Weekly BioML Digest [February 16, 2026]

Machine Learning × Computational Biology paper compilation

Hey! It's your weekly digest of machine learning papers in CompBio and Drug Discovery.

This weeks digest contains only preprint section due to technical issues.

Feedback? Email me at biomldigest@gmail.com.

🧬 Preprints (arXiv + bioRxiv)

155 papers matched filters → 20 selected after LLM relevance + novelty ranking.

• 🧬 Designing AI-programmable therapeutics with the EDEN family of foundation models
  Munsamy, G.; Ayres, G.; Greco, C.; Kam, K.; Minto-Cowcher, G.; St John, J.; Bohnuud, T.; Bakalar, M.; Chow, W.; Pecoraro, R.; D.T. Torres, M.; Kollasch, A.; Leung, M.; Sirelkhatim, H.; Farina, F.; McGinnis, C.; Sridhar, S.; Anderson, D.; Oteri, F.; Taghibakhshi, A.; Dona, J.; Shimko, T.; Steenbeke, C.; Papadopoulos, A.; Krolick, M.; Spoendlin, F.; Gupta, P.; Kumar, S.; Bara, A.; Wilber, J.; Ferruz, N.; Rvachoc, T.; Wan, F.; Cao, H.; Lee, H.-S.; Mehta, J.; Chaleil, R.; Pereno, V.; Potti, S.; Emerson, C.; Dew, R. T.; Yang, K. K.; Nguyen, E.; Tadimeti, N.; Banfield, J. F.; Frame, A.; Bolton, E.; — bioRxiv, 2026-02-09
  abs

• 🧬 IntelliFold-2: Surpassing AlphaFold 3 via Architectural Refinement and Structural Consistency
  Qiao, L.; Yan, H.; Liu, G.; Guo, G.; Sun, S. — bioRxiv, 2026-02-10
  abs

• 🧬 Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics
  Feng, B.; Zhang, J.; Zhang, X.; Zhang, M.; Barth, P.; Liu, Z.; Li, Y. — bioRxiv, 2026-02-15
  abs

• 🧬 Disentangled multimodal evolutionary representations for cross-virus predictive modeling of antigenic change
  Zhang, Z.; Lin, Y.; Zhong, S.; Zhou, P.; Li, Y.; Yu, F. — bioRxiv, 2026-02-13
  abs

• 🧬 A Unified Framework for Model-Informed and Agentic RNA Design
  Riley, A. T.; Vlasity, M.; Becicka, W. M.; Huang, J. Z.; Pang, S.; Wong, W. W.; Grinstaff, M. W.; Green, A. A. — bioRxiv, 2026-02-09
  abs

• 🧬 AI-driven discovery and engineering of human endogenous nanocage proteins for mRNA delivery
  Xun, D.; Li, L.; Liu, Y.; Yang, Z.; Zou, J.; Liang, Q.; Li, K.; Zhu, Z.; Zhang, J.; Lang, L.; Liu, K.; Wang, X.; Tian, M.; Chen, G.; An, B.; Heng, P.-A.; Zhong, C. — bioRxiv, 2026-02-09
  abs

• 🧬 Generative AI Guided Design of High-Affinity T cell Receptors
  Min, M. R.; Li, T.; Onoguchi, K.; Mori, D.; Demachi-Okamura, A.; Warrell, J.; Machart, P.; Moesch, A.; Meiser, A.; Pait, I. G.; Muraoka, D.; Matsushita, H.; Paiardi, G.; Ferraz, M.; Bendjama, K. — bioRxiv, 2026-02-12
  abs

• 🧬 ChatDIA: A zero-shot large language model workflow for targeted analysis of data-independent acquisition mass spectrometry data
  Li, J.; Charkow, J.; Gao, M.; Li, J.; Rost, H. — bioRxiv, 2026-02-13
  abs

• 📄 Central Dogma Transformer II: An AI Microscope for Understanding Cellular Regulatory Mechanisms
  Nobuyuki Ota — arXiv, 2026-02-09
  abs

• 📄 dnaHNet: A Scalable and Hierarchical Foundation Model for Genomic Sequence Learning
  Arnav Shah, Junzhe Li, Parsa Idehpour, Adibvafa Fallahpour, Brandon Wang, Sukjun Hwang, Bo Wang, Patrick D. Hsu, Hani Goodarzi, Albert Gu — arXiv, 2026-02-11
  abs

• 🧬 Decoding the Molecular Language of Proteins with Evolla
  Zhou, X.; Han, C.; Zhang, Y.; Du, H.; Tian, J.; Su, J.; Liu, R.; Zhuang, K.; Jiang, S.; Gitter, A.; Liu, L.; Li, H.; Wu, M.; You, S.; Yuan, Z.; Ju, F.; Zhang, H.; Zheng, W.; Dai, F.; Zhou, Y.; Tao, Y.; Wu, D.; Shao, Z.; Liu, Y.; Lu, H.; Yuan, F. — bioRxiv, 2026-02-11
  abs

• 🧬 TM-Vec 2: Accelerated Protein Homology Detection for Structural Similarity
  Keluskar, A.; Batra, P.; Bezshapkin, V.; Morton, J. T.; Zhu, Q. — bioRxiv, 2026-02-09
  abs

• 🧬 Genetic variation shapes human mRNA translation and disease risk
  Wang, S.; Chen, C.; Xiao, X.; Wang, Z. — bioRxiv, 2026-02-12
  abs

• 🧬 SLECA: a single-cell atlas of systemic lupus erythematosus enabling rare cell discovery using graph transformer
  Duan, M.; Shi, Y.; Tian, H.; Wu, Q.; Wang, X.; Liu, B. — bioRxiv, 2026-02-12
  abs

• 🧬 Augmented prediction of multi-species protein--RNA interactions using evolutionary conservation of RNA-binding proteins
  He, J.; Zhou, T.; Hu, L.-F.; Jiao, Y.; Wang, J.; Yan, S.; Jia, S.; Chen, Q.; Zhu, W.; Zhang, J.; Jia, M.; Li, Y.; Wang, X.; Wang, Y.; Yang, Y. T.; Sun, L. — bioRxiv, 2026-02-11
  abs

• 🧬 A single-cell atlas and aging clock define biological age and risk-associated stem cell states in human hematopoiesis
  Chen, H.; Dong, P.; Xu, J.; Wang, G. — bioRxiv, 2026-02-13
  abs

• 🧬 Metadiffusion: inference-time meta-energy biasing of biomolecular diffusion models
  Lam, H. Y. I.; Pujalte Ojeda, S.; Brezinova, M.; Hanke, J.; Ong, X. E.; Mu, Y.; Vendruscolo, M. — bioRxiv, 2026-02-11
  abs

• 📄 Protein Language Model Embeddings Improve Generalization of Implicit Transfer Operators
  Panagiotis Antoniadis, Beatrice Pavesi, Simon Olsson, Ole Winther — arXiv, 2026-02-11
  abs

• 📄 Coarse-Grained Boltzmann Generators
  Weilong Chen, Bojun Zhao, Jan Eckwert, Julija Zavadlav — arXiv, 2026-02-11
  abs

• 📄 FlashSchNet: Fast and Accurate Coarse-Grained Neural Network Molecular Dynamics
  Pingzhi Li, Hongxuan Li, Zirui Liu, Xingcheng Lin, Tianlong Chen — arXiv, 2026-02-13
  abs