Weekly BioML Digest [November 24, 2025]

Machine Learning × Computational Biology compilation from arXiv + bioRxiv

Hey! It's your weekly automated digest of machine learning papers in CompBio and Drug Discovery. Here is how it was created:

• Both arXiv and bioRxiv queried for new papers published in the past week [November 17, 2025 - November 23, 2025].
• Found 4512 new arXiv papers and 1206 new bioRxiv papers.
• 25 arXiv papers and 69 bioRxiv papers matched keyword filters.
• 30 papers are included in this digest after deduplication and ChatGPT relevance+novelty reranking.

Here are your top 30 papers:

• 📄 Unified all-atom molecule generation with neural fields
  Matthieu Kirchmeyer, Pedro O. Pinheiro, Emma Willett, Karolis Martinkus, Joseph Kleinhenz, Emily K. Makowski, Andrew M. Watkins, Vladimir Gligorijevic, Richard Bonneau, Saeed Saremi — cs.LG, 2025-11-19
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• 🧬 Targeting peptide-MHC complexes with designed T cell receptors and antibodies
  Motmaen, A.; Jude, K. M.; Wang, N.; Minervina, A.; Feldman, D.; Lichtenstein, M. A.; Ebenezer, A.; Correnti, C.; Thomas, P. G.; Garcia, K. C.; Baker, D.; Bradley, P. — bioRxiv:immunology, 2025-11-20
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• 🧬 Computational design of metalloproteases
  Chen, A.; Wu, K.; Choi, H.; Venkatesh, P.; Pellock, S. J.; Hanikel, N.; Coventry, B.; Kim, D.; Woodbury, S. M.; Ji, P.; Honda, S.; Li, X.; Gerben, S.; Chang, L.; Yan, X.; Hyman, A. A.; Hilvert, D.; Baker, D. — bioRxiv:biochemistry, 2025-11-21
  abs · pdf

• 🧬 Computational design of cysteine proteases
  Choi, H.; Coventry, B.; Bauer, M. S.; Venkatesh, P.; Chen, A.; Kim, D.; Bera, A. K.; Kang, A.; Nguyen, H.; Joyce, E.; Shankaran, B.; Thompson, T. R.; Gershon, J.; Shida, A. F.; Lee, G. R.; Hilvert, D.; Pellock, S. J.; Baker, D. — bioRxiv:biochemistry, 2025-11-22
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• 🧬 OPUS-ET: Resolving Compositional and Conformational Heterogeneities of Biomolecules in Cryo-Electron Tomography
  Luo, Z.; Chen, X.; Wang, Q.; Ma, J. — bioRxiv:molecular biology, 2025-11-23
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• 📄 Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models
  Xinzhe Zheng, Shiyu Jiang, Gustavo Seabra, Chenglong Li, Yanjun Li — q-bio.BM, 2025-11-18
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• 🧬 De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of Hydrogenase
  Sun, X.; Li, W.; Li, W.; Luo, H.; Xiao, Q.; Zhang, L.; Jiang, P.; Wu, G.; Zhang, L. — bioRxiv:biochemistry, 2025-11-19
  abs · pdf

• 🧬 RegFormer: A Single-Cell Foundation Model Powered by Gene Regulatory Hierarchies
  Hu, L.; Qin, H.; Zhang, Y.; Lu, Y.; Qiu, P.; Cao, L.; Jiang, W.; Feng, B.; Zhang, Y.; Chen, Q.; Shang, Y.; Xia, T.; Deng, Z.; Xu, X.; Fang, S.; Li, Y.; Zhang, Y. — bioRxiv:bioinformatics, 2025-11-19
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• 🧬 CONCERT predicts niche-aware perturbation responses in spatial transcriptomics
  Lin, X.; Kong, Z.; Ghosh, S.; Kellis, M.; Zitnik, M. — bioRxiv:bioinformatics, 2025-11-20
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• 🧬 SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data
  Zhou, H.; Chen, H.; Rudnick, Z.; Baalbaki, S. I.; Lee, Y. J.; Lugo-Martinez, J. — bioRxiv:bioinformatics, 2025-11-21
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• 🧬 ARCADIA Reveals Spatially Dependent Transcriptional Programs through Integration of scRNA-seq and Spatial Proteomics
  Rozenman, B.; Hoffer-Hawlik, K.; Djedjos, N.; Azizi, E. — bioRxiv:bioinformatics, 2025-11-21
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• 📄 FlexiFlow: decomposable flow matching for generation of flexible molecular ensemble
  Riccardo Tedoldi, Ola Engkvist, Patrick Bryant, Hossein Azizpour, Jon Paul Janet, Alessandro Tibo — cs.LG, 2025-11-21
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• 📄 Generating transition states of chemical reactions via distance-geometry-based flow matching
  Yufei Luo, Xiang Gu, Jian Sun — cs.LG, 2025-11-21
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• 🧬 STAMPS: Signal-peptide Transformer for Augmenting Mammalian Protein Secretion
  Gabrielli, J.; Esposito, M.; Briliute, J.; Burrell, M.; Thom, G.; Kontoravdi, C.; Ceroni, F. — bioRxiv:synthetic biology, 2025-11-20
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• 🧬 A Global Discovery of Antimicrobial Peptides in Deep-Sea Microbiomes Driven by an ESM-2 and Transformer-based Dual-Engine Framework
  Chen, B.; Mou, X.; Song, Z.; Lin, H.; Zhang, Y.; Li, J. — bioRxiv:bioinformatics, 2025-11-20
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• 🧬 Semantic-Aware Graph Embedding Approach Uncovers LC-61, a Potent Anti-Leishmania infantum Compound
  Costa, V. A. F.; Carvalho, A. M. d. S.; Chelucci, R. C.; Felizardo, G. S. S.; Bernardes, C. A. C.; Martin, H.-J.; Braga, R. d. C.; Charneau, S.; Muratov, E.; Andricopulo, A. D.; Bastos, I. M. D.; Neves, B. J. — bioRxiv:bioinformatics, 2025-11-20
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• 🧬 Supervised Deep Learning for Efficient Cryo-EM Image Alignment in Drug Discovery with cryoPARES
  Sanchez-Garcia, R.; Berndt, A.; Apelbaum, A.; Reeks, J.; Williams, P. A.; Poelking, C.; Deane, C.; Saur, M. — bioRxiv:bioinformatics, 2025-11-19
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• 🧬 PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms
  Zhai, J.; Gokaslan, A.; Hsu, S.-K.; Chen, S.-P.; Liu, Z.-Y.; Marroquin, E.; Czech, E.; Cannon, B.; Berthel, A.; Romay, C.; Pennell, M.; Kuleshov, V.; Buckler, E. S. — bioRxiv:bioinformatics, 2025-11-19
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• 🧬 The Human-In-the-Loop Drug Design Framework with Equivariant Rectified Flow
  Zhao, Y.; Huang, Y.; Peng, X.; Lin, H.; Xu, Q.; Shi, Y.; Liu, X.; Wang, Y.; Liu, Q.; Peng, J.; Ma, J. — bioRxiv:bioinformatics, 2025-11-21
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• 🧬 ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering
  Li, J.; Lai, H.-s.; Liang, L.; Du, S.; Tang, S.; Kingsford, C. — bioRxiv:bioinformatics, 2025-11-21
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• 📄 PepEVOLVE: Position-Aware Dynamic Peptide Optimization via Group-Relative Advantage
  Trieu Nguyen, Hao-Wei Pang, Shasha Feng — cs.LG, 2025-11-21
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• 📄 AssayMatch: Learning to Select Data for Molecular Activity Models
  Vincent Fan, Regina Barzilay — cs.LG, 2025-11-20
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• 🧬 Quantum and Classical Graph Convolutional Neural Networks for Protein Ligand Dissociation Constant Prediction
  Salamatov, A.; Atluri, G. — bioRxiv:bioinformatics, 2025-11-22
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• 🧬 MicroSplit: Semantic Unmixing of Fluorescent Microscopy Data
  Ashesh, A.; Carrara, F.; Zubarev, I.; Galinova, V.; Croft, M.; Pezzotti, M.; Gong, D.; Casagrande, F.; Colombo, E.; Giussani, S.; Restelli, E.; Cammarota, E.; Battagliotti, J. M.; Klena, N.; Di Sante, M.; Adhikari, R.; Feliciano, D.; Pigino, G.; Taverna, E.; Harschnitz, O.; Maghelli, N.; Scherer, N. F.; Dalle Nogare, D. E.; Dechamps, J.; Pasqualini, F.; Jug, F. — bioRxiv:bioinformatics, 2025-11-19
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• 🧬 SHEST: Single-cell-level artificial intelligence from haematoxylin and eosin morphology for cell type prediction and spatial transcriptomics reconstruction
  Jeong, H.; Oh, J.; Lee, D.; Kang, J. H.; Choi, Y.-L. — bioRxiv:bioinformatics, 2025-11-19
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• 🧬 Deep Learning-Augmented Stimulated Raman Imaging for Cell-Type-Specific Metabolic Profiling in Live Neuronal Co-Cultures
  Lin, L.-E.; Bi, X.; Colazo, A.; Wang, H.; Wei, L. — bioRxiv:neuroscience, 2025-11-18
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• 🧬 CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs
  Kolodziej, A. R.; Abulnaga, S. M.; Ovchinnikov, S. — bioRxiv:biophysics, 2025-11-18
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• 🧬 Generating Hybrid Proteins with the MSA-Transformer
  Tule, S.; Davis, S.; Koludarov, I.; Mora, A.; Boden, M. — bioRxiv:bioinformatics, 2025-11-20
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• 🧬 Multimodal Cross-Attentive Graph-Based Framework for Predicting In Vivo Endocrine Disruptors
  Santos, E. S. d. A.; Felizardo, G. S. S.; da Silva, A. C. G.; Martin, H.-J.; Muratov, E. N.; Braga, R. d. C.; Neves, B. J. — bioRxiv:pharmacology and toxicology, 2025-11-19
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