arXiv:2605.25577v1 Announce Type: cross Abstract: The generation of accurate 3D molecular conformations is a pivotal challenge in computational chemistry and drug discovery. Recently, diffusion and flow matching models have achieved remarkable success. However, there is a critical misalignment between their mathematical formulation and the physical reality of molecules. Existing approaches predominantly treat molecules as unstructured point clouds in Cartesian space, overlooking the intrinsic hierarchical mechanics where bond lengths and bond angles are relatively stiff, whereas torsion angles constitute the dominant flexible degrees of freedom. This lack of manifold awareness forces models to relearn fundamental geometric constraints from scratch, often leading to physically implausible intermediate structures. To address this, we propose GO-Flow that aligns generative modeling with molecular geometry via manifold decomposition. Instead of forcing motion through Euclidean space, GO-Flow decomposes the generation process into three physically motivated subspaces: translation space with linear optimal transport, rotation space with geodesic flows on $SO(3)$, and conformation space with entropic optimal transport. This decomposition injects geometric inductive biases and makes the generative paths better aligned with molecular degrees of freedom. When combined with equivariant neural architectures, it encourages rotation-consistent generation and improves geometric validity. Extensive experiments on GEOM-Drugs and GEOM-QM9 demonstrate that GO-Flow achieves state-of-the-art generation quality. Notably, by learning straighter probability paths on the correct manifolds naturally, our method enables high-fidelity sampling with as few as 50 steps, effectively bridging the gap between structural precision and computational efficiency.

arXiv:2605.25698v1 Announce Type: cross Abstract: High-quality data is scarce in large language model (LLM) training, yet how to schedule its use jointly with training dynamics lacks theoretical guidance. We extend functional scaling laws by incorporating a data-quality dimension, and solve the joint data-quality and batch-size scheduling problem in asymptotic closed form. The solution reveals two regimes and a dual role of high-quality data. In the noise-limited regime, high-quality data should be used as a signal amplifier: lowering the batch size converts cleaner data into more signal without amplifying noise. In the signal-limited regime, it should be used as a noise suppressor: late placement reduces terminal noise without sacrificing signal accumulation. Existing curriculum-style pipelines primarily exploit the second role by placing cleaner data late, but miss the first role because conventional decay schedules reduce update intensity exactly when high-quality data becomes available. Guided by this, we propose Drop-Stable-Rampup for LLM midtraining: upon the quality transition, drop the batch size, hold it stable to accumulate signal, then ramp up to suppress terminal noise. On a 15B Mixture-of-Experts model midtrained on 108B tokens, Drop-Stable-Rampup improves average accuracy over Warmup-Stable-Decay (WSD) by +1.70 and over Cosine-decay by +2.98, with particularly large gains on mathematical reasoning benchmarks such as GSM8K (+4.23) and MATH (+2.80).

arXiv:2604.01007v2 Announce Type: replace Abstract: AI agents increasingly operate over extended time horizons, yet their ability to retain, organize, and recall multimodal experiences remains a critical bottleneck. Building effective lifelong memory requires navigating a vast design space spanning architecture, retrieval strategies, prompt engineering, and data pipelines; this space is too large and interconnected for manual exploration or traditional AutoML to explore effectively. We deploy an autonomous research pipeline to discover Omni-SimpleMem, a unified multimodal memory framework for lifelong AI agents. Starting from a na\"ive baseline (F1=0.117 on LoCoMo), the pipeline autonomously executes ${\sim}50$ experiments across two benchmarks, diagnosing failure modes, proposing architectural modifications, and repairing data pipeline bugs, all without human intervention in the inner loop. The resulting system achieves state-of-the-art on both benchmarks, improving F1 by +411% on LoCoMo (0.117$\to$0.598) and +214% on Mem-Gallery (0.254$\to$0.797) relative to the initial configurations. Critically, the most impactful discoveries are not hyperparameter adjustments: bug fixes (+175%), architectural changes (+44%), and prompt engineering (+188% on specific categories) each individually exceed the cumulative contribution of all hyperparameter tuning, demonstrating capabilities fundamentally beyond the reach of traditional AutoML. We provide a taxonomy of six discovery types and identify four properties that make multimodal memory particularly suited for autoresearch, offering guidance for applying autonomous research pipelines to other AI system domains. Code is available at this https://github.com/aiming-lab/SimpleMem.

A multi-omic single-cell atlas of the aging mouse brain reveals cell-type-specific transposon methylation changes, strengthening of 3D genome boundaries, and regionally heterogeneous aging signatures. These findings offer a resource to understand the molecular mechanisms of brain aging and guide future research on neurodegeneration.

arXiv:2508.09537v2 Announce Type: replace-cross Abstract: The growing capabilities of Large Language Models (LLMs) have led to their widespread adoption for function completion within code repositories. Recent studies on such tasks show promising results when explicit instructions, often in the form of docstrings, are available to guide the completion. However, in real-world scenarios, clear docstrings are frequently absent. Under such conditions, LLMs typically fail to produce accurate completions. To enable more automated and accurate function completion in such settings, we aim to enable LLMs to accurately infer the developer's intent prior to code completion. Our key insight is that the preceding code, namely the code context before the function to be completed, often contains valuable cues that help the model understand the intended functionality. However, inferring intent from such implicit context is non-trivial and constitutes a core challenge in function-level code completion. To tackle this challenge, inspired by how humans interpret context, we propose a reasoning-based prompting framework that guides LLMs to utilize these contextual cues to infer intent step by step. To incentivize LLMs to reason through the preceding code and infer intent, we further curate a dataset of 40k examples, each annotated with intermediate reasoning traces and corresponding docstrings. Extensive experiments on DevEval and ComplexCodeEval demonstrate consistent performance improvements across multiple models, achieving over 25% relative gains in pass@1 for both DeepSeekCoder and CodeLLaMA families. Building upon our framework, we further develop an intent-interactive platform that supports lightweight human feedback. This platform allows developers to select from a set of candidate intentions or edit the intent to better guide the model. Our experiments show that this interactive approach leads to further performance improvements.

arXiv:2602.12670v3 Announce Type: replace Abstract: Agent Skills are structured packages of procedural knowledge that augment LLM agents at inference time. Despite rapid adoption, there is no standard way to measure whether they actually help. We present SkillsBench, a benchmark of 86 tasks across 11 domains paired with curated Skills and deterministic verifiers. Each task is evaluated under three conditions: no Skills, curated Skills, and self-generated Skills. We test 7 agent-model configurations over 7,308 trajectories. Curated Skills raise average pass rate by 16.2 percentage points(pp), but effects vary widely by domain (+4.5pp for Software Engineering to +51.9pp for Healthcare) and 16 of 84 tasks show negative deltas. Self-generated Skills provide no benefit on average, showing that models cannot reliably author the procedural knowledge they benefit from consuming. Focused Skills with 2--3 modules outperform comprehensive documentation, and smaller models with Skills can match larger models without them.

arXiv:2601.15369v2 Announce Type: replace-cross Abstract: This paper presents a family of advanced vision encoder, named OpenVision 3, that learns a single, unified visual representation that can serve both image understanding and image generation. Our core architecture is simple: we feed VAE-compressed image latents to a ViT encoder and train its output to support two complementary roles. First, the encoder output is passed to the ViT-VAE decoder to reconstruct the original image, encouraging the representation to capture generative structure. Second, the same representation is optimized with contrastive learning and image-captioning objectives, strengthening semantic features. By jointly optimizing reconstruction- and semantics-driven signals in a shared latent space, the encoder learns representations that synergize and generalize well across both regimes. We validate this unified design through extensive downstream evaluations with the encoder frozen. For generation, we test it under the RAE framework: ours substantially surpasses the standard CLIP-based encoder (e.g., gFID: 1.87 vs. 2.54 on ImageNet). For multimodal understanding, we plug the encoder into the LLaVA-1.5 and LLaVA-NeXT framework: it performs comparably with a standard CLIP vision encoder (e.g., 63.3 vs. 61.2 on SeedBench, and 59.2 vs. 58.1 on GQA). We provide empirical evidence that generation and understanding are mutually beneficial in our architecture, while further underscoring the critical role of the VAE latent space. We hope this work can spur future research on unified modeling.

arXiv:2603.07540v1 Announce Type: cross Abstract: Unified multimodal models hold the promise of generating extensive, interleaved narratives, weaving text and imagery into coherent long-form stories. However, current systems suffer from a critical reliability gap: as sequences grow, generation quality rapidly collapses. In this work, we investigate the mechanism behind this failure and argue that it is distinct from standard long-context challenges. We reveal that in generation, accumulated visual history acts as a source of active pollution, a decay governed specifically by the number of image events rather than raw token count. We identify a structural vulnerability where dense visual tokens overwhelm the attention mechanism, creating noise that distorts future synthesis. Guided by these mechanistic insights, we propose UniLongGen, a training-free inference strategy that prioritizes safe conditioning over total recall. Instead of retaining all history, UniLongGen dynamically curates the model's memory, identifying and discarding interfering visual signals based on the model's own internal relevance rankings. Extensive experiments demonstrate that this active forgetting approach is essential for stability: UniLongGen significantly outperforms baselines in long-horizon fidelity and consistency, while simultaneously reducing memory footprint and inference time.

arXiv:2602.12670v2 Announce Type: replace Abstract: Agent Skills are structured packages of procedural knowledge that augment LLM agents at inference time. Despite rapid adoption, there is no standard way to measure whether they actually help. We present SkillsBench, a benchmark of 86 tasks across 11 domains paired with curated Skills and deterministic verifiers. Each task is evaluated under three conditions: no Skills, curated Skills, and self-generated Skills. We test 7 agent-model configurations over 7,308 trajectories. Curated Skills raise average pass rate by 16.2 percentage points(pp), but effects vary widely by domain (+4.5pp for Software Engineering to +51.9pp for Healthcare) and 16 of 84 tasks show negative deltas. Self-generated Skills provide no benefit on average, showing that models cannot reliably author the procedural knowledge they benefit from consuming. Focused Skills with 2--3 modules outperform comprehensive documentation, and smaller models with Skills can match larger models without them.

arXiv:2511.02860v2 Announce Type: replace-cross Abstract: The distribution and interactions of cellular organelles play a critical role in mediating cellular physiology and pathology. Large-scale electron microscopy enables visualization of organelle distribution and interactions at the tissue level with nanometer resolution, but robust and efficient computational analysis tools are lacking. Here, we present a deep learning tool for universal large-scale 2D/3D electron microscopy analysis, DeepOrganelle. This new tool enables high-throughput, cell-resolved spatiotemporal mapping and digitization of organelle distribution and interactions. When applied to spermatogenesis across 12 stages and 22 differentiation status of the germ cells, DeepOrganelle uncovered previously unrecognized, stage-dependent dynamics of mitochondria-endoplasmic reticulum contact sites within one subphase of prophase I during meiosis. It also revealed coordinated organelle redistribution in Sertoli cells towards the blood-testis barrier, digitizing the remodeling dynamics of the tissue. This study demonstrates that DeepOrganelle provides a powerful framework that captures subcellular dynamics at the whole-tissue level.