arXiv:2604.01545v1 Announce Type: new Abstract: The latent space of generative modeling is long dominated by the VAE encoder. The latents from the pretrained representation encoders (e.g., DINO, SigLIP, MAE) are previously considered inappropriate for generative modeling. Recently, RAE method lights the hope and reveals that the representation autoencoder can also achieve competitive performance as the VAE encoder. However, the integration of representation autoencoder into continuous autoregressive (AR) models, remains largely unexplored. In this work, we investigate the challenges of employing high-dimensional representation autoencoders within the AR paradigm, denoted as \textit{RAE-AR}. We focus on the unique properties of AR models and identify two primary hurdles: complex token-wise distribution modeling and the high-dimensionality amplified training-inference gap (exposure bias). To address these, we introduce token simplification via distribution normalization to ease modeling difficulty and improve convergence. Furthermore, we enhance prediction robustness by incorporating Gaussian noise injection during training to mitigate exposure bias. Our empirical results demonstrate that these modifications substantially bridge the performance gap, enabling representation autoencoder to achieve results comparable to traditional VAEs on AR models. This work paves the way for a more unified architecture across visual understanding and generative modeling.

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.