Clay weekly context brief for the Quantitative Biology category (ISO week 2026-W44). Clay tracks publications from the Quantitative Biology feed list. Below are recent items from this category, each with its source and a short description of what the publication covers when one is available in the source feed. Recent publications: 1. Behavioral Mapping of Hierarchical Dynamical Models Accelerates Bayesian Parameter Inference Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2610.30683 Bayesian parameter inference for complex nonlinear dynamical models is often limited by the cost of repeated model simulation. 2. Structural properties of distance-bounded phylogenetic reconciliation Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2601.22193 Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. 3. A Formalizable Proof of the No-Supervenience Theorem: A Diagonal Limitation on the Viability of Physicalist Theories of Consciousness Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2307.10178 The no-supervenience theorem limits the capacity of physicalist theories to provide a comprehensive account of human consciousness. 4. Advances in Machine Learning for Directed Evolution: A Five-Year Retrospective Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2609.03046 The last five-plus years have seen many protein engineering disciplines transformed by advances in machine learning (ML), but the same cannot be said for directed evolution. 5. manylp: reproducible, exact, and batched linear programming for genome-scale dynamic flux balance analysis Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2610.14566 Dynamic flux balance analysis (dFBA) and its community, spatial and ensemble variants predict microbial metabolism by solving one linear program (LP) per species and time step, often 10^6 to 10^8 LPs per study. 6. Orchestra: Corroboration-Based Regulatory Candidate Discovery via Composed Bioinformatics MCP Agents Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2609.05496 Orchestra composes two independently built bioinformatics MCP servers -- RegNetAgents, which infers regulatory network topology, and CASCADE, which provides independent functional evidence (LINCS knockdown, DepMap essentiality, super-enhancer status, DoRothEA transcription-factor confidence) -- into one multi-agent LangGraph workflow. 7. Forecasting Without Full Identification: Reliability and Computational Cost in Clot-Growth Simulation Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/2608.08165 We forecast clot growth from sparse early measurements with incomplete biochemical information. 8. Generalizable single-cell perturbation response prediction using energy-guided flow matching Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2610.02232 Predicting phenotypic and transcriptional responses to perturbations at single-cell resolution provides a powerful tool for probing biological systems. 9. Uncertainty-aware neural emulation reveals climate-resilient maize traits at scale Source: q-bio.OT (Other Quantitative Biology) Link: https://arxiv.org/abs/2605.22848 Global food security depends on predicting crop responses to climate variability, yet process based crop models remain too computationally expensive for large scale exploration of genotype and environment interactions. 10. Quantifying reticulocyte biomechanics in health and disease Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2607.21810 Red blood cell (RBC) populations are mechanically and morphologically heterogeneous, yet how this heterogeneity governs transport, splenic retention and blood rheology in confinement remains unclear. 11. Generalized modeling reveals stabilizing mechanisms in cross-feeding microbial communities Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2610.31154 Understanding what makes microbial communities stable and able to resist perturbation is a fundamental question in microbial ecology. 12. Music Between Two Minds: Individual Signatures, Shared States, and the Emergence of Creative Interaction Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2610.31131 Some of the most valued forms of human creativity arise between people-in conversation, collaboration, and improvised music-yet how two minds jointly regulate the flow of novelty in real time remains unknown. 13. RiboBridge: protein-conditioned de novo RNA binder structure design Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2610.30668 Designing RNA molecules that bind to target protein structures requires generating both an RNA conformation and its bound complex geometry, without assuming a predefined binding site. 14. Data-Driven Soft Labeling Scales DNA Read Classification to Whole-Body Cell-Type Deconvolution Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2607.04987 Cell-type deconvolution, the task of estimating the proportions of constituent cell types in a heterogeneous biological sample, is a core problem in computational biology. 15. Graph Neural Network-Based Reinforcement Learning for Controlling Biological Networks - the GATTACA Framework Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2505.02712 Cellular reprogramming, the artificial transformation of one cell type into another, has been attracting increasing research attention due to its therapeutic potential for complex diseases. 16. Semantic Context Forests for Learning-Based Knee Cartilage Segmentation in 3D MR Images Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/1307.2965 The automatic segmentation of human knee cartilage from 3D MR images is a useful yet challenging task due to the thin sheet structure of the cartilage with diffuse boundaries and inhomogeneous intensities. 17. Multimodal reasoning for broadly neutralizing antibody discovery from label-free human B cell repertoires across virus families Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2610.03160 Discovering broadly neutralizing antibodies (bnAbs) from human natural immune repertoires remains a fundamental challenge in immunology, hindered by: the extreme rarity of bnAb, incomplete understanding of their cellular origins across pathogens, and the inability of existing computational tools to generalize across emerging viral threats. 18. Can synthetic data reproduce real-world findings in epidemiology? A replication study using adversarial random forests Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2508.14936 Synthetic data hold substantial potential to address practical challenges in epidemiology due to restricted data access and privacy concerns. 19. Report the tolerance, not the count: exact phylogenetic distance deconvolution with incomplete references Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2610.30776 Phylogenetic distance deconvolution represents mixture-to-reference distances by weighted sources placed on a reference tree. 20. Gate-Based Feature Importance in Simulation-Based Inference for EEG: A Cautionary Tale Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2610.30364 Simulation-based inference (SBI) provides a powerful way to fit mechanistic models to data, but offers little insight into which information in the data shapes the inferred parameter values. 21. Escaping the Phylogenetic Trap: Persistent Homology Enables Cross-Species Ion Channel Classification via Multimodal Graph Neural Networks Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2610.30394 Protein classifiers are highly sensitive to evaluation protocol: random train/test splits induce phylogenetic leakage, allowing models to exploit taxon-specific correlations and substantially overestimate out-of-distribution performance. 22. GenoMAS: Guided Multi-Agent Programming for Scientific Discovery from Genomic Data Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2507.21035 Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains challenging due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. 23. On the Regularity of Reaction Systems Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2409.05340 Reaction networks have been widely used as generic models in diverse areas of applied sciences, such as biology, chemistry, ecology, epidemiology, and computer science. 24. An Octahedral Fibrous Constitutive Model for Heart Valve Mechanics and Function Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/2606.04234 Fibrous soft tissues derive their nonlinear mechanical response from networks of extracellular matrix fibers. 25. Reduced Hodgkin-Huxley models based on the correlation between sodium and potassium gating variables Source: q-bio.CB (Cell Behavior) Link: https://arxiv.org/abs/2402.19185 We analyse the interaction between the sodium (Na$^+$) and potassium (K$^+$) gating variables in the 4D Hodgkin-Huxley axonal electrophysiological model. 26. Do Vision CIL Methods Transfer to Protein? A Diagnostic Benchmark of Frozen Protein Encoders Source: q-bio.QM (Quantitative Methods) Link: https://arxiv.org/abs/2610.18879 Protein function annotation operates over an expanding label space, making class-incremental learning (CIL) a natural framework for incorporating newly discovered functions without full retraining. 27. Short-wave signal versus indirect prey-taxis Source: q-bio.PE (Populations and Evolution) Link: https://arxiv.org/abs/2604.20469 We address a short-wave asymptotic for one class of quasi-linear second-order PDE systems involving the cross-diffusion described by the so-called Patlak-Keller-Segel law. 28. Word-Class and Construction-Like Structure Emerges in Neural Successor Representations Trained on Natural Language Source: q-bio.NC (Neurons and Cognition) Link: https://arxiv.org/abs/2605.24585 Neural language models are typically trained on next-token prediction, although linguistic structure spans multiple temporal scales. 29. AI Mindmeld: A Latent Interconnect Protocol Source: q-bio.BM (Biomolecules) Link: https://arxiv.org/abs/2610.30215 LLMs can act as scientific agents using tools to consult specialists and run experiments. 30. PACE: Geometry-Aware Bridge Transport for Single-Cell Trajectory Inference Source: q-bio.GN (Genomics) Link: https://arxiv.org/abs/2605.18587 Single-cell trajectory inference from destructive time-course snapshots is fundamentally ill-posed: neither cross-time cell correspondences nor continuous trajectories are observed, so the snapshot distributions alone do not uniquely determine the underlying dynamics. 31. The influence of decay in dynamic models of gene regulatory networks Source: q-bio.MN (Molecular Networks) Link: https://arxiv.org/abs/2610.18261 We investigate the influence of decay rates on the dynamics of three-dimensional gene regulatory networks modeled by nonlinear differential equations with logistic sigmoidal regulatory functions. 32. MP-MNCA: Morphology-Prior Masked Neighbor Cross-Attention for Efficient Spatial Domain Identification Source: q-bio.TO (Tissues and Organs) Link: https://arxiv.org/abs/2610.16212 Spatial transcriptomics jointly captures molecular state, tissue morphology, and spatial organization, yet spatial-domain methods are typically compared only at late training checkpoints, obscuring differences in convergence efficiency. Sources in this brief: q-bio.BM (Biomolecules); q-bio.CB (Cell Behavior); q-bio.GN (Genomics); q-bio.MN (Molecular Networks); q-bio.NC (Neurons and Cognition); q-bio.OT (Other Quantitative Biology); q-bio.PE (Populations and Evolution); q-bio.QM (Quantitative Methods); q-bio.TO (Tissues and Organs). Selected 32 of 469 available items for this weekly brief.