Weekly BioML Digest [April 20, 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)

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

• Phenotypic prediction of missense variants via deep contrastive learning
  Wen, Jun, Zeng, Sihang, Bonzel, Clara-Lea, Kobren, Shilpa Nadimpalli, Du, Jiangchuan, Chai, Yi, Wang, Hao, Zhu, Meng, Chen, Siwei, Leng, Fangwei, Zhang, Harrison G., Liao, Katherine P., Cho, Kelly, Kohane, Isaac S., Zitnik, Marinka, Pereira, Alexandre C., Liu, Jun S., Cai, Tianxi — Nature Biomedical Engineering, 2026-04-14
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• Steering semi-flexible molecular diffusion model for structure-based drug design with reinforcement learning
  Xudong Zhang, Sanqing Qu, Fan Lu, Jianmin Wang, Zhixin Tian, Shangding Gu, Yanping Zhang, Alois Knoll, Shaorong Gao, Guang Chen, Changjun Jiang — Science Advances, 2026-04-17
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• DualGPT-AB: a dual-stage generative optimization framework for therapeutic antibody design
  Xie, Dongna, Chen, Siyuan, Zeng, Xi, Lu, Dazhi, Jiao, Shaoqing, Xiao, Shuyuan, Liu, Jiaming, Hao, Jianye, Dai, Hui, Peng, Jiajie — Nature Computational Science, 2026-04-15
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• KIMMDY: a biomolecular reaction emulator
  Hartmann, Eric, Buhr, Jannik, Riedmiller, Kai, Ulanov, Evgeni, Schüpp, Boris N., Kiesewetter, Denis, Sucerquia, Daniel, Aponte-Santamaría, Camilo, Gräter, Frauke — Nature Communications, 2026-04-14
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• A multi-modal diffusion model with dual-cross-attention for multi-omics data generation and translation
  Luo, Erpai, Wei, Lei, Hao, Minsheng, Zhang, Xuegong, Liu, Qiao — Nature Communications, 2026-04-14
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• A sequence knowledge-guided deep learning method for single-cell multi-omics translation
  Zhao, Mengyuan, Li, Jiawei, Jiang, Yanlin, Yan, Jiahui, Tang, Xinyue, Liang, Cheng, Tang, Jijun, Guo, Fei — Genome Biology, 2026-04-14
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• DrugBLIP: Exploring the Protein-Molecule Interaction Mechanisms with a Multi-task Learning Graph Transformer
  Rubo Wang, Xingyu Gao, Peilin Zhao — Bioinformatics, 2026-04-15
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• Making invisible excited-state structures of pro-interleukin-18 visible by combining NMR and machine learning
  Jeffrey P. Bonin, Jin Sub Lee, Zi Hao Liu, Philip M. Kim, Lewis E. Kay — Proceedings of the National Academy of Sciences, 2026-04-17
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• DRUMBEAT temporally resolved interpretable machine learning model for characterizing state transitions in protein dynamics
  Manookian, Babgen, Mukhaleva, Elizaveta, Gogoshin, Grigoriy, Bhattacharya, Supriyo, Vaidehi, Nagarajan, Rodin, Andrei S., Branciamore, Sergio — Communications Biology, 2026-04-15
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• Deep learning inference of cell type-specific gene expression from breast tumor histopathology
  Wang, Andrew T., Dhruba, Saugato Rahman, Campagnolo, Emma M., Yao, Keluo, Jiang, Peng, Wang, Kun, Hoang, Danh-Tai, Ruppin, Eytan, Shulman, Eldad D. — npj Precision Oncology, 2026-04-16
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• iPalmT: a new paradigm for palmitoyltransferase discovery via end-to-end deep learning
  Li, Tengda, Li, Xiang — Oncogene, 2026-04-18
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• M-GNN: A Topology-Enhanced Multi-Modal Graph Neural Network for Cancer Driver Gene Prediction
  Lu Qin, Wen Zhu, Xinyi Liao, Yujing Zhang — Metabolites, 2026-04-16
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• Reconstructing cell-cell interaction network in single-cell spatial transcriptomics via directed heterogeneous graph autoencoder
  Jin-Xian Hu, Xiaoyong Pan, Yuan Ye, Hongbin Shen — Bioinformatics, 2026-04-18
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• Active Learning on Protein Language Model Embeddings Accelerates Rubisco Variant Discovery for Desired Traits
  James Young, Dillon Nelson, Liping Gu, Ruanbao Zhou — AI Chemistry, 2026-04-15
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• Abstract LB168: Advancing peptide-MHC binding prediction with JANUS through iterative multi-allele deconvolution and ensemble deep learning
  Alan Perez-Rathke, J. Balko, Jens Meiler — Cancer Research, 2026-04-17
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• Abstract LB003: Integrated computational design and cDNA display selection enable cyclic peptide radiopharmaceutical ligand discovery
  Josie Fieger, Braxton Bell — Cancer Research, 2026-04-17
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• Abstract LB027: AI guided engineering of pH responsive antibodies enables tumor selective targeting and improves the therapeutic index
  Qilin Yu, Mingchen Chen, Ying Lu, Yuxi Wang — Cancer Research, 2026-04-17
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• AI-guided discovery of the IRF4-PAICS-LDHA axis as a multitarget hub linking tumor metabolism to CD8+ T cell exhaustion in DLBCL
  Wang, Zeyuan, wang, Liye, Qian, Siyu, Zhang, Yue, Yang, Qing, Yang, Zhenzhen, Wu, Shaoxuan, Dong, Meng, Zhang, Zhiqi, Wei, Xufeng, Yang, Minglei, Meng, Hui, Liu, Enjie, Jiang, Guozhong, Zhang, Xudong, Li, Wencai, Chen, Qingjiang — npj Precision Oncology, 2026-04-16
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• CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms
  Yu, Yu-Huai, He, Guan-Liang, Yang, Tzu-Hsien — BioData Mining, 2026-04-14
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• A Unified Information Bottleneck Framework for Multimodal Biomedical Machine Learning
  Liang Dong — Entropy, 2026-04-14
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🧬 Preprints (arXiv + bioRxiv)

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

• 🧬 Enabling the prediction of phage receptor specificity from genome data
  Moriniere, L.; Noonan, A. J. C.; Kazakov, A.; Pena, M.; Svab, M.; Rivera-Lopez, E. O.; Maucourt, F.; Johnson, M. S.; Roux, S.; Koskella, B.; Deutschbauer, A. M.; Dudley, E. G.; Mutalik, V. K.; Arkin, A. P. — bioRxiv, 2026-04-19
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• 🧬 Efficient generation of epitope-targeted de novo antibodies with Germinal
  Mille-Fragoso, L. S.; Driscoll, C. L.; Wang, J. N.; Dai, H.; Widatalla, T. M.; Zhang, J. L.; Zhang, X.; Rao, B.; Feng, L.; Hie, B. L.; Gao, X. J. — bioRxiv, 2026-04-15
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• 🧬 Zero-Shot Generation of Protein Conformational Ensembles Through AlphaFold Latent Flooding
  QIAN, R.; Zhan, R.; Song, Z.; Huang, J. — bioRxiv, 2026-04-18
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• 📄 PRiMeFlow: Capturing Complex Expression Heterogeneity in Perturbation Response Modelling
  Zichao Yan, Yan Wu, Mica Xu Ji, Chaitra Agrahar, Esther Wershof, Marcel Nassar, Mehrshad Sadria, Ridvan Eksi, Vladimir Trifonov, Ignacio Ibarra, Telmo Felgueira, Błażej Osiński, Rory Stark — arXiv, 2026-04-15
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• 🧬 Hybrid Gated Fusion: A Multimodal Deep Learning Framework for Protein Function Annotation
  Zhou, Z.; Buchan, D. W. — bioRxiv, 2026-04-17
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• 🧬 Highly Accurate Estimation of the Fold Accuracy of Protein Structural Models
  Xie, L.; Ye, E.; Wang, H.; Zhang, T.; Zhen, Q.; Liang, F.; Liu, D.; Zhang, G. — bioRxiv, 2026-04-16
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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.; Shao, Y.; Lee, Y. J.; Lugo-Martinez, J. — bioRxiv, 2026-04-19
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• 🧬 TFBindFormer: A Cross-Attention Transformer for Transcription Factor-DNA Binding Prediction
  Liu, P.; Wang, L.; Basnet, S.; Cheng, J. — bioRxiv, 2026-04-15
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• 🧬 A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins
  Galvin, C. V.; Guo, A. B.; Chen, M. N.; Alfonso, I. L.; Grisingher, D.; Kretschmer, S.; Kranthi, D.; Kelly, M. J.; Kortemme, T. — bioRxiv, 2026-04-15
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• 🧬 Generative design of intrinsically disordered proteins based on conditioned protein language models: Data is the limit
  Carriere, L.; Huyghe, A.; Pajkos, M.; Bernado, P.; Cortes, J. — bioRxiv, 2026-04-16
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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, 2026-04-17
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• 🧬 PathwaySeeker: Evidence-Grounded AI Reasoning over Organism-Specific Metabolic Networks
  Oliveira Monteiro, L. M.; Chowdhury, N. B.; Oostrom, M.; McDermott, J. E.; Stratton, K. G.; Choudhury, S.; Bardhan, J. P. — bioRxiv, 2026-04-17
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• 🧬 LinkLlama: Enabling Large Language Model for Chemically Reasonable Linker Design
  Sun, K.; Wang, Y. E.; Purnomo, J. C.; Cavanagh, J. M.; Alteri, G. B.; Head-Gordon, T. — bioRxiv, 2026-04-16
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• 🧬 TB-Bench: A Systematic Benchmark of Machine Learning and Deep Learning Methods for Second-Line TB Drug Resistance Prediction
  VP, B.; Jaiswal, S.; Meshram, A.; PVS, D.; S C, S.; Narayanan, M. — bioRxiv, 2026-04-13
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• 🧬 VeloTrace Reconciles Divergent Velocity and Trajectory in Single-cell Transcriptomics with Deep Neural ODE
  Cheng, H.; Qiao, Y.; Feng, Y.; Wei, Y.; Li, J.; Cai, J.; Zheng, S.; Chen, S.; Li, G.; Simons, B. D.; Lian, Q.; Xin, H. — bioRxiv, 2026-04-13
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• 📄 BOAT: Navigating the Sea of In Silico Predictors for Antibody Design via Multi-Objective Bayesian Optimization
  Jackie Rao, Ferran Gonzalez Hernandez, Leon Gerard, Alexandra Gessner — arXiv, 2026-04-15
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• 📄 Pareto-Optimal Offline Reinforcement Learning via Smooth Tchebysheff Scalarization
  Aadyot Bhatnagar, Peter Mørch Groth, Ali Madani — arXiv, 2026-04-14
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• 📄 Scaffold-Conditioned Preference Triplets for Controllable Molecular Optimization with Large Language Models
  Yi Xiong, Liang Xiong, Xiaohong Ji, Sen Yang, Zhifeng Gao, Huaimin Wang, Kele Xu — arXiv, 2026-04-14
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• 📄 MolMem: Memory-Augmented Agentic Reinforcement Learning for Sample-Efficient Molecular Optimization
  Ziqing Wang, Yibo Wen, Abhishek Pandy, Han Liu, Kaize Ding — arXiv, 2026-04-14
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• 📄 CAGenMol: Condition-Aware Diffusion Language Model for Goal-Directed Molecular Generation
  Yanting Li, Zhuoyang Jiang, Enyan Dai, Lei Wang, Wen-Cai Ye, Li Liu — arXiv, 2026-04-13
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