arXiv:2603.22791v1 Announce Type: new Abstract: How should multi-agent systems be designed, and can that design knowledge be captured in a form that is inspectable, revisable, and transferable? We introduce ABSTRAL, a framework that treats MAS architecture as an evolving natural-language document, an artifact refined through contrastive trace analysis. Three findings emerge. First, we provide a precise measurement of the multi-agent coordination tax: under fixed turn budgets, ensembles achieve only 26% turn efficiency, with 66% of tasks exhausting the limit, yet still improve over single-agent baselines by discovering parallelizable task decompositions. Second, design knowledge encoded in documents transfers: topology reasoning and role templates learned on one domain provide a head start on new domains, with transferred seeds matching coldstart iteration 3 performance in a single iteration. Third, contrastive trace analysis discovers specialist roles absent from any initial design, a capability no prior system demonstrates. On SOPBench (134 bank tasks, deterministic oracle), ABSTRAL reaches 70% validation / 65.96% test pass rate with a GPT-4o backbone. We release the converged documents as inspectable design rationale.

arXiv:2602.22263v2 Announce Type: replace-cross Abstract: High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta are computationally expensive, demand extensive manual tuning, and present a significant bottleneck for researchers. We present CryoNet.Refine, an end-to-end deep learning framework that automates and accelerates molecular structure refinement. Our approach utilizes a one-step diffusion model that integrates a density-aware loss function with robust stereochemical restraints, enabling rapid optimization of a structure against experimental data. CryoNet.Refine provides a unified and versatile solution capable of refining protein complexes as well as DNA/RNA-protein complexes. In benchmarks against Phenix.real_space_refine, CryoNet.Refine consistently achieves substantial improvements in both model-map correlation and overall geometric quality metrics. By offering a scalable, automated, and powerful alternative, CryoNet.Refine aims to serve as an essential tool for next-generation cryo-EM structure refinement. Web server: https://cryonet.ai/refine; Source code: https://github.com/kuixu/cryonet.refine.