arXiv:2603.06615v1 Announce Type: cross Abstract: For multivariate co-generation in scientific applications, we advocate pairwise block rather than joint modeling of all variables. This design mitigates the computational burden and data imbalance. To this end, we propose an Annealed Co-Generation (ACG) framework that replaces high-dimensional diffusion modeling with a low-dimensional diffusion model, which enables multivariate co-generation by composing pairwise variable generations. We first train an unconditional diffusion model over causal variables that are disentangled into pairs. At inference time, we recover the joint distribution by coupling these pairwise models through shared common variables, enabling coherent multivariate generation without any additional training. By employing a three-stage annealing process-Consensus, Heating, and Cooling-our method enforces consistency across shared common variables and progressively constrains each pairwise data distribution to lie on a learnable manifold, while maintaining high likelihood within each pair. We demonstrate the framework's flexibility and efficacy on two distinct scientific tasks: flow-field completion and antibody generation. All datasets and code will be made publicly available upon publication.

arXiv:2603.06617v1 Announce Type: cross Abstract: We introduce \textbf{Evo}, a duality latent trajectory model that bridges autoregressive (AR) and diffusion-based language generation within a continuous evolutionary generative framework. Rather than treating AR decoding and diffusion generation as separate paradigms, Evo reconceptualizes text generation as a latent flow: each token is associated with a vector-valued embedding that evolves over a progression variable $t_i \in [0, 1]$, indicating its semantic maturity. Low $t_i$ values correspond to confident AR-like refinement, while high values invoke diffusion-style planning, allowing the model to adaptively balance AR and diffusion based on uncertainty. Theoretically, we show that both AR and diffusion models emerge as discretizations of a shared probability flow, and we derive Evo's training objective from a unified variational ELBO. The model is implemented as a time-conditioned Transformer governed by a shared vector field, trained end-to-end to jointly infer latent codes and their progression times. During decoding, Evo performs efficient, semantics-aware refinement, achieving high-quality outputs without sacrificing speed. Empirically, Evo 8B achieves state-of-the-art or highly competitive results on 15 diverse benchmarks, including reasoning (GSM8K, ARC-C), code generation (HumanEval, MBPP), and general language understanding, while maintaining fast inference speed. Our results demonstrate that Evo delivers a new paradigm for LLM design with strong generation quality, robust symbolic reasoning, and decoding efficiency.

arXiv:2603.06618v1 Announce Type: cross Abstract: Multiplex Biological Networks (MBNs), which represent multiple interaction types between entities, are crucial for understanding complex biological systems. Yet, existing methods often inadequately model multiplexity, struggle to integrate structural and sequence information, and face difficulties in zero-shot prediction for unseen entities with no prior neighbourhood information. To address these limitations, we propose a novel framework for zero-shot interaction prediction in MBNs by leveraging context-aware representation learning and knowledge distillation. Our approach leverages domain-specific foundation models to generate enriched embeddings, introduces a topology-aware graph tokenizer to capture multiplexity and higher-order connectivity, and employs contrastive learning to align embeddings across modalities. A teacher-student distillation strategy further enables robust zero-shot generalization. Experimental results demonstrate that our framework outperforms state-of-the-art methods in interaction prediction for MBNs, providing a powerful tool for exploring various biological interactions and advancing personalized therapeutics.

arXiv:2603.07886v1 Announce Type: cross Abstract: Enhancing the ability of large language models (LLMs) to follow complex instructions is critical for their deployment in real-world applications. However, existing evaluation methods often oversimplify instruction complexity as a mere additive combination of atomic constraints, failing to adequately capture the high-dimensional complexity arising from the intricate interplay of content and format, logical workflow control, and real-world applications. This leads to a significant gap between current evaluation practices and practical demands. To bridge this gap, we introduce CCR-Bench, a novel benchmark designed to assess LLMs' adherence to complex instructions. CCR-Bench is characterized by: (1) deep entanglement of content and formatting requirements in task specifications; (2) instructions that involve intricate task decomposition, conditional reasoning, and procedural planning; and (3) evaluation samples derived entirely from real-world industrial scenarios. Extensive experiments on CCR-Bench demonstrate that even state-of-the-art models exhibit substantial performance deficiencies, clearly quantifying the gap between current LLM capabilities and the demands of realworld instruction understanding. We believe that CCR-Bench offers a more rigorous and realistic evaluation framework, advancing the development of LLMs toward the next generation of models capable of understanding and executing complex tasks in industrial applications.

arXiv:2603.01396v2 Announce Type: replace Abstract: Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.

arXiv:2602.04265v2 Announce Type: replace-cross Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a promising paradigm for enhancing reasoning in Large Language Models (LLMs). However, it frequently encounters challenges such as entropy collapse, excessive verbosity, and insufficient exploration for hard problems. Crucially, existing reward schemes fail to distinguish between the need for extensive search during problem-solving and the efficiency required for mastered knowledge. In this work, we introduce T2T(Thickening-to-Thinning), a dynamic reward framework inspired by human learning processes. Specifically, it implements a dual-phase mechanism: (1) On incorrect attempts, T2T incentivizes "thickening" (longer trajectories) to broaden the search space and explore novel solution paths; (2) Upon achieving correctness, it shifts to "thinning", imposing length penalties to discourage redundancy, thereby fostering model confidence and crystallizing reasoning capabilities. Extensive experiments on mathematical benchmarks (MATH-500, AIME, AMC) across Qwen-series and Deepseek models demonstrate that T2T significantly outperforms standard GRPO and recent baselines, achieving superior performance.

arXiv:2602.14536v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) have seen remarkable advancements, achieving state-of-the-art results in diverse applications. Fine-tuning, an important step for adapting LLMs to specific downstream tasks, typically involves further training on corresponding datasets. However, a fundamental discrepancy exists between current fine-tuning datasets and the token-level optimization mechanism of LLMs: most datasets are designed at the sentence-level, which introduces token-level noise, causing negative influence to final performance. In this paper, we propose XTF, an explainable token-level noise filtering framework. XTF decomposes the complex and subtle contributions of token-level data to the fine-tuning process into three distinct and explicit attributes (reasoning importance, knowledge novelty, and task relevance), which can be assessed using scoring methods, and then masks the gradients of selected noisy tokens accordingly to optimize the performance of fine-tuned LLMs. We conduct extensive experiments on three representative downstream tasks (math, code and medicine) across 7 mainstream LLMs. The results demonstrate that XTF can significantly improve downstream performance by up to 13.7% compared to regular fine-tuning. Our work highlights the importance of token-level dataset optimization, and demonstrates the potential of strategies based on attribute decomposition for explaining complex training mechanisms.

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.