Weekly BioML Digest [May 18, 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)

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

• A generative artificial intelligence approach for peptide antibiotic optimization
  Torres, Marcelo D. T., Zeng, Yimeng, Wan, Fangping, Maus, Natalie, Gardner, Jacob, de la Fuente-Nunez, Cesar — Nature Machine Intelligence, 2026-05-13
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• Cell-free chromatin state tracing reveals disease origin and therapy responses
  Chen, Xubin, Meng, Xiaoxuan, Zhang, Weilong, Zhang, Xiawei, Zhang, Yaping, Yang, Ping, Liu, Yan, Bao, Fang, Li, Sen, Wang, Jing, Yan, Changjian, Li, Chunyuan, Zhang, Lingke, Hao, Xiaoyu, Liu, Jia, Sun, Jing, Wang, Zhengting, Tian, Yu, Zhu, Liqing, Hou, Yan, Liu, Zongchao, Li, Wenqing, Mi, Lan, Qi, Xinyu, Yue, Yanzhu, Du, Peng, Chen, Guoqiang, Zheng, Junke, Dou, Liping, Jing, Hongmei, He, Aibin — Nature, 2026-05-14
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• Large-scale discovery, analysis and design of protein energy landscapes
  Ferrari, Állan J. R., Dixit, Sugyan M., Thibeault, Jane, Garcia, Mario, Houliston, Scott, Ludwig, Robert W., Notin, Pascal, Phoumyvong, Claire M., Martell, Cydney M., Jung, Michelle D., Tsuboyama, Kotaro, Carter, Lauren, Arrowsmith, Cheryl H., Guttman, Miklos, Rocklin, Gabriel J. — Nature, 2026-05-13
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• SmileyLlama: modifying large language models for directed chemical space exploration
  Cavanagh, Joseph M., Sun, Kunyang, Gritsevskiy, Andrew, Bagni, Dorian, Wang, Yingze, Bannister, Thomas D., Head-Gordon, Teresa — Nature Computational Science, 2026-05-11
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• Learning the PTM code through a coarse-to-fine mechanism-aware framework
  Zhang, Jingjie, Cao, Hanqun, Gao, Zijun, Wang, Yu, Li, Shaoning, Xu, Jun, Tan, Cheng, Zhu, Jun, Hsieh, Chang-Yu, Gu, Chunbin, Heng, Pheng Ann — Nature Communications, 2026-05-15
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• De novo design of peptides localizing at the interface of biomolecular condensates
  Schneider, Timo N., Gil-Garcia, Marcos, Bühler, Marco A., Santos, Lucas F., Faltova, Lenka, Guillén-Gosálbez, Gonzalo, Arosio, Paolo — Nature Communications, 2026-05-16
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• HESpotEx: a dual-stream deep learning framework for spot-level gene expression prediction from histological images
  Yin, Wang, Peng, Qin, Meng, Fanyi, Wan, You, Zhang, Weilong, Zhou, Yuan — Nature Computational Science, 2026-05-15
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• Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery
  Wang, Nan, Yeh, Hugh, Lai, Ben, Perera, Jason, Jude, Kevin M., Risch, Isabel, Um, Joy, Chen, Xiaojing, Xiang, Xinyu, Wang, Chunyu, Liu, Liu Daisy, Yang, Xinbo, Paley, Michael A., Khan, Aly A., Garcia, K. Christopher — Nature Biotechnology, 2026-05-13
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• Multiscale machine learning molecular mechanics for mechanism and stereoselectivity of Diels-Alderase catalysis
  Wang, Xujian, Tang, Haocheng, Wu, Xiongwu, Brooks, Bernard R., Wang, Junmei, Li, Wan-Lu — Nature Communications, 2026-05-13
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• Aberration-aware 3D localization microscopy via self-supervised neural-physics learning
  Fu, Shuang, Shi, Wei, Katrukha, Eugene A., Chen, Xi, Fei, Yue, Fang, Ke, Wang, Ruixiong, Zhang, Tianlun, Ma, Donghan, Li, Yiming — Nature Communications, 2026-05-16
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• PromoterAtlas: decoding regulatory sequences across Gammaproteobacteria using a transformer model
  Coppens, Lucas, Ledesma-Amaro, Rodrigo — Nature Communications, 2026-05-15
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• An SE(3)-equivariant and dynamic multi-modal engine advancing from PTM site prediction to network understanding
  Lin, Yiyu, Wu, Jiahui, Yang, Sen, Wang, Yan — Communications Chemistry, 2026-05-11
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• SPECTRAL: An Intelligent and Ultra‐Sensitive Photonic Hydrogel Platform for Biomarker‐Based Cancer Prediction
  Junjie Qin, Xingxing Yang, Jia Guo, Chengrui Hu, Shao Q. Yao, Chengxi Li — Angewandte Chemie International Edition, 2026-05-12
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• Critical evaluation of drug response prediction models with DrEval
  Bernett, Judith, Iversen, Pascal, Picciani, Mario, Wilhelm, Mathias, Baum, Katharina, List, Markus — Nature Communications, 2026-05-12
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• scArchon: a scalable benchmarking framework for assessing single-cell perturbation models
  Radig, Jean, Droit, Robin, Doncevic, Daria, Li, Albert, Bui, Duc Thien, Herfurth, Luis, Kühn, Thaddeus, Herrmann, Carl — Genome Biology, 2026-05-12
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• Multimodal interpretable deep learning for transcriptome-informed precision oncology and drug mechanism analysis
  Qu, Ning, Tong, Xiaochu, Wang, Zhaokun, Shao, Panpan, Zhang, Lehan, Zhang, Xiaoya, Xing, Yuxin, Liu, Jin, Wang, Yitian, Zhang, Sulin, Zheng, Mingyue, Li, Xutong — npj Digital Medicine, 2026-05-13
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• Protein language models accurately predict polymorphic peptide–modulated NK cell receptor–HLA class I interaction strengths
  Abdallah AlShafey, Madeline Nelson, Mubasher Hassan, A. Kloczkowski, William Ray, Salim I. Khakoo, Jayajit Das — Science Advances, 2026-05-12
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• Accurate proteome-wide prediction of enzymes and catalytic sites using graph deep learning and protein language model
  Yui-Lun Ng, Xiaomei Wang, Yingqi Li, Junzhe Huang, H. Lai, J. Y. Chan, Billy Wai-Lung Ng, Ho Ko, Ka‐Wai Kwok — GigaScience, 2026-05-13
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• CDMed: Medication Recommendation via Causal Inference and Dual-Granularity Information Enhancement
  Jialei Liu, Haitao Wang, Jianfeng He — Electronics, 2026-05-13
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• Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population
  Zhou, Ziyun, Lamanna, Arianna, Halder, Rashi, Pansart, Emeline, Narayanasamy, Shaman, Boussoufa, Besma, Kerkour, Thamila, Wilmes, Paul, Williams, Evan — Microbiome, 2026-05-12
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🧬 Preprints (arXiv + bioRxiv)

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

• 🧬 ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications
  Qian, Q.; Peng, J.; Ma, D.; Liu, K.; Cheng, Y.; Deng, Y.; Zhao, J.; Su, S.; Yao, Y.; Qu, Y.; Fu, R.; Liu, J.; Zhao, M.; Xiao, Y.; Wang, K.; Wu, Y.; Wang, Y.; Xu, Q.; Wang, J.; Hay, D. C.; Ke, Y.; Wang, Y.; Shipston, M. J.; Chi, Y. — bioRxiv, 2026-05-11
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• 🧬 A Scalable Sign-Aware Multi-Omics Knowledge Graph Foundation Model for Mechanistic Drug Action and Clinical Response Predictions
  Mottaqi, M.; Zhang, S.; Adoremos, I.; Zhang, P.; Xie, L. — bioRxiv, 2026-05-11
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• 📄 CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography
  Minseo Kim, Huanghao Mai, Jay Shenoy, Alec Follmer, Gordon Wetzstein, Frederic Poitevin — arXiv, 2026-05-15
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• 📄 Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design
  Ziyu Xu, Zijian Zhang, Liang Wang, Zhiyuan Liu, Qiang Liu, Shu Wu, Liang Wang — arXiv, 2026-05-14
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• 🧬 A structure-informed evolutionary model for predicting viral immune escape and evolution
  Wang, C.; Zhang, L. — bioRxiv, 2026-05-11
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• 🧬 MuseDrift: Navigating Protein Evolutionary Manifolds with Conditional Discrete Diffusion
  Wang, C.; Wang, Y. — bioRxiv, 2026-05-12
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• 🧬 Simpatico: accurate and ultra-fast virtual drug screening with atomic embeddings
  Gaiser, J.; Wheeler, T. J. — bioRxiv, 2026-05-13
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• 🧬 CatIF-RL: Activity-Oriented Enzyme Sequence Design by Steered Inverse Protein Folding
  Li, Y.; Xiong, J.; Zhang, Y.; Cai, T.; Gong, X.; Wang, F. — bioRxiv, 2026-05-15
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• 🧬 Keeping SCORE enables interpretable uncertainty-aware classification from diffusion models for genomics
  Kuznets-Speck, B.; Jung, J.; Pholraksa, P.; Zhong, A.; Schwartz, L.; Prashnani, E.; Vaikuntanathan, S.; Goyal, Y. — bioRxiv, 2026-05-13
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• 🧬 Machine Learning-Driven Optimization of Specific, Compact, and Efficient Base Editors via Single-Round Diversification
  Ielanskyi, M.; Wang, M.; Scott, L.; Rieber, L.; Merrett, S.; Schimunek, J.; Mayr, A.; McDowell, I.; Klambauer, G.; Bowen, T. — bioRxiv, 2026-05-12
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• 📄 MetaGEM: Bottom-Up Reconstruction of Genome-Scale Metabolic Networks via Deep Enzyme-Metabolite Anchoring
  Weiyu Xiao, Jiangbin Zheng, Stan Z. Li — arXiv, 2026-05-14
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• 🧬 OmniGene-4: A Unified Bio-Language MoE Model with Router-Level Interpretability
  Wang, L. — bioRxiv, 2026-05-14
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• 📄 StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction
  Peiting Shi, Ningfeng Que, Xianzhe Huang, Xiaofei Wang, Jianzhong Jeff Xi — arXiv, 2026-05-15
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• 🧬 Integrating Diffusion and Liquid AI Models for Predicting Peptide Affinity from mRNA Display Selections
  Leaf, C. M.; Qi, P.; Gandhi, Y. P.; Jalali-Yazdi, F.; Ong, J. N.; Takahashi, T. T.; Kalia, R.; Roberts, R. W. — bioRxiv, 2026-05-11
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• 🧬 Knowledge Inclusive Machine Learning for Disease Gene Prioritisation
  Gamage, C. J.; Xia, Y.; Rupasinghe, R.; Seneviratne, S.; Senanayake, D.; Malepathirana, T.; Hevapathige, A.; Corbett, M.; O'Brien, T. J.; Petrou, S.; Berkovic, S. F.; Scheffer, I. E.; Gecz, J.; Bahlo, M.; Bennett, M. F.; Halgamuge, S. K. — bioRxiv, 2026-05-17
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• 🧬 pyTrance finds co-localizing RNAs in subcellular spatial transcriptomics data
  Strenger, L.; Cerda-Jara, C. A.; Karaiskos, N.; Rajewsky, N. — bioRxiv, 2026-05-11
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• 📄 ENSEMBITS: an alphabet of protein conformational ensembles
  Kaiwen Shi, Carlos Oliver — arXiv, 2026-05-13
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• 🧬 Improving Variant Effect Prediction by Steering Sparse Mechanistic Features in Protein Language Models
  Wang, M.; Yuan, M.; Vasilakos, A. V.; He, Y.; Ren, Z. — bioRxiv, 2026-05-15
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• 📄 Controllable Molecular Generative Foundation Models
  Yihan Zhu, Yuhan Liu, Weijiang Li, Tengfei Luo, Meng Jiang — arXiv, 2026-05-14
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• 📄 FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization
  Qingchuan Zhang, He Cao, Hao Li, Yanjun Shao, Zhiyuan Liu, Shihang Wang, Shufang Xie, Shenghua Gao, Xinwu Ye — arXiv, 2026-05-11
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