhang, Z.; Zhou, A.; Loscalzo, J.; Pentelute, B. L.; Zitnik, M. — bioRxiv, 2026-03-16
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• 🧬 RNAElectra: An ELECTRA-Style RNA Foundation Model for RNA Regulatory Inference
  Ding, K.; Liu, L.; Parker, B.; Wen, J. — bioRxiv, 2026-03-17
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• 🧬 Single-Pass Discrete Diffusion Predicts High-Affinity Peptide Binders at >1,000 Sequences per Second across 150 Receptor Targets
  Watson, A. — bioRxiv, 2026-03-17
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• 🧬 Protein Diffusion Models as Statistical Potentials
  Roney, J.; Ou, C.; Ovchinnikov, S. — bioRxiv, 2026-03-18
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• 🧬 ProteinSage: From implicit learning to explicit structural constraints for efficient protein language modeling
  Shen, L.; Chao, L.; Liu, T.; Liu, Q.; Zhou, G.; Wang, H.; Dong, X.; Li, T.; Zhang, X.; Ni, J. — bioRxiv, 2026-03-19
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• 🧬 Enhancing non-local interaction modeling for ab initio biomolecular calculations and simulations with ViSNet-PIMA
  Cui, T.; Wang, Z.; Wang, T. — bioRxiv, 2026-03-20
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• 📄 Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention
  Jeffrey D. Varner — arXiv, 2026-03-16
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• 📄 Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
  Liang Shi, Jiarui Lu, Junqi Liu, Chence Shi, Zhi Yang, Jian Tang — arXiv, 2026-03-18
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• 📄 Generative Replica-Exchange: A Flow-based Framework for Accelerating Replica Exchange Simulations
  Shengjie Huang, Sijie Yang, Jianqiao Yi, Rui Zheng, Haocong Liao, Muzammal Hussain, Yaoquan Tu, Xiaoyun Lu, Yang Zhou — arXiv, 2026-03-18
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• 📄 RiboSphere: Learning Unified and Efficient Representations of RNA Structures
  Zhou Zhang, Hanqun Cao, Cheng Tan, Fang Wu, Pheng Ann Heng, Tianfan Fu — arXiv, 2026-03-20
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• 📄 Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids
  Lucas Ferraz, Ana F. Rodrigues, Pedro Giesteira Cotovio, Mafalda Ventura, Gabriela Silva, Ana Sofia Coroadinha, Miguel Machuqueiro, Catia Pesquita — arXiv, 2026-03-19
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• 🧬 ST-PARM: Pareto-Complete Inference-Time Alignment for Multi-Objective Protein Design
  Yin, R.; Shen, Y. — bioRxiv, 2026-03-19
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• 🧬 Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA
  Bian, B.; Zhang, Y.; Zhang, J.; Asai, K.; Saito, Y. — bioRxiv, 2026-03-20
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• 🧬 VarDCL: A Multimodal PLM-Enhanced Framework for Missense Variant Effect Prediction via Self-distilled Contrastive Learning
  Zhang, H.; Zheng, G.; Xu, Z.; Zhao, H.; Cai, S.; Huang, Y.; Zhou, Z.; Wei, Y. — bioRxiv, 2026-03-17
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• 📄 IgPose: A Generative Data-Augmented Pipeline for Robust Immunoglobulin-Antigen Binding Prediction
  Tien-Cuong Bui, Injae Chung, Wonjun Lee, Junsu Ko, Juyong Lee — arXiv, 2026-03-16
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• 🧬 HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism
  Davuluri, R. V.; Dutta, P.; Vaska, J.; Surana, P.; Sathian, R.; Chao, M.; Zhou, Z.; Liu, H. — bioRxiv, 2026-03-20
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• 🧬 HARVEST: Unlocking the Dark Bioactivity Data of Pharmaceutical Patents via Agentic AI
  Shepard, V.; Musin, A.; Chebykina, K.; Zeninskaya, N. A.; Mistryukova, L.; Avchaciov, K.; Fedichev, P. O. — bioRxiv, 2026-03-18
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