Weekly BioML Digest [May 04, 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)

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

• Genome modelling and design across all domains of life with Evo 2
  Brixi, Garyk, Durrant, Matthew G., Ku, Jerome, Naghipourfar, Mohsen, Poli, Michael, Sun, Gwanggyu, Brockman, Greg, Chang, Daniel, Fanton, Alison, Gonzalez, Gabriel A., King, Samuel H., Li, David B., Merchant, Aditi T., Nguyen, Eric, Ricci-Tam, Chiara, Romero, David W., Schmok, Jonathan C., Taghibakhshi, Ali, Vorontsov, Anton, Yang, Brandon, Deng, Myra, Gorton, Liv, Nguyen, Nam, Wang, Nicholas K., Pearce, Michael T., Simon, Elana, Adams, Etowah, Amador, Zachary J., Ashley, Euan A., Baccus, Stephen A., Dai, Haoyu, Dillmann, Steven, Ermon, Stefano, Guo, Daniel, Herschl, Michael H., Ilango, Rajesh, Janik, Ken, Lu, Amy X., Mehta, Reshma, Mofrad, Mohammad R. K., Ng, Madelena Y., Pannu, Jaspreet, Ré, Christopher, John, John, Sullivan, Jeremy, Tey, Joseph, Viggiano, Ben, Zhu, Kevin, Zynda, Greg, Balsam, Daniel, Collison, Patrick, Costa, Anthony B., Hernandez-Boussard, Tina, Ho, Eric, Liu, Ming-Yu, McGrath, Thomas, Powell, Kimberly, Pinglay, Sudarshan, Burke, Dave P., Goodarzi, Hani, Hsu, Patrick D., Hie, Brian L. — Nature, 2026-04-30
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• eSIG-Net: an interaction language model that decodes the protein code of single mutations
  Pan, Xingxin, Shrawat, Aditya, Raghavan, Sidharth, Dong, Chuanpeng, Yang, Yuntao, Li, Zhao, Zheng, W. Jim, Eckhardt, S. Gail, Wu, Erxi, Fuxman Bass, Juan I., Jarosz, Daniel F., Chen, Sidi, McGrail, Daniel J., Sheynkman, Gloria M., Huang, Jason H., Sahni, Nidhi, Yi, S. Stephen — Nature Methods, 2026-04-29
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• DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model
  Xu, Tingjun, Yang, Yuwei, Zhu, Ruixin, Lin, Weili, Li, Jixuan, Zheng, Yan, Zhang, Peng, Zhang, Guoqing, Zhao, Guoping, Jiao, Na — Nature Computational Science, 2026-04-30
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• Improving protein-ligand complex generation with force field guidance
  Lai, Helen, Wang, Tingyu, Sirelkhatim, Hassan, Eaton, Joe, Huang, Howard, Rees, Brad, Engkvist, Ola, Janet, Jon Paul, Wang, Xiaoyun, Tibo, Alessandro — Journal of Cheminformatics, 2026-05-02
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• Benchmarking co-folding methods to predict the structures of covalent protein–ligand complexes
  Zhang, Tong-han, Zhu, Jin-tao, Huang, Zhi-xian, Xie, Juan, Pei, Jian-feng, Lai, Lu-hua — Acta Pharmacologica Sinica, 2026-05-01
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• Augmented prediction of multi-species protein–RNA interactions using evolutionary conservation of RNA-binding proteins
  He, Jiale, Zhou, Tong, Hu, Lu-Feng, Jiao, Yuhua, Wang, Junhao, Yan, Shengwen, Jia, Siyao, Chen, Qiuzhen, Zhu, Wentao, Zhang, Jilin, Jia, Mutian, Li, Yuanning, Wang, Xianwei, Wang, Yangming, Yang, Yucheng T., Sun, Lei — Nature Communications, 2026-04-27
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• Pharmacology knowledge graphs enable drug repurposing without chemical structure information
  Abo-Dahab, Youssef, Hernandez, Ruby, Duran, Ismael Caleb Arechiga — Discover Artificial Intelligence, 2026-04-28
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• Deep Learning-Based Protein Half-Life Prediction for Identifying Rate-Limiting Enzymes in Metabolic Pathways to Alleviate Bottleneck Reactions
  Yunhyeok Lee, Jun Ren, Jingyu Lee, Minh Thi-Hong Tran, Yu-Kyung Kim, Youngseop Chang, So-Hee Oh, Hyang-Mi Lee, D. Na — Journal of Microbiology and Biotechnology, 2026-04-28
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• Physics-informed deep learning for molecular solubility prediction: integrating thermodynamic constraints with neural network architectures
  Amiri, Masoud — Scientific Reports, 2026-04-27
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• A Comprehensive Dataset of Chemical Reactions Covering Second and Third Row Elements with Million-Scale Quantum Chemical Calculations
  Lee, Kyunghoon, Kang, Sungwoo, Kang, Beomgyu, Son, Won-Joon, Lee, Seungmin, Kim, Dae Sin, Kim, Woo Youn — Scientific Data, 2026-04-29
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• Experimentally validated deep learning control of protein aggregation
  Cima, Vojtech, Kunka, Antonin, Planas-Iglesias, Joan, Grakova, Ekaterina, Havlasek, Martin, Subramanian, Madhumalar, Beloch, Michal, Marek, Martin, Slaninova, Katerina, Damborsky, Jiri, Prokop, Zbynek, Bednar, David, Martinovic, Jan — Communications Chemistry, 2026-04-28
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• Hypervariable loop profiling decodes sequence determinants of antibody stability
  Wan, Yue, Liang, Jiahao, Dai, Yile, Srinivasan, Karthik, Billesbølle, Christian, Zhu, Ju-Fen, Shin, Jung-Eun, Paul, Steffanie, Marks, Debora, Song, Yun S., Myers, Benjamin R., Koehl, Antoine, Manglik, Aashish — Nature Structural & Molecular Biology, 2026-04-30
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• Accelerating natural product discovery with linked MS-genomics and language/transformer-based models
  Tay, Dillon W. P., Koh, Winston, Ang, Shi Jun, Wong, Zicong Marvin, Lim, Yi Wee, Heng, Elena, Ng, Yu Hung, Yeo, Naythan Z. X., Adaikkappan, Krishnan, Wong, Fong Tian, Lim, Yee Hwee — npj Antimicrobials and Resistance, 2026-04-30
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• Integration of in vitro and in silico approaches enables prediction of drug-induced liver injury
  Geci, René, Sayin, Ahenk Zeynep, Schaller, Stephan, Kuepfer, Lars — Archives of Toxicology, 2026-05-01
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• plasmaCHORD: A Machine Learning Approach to Distinguish Clonal Hematopoiesis–Derived Variants in Liquid Biopsies from Patients with Solid Tumors
  J. Canzoniero, D. Rabizadeh, I. Ziakas, Jaime Wehr, A. Balan, Amna Jamali, Blair V. Landon, L. Sivapalan, S. Scott, Gavin Pereira, V. Lam, C. Hann, C. Lovly, Jessica Tao, P. Forde, Joseph C. Murray, M. Sausen, G. Meijer, G. Vink, R. Fijneman, E.J.T. M.A. I.H.J.T. A.I. J.W.T. A.W. M.P. R. J. J.J.B. F Belt Davidis de Hingh de Vos Dekker Haringhuizen H, E. Belt, M. A. Davidis, I. D. de Hingh, A. De Vos, J. Dekker, A. Haringhuizen, M. Hendriks, R. Hoekstra, J. Jansen, Jacob Janssen, F. Jeurissen, F. Kloppenberg, J. Konsten, M. Koopman, M. Los, P. Nieboer, Nandette Peters, J. Pruijt, R. Rietbroek, A. Schiphorst, R. Schrauwen, J. Schreinemakers, L. Simkens, D. W. Sommeijer, H. Stockmann, Koen Talsma, F. Terheggen, M. Tjin‐A‐Ton, Liselot Valkenburg, H. van Cruijsen, J. van der Bilt, A. Van Der Velden, Joyce M. van Dodewaard, Teo van Voorthuizen, W. Vles, D. Zimmerman, V. Velculescu, J. Phallen, R. Scharpf, Valsamo Anagnostou — Clinical Cancer Research, 2026-05-01
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• EpitopeGNN: A Graph Neural Network for Influenza A Virus Hemagglutinin Subtype Classification Based on 3D Structure
  A. Timofeev, Alexander Anufriev, O. Ergashev, I. Isakova-Sivak — BioMedInformatics, 2026-04-28
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• MS-ConTab: Multi-Scale Contrastive Learning of Mutation Signatures for Pan-Cancer Representation and Stratification
  Yifan Dou, Adam Khadre, Ruben C. Petreaca, Mirzaei Golrokh — Bioinformatics, 2026-04-28
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• 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, 2026-04-27
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• Hybrid deep learning model (E2BNet) combining ESM2 and BiLSTM for 8-state protein secondary structure prediction
  Droba, Diganta Das, Banu, Ayesha, Sami, Miftiaz Inti, Hossain, Riad, Chowdhury, Mahfuzulhoq — Discover Applied Sciences, 2026-04-27
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• PRGNet: a Parallel Residual Graph Network for enhanced drug-target binding affinity prediction
  Liu, Jing, Mehmood, Aamir, Liu, Haiqi, Liu, Yishu, Wei, Dongqing, Li, Daixi — BMC Genomics, 2026-04-28
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🧬 Preprints (arXiv + bioRxiv)

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

• 🧬 Programming Biomolecular Interactions with All-Atom Generative Model
  Kong, X.; Chen, J.; Zhang, Z.; Li, G.; Zhu, Q.; Wei, L.; Li, M.; Shi, Y.; Dai, W.; Zhang, Z.; Tan, W.; Jiao, R.; Wang, X.; Zheng, J.; Yu, Z.; Wu, Q.; Guo, Z.; Zhang, L.; Li, W.; Huang, Q.; Zhu, T.; Wang, X.; Huang, W.; She, Y.; Zhang, J.; Liu, Y.; Liu, K.; Ma, J. — bioRxiv, 2026-04-30
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• 📄 MIMIC: A Generative Multimodal Foundation Model for Biomolecules
  Siavash Golkar, Jake Kovalic, Irina Espejo Morales, Samuel Sledzieski, Minhuan Li, Ksenia Sokolova, Geraud Krawezik, Alberto Bietti, Claudia Skok Gibbs, Roman Klypa, Shengwei Xiong, Francois Lanusse, Liam Parker, Kyunghyun Cho, Miles Cranmer, Tom Hehir, Michael McCabe, Lucas Meyer, Rudy Morel, Payel Mukhopadhyay, Mariel Pettee, Helen Qu, Jeff Shen, David Fouhey, Hadi Sotoudeh, Vikram Mulligan, Pilar Cossio, Sonya M. Hanson, Alisha N. Jones, Olga G. Troyanskaya, Shirley Ho — arXiv, 2026-04-27
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• 🧬 Learning the All-Atom Equilibrium Distribution of Biomolecular Interactions at Scale
  Wang, Y.; Xu, Y.; Li, W.; Yu, H.; Tan, W.; Li, S.; Huang, Q.; Chen, N.; Wu, X.; Wu, Q.; Liu, K. — bioRxiv, 2026-04-29
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• 🧬 Generative design of sequence specific DNA binding proteins
  Sehgal, E.; Politanska, Y.; Mitra, R.; Kim, P. T.; Gonzalez Rodriguez, N.; Warrier, T.; Kubaney, A.; Morishita, A.; Quijano, R.; Butcher, J.; Krishna, R.; Pecoraro, R.; Belmont, B.; Roullier, N.; Goreshnik, I.; Vafeados, D. K.; Kwon, P.; Ramarao, R.; Taipale, J.; Glasscock, C. J.; Baker, D. — bioRxiv, 2026-04-27
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• 🧬 Pan-cancer virtual spatial transcriptomics from routine histology with Phoenix
  Tran, M.; Gindra, R. H.; Putze, P.; Senbai, K.; Palla, G.; Kos, T.; Falcomata, C.; Wang, C.; Guo, R.; Boxberg, M.; Berclaz, L. M.; Lindner, L. H.; Bergmayr, L.; Knoesel, T.; Jurmeister, P.; Klauschen, F.; Homicsko, K.; Gottardo, R.; Eckstein, M.; Matek, C.; Mock, A.; Theis, F. J.; Saur, D.; Peng, T. — bioRxiv, 2026-04-29
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• 🧬 Aiki-GeNano: Multi-Stage Preference Optimization for Generative Design of Developable Nanobodies
  Meda, R. S.; Doshi, J.; Iyer, E.; Shastry, S.; Mysore, V. — bioRxiv, 2026-05-01
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• 🧬 Advancing ab initio genome annotation with OrionGeno
  Liu, L.; Cai, X.; Wang, S.; Deng, Y.; Wu, Y.; Pan, Y.; Wang, J.; Zhang, C.; Xia, H.; Tan, N.; Su, K.; Liu, Y.; Zhou, X.; Liu, L.; Wei, T.; Zhang, Y.; Li, Q.; Li, Y.; Yin, P.; Xu, X. — bioRxiv, 2026-04-29
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• 🧬 Reconstructing True 3D Spatial Omics at Single-Cell Resolution
  Yang, Y.; Luo, Y.; Zhang, K.; Bu, Y.; Xia, Z.; Peng, H.; Yan, R.; Liu, Q.; Chen, Y.; Shen, L.; Chen, E. — bioRxiv, 2026-05-01
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• 🧬 Scalable machine learning improves resistance prediction and identifies novel determinants in Mycobacterium tuberculosis
  Serajian, M.; Lotfollahi, M.; Green, O.; Smith, K.; Marini, S.; Prosperi, M.; Boucher, C. — bioRxiv, 2026-04-29
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• 📄 Learning biophysical models of gene regulation with probability flow matching
  Suryanarayana Maddu, Victor Chardès, Michael J. Shelley — arXiv, 2026-04-27
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• 📄 Computational Design and Experimental Validation of Photoactive PARP1 Inhibitors
  Simon Axelrod, Miroslav Kašpar, Kristýna Jelínková, Markéta Šmídková, Erika Bartůňková, Sille Štěpánová, Eugene Shakhnovich, Václav Kašička, Martin Dračínský, Zlatko Janeba, Rafael Gómez-Bombarelli — arXiv, 2026-04-27
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• 🧬 Reference-free compound identification using computational prediction of molecular properties and multi-dimensional spectrometric measurements: a fentanyl case study
  Harrilal, C. P.; Hollerbach, A. L.; Ciesielski, D.; Schultz, K. J.; Overstreet, R.; Rice, P. S.; King, E.; Nguyen, J.; Ross, D. H.; Lin, V. S.; Deng, G. Y.; Brayfindley, E.; Webb-Robertson, B.-J.; Raugei, S.; Ibrahim, Y. M.; Ewing, R. G.; Metz, T. — bioRxiv, 2026-04-27
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• 🧬 MissAlignment Teaches Itself Better Cryo-ET Tilt-Series Alignment by Making It Worse
  Chaillet, M. L.; van Loenhout, J.; Leung, M. R.; Burt, A.; Tegunov, D. — bioRxiv, 2026-05-02
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• 🧬 Designing biochemical circuits with tree search
  Bhamidipati, P. S.; Thomson, M. — bioRxiv, 2026-05-03
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• 📄 Towards A Generative Protein Evolution Machine with DPLM-Evo
  Xinyou Wang, Liang Hong, Jiasheng Ye, Zaixiang Zheng, Yu Li, Shujian Huang, Quanquan Gu — arXiv, 2026-04-30
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• 📄 Hyper-Dimensional Fingerprints as Molecular Representations
  Jonas Teufel, Luca Torresi, André Eberhard, Pascal Friederich — arXiv, 2026-04-30
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• 📄 VQ-SAD: Vector Quantized Structure Aware Diffusion For Molecule Generation
  Farshad Noravesh, Reza Haffari, Layki Soon, Arghya Pal — arXiv, 2026-05-01
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• 🧬 Overcoming systematic data biases enables accurate prediction of enzyme kcat fold-changes for computational protein design
  Rousset, Y.; Kroll, A.; Lercher, M. — bioRxiv, 2026-04-30
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• 🧬 Knowledge Inclusive Machine Learning for Disease Gene Prioritisation
  Gamage, C. J.; Xia, Y.; Rupasinghe, R.; Senevirathne, 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, 2026-05-02
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• 🧬 UshEffect-3D: Structure-informed Classification of USH2A Missense Variants for Inherited Retinal Disease
  Choudhary, D.; Portelli, S.; Ascher, D. B. — bioRxiv, 2026-04-27
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