Human-Guided Causal Knowledge Injection for Virtual Cells

Virtual cells employ machine learning models to simulate and predict cellular behaviors, serving as a critical computational framework for investigating health and disease. Injecting causal graphs into virtual cells can improve the interpretability, but such graphs are usually not available in real-world applications. Recently, many methods have been proposed to construct causal graphs from data, which group genes based on their similarities to form concepts and extract their causal relationships. However, since this automatic process is unsupervised, the causal graphs usually contain errors. In this paper, we propose a human-guided causal knowledge injection method for virtual cells. We developed a gene-similarity-aware causal graph visualization supported by a hybrid optimization algorithm to help explore both the causal relationships between concepts and the similarities between genes. Based on the exploration, we further developed a counterfactual analysis strategy supported by a counterfactual visualization and a causal path visualization to help validate and refine causal graphs. The effectiveness of our method is demonstrated through two real-world case studies, the extraction of scientifically meaningful causal insights, and positive feedback from domain experts.

Explore or Converge? Stage-Guided Per-Step Optimization for Diffusion Models

Diffusion models have strong generative capabilities. However, their maximum likelihood training objective only focuses on reconstructing the data distribution, making it difficult to align with specific preferences. Reinforcement learning (RL) for preference alignment in diffusion models is promising but limited by reward sparsity. Since a single reward cannot support optimization, existing RL methods usually backpropagate the final reward to all previous steps. However, denoising is stage-wise, with distinct semantics and controllability. Repeating the final reward across all steps creates a temporal objective mismatch, encouraging reward shortcuts that lead to reward hacking. At the same time, due to reward backfilling, each time step receives the same reward, making it impossible to distinguish between actions, thereby weakening the optimization process. To resolve this issue, we propose Stage-Guided Per-Step Optimization (SGPO) for diffusion models, which jointly leverages signal-to-noise ratio and semantic changes to identify generation stages and adaptively assign stage-specific objectives. Early denoising is chaotic and far from the final reward, resulting in weak reward-behavior correlation. This stage should prioritize exiting the chaotic state. In the mid stage, the latent transitions to a stable structure, where the final reward better corresponds to generative behavior. Therefore, this stage optimizes the final reward while exploring diversity to avoid early convergence to a single mode. In the late stage, the latent's core structure is largely fixed, and preference optimization mainly amplifies local details, risking overfitting. Therefore, stable convergence is preferred to avoid quality degradation. Results from 16 comparative experiments validate SGPO. Our method achieves 26.7% average gains in generative quality and 36.7% higher convergence speed.

PAST: Prompt-Adaptive Sampling Termination for Efficient Diffusion Model

While diffusion models have made significant progress in text-to-image tasks, they still exhibit limitations when directly optimizing downstream objectives. Although Reinforcement Learning (RL) enables targeted optimization, existing methods are generally constrained by low-efficiency fine-tuning and sparse rewards. To address these challenges, we propose PAST, which provides differentiated rewards while adaptively regulating training episode length by jointly perceiving denoising progress and prompt difficulty. Specifically, we design an intrinsic reward paradigm to compensate for sparse extrinsic rewards and guide the model to explore paths that diverge more efficiently from noise patterns. We further provide theoretical justification for intrinsic rewards. Then, PAST dynamically monitors denoising completion and semantic alignment between image structures and prompt semantics. When both metrics satisfy generation requirements, the system adaptively terminates training. This enables appropriate allocation of episode lengths based on prompt difficulty and the current generation process. Finally, based on the predicted residual noise level, we establish a dual adaptive coordination mechanism. Specifically, it not only balances the extrinsic and intrinsic rewards but also balances the exploration and convergence. Experimental results demonstrate that PAST enhances computational efficiency of existing RL fine-tuning methods by up to 66.7%, while improving preference optimization quality by up to 29.5% through its dual adaptive regulation mechanism.

S$^4$R: Selective Sampling, Subspaces, and Sparse Reconstruction for Compressed Long-Context KV Caching

The growth of context window lengths in Large Language Models (LLMs) significantly enhances their long-context capabilities but incurs prohibitive memory costs due to the Key-Value (KV) cache. Although low-rank compression of KV cache is a promising remedy, existing methods face a dilemma: offline approaches depend on external calibration data, whereas online approaches incur substantial compute for full-prompt decomposition and reconstruction. In this paper, we propose S$^4$R, which builds low-rank subspaces from selectively sampled tokens and computes attention over a sparsely reconstructed KV representation. S$^4$R uses prompt-aware initialization to build initial key/value bases from a representative prompt subset, trading off calibration-data dependence against prefilling cost. Because fully reconstructing the cache at every decoding step is prohibitively expensive and hurts throughput, we further adopt sparse reconstruction to retain only informative positions during decoding. Extensive experiments on LongBench and RULER with Llama and Qwen model families show that S$^4$R achieves up to 5$\times$ KV compression with near full-cache accuracy, combining the efficiency of fixed compression with the adaptability of prompt-dependent methods.

Pixel-Space Diffusion Transformers

Latent diffusion models (LDMs) enable efficient high-resolution image synthesis by denoising in a VAE-compressed latent space. However, fixed visual tokenizers can discard fine textures and structural details, while separate representation and diffusion training creates a mismatch between reconstruction and generation objectives. These limitations have renewed interest in pixel-space diffusion, which models raw pixels directly, removes the VAE bottleneck, and supports end-to-end optimization. This formulation better matches the demands of high-fidelity generation but introduces challenges in high-dimensional modeling, including noise scheduling, loss weighting, token efficiency, and scalable architecture design. Pixel-space modeling also offers a promising basis for unified multimodal systems: raw pixels, text, and task conditions can be represented in a shared token space and jointly processed by a single Transformer, narrowing the gap between visual understanding and generation. This paper reviews Pixel-Space Diffusion Transformers (pDiTs) from the perspectives of model architecture, continuous generative mechanisms, and unified multimodal modeling. We summarize representative methods, identify key technical challenges, and discuss future directions toward high-fidelity, end-to-end vision foundation models that integrate generation and understanding.

GRKV: Global Regression for Training-Free KV Cache Compression in Long-Context LLMs

Large language models (LLMs) with extended context lengths rely on the key-value (KV) cache to support attention over prior tokens. However, maintaining the KV cache incurs substantial memory overhead, motivating KV-cache compression methods that enforce a fixed budget through eviction and merging. Modern eviction methods increasingly adopt span-based retention because preserving contiguous spans is empirically effective and better preserves semantic coherence. Yet, when combined with post-eviction merging, span-based retention concentrates merges onto a small set of span-boundary carrier tokens, producing a highly imbalanced merge pattern that exacerbates over-merging and increases information loss. To address this imbalance, we propose GRKV (Global Regression for KV Cache), a training-free KV-cache merging method that directly minimizes the discrepancy between compressed-cache and full-cache attention outputs. GRKV uses ridge-regression-based merge steps to distribute information from evicted tokens across retained tokens, while regularizing the updates to prevent over-smoothing. Across the LongBench and RULER long-context benchmarks, GRKV is the only merging method that improves overall performance with minimal overhead.

YOCO++: Enhancing YOCO with KV Residual Connections for Efficient LLM Inference

Cross-layer key-value (KV) compression has been found to be effective in efficient inference of large language models (LLMs). Although they reduce the memory consumption of the KV cache, such methods usually introduce non-negligible performance degradation. In this work, we aim to enhance the performance of YOCO, a cross-layer KV compression method that shares the KVs of the middle layer with the top-half layers. We propose YOCO++, an enhanced YOCO that incorporates a weighted residual connection between the KVs of each bottom-half layer and the bottom layer. Compared to YOCO, YOCO++ increases model capacity while maintaining the same training and inference efficiency. Our experiments show that YOCO++ achieves state-of-the-art performance among the cross-layer KV compression methods at a 50% KV cache compression rate, outperforming the standard Transformer.

ST-VLA: Enabling 4D-Aware Spatiotemporal Understanding for General Robot Manipulation

Robotic manipulation in open-world environments requires reasoning across semantics, geometry, and long-horizon action dynamics. Existing hierarchical Vision-Language-Action (VLA) frameworks typically use 2D representations to connect high-level reasoning with low-level control, but lack depth awareness and temporal consistency, limiting robustness in complex 3D scenes. We propose ST-VLA, a hierarchical VLA framework using a unified 3D-4D representation to bridge perception and action. ST-VLA converts 2D guidance into 3D trajectories and generates smooth spatial masks that capture 4D spatio-temporal context, providing a stable interface between semantic reasoning and continuous control. To enable effective learning of such representations, we introduce ST-Human, a large-scale human manipulation dataset with 14 tasks and 300k episodes, annotated with 2D, 3D, and 4D supervision via a semi-automated pipeline. Using ST-Human, we train ST-VLM, a spatio-temporal vision-language model that generates spatially grounded and temporally coherent 3D representations to guide policy execution. The smooth spatial masks focus on task-relevant geometry and stabilize latent representations, enabling online replanning and long-horizon reasoning. Experiments on RLBench and real-world manipulation tasks show that \method significantly outperforms state-of-the-art baselines, improving zero-shot success rates by 44.6% and 30.3%. These results demonstrate that offloading spatio-temporal reasoning to VLMs with unified 3D-4D representations substantially improves robustness and generalization for open-world robotic manipulation. Project website: https://oucx117.github.io/ST-VLA/.

From AI Weather Prediction to Infrastructure Resilience: A Correction-Downscaling Framework for Tropical Cyclone Impacts

This paper addresses a missing capability in infrastructure resilience: turning fast, global AI weather forecasts into asset-scale, actionable risk. We introduce the AI-based Correction-Downscaling Framework (ACDF), which transforms coarse AI weather prediction (AIWP) into 500-m, unbiased wind fields and transmission tower/line failure probabilities for tropical cyclones. ACDF separates storm-scale bias correction from terrain-aware downscaling, preventing error propagation while restoring sub-kilometer variability that governs structural loading. Tested on 11 typhoons affecting Zhejiang, China under leave-one-storm-out evaluation, ACDF reduces station-scale wind-speed MAE by 38.8% versus Pangu-Weather, matches observation-assimilated mesoscale analyses, yet runs in 25 s per 12-h cycle on a single GPU. In the Typhoon Hagupit case, ACDF reproduced observed high-wind tails, isolated a coastal high-risk corridor, and flagged the line that failed, demonstrating actionable guidance at tower and line scales. ACDF provides an end-to-end pathway from AI global forecasts to operational, impact-based early warning for critical infrastructure.

SpiralFormer: Looped Transformers Can Learn Hierarchical Dependencies via Multi-Resolution Recursion

Recursive (looped) Transformers decouple computational depth from parameter depth by repeatedly applying shared layers, providing an explicit architectural primitive for iterative refinement and latent reasoning. However, early looped Transformers often underperform non-recursive baselines of equal compute. While recent literature has introduced more effective recursion mechanisms to mitigate this gap, existing architectures still operate at a fixed, full-token resolution, neglecting the potential efficiency of computing over compressed latent representations. In this paper, we propose SpiralFormer, a looped Transformer that executes recurrence under a multi-resolution recursion schedule. We provide probing evidence that multi-resolution recursion enables the model to learn hierarchical dependencies by inducing iteration-wise functional specialization across different scales. Empirically, SpiralFormer achieves better parameter and compute efficiency than both looped and non-looped baselines across model scales from 160M to 1.4B, establishing sequence resolution as a potential axis for scaling recursive architectures.